Magnesium in PDB 7tgk: Crystal Structure of Atp Bound Desd, the Desferrioxamine Synthetase From the Streptomyces Griseoflavus Ferrimycin Biosynthetic Pathway
Protein crystallography data
The structure of Crystal Structure of Atp Bound Desd, the Desferrioxamine Synthetase From the Streptomyces Griseoflavus Ferrimycin Biosynthetic Pathway, PDB code: 7tgk
was solved by
K.D.Patel,
A.M.Gulick,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
48.95 /
2.30
|
|
Space group
|
C 2 2 21
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
126.407,
237.528,
326.829,
90,
90,
90
|
|
R / Rfree (%)
|
18.3 /
21.6
|
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Crystal Structure of Atp Bound Desd, the Desferrioxamine Synthetase From the Streptomyces Griseoflavus Ferrimycin Biosynthetic Pathway
(pdb code 7tgk). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 10 binding sites of Magnesium where determined in the
Crystal Structure of Atp Bound Desd, the Desferrioxamine Synthetase From the Streptomyces Griseoflavus Ferrimycin Biosynthetic Pathway, PDB code: 7tgk:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Magnesium binding site 1 out
of 10 in 7tgk
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Magnesium Binding Sites List in 7tgk
Magnesium binding site 1 out
of 10 in the Crystal Structure of Atp Bound Desd, the Desferrioxamine Synthetase From the Streptomyces Griseoflavus Ferrimycin Biosynthetic Pathway
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Crystal Structure of Atp Bound Desd, the Desferrioxamine Synthetase From the Streptomyces Griseoflavus Ferrimycin Biosynthetic Pathway within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg613
b:35.8
occ:1.00
|
OE2
|
D:GLU463
|
2.0
|
48.3
|
1.0
|
|
OE2
|
D:GLU464
|
2.2
|
46.1
|
1.0
|
|
O1B
|
D:ATP612
|
2.3
|
40.4
|
1.0
|
|
O
|
D:HOH760
|
2.3
|
52.2
|
1.0
|
|
OD2
|
D:ASP460
|
2.4
|
50.0
|
1.0
|
|
OD1
|
D:ASP460
|
2.8
|
46.0
|
1.0
|
|
O1A
|
D:ATP612
|
2.8
|
52.2
|
1.0
|
|
CG
|
D:ASP460
|
2.9
|
48.4
|
1.0
|
|
CD
|
D:GLU463
|
3.1
|
48.6
|
1.0
|
|
HG3
|
D:GLU463
|
3.2
|
57.2
|
1.0
|
|
CD
|
D:GLU464
|
3.3
|
46.9
|
1.0
|
|
PA
|
D:ATP612
|
3.3
|
54.0
|
1.0
|
|
PB
|
D:ATP612
|
3.4
|
42.8
|
1.0
|
|
HZ1
|
D:LYS291
|
3.4
|
63.7
|
1.0
|
|
O3A
|
D:ATP612
|
3.5
|
46.0
|
1.0
|
|
CG
|
D:GLU463
|
3.6
|
47.6
|
1.0
|
|
O2A
|
D:ATP612
|
3.6
|
47.7
|
1.0
|
|
HG2
|
D:GLU464
|
3.6
|
53.1
|
1.0
|
|
HG2
|
D:GLU463
|
3.7
|
57.2
|
1.0
|
|
HH21
|
D:ARG277
|
3.8
|
54.4
|
1.0
|
|
CG
|
D:GLU464
|
3.8
|
44.3
|
1.0
|
|
HG3
|
D:GLU464
|
3.9
|
53.1
|
1.0
|
|
HZ2
|
D:LYS291
|
3.9
|
63.7
|
1.0
|
|
NZ
|
D:LYS291
|
4.1
|
53.1
|
1.0
|
|
OE1
|
D:GLU463
|
4.2
|
46.6
|
1.0
|
|
HH22
|
D:ARG277
|
4.2
|
54.4
|
1.0
|
|
MG
|
D:MG614
|
4.2
|
49.1
|
1.0
|
|
OE1
|
D:GLU464
|
4.3
|
45.6
|
1.0
|
|
NH2
|
D:ARG277
|
4.3
|
45.3
|
1.0
|
|
O1G
|
D:ATP612
|
4.3
|
47.9
|
1.0
|
|
HZ3
|
D:LYS291
|
4.4
|
63.7
|
1.0
|
|
CB
|
D:ASP460
|
4.4
|
46.1
|
1.0
|
|
O2B
|
D:ATP612
|
4.5
|
43.5
|
1.0
|
|
O3B
|
D:ATP612
|
4.6
|
49.6
|
1.0
|
|
HB2
|
D:ASP460
|
4.8
|
55.4
|
1.0
|
|
HD21
|
D:ASN443
|
4.8
|
59.6
|
1.0
|
|
HB3
|
D:ASP460
|
4.8
|
55.4
|
1.0
|
|
HH12
|
D:ARG303
|
4.9
|
50.1
|
1.0
|
|
O5'
|
D:ATP612
|
4.9
|
51.8
|
1.0
|
|
PG
|
D:ATP612
|
4.9
|
46.0
|
1.0
|
|
O2G
|
D:ATP612
|
5.0
|
45.6
|
1.0
|
|
HH11
|
D:ARG303
|
5.0
|
50.1
|
1.0
|
|
CB
|
D:GLU463
|
5.0
|
44.4
|
1.0
|
|
Magnesium binding site 2 out
of 10 in 7tgk
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Magnesium Binding Sites List in 7tgk
Magnesium binding site 2 out
of 10 in the Crystal Structure of Atp Bound Desd, the Desferrioxamine Synthetase From the Streptomyces Griseoflavus Ferrimycin Biosynthetic Pathway
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Crystal Structure of Atp Bound Desd, the Desferrioxamine Synthetase From the Streptomyces Griseoflavus Ferrimycin Biosynthetic Pathway within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg614
b:49.1
occ:1.00
|
O2G
|
D:ATP612
|
2.0
|
45.6
|
1.0
|
|
OD1
|
D:ASN443
|
2.3
|
49.8
|
1.0
|
|
O3A
|
D:ATP612
|
2.3
|
46.0
|
1.0
|
|
O2A
|
D:ATP612
|
2.3
|
47.7
|
1.0
|
|
OE1
|
D:GLU442
|
2.3
|
51.0
|
1.0
|
|
OD2
|
D:ASP460
|
2.6
|
50.0
|
1.0
|
|
PA
|
D:ATP612
|
2.8
|
54.0
|
1.0
|
|
HB2
|
D:ASP460
|
3.2
|
55.4
|
1.0
|
|
PG
|
D:ATP612
|
3.2
|
46.0
|
1.0
|
|
CG
|
D:ASN443
|
3.3
|
49.0
|
1.0
|
|
CD
|
D:GLU442
|
3.3
|
51.3
|
1.0
|
|
HD21
|
D:ASN443
|
3.3
|
59.6
|
1.0
|
|
HE1
|
D:HIS440
|
3.4
|
54.9
|
1.0
|
|
O5'
|
D:ATP612
|
3.4
|
51.8
|
1.0
|
|
CG
|
D:ASP460
|
3.4
|
48.4
|
1.0
|
|
PB
|
D:ATP612
|
3.5
|
42.8
|
1.0
|
|
HZ2
|
D:LYS459
|
3.5
|
76.0
|
1.0
|
|
OE2
|
D:GLU442
|
3.5
|
52.2
|
1.0
|
|
O3B
|
D:ATP612
|
3.5
|
49.6
|
1.0
|
|
CB
|
D:ASP460
|
3.7
|
46.1
|
1.0
|
|
ND2
|
D:ASN443
|
3.7
|
49.6
|
1.0
|
|
HB3
|
D:ASP460
|
3.8
|
55.4
|
1.0
|
|
HZ1
|
D:LYS459
|
3.8
|
76.0
|
1.0
|
|
O1G
|
D:ATP612
|
3.9
|
47.9
|
1.0
|
|
O1B
|
D:ATP612
|
3.9
|
40.4
|
1.0
|
|
HE2
|
D:HIS440
|
4.0
|
55.3
|
1.0
|
|
NZ
|
D:LYS459
|
4.0
|
63.4
|
1.0
|
|
O1A
|
D:ATP612
|
4.1
|
52.2
|
1.0
|
|
CE1
|
D:HIS440
|
4.1
|
45.7
|
1.0
|
|
HZ3
|
D:LYS459
|
4.1
|
76.0
|
1.0
|
|
HB3
|
D:SER275
|
4.2
|
52.1
|
1.0
|
|
MG
|
D:MG613
|
4.2
|
35.8
|
1.0
|
|
HA
|
D:ASN443
|
4.3
|
53.3
|
1.0
|
|
NE2
|
D:HIS440
|
4.4
|
46.1
|
1.0
|
|
O3G
|
D:ATP612
|
4.5
|
45.2
|
1.0
|
|
HB3
|
D:GLU442
|
4.5
|
53.6
|
1.0
|
|
OD1
|
D:ASP460
|
4.5
|
46.0
|
1.0
|
|
HD22
|
D:ASN443
|
4.6
|
59.6
|
1.0
|
|
CB
|
D:ASN443
|
4.6
|
45.5
|
1.0
|
|
C5'
|
D:ATP612
|
4.7
|
51.2
|
1.0
|
|
O2B
|
D:ATP612
|
4.7
|
43.5
|
1.0
|
|
CG
|
D:GLU442
|
4.7
|
48.3
|
1.0
|
|
HB2
|
D:SER275
|
4.8
|
52.1
|
1.0
|
|
HG3
|
D:LYS459
|
4.8
|
65.3
|
1.0
|
|
CA
|
D:ASN443
|
4.8
|
44.4
|
1.0
|
|
O
|
D:GLU442
|
4.8
|
40.5
|
1.0
|
|
H4'
|
D:ATP612
|
4.9
|
58.6
|
1.0
|
|
CB
|
D:SER275
|
4.9
|
43.4
|
1.0
|
|
N
|
D:ASN443
|
4.9
|
44.4
|
1.0
|
|
C
|
D:GLU442
|
5.0
|
40.3
|
1.0
|
|
Magnesium binding site 3 out
of 10 in 7tgk
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Magnesium Binding Sites List in 7tgk
Magnesium binding site 3 out
of 10 in the Crystal Structure of Atp Bound Desd, the Desferrioxamine Synthetase From the Streptomyces Griseoflavus Ferrimycin Biosynthetic Pathway
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Crystal Structure of Atp Bound Desd, the Desferrioxamine Synthetase From the Streptomyces Griseoflavus Ferrimycin Biosynthetic Pathway within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg610
b:33.8
occ:1.00
|
OE2
|
B:GLU464
|
2.3
|
48.1
|
1.0
|
|
O1A
|
B:ATP609
|
2.3
|
44.7
|
1.0
|
|
O
|
B:HOH755
|
2.3
|
41.6
|
1.0
|
|
OD2
|
B:ASP460
|
2.3
|
53.3
|
1.0
|
|
O1B
|
B:ATP609
|
2.3
|
46.6
|
1.0
|
|
OE1
|
B:GLU463
|
2.5
|
52.4
|
1.0
|
|
OD1
|
B:ASP460
|
2.8
|
52.5
|
1.0
|
|
CG
|
B:ASP460
|
2.9
|
50.8
|
1.0
|
|
PA
|
B:ATP609
|
3.3
|
43.8
|
1.0
|
|
HZ1
|
B:LYS291
|
3.4
|
60.9
|
1.0
|
|
CD
|
B:GLU464
|
3.4
|
47.2
|
1.0
|
|
PB
|
B:ATP609
|
3.5
|
47.9
|
1.0
|
|
HG2
|
B:GLU464
|
3.6
|
55.4
|
1.0
|
|
O3A
|
B:ATP609
|
3.7
|
45.2
|
1.0
|
|
HH21
|
B:ARG277
|
3.7
|
55.7
|
1.0
|
|
HB2
|
B:GLU463
|
3.7
|
58.5
|
1.0
|
|
CD
|
B:GLU463
|
3.8
|
55.6
|
1.0
|
|
HZ2
|
B:LYS291
|
3.8
|
60.9
|
1.0
|
|
CG
|
B:GLU464
|
3.9
|
46.1
|
1.0
|
|
HG3
|
B:GLU464
|
3.9
|
55.4
|
1.0
|
|
NZ
|
B:LYS291
|
4.0
|
50.8
|
1.0
|
|
HB3
|
B:GLU463
|
4.0
|
58.5
|
1.0
|
|
O2A
|
B:ATP609
|
4.0
|
41.8
|
1.0
|
|
MG
|
B:MG611
|
4.2
|
50.9
|
1.0
|
|
HZ3
|
B:LYS291
|
4.2
|
60.9
|
1.0
|
|
HH22
|
B:ARG277
|
4.3
|
55.7
|
1.0
|
|
CB
|
B:GLU463
|
4.3
|
48.8
|
1.0
|
|
NH2
|
B:ARG277
|
4.3
|
46.4
|
1.0
|
|
OE1
|
B:GLU464
|
4.4
|
51.2
|
1.0
|
|
O1G
|
B:ATP609
|
4.4
|
48.4
|
1.0
|
|
CB
|
B:ASP460
|
4.4
|
42.6
|
1.0
|
|
O2B
|
B:ATP609
|
4.5
|
42.1
|
1.0
|
|
OE2
|
B:GLU463
|
4.6
|
59.3
|
1.0
|
|
CG
|
B:GLU463
|
4.6
|
53.6
|
1.0
|
|
O3B
|
B:ATP609
|
4.7
|
48.2
|
1.0
|
|
HB2
|
B:ASP460
|
4.8
|
51.1
|
1.0
|
|
O5'
|
B:ATP609
|
4.8
|
44.4
|
1.0
|
|
HB3
|
B:ASP460
|
4.8
|
51.1
|
1.0
|
|
HD21
|
B:ASN443
|
4.9
|
56.2
|
1.0
|
|
Magnesium binding site 4 out
of 10 in 7tgk
Go back to
Magnesium Binding Sites List in 7tgk
Magnesium binding site 4 out
of 10 in the Crystal Structure of Atp Bound Desd, the Desferrioxamine Synthetase From the Streptomyces Griseoflavus Ferrimycin Biosynthetic Pathway
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Crystal Structure of Atp Bound Desd, the Desferrioxamine Synthetase From the Streptomyces Griseoflavus Ferrimycin Biosynthetic Pathway within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg611
b:50.9
occ:1.00
|
O2G
|
B:ATP609
|
2.2
|
53.2
|
1.0
|
|
OD1
|
B:ASN443
|
2.3
|
46.8
|
1.0
|
|
O3A
|
B:ATP609
|
2.3
|
45.2
|
1.0
|
|
O2A
|
B:ATP609
|
2.3
|
41.8
|
1.0
|
|
OE1
|
B:GLU442
|
2.5
|
51.5
|
1.0
|
|
OD2
|
B:ASP460
|
2.5
|
53.3
|
1.0
|
|
PA
|
B:ATP609
|
2.8
|
43.8
|
1.0
|
|
HB2
|
B:ASP460
|
3.1
|
51.1
|
1.0
|
|
H5'2
|
B:ATP609
|
3.2
|
46.2
|
1.0
|
|
HD21
|
B:ASN443
|
3.2
|
56.2
|
1.0
|
|
CG
|
B:ASN443
|
3.3
|
46.7
|
1.0
|
|
CG
|
B:ASP460
|
3.3
|
50.8
|
1.0
|
|
PG
|
B:ATP609
|
3.4
|
50.2
|
1.0
|
|
HE1
|
B:HIS440
|
3.4
|
54.4
|
1.0
|
|
PB
|
B:ATP609
|
3.5
|
47.9
|
1.0
|
|
CD
|
B:GLU442
|
3.5
|
54.2
|
1.0
|
|
CB
|
B:ASP460
|
3.6
|
42.6
|
1.0
|
|
O3B
|
B:ATP609
|
3.6
|
48.2
|
1.0
|
|
HZ2
|
B:LYS459
|
3.6
|
70.1
|
1.0
|
|
HB3
|
B:ASP460
|
3.6
|
51.1
|
1.0
|
|
ND2
|
B:ASN443
|
3.6
|
46.8
|
1.0
|
|
OE2
|
B:GLU442
|
3.8
|
54.9
|
1.0
|
|
O1B
|
B:ATP609
|
3.8
|
46.6
|
1.0
|
|
O1A
|
B:ATP609
|
3.9
|
44.7
|
1.0
|
|
O1G
|
B:ATP609
|
3.9
|
48.4
|
1.0
|
|
HE2
|
B:HIS440
|
3.9
|
53.1
|
1.0
|
|
O5'
|
B:ATP609
|
4.0
|
44.4
|
1.0
|
|
C5'
|
B:ATP609
|
4.0
|
38.5
|
1.0
|
|
CE1
|
B:HIS440
|
4.1
|
45.3
|
1.0
|
|
HZ1
|
B:LYS459
|
4.2
|
70.1
|
1.0
|
|
MG
|
B:MG610
|
4.2
|
33.8
|
1.0
|
|
NZ
|
B:LYS459
|
4.2
|
58.4
|
1.0
|
|
HA
|
B:ASN443
|
4.3
|
48.3
|
1.0
|
|
NE2
|
B:HIS440
|
4.3
|
44.3
|
1.0
|
|
HB3
|
B:SER275
|
4.4
|
48.0
|
1.0
|
|
HZ3
|
B:LYS459
|
4.4
|
70.1
|
1.0
|
|
OD1
|
B:ASP460
|
4.4
|
52.5
|
1.0
|
|
HD22
|
B:ASN443
|
4.5
|
56.2
|
1.0
|
|
O3G
|
B:ATP609
|
4.5
|
46.1
|
1.0
|
|
HB3
|
B:GLU442
|
4.6
|
53.3
|
1.0
|
|
CB
|
B:ASN443
|
4.6
|
43.0
|
1.0
|
|
H5'1
|
B:ATP609
|
4.7
|
46.2
|
1.0
|
|
O2B
|
B:ATP609
|
4.7
|
42.1
|
1.0
|
|
HG3
|
B:LYS459
|
4.8
|
59.0
|
1.0
|
|
CA
|
B:ASN443
|
4.8
|
40.2
|
1.0
|
|
CG
|
B:GLU442
|
4.9
|
53.0
|
1.0
|
|
H4'
|
B:ATP609
|
4.9
|
47.2
|
1.0
|
|
HG3
|
B:GLU464
|
5.0
|
55.4
|
1.0
|
|
O
|
B:GLU442
|
5.0
|
39.3
|
1.0
|
|
Magnesium binding site 5 out
of 10 in 7tgk
Go back to
Magnesium Binding Sites List in 7tgk
Magnesium binding site 5 out
of 10 in the Crystal Structure of Atp Bound Desd, the Desferrioxamine Synthetase From the Streptomyces Griseoflavus Ferrimycin Biosynthetic Pathway
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of Crystal Structure of Atp Bound Desd, the Desferrioxamine Synthetase From the Streptomyces Griseoflavus Ferrimycin Biosynthetic Pathway within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Mg608
b:44.0
occ:1.00
|
O1B
|
E:ATP607
|
2.3
|
46.7
|
1.0
|
|
OE2
|
E:GLU464
|
2.3
|
52.7
|
1.0
|
|
O
|
E:HOH774
|
2.3
|
53.1
|
1.0
|
|
OD2
|
E:ASP460
|
2.4
|
55.5
|
1.0
|
|
O1A
|
E:ATP607
|
2.4
|
51.8
|
1.0
|
|
OE1
|
E:GLU463
|
2.6
|
54.6
|
1.0
|
|
OD1
|
E:ASP460
|
2.8
|
53.8
|
1.0
|
|
CG
|
E:ASP460
|
2.9
|
52.1
|
1.0
|
|
HZ1
|
E:LYS291
|
3.3
|
64.8
|
1.0
|
|
CD
|
E:GLU464
|
3.4
|
57.5
|
1.0
|
|
PA
|
E:ATP607
|
3.4
|
53.3
|
1.0
|
|
PB
|
E:ATP607
|
3.4
|
49.8
|
1.0
|
|
HH21
|
E:ARG277
|
3.6
|
67.0
|
1.0
|
|
O3A
|
E:ATP607
|
3.6
|
54.6
|
1.0
|
|
HG2
|
E:GLU464
|
3.7
|
65.7
|
1.0
|
|
HB2
|
E:GLU463
|
3.7
|
66.2
|
1.0
|
|
CD
|
E:GLU463
|
3.8
|
60.2
|
1.0
|
|
HZ2
|
E:LYS291
|
3.9
|
64.8
|
1.0
|
|
CG
|
E:GLU464
|
4.0
|
54.8
|
1.0
|
|
NZ
|
E:LYS291
|
4.0
|
54.0
|
1.0
|
|
HG3
|
E:GLU464
|
4.0
|
65.7
|
1.0
|
|
O2A
|
E:ATP607
|
4.0
|
48.0
|
1.0
|
|
HB3
|
E:GLU463
|
4.1
|
66.2
|
1.0
|
|
HH22
|
E:ARG277
|
4.1
|
67.0
|
1.0
|
|
NH2
|
E:ARG277
|
4.2
|
55.9
|
1.0
|
|
HZ3
|
E:LYS291
|
4.3
|
64.8
|
1.0
|
|
CB
|
E:GLU463
|
4.3
|
55.2
|
1.0
|
|
MG
|
E:MG609
|
4.3
|
51.0
|
1.0
|
|
O1G
|
E:ATP607
|
4.4
|
48.4
|
1.0
|
|
OE1
|
E:GLU464
|
4.4
|
60.3
|
1.0
|
|
O2B
|
E:ATP607
|
4.5
|
47.7
|
1.0
|
|
CB
|
E:ASP460
|
4.5
|
49.2
|
1.0
|
|
O3B
|
E:ATP607
|
4.7
|
52.1
|
1.0
|
|
OE2
|
E:GLU463
|
4.7
|
63.0
|
1.0
|
|
CG
|
E:GLU463
|
4.7
|
60.0
|
1.0
|
|
HB3
|
E:ASP460
|
4.8
|
59.1
|
1.0
|
|
HB2
|
E:ASP460
|
4.8
|
59.1
|
1.0
|
|
HD21
|
E:ASN443
|
4.8
|
65.1
|
1.0
|
|
HH12
|
E:ARG303
|
4.8
|
65.4
|
1.0
|
|
O5'
|
E:ATP607
|
4.9
|
49.4
|
1.0
|
|
O
|
E:HOH702
|
5.0
|
48.9
|
1.0
|
|
Magnesium binding site 6 out
of 10 in 7tgk
Go back to
Magnesium Binding Sites List in 7tgk
Magnesium binding site 6 out
of 10 in the Crystal Structure of Atp Bound Desd, the Desferrioxamine Synthetase From the Streptomyces Griseoflavus Ferrimycin Biosynthetic Pathway
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 6 of Crystal Structure of Atp Bound Desd, the Desferrioxamine Synthetase From the Streptomyces Griseoflavus Ferrimycin Biosynthetic Pathway within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Mg609
b:51.0
occ:1.00
|
O2G
|
E:ATP607
|
2.1
|
51.8
|
1.0
|
|
OD1
|
E:ASN443
|
2.2
|
55.1
|
1.0
|
|
O3A
|
E:ATP607
|
2.3
|
54.6
|
1.0
|
|
OE1
|
E:GLU442
|
2.4
|
53.4
|
1.0
|
|
O2A
|
E:ATP607
|
2.4
|
48.0
|
1.0
|
|
OD2
|
E:ASP460
|
2.5
|
55.5
|
1.0
|
|
PA
|
E:ATP607
|
3.0
|
53.3
|
1.0
|
|
HB2
|
E:ASP460
|
3.0
|
59.1
|
1.0
|
|
CG
|
E:ASN443
|
3.2
|
55.8
|
1.0
|
|
H5'2
|
E:ATP607
|
3.2
|
56.9
|
1.0
|
|
PG
|
E:ATP607
|
3.3
|
49.4
|
1.0
|
|
HD21
|
E:ASN443
|
3.3
|
65.1
|
1.0
|
|
CD
|
E:GLU442
|
3.4
|
55.4
|
1.0
|
|
CG
|
E:ASP460
|
3.4
|
52.1
|
1.0
|
|
HE1
|
E:HIS440
|
3.4
|
60.5
|
1.0
|
|
PB
|
E:ATP607
|
3.5
|
49.8
|
1.0
|
|
O3B
|
E:ATP607
|
3.5
|
52.1
|
1.0
|
|
CB
|
E:ASP460
|
3.5
|
49.2
|
1.0
|
|
OE2
|
E:GLU442
|
3.6
|
56.8
|
1.0
|
|
HB3
|
E:ASP460
|
3.6
|
59.1
|
1.0
|
|
ND2
|
E:ASN443
|
3.6
|
54.2
|
1.0
|
|
O1G
|
E:ATP607
|
3.8
|
48.4
|
1.0
|
|
O1B
|
E:ATP607
|
3.9
|
46.7
|
1.0
|
|
O1A
|
E:ATP607
|
4.0
|
51.8
|
1.0
|
|
O5'
|
E:ATP607
|
4.1
|
49.4
|
1.0
|
|
C5'
|
E:ATP607
|
4.1
|
47.5
|
1.0
|
|
CE1
|
E:HIS440
|
4.2
|
50.5
|
1.0
|
|
HA
|
E:ASN443
|
4.2
|
59.3
|
1.0
|
|
HE2
|
E:HIS440
|
4.2
|
59.7
|
1.0
|
|
MG
|
E:MG608
|
4.3
|
44.0
|
1.0
|
|
HB3
|
E:SER275
|
4.3
|
54.4
|
1.0
|
|
OD1
|
E:ASP460
|
4.4
|
53.8
|
1.0
|
|
HD22
|
E:ASN443
|
4.5
|
65.1
|
1.0
|
|
O3G
|
E:ATP607
|
4.5
|
54.9
|
1.0
|
|
HE3
|
E:LYS459
|
4.5
|
77.7
|
1.0
|
|
CB
|
E:ASN443
|
4.5
|
53.0
|
1.0
|
|
NE2
|
E:HIS440
|
4.5
|
49.8
|
1.0
|
|
HB3
|
E:GLU442
|
4.5
|
63.7
|
1.0
|
|
HG3
|
E:LYS459
|
4.5
|
67.8
|
1.0
|
|
CA
|
E:ASN443
|
4.7
|
49.4
|
1.0
|
|
O2B
|
E:ATP607
|
4.7
|
47.7
|
1.0
|
|
H5'1
|
E:ATP607
|
4.7
|
56.9
|
1.0
|
|
CG
|
E:GLU442
|
4.8
|
54.0
|
1.0
|
|
O
|
E:GLU442
|
4.8
|
46.7
|
1.0
|
|
N
|
E:ASN443
|
4.8
|
51.0
|
1.0
|
|
H4'
|
E:ATP607
|
4.9
|
57.9
|
1.0
|
|
C
|
E:GLU442
|
4.9
|
48.3
|
1.0
|
|
HB2
|
E:SER275
|
5.0
|
54.4
|
1.0
|
|
CA
|
E:ASP460
|
5.0
|
50.2
|
1.0
|
|
Magnesium binding site 7 out
of 10 in 7tgk
Go back to
Magnesium Binding Sites List in 7tgk
Magnesium binding site 7 out
of 10 in the Crystal Structure of Atp Bound Desd, the Desferrioxamine Synthetase From the Streptomyces Griseoflavus Ferrimycin Biosynthetic Pathway
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 7 of Crystal Structure of Atp Bound Desd, the Desferrioxamine Synthetase From the Streptomyces Griseoflavus Ferrimycin Biosynthetic Pathway within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg613
b:36.2
occ:1.00
|
OE2
|
A:GLU463
|
1.9
|
51.4
|
1.0
|
|
OE2
|
A:GLU464
|
2.2
|
55.9
|
1.0
|
|
O
|
A:HOH770
|
2.3
|
52.3
|
1.0
|
|
O1B
|
A:ATP612
|
2.3
|
49.0
|
1.0
|
|
OD2
|
A:ASP460
|
2.4
|
49.0
|
1.0
|
|
OD1
|
A:ASP460
|
2.8
|
49.8
|
1.0
|
|
O1A
|
A:ATP612
|
2.9
|
48.1
|
1.0
|
|
CG
|
A:ASP460
|
3.0
|
48.6
|
1.0
|
|
CD
|
A:GLU463
|
3.0
|
55.3
|
1.0
|
|
HG3
|
A:GLU463
|
3.2
|
65.9
|
1.0
|
|
CD
|
A:GLU464
|
3.3
|
55.7
|
1.0
|
|
PA
|
A:ATP612
|
3.4
|
48.4
|
1.0
|
|
HZ1
|
A:LYS291
|
3.5
|
53.4
|
1.0
|
|
PB
|
A:ATP612
|
3.5
|
43.6
|
1.0
|
|
CG
|
A:GLU463
|
3.5
|
54.9
|
1.0
|
|
O3A
|
A:ATP612
|
3.5
|
50.9
|
1.0
|
|
HH21
|
A:ARG277
|
3.6
|
58.9
|
1.0
|
|
HG2
|
A:GLU464
|
3.7
|
63.7
|
1.0
|
|
HG2
|
A:GLU463
|
3.7
|
65.9
|
1.0
|
|
O2A
|
A:ATP612
|
3.8
|
53.5
|
1.0
|
|
CG
|
A:GLU464
|
3.9
|
53.1
|
1.0
|
|
HG3
|
A:GLU464
|
3.9
|
63.7
|
1.0
|
|
HZ2
|
A:LYS291
|
4.0
|
53.4
|
1.0
|
|
NZ
|
A:LYS291
|
4.1
|
44.5
|
1.0
|
|
OE1
|
A:GLU463
|
4.2
|
54.0
|
1.0
|
|
MG
|
A:MG614
|
4.2
|
47.0
|
1.0
|
|
NH2
|
A:ARG277
|
4.3
|
49.1
|
1.0
|
|
OE1
|
A:GLU464
|
4.3
|
58.3
|
1.0
|
|
HH22
|
A:ARG277
|
4.3
|
58.9
|
1.0
|
|
HZ3
|
A:LYS291
|
4.4
|
53.4
|
1.0
|
|
CB
|
A:ASP460
|
4.5
|
46.2
|
1.0
|
|
O2B
|
A:ATP612
|
4.5
|
44.5
|
1.0
|
|
O1G
|
A:ATP612
|
4.5
|
45.5
|
1.0
|
|
O3B
|
A:ATP612
|
4.6
|
44.3
|
1.0
|
|
HB3
|
A:ASP460
|
4.8
|
55.4
|
1.0
|
|
HD21
|
A:ASN443
|
4.8
|
55.3
|
1.0
|
|
HH12
|
A:ARG303
|
4.8
|
52.7
|
1.0
|
|
HB2
|
A:ASP460
|
4.8
|
55.4
|
1.0
|
|
O2G
|
A:ATP612
|
4.9
|
48.5
|
1.0
|
|
CB
|
A:GLU463
|
4.9
|
55.6
|
1.0
|
|
HH11
|
A:ARG303
|
5.0
|
52.7
|
1.0
|
|
O5'
|
A:ATP612
|
5.0
|
65.0
|
1.0
|
|
PG
|
A:ATP612
|
5.0
|
48.4
|
1.0
|
|
Magnesium binding site 8 out
of 10 in 7tgk
Go back to
Magnesium Binding Sites List in 7tgk
Magnesium binding site 8 out
of 10 in the Crystal Structure of Atp Bound Desd, the Desferrioxamine Synthetase From the Streptomyces Griseoflavus Ferrimycin Biosynthetic Pathway
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 8 of Crystal Structure of Atp Bound Desd, the Desferrioxamine Synthetase From the Streptomyces Griseoflavus Ferrimycin Biosynthetic Pathway within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg614
b:47.0
occ:1.00
|
O2A
|
A:ATP612
|
2.0
|
53.5
|
1.0
|
|
OD1
|
A:ASN443
|
2.1
|
46.7
|
1.0
|
|
O2G
|
A:ATP612
|
2.1
|
48.5
|
1.0
|
|
O3A
|
A:ATP612
|
2.3
|
50.9
|
1.0
|
|
OE1
|
A:GLU442
|
2.4
|
55.5
|
1.0
|
|
OD2
|
A:ASP460
|
2.5
|
49.0
|
1.0
|
|
PA
|
A:ATP612
|
2.6
|
48.4
|
1.0
|
|
HD21
|
A:ASN443
|
3.0
|
55.3
|
1.0
|
|
CG
|
A:ASN443
|
3.1
|
47.3
|
1.0
|
|
HB2
|
A:ASP460
|
3.1
|
55.4
|
1.0
|
|
O5'
|
A:ATP612
|
3.3
|
65.0
|
1.0
|
|
CG
|
A:ASP460
|
3.4
|
48.6
|
1.0
|
|
HE1
|
A:HIS440
|
3.4
|
52.2
|
1.0
|
|
ND2
|
A:ASN443
|
3.4
|
46.1
|
1.0
|
|
PG
|
A:ATP612
|
3.4
|
48.4
|
1.0
|
|
CD
|
A:GLU442
|
3.4
|
52.8
|
1.0
|
|
PB
|
A:ATP612
|
3.6
|
43.6
|
1.0
|
|
CB
|
A:ASP460
|
3.6
|
46.2
|
1.0
|
|
HB3
|
A:ASP460
|
3.6
|
55.4
|
1.0
|
|
OE2
|
A:GLU442
|
3.7
|
53.0
|
1.0
|
|
O3B
|
A:ATP612
|
3.7
|
44.3
|
1.0
|
|
HZ2
|
A:LYS459
|
3.8
|
72.5
|
1.0
|
|
O1A
|
A:ATP612
|
3.9
|
48.1
|
1.0
|
|
O1G
|
A:ATP612
|
4.0
|
45.5
|
1.0
|
|
O1B
|
A:ATP612
|
4.0
|
49.0
|
1.0
|
|
HE2
|
A:HIS440
|
4.1
|
50.7
|
1.0
|
|
CE1
|
A:HIS440
|
4.1
|
43.5
|
1.0
|
|
MG
|
A:MG613
|
4.2
|
36.2
|
1.0
|
|
HD22
|
A:ASN443
|
4.2
|
55.3
|
1.0
|
|
HA
|
A:ASN443
|
4.3
|
57.3
|
1.0
|
|
HZ1
|
A:LYS459
|
4.3
|
72.5
|
1.0
|
|
NZ
|
A:LYS459
|
4.4
|
60.4
|
1.0
|
|
HB3
|
A:SER275
|
4.4
|
50.9
|
1.0
|
|
HB3
|
A:GLU442
|
4.4
|
58.0
|
1.0
|
|
NE2
|
A:HIS440
|
4.4
|
42.2
|
1.0
|
|
CB
|
A:ASN443
|
4.4
|
46.6
|
1.0
|
|
HZ3
|
A:LYS459
|
4.4
|
72.5
|
1.0
|
|
OD1
|
A:ASP460
|
4.5
|
49.8
|
1.0
|
|
O3G
|
A:ATP612
|
4.6
|
48.5
|
1.0
|
|
C5'
|
A:ATP612
|
4.7
|
59.5
|
1.0
|
|
CA
|
A:ASN443
|
4.7
|
47.7
|
1.0
|
|
CG
|
A:GLU442
|
4.8
|
50.7
|
1.0
|
|
O2B
|
A:ATP612
|
4.8
|
44.5
|
1.0
|
|
HG3
|
A:LYS459
|
4.8
|
66.2
|
1.0
|
|
N
|
A:ASN443
|
4.9
|
46.3
|
1.0
|
|
HG3
|
A:GLU464
|
5.0
|
63.7
|
1.0
|
|
HB3
|
A:ASN443
|
5.0
|
55.9
|
1.0
|
|
HB2
|
A:ASN443
|
5.0
|
55.9
|
1.0
|
|
Magnesium binding site 9 out
of 10 in 7tgk
Go back to
Magnesium Binding Sites List in 7tgk
Magnesium binding site 9 out
of 10 in the Crystal Structure of Atp Bound Desd, the Desferrioxamine Synthetase From the Streptomyces Griseoflavus Ferrimycin Biosynthetic Pathway
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 9 of Crystal Structure of Atp Bound Desd, the Desferrioxamine Synthetase From the Streptomyces Griseoflavus Ferrimycin Biosynthetic Pathway within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg605
b:44.7
occ:1.00
|
OE2
|
C:GLU464
|
2.0
|
56.0
|
1.0
|
|
O1B
|
C:ATP604
|
2.4
|
50.2
|
1.0
|
|
OE1
|
C:GLU463
|
2.5
|
57.0
|
1.0
|
|
OD2
|
C:ASP460
|
2.5
|
54.6
|
1.0
|
|
OD1
|
C:ASP460
|
2.8
|
56.7
|
1.0
|
|
O1A
|
C:ATP604
|
2.9
|
47.1
|
1.0
|
|
CG
|
C:ASP460
|
3.0
|
55.3
|
1.0
|
|
CD
|
C:GLU464
|
3.2
|
62.4
|
1.0
|
|
HB2
|
C:GLU463
|
3.5
|
70.3
|
1.0
|
|
HZ1
|
C:LYS291
|
3.5
|
59.1
|
1.0
|
|
PA
|
C:ATP604
|
3.6
|
55.4
|
1.0
|
|
HG2
|
C:GLU464
|
3.6
|
70.5
|
1.0
|
|
PB
|
C:ATP604
|
3.7
|
46.8
|
1.0
|
|
O2A
|
C:ATP604
|
3.7
|
53.8
|
1.0
|
|
CD
|
C:GLU463
|
3.7
|
60.8
|
1.0
|
|
HH21
|
C:ARG277
|
3.8
|
64.5
|
1.0
|
|
HB3
|
C:GLU463
|
3.8
|
70.3
|
1.0
|
|
CG
|
C:GLU464
|
3.9
|
58.7
|
1.0
|
|
O3A
|
C:ATP604
|
3.9
|
54.2
|
1.0
|
|
HG3
|
C:GLU464
|
4.0
|
70.5
|
1.0
|
|
CB
|
C:GLU463
|
4.1
|
58.6
|
1.0
|
|
HZ2
|
C:LYS291
|
4.1
|
59.1
|
1.0
|
|
NZ
|
C:LYS291
|
4.2
|
49.2
|
1.0
|
|
OE1
|
C:GLU464
|
4.2
|
68.0
|
1.0
|
|
HH22
|
C:ARG277
|
4.3
|
64.5
|
1.0
|
|
NH2
|
C:ARG277
|
4.4
|
53.7
|
1.0
|
|
MG
|
C:MG606
|
4.4
|
53.6
|
1.0
|
|
HZ3
|
C:LYS291
|
4.4
|
59.1
|
1.0
|
|
O1G
|
C:ATP604
|
4.4
|
49.0
|
1.0
|
|
CG
|
C:GLU463
|
4.5
|
61.2
|
1.0
|
|
CB
|
C:ASP460
|
4.6
|
52.5
|
1.0
|
|
OE2
|
C:GLU463
|
4.6
|
62.0
|
1.0
|
|
O2B
|
C:ATP604
|
4.6
|
50.1
|
1.0
|
|
O3B
|
C:ATP604
|
4.8
|
51.0
|
1.0
|
|
HB3
|
C:ASP460
|
4.9
|
63.0
|
1.0
|
|
HD21
|
C:ASN443
|
4.9
|
53.4
|
1.0
|
|
HB2
|
C:ASP460
|
5.0
|
63.0
|
1.0
|
|
HH12
|
C:ARG303
|
5.0
|
55.2
|
1.0
|
|
Magnesium binding site 10 out
of 10 in 7tgk
Go back to
Magnesium Binding Sites List in 7tgk
Magnesium binding site 10 out
of 10 in the Crystal Structure of Atp Bound Desd, the Desferrioxamine Synthetase From the Streptomyces Griseoflavus Ferrimycin Biosynthetic Pathway
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 10 of Crystal Structure of Atp Bound Desd, the Desferrioxamine Synthetase From the Streptomyces Griseoflavus Ferrimycin Biosynthetic Pathway within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg606
b:53.6
occ:1.00
|
O2G
|
C:ATP604
|
1.9
|
53.6
|
1.0
|
|
O2A
|
C:ATP604
|
2.2
|
53.8
|
1.0
|
|
OD1
|
C:ASN443
|
2.2
|
50.5
|
1.0
|
|
OE1
|
C:GLU442
|
2.3
|
52.0
|
1.0
|
|
OD2
|
C:ASP460
|
2.5
|
54.6
|
1.0
|
|
O3A
|
C:ATP604
|
2.5
|
54.2
|
1.0
|
|
PA
|
C:ATP604
|
2.9
|
55.4
|
1.0
|
|
HB2
|
C:ASP460
|
3.1
|
63.0
|
1.0
|
|
PG
|
C:ATP604
|
3.2
|
50.9
|
1.0
|
|
CD
|
C:GLU442
|
3.3
|
56.2
|
1.0
|
|
CG
|
C:ASP460
|
3.3
|
55.3
|
1.0
|
|
CG
|
C:ASN443
|
3.3
|
47.4
|
1.0
|
|
HZ2
|
C:LYS459
|
3.4
|
78.9
|
1.0
|
|
HD21
|
C:ASN443
|
3.4
|
53.4
|
1.0
|
|
HE1
|
C:HIS440
|
3.5
|
63.3
|
1.0
|
|
O3B
|
C:ATP604
|
3.5
|
51.0
|
1.0
|
|
PB
|
C:ATP604
|
3.5
|
46.8
|
1.0
|
|
O5'
|
C:ATP604
|
3.6
|
54.2
|
1.0
|
|
OE2
|
C:GLU442
|
3.6
|
59.6
|
1.0
|
|
CB
|
C:ASP460
|
3.6
|
52.5
|
1.0
|
|
ND2
|
C:ASN443
|
3.7
|
44.5
|
1.0
|
|
O1G
|
C:ATP604
|
3.7
|
49.0
|
1.0
|
|
HB3
|
C:ASP460
|
3.8
|
63.0
|
1.0
|
|
O1B
|
C:ATP604
|
3.8
|
50.2
|
1.0
|
|
HZ1
|
C:LYS459
|
3.9
|
78.9
|
1.0
|
|
NZ
|
C:LYS459
|
4.0
|
65.7
|
1.0
|
|
O1A
|
C:ATP604
|
4.1
|
47.1
|
1.0
|
|
HA
|
C:ASN443
|
4.2
|
61.7
|
1.0
|
|
HZ3
|
C:LYS459
|
4.2
|
78.9
|
1.0
|
|
HB3
|
C:SER275
|
4.2
|
55.5
|
1.0
|
|
CE1
|
C:HIS440
|
4.3
|
52.7
|
1.0
|
|
HE2
|
C:HIS440
|
4.3
|
62.9
|
1.0
|
|
OD1
|
C:ASP460
|
4.3
|
56.7
|
1.0
|
|
O3G
|
C:ATP604
|
4.4
|
48.1
|
1.0
|
|
MG
|
C:MG605
|
4.4
|
44.7
|
1.0
|
|
HB3
|
C:GLU442
|
4.5
|
64.7
|
1.0
|
|
HD22
|
C:ASN443
|
4.6
|
53.4
|
1.0
|
|
CB
|
C:ASN443
|
4.6
|
49.6
|
1.0
|
|
HG3
|
C:LYS459
|
4.6
|
71.0
|
1.0
|
|
NE2
|
C:HIS440
|
4.6
|
52.4
|
1.0
|
|
CG
|
C:GLU442
|
4.7
|
54.4
|
1.0
|
|
CA
|
C:ASN443
|
4.7
|
51.4
|
1.0
|
|
O2B
|
C:ATP604
|
4.8
|
50.1
|
1.0
|
|
HB2
|
C:SER275
|
4.8
|
55.5
|
1.0
|
|
C5'
|
C:ATP604
|
4.9
|
54.2
|
1.0
|
|
O
|
C:GLU442
|
4.9
|
48.5
|
1.0
|
|
N
|
C:ASN443
|
4.9
|
50.5
|
1.0
|
|
H4'
|
C:ATP604
|
4.9
|
59.7
|
1.0
|
|
C
|
C:GLU442
|
5.0
|
49.9
|
1.0
|
|
CB
|
C:SER275
|
5.0
|
46.3
|
1.0
|
|
CA
|
C:ASP460
|
5.0
|
50.6
|
1.0
|
|
Reference:
J.Yang,
V.S.Banas,
K.D.Patel,
G.S.M.Rivera,
L.S.Mydy,
A.M.Gulick,
T.A.Wencewicz.
An Acyl-Adenylate Mimic Reveals the Structural Basis For Substrate Recognition By the Iterative Siderophore Synthetase Desd. J.Biol.Chem. V. 298 02166 2022.
ISSN: ESSN 1083-351X
PubMed: 35750210
DOI: 10.1016/J.JBC.2022.102166
Page generated: Thu Oct 3 09:09:49 2024
|
