Magnesium in PDB 6pjw: Adenylate Kinase From Methanococcus Igneus - Amp Bound Form
Enzymatic activity of Adenylate Kinase From Methanococcus Igneus - Amp Bound Form
All present enzymatic activity of Adenylate Kinase From Methanococcus Igneus - Amp Bound Form:
2.7.4.3;
Protein crystallography data
The structure of Adenylate Kinase From Methanococcus Igneus - Amp Bound Form, PDB code: 6pjw
was solved by
S.Moon,
J.Kim,
J.L.Olmos,
E.Bae,
G.N.Phillips,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
44.33 /
2.40
|
|
Space group
|
P 1 21 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
88.770,
121.390,
121.040,
90.00,
102.95,
90.00
|
|
R / Rfree (%)
|
20 /
24.8
|
Magnesium Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
12;
Binding sites:
The binding sites of Magnesium atom in the Adenylate Kinase From Methanococcus Igneus - Amp Bound Form
(pdb code 6pjw). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 12 binding sites of Magnesium where determined in the
Adenylate Kinase From Methanococcus Igneus - Amp Bound Form, PDB code: 6pjw:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Magnesium binding site 1 out
of 12 in 6pjw
Go back to
Magnesium Binding Sites List in 6pjw
Magnesium binding site 1 out
of 12 in the Adenylate Kinase From Methanococcus Igneus - Amp Bound Form
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Adenylate Kinase From Methanococcus Igneus - Amp Bound Form within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg303
b:70.5
occ:1.00
|
O
|
A:HOH408
|
2.0
|
73.3
|
1.0
|
|
O
|
A:HOH407
|
2.0
|
73.2
|
1.0
|
|
O
|
A:HOH410
|
2.0
|
67.9
|
1.0
|
|
O
|
A:HOH412
|
2.1
|
68.3
|
1.0
|
|
O
|
A:HOH402
|
2.1
|
69.8
|
1.0
|
|
OG1
|
A:THR17
|
2.1
|
67.2
|
1.0
|
|
HB
|
A:THR17
|
3.1
|
53.5
|
1.0
|
|
CB
|
A:THR17
|
3.2
|
68.0
|
1.0
|
|
HH22
|
A:ARG140
|
3.2
|
53.5
|
1.0
|
|
HH21
|
A:ARG140
|
3.3
|
53.5
|
1.0
|
|
H
|
A:THR17
|
3.5
|
53.5
|
1.0
|
|
HOP3
|
A:AMP301
|
3.5
|
53.5
|
1.0
|
|
NH2
|
A:ARG140
|
3.6
|
79.1
|
1.0
|
|
OD2
|
A:ASP90
|
3.9
|
64.7
|
1.0
|
|
HH12
|
A:ARG138
|
3.9
|
53.5
|
1.0
|
|
HG21
|
A:THR17
|
4.0
|
53.5
|
1.0
|
|
O3P
|
A:AMP302
|
4.0
|
70.0
|
1.0
|
|
O2P
|
A:AMP301
|
4.0
|
59.9
|
1.0
|
|
HD21
|
A:ASN38
|
4.1
|
53.5
|
1.0
|
|
HOP2
|
A:AMP302
|
4.1
|
53.5
|
1.0
|
|
N
|
A:THR17
|
4.1
|
66.5
|
1.0
|
|
CG2
|
A:THR17
|
4.2
|
71.0
|
1.0
|
|
O3P
|
A:AMP301
|
4.2
|
62.3
|
1.0
|
|
CA
|
A:THR17
|
4.2
|
69.2
|
1.0
|
|
OD1
|
A:ASP90
|
4.3
|
61.0
|
1.0
|
|
O1P
|
A:AMP301
|
4.3
|
60.0
|
1.0
|
|
P
|
A:AMP301
|
4.3
|
60.9
|
1.0
|
|
O2P
|
A:AMP302
|
4.3
|
64.9
|
1.0
|
|
HH11
|
A:ARG138
|
4.5
|
53.5
|
1.0
|
|
NH1
|
A:ARG138
|
4.5
|
78.8
|
1.0
|
|
CG
|
A:ASP90
|
4.5
|
63.1
|
1.0
|
|
HA
|
A:THR17
|
4.6
|
53.5
|
1.0
|
|
HG23
|
A:THR17
|
4.6
|
53.5
|
1.0
|
|
HOP3
|
A:AMP302
|
4.6
|
53.5
|
1.0
|
|
P
|
A:AMP302
|
4.6
|
67.4
|
1.0
|
|
ND2
|
A:ASN38
|
4.7
|
64.3
|
1.0
|
|
HD22
|
A:ASN38
|
4.7
|
53.5
|
1.0
|
|
HOP2
|
A:AMP301
|
4.8
|
53.5
|
1.0
|
|
HE1
|
A:HIS92
|
4.9
|
53.5
|
1.0
|
|
CZ
|
A:ARG140
|
5.0
|
79.0
|
1.0
|
|
HG22
|
A:THR17
|
5.0
|
53.5
|
1.0
|
|
Magnesium binding site 2 out
of 12 in 6pjw
Go back to
Magnesium Binding Sites List in 6pjw
Magnesium binding site 2 out
of 12 in the Adenylate Kinase From Methanococcus Igneus - Amp Bound Form
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Adenylate Kinase From Methanococcus Igneus - Amp Bound Form within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg303
b:49.1
occ:1.00
|
O
|
B:HOH405
|
2.0
|
52.5
|
1.0
|
|
O
|
B:HOH413
|
2.0
|
49.4
|
1.0
|
|
O
|
B:HOH404
|
2.1
|
49.4
|
1.0
|
|
O
|
B:HOH417
|
2.1
|
49.9
|
1.0
|
|
O
|
B:HOH421
|
2.1
|
46.0
|
1.0
|
|
OG1
|
B:THR17
|
2.2
|
42.7
|
1.0
|
|
HB
|
B:THR17
|
3.1
|
53.5
|
1.0
|
|
CB
|
B:THR17
|
3.2
|
43.9
|
1.0
|
|
H
|
B:THR17
|
3.4
|
53.5
|
1.0
|
|
O
|
B:HOH401
|
3.6
|
50.3
|
1.0
|
|
HH12
|
B:ARG138
|
3.7
|
53.5
|
1.0
|
|
HOP3
|
B:AMP301
|
3.7
|
53.5
|
1.0
|
|
HH22
|
B:ARG140
|
3.9
|
53.5
|
1.0
|
|
HD21
|
B:ASN38
|
3.9
|
53.5
|
1.0
|
|
HG21
|
B:THR17
|
4.0
|
53.5
|
1.0
|
|
O3P
|
B:AMP302
|
4.0
|
45.8
|
1.0
|
|
HH21
|
B:ARG140
|
4.0
|
53.5
|
1.0
|
|
OD2
|
B:ASP90
|
4.1
|
45.9
|
1.0
|
|
N
|
B:THR17
|
4.1
|
44.6
|
1.0
|
|
O2P
|
B:AMP302
|
4.1
|
44.8
|
1.0
|
|
O1P
|
B:AMP301
|
4.1
|
47.9
|
1.0
|
|
O2P
|
B:AMP301
|
4.1
|
44.8
|
1.0
|
|
CG2
|
B:THR17
|
4.2
|
45.2
|
1.0
|
|
O3P
|
B:AMP301
|
4.2
|
49.9
|
1.0
|
|
CA
|
B:THR17
|
4.2
|
45.4
|
1.0
|
|
P
|
B:AMP301
|
4.3
|
46.8
|
1.0
|
|
NH2
|
B:ARG140
|
4.3
|
60.5
|
1.0
|
|
NH1
|
B:ARG138
|
4.3
|
58.3
|
1.0
|
|
O
|
B:HOH424
|
4.3
|
50.7
|
1.0
|
|
HH11
|
B:ARG138
|
4.4
|
53.5
|
1.0
|
|
HD22
|
B:ASN38
|
4.4
|
53.5
|
1.0
|
|
OD1
|
B:ASP90
|
4.4
|
43.7
|
1.0
|
|
P
|
B:AMP302
|
4.5
|
45.9
|
1.0
|
|
ND2
|
B:ASN38
|
4.5
|
46.3
|
1.0
|
|
HA
|
B:THR17
|
4.6
|
53.5
|
1.0
|
|
HOP3
|
B:AMP302
|
4.7
|
53.5
|
1.0
|
|
CG
|
B:ASP90
|
4.7
|
44.4
|
1.0
|
|
O
|
B:HOH416
|
4.8
|
50.7
|
1.0
|
|
HE2
|
B:HIS92
|
4.8
|
53.5
|
1.0
|
|
HG23
|
B:THR17
|
4.8
|
53.5
|
1.0
|
|
O1P
|
B:AMP302
|
4.8
|
44.8
|
1.0
|
|
HG22
|
B:THR17
|
4.8
|
53.5
|
1.0
|
|
HOP2
|
B:AMP302
|
4.9
|
53.5
|
1.0
|
|
Magnesium binding site 3 out
of 12 in 6pjw
Go back to
Magnesium Binding Sites List in 6pjw
Magnesium binding site 3 out
of 12 in the Adenylate Kinase From Methanococcus Igneus - Amp Bound Form
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Adenylate Kinase From Methanococcus Igneus - Amp Bound Form within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg303
b:54.5
occ:1.00
|
OG1
|
C:THR17
|
2.0
|
52.3
|
1.0
|
|
O
|
C:HOH406
|
2.0
|
57.8
|
1.0
|
|
O
|
C:HOH419
|
2.0
|
51.9
|
1.0
|
|
O
|
C:HOH413
|
2.1
|
56.4
|
1.0
|
|
O
|
C:HOH408
|
2.1
|
53.1
|
1.0
|
|
O
|
C:HOH414
|
2.1
|
53.9
|
1.0
|
|
HB
|
C:THR17
|
3.0
|
53.5
|
1.0
|
|
CB
|
C:THR17
|
3.1
|
52.9
|
1.0
|
|
H
|
C:THR17
|
3.5
|
53.5
|
1.0
|
|
HOP3
|
C:AMP301
|
3.7
|
53.5
|
1.0
|
|
O2P
|
C:AMP301
|
3.9
|
55.8
|
1.0
|
|
HH12
|
C:ARG138
|
3.9
|
53.5
|
1.0
|
|
HG21
|
C:THR17
|
3.9
|
53.5
|
1.0
|
|
HOP2
|
C:AMP302
|
4.0
|
53.5
|
1.0
|
|
HD21
|
C:ASN38
|
4.0
|
53.5
|
1.0
|
|
N
|
C:THR17
|
4.0
|
49.2
|
1.0
|
|
OD2
|
C:ASP90
|
4.1
|
54.5
|
1.0
|
|
O1P
|
C:AMP301
|
4.1
|
55.6
|
1.0
|
|
CA
|
C:THR17
|
4.1
|
51.5
|
1.0
|
|
CG2
|
C:THR17
|
4.1
|
55.4
|
1.0
|
|
O3P
|
C:AMP301
|
4.1
|
56.1
|
1.0
|
|
P
|
C:AMP301
|
4.2
|
56.9
|
1.0
|
|
OD1
|
C:ASP90
|
4.2
|
51.2
|
1.0
|
|
O2P
|
C:AMP302
|
4.3
|
49.9
|
1.0
|
|
HA
|
C:THR17
|
4.3
|
53.5
|
1.0
|
|
O3P
|
C:AMP302
|
4.3
|
50.0
|
1.0
|
|
HD22
|
C:ASN38
|
4.4
|
53.5
|
1.0
|
|
O1P
|
C:AMP302
|
4.4
|
52.8
|
1.0
|
|
HOP3
|
C:AMP302
|
4.5
|
53.5
|
1.0
|
|
ND2
|
C:ASN38
|
4.5
|
57.5
|
1.0
|
|
P
|
C:AMP302
|
4.6
|
51.9
|
1.0
|
|
CG
|
C:ASP90
|
4.6
|
53.1
|
1.0
|
|
HOP2
|
C:AMP301
|
4.6
|
53.5
|
1.0
|
|
HG23
|
C:THR17
|
4.7
|
53.5
|
1.0
|
|
NH1
|
C:ARG138
|
4.7
|
79.3
|
1.0
|
|
HG22
|
C:THR17
|
4.8
|
53.5
|
1.0
|
|
HH11
|
C:ARG138
|
5.0
|
53.5
|
1.0
|
|
Magnesium binding site 4 out
of 12 in 6pjw
Go back to
Magnesium Binding Sites List in 6pjw
Magnesium binding site 4 out
of 12 in the Adenylate Kinase From Methanococcus Igneus - Amp Bound Form
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Adenylate Kinase From Methanococcus Igneus - Amp Bound Form within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg303
b:57.7
occ:1.00
|
O
|
D:HOH404
|
2.0
|
60.2
|
1.0
|
|
O
|
D:HOH414
|
2.0
|
55.4
|
1.0
|
|
O
|
D:HOH411
|
2.1
|
58.9
|
1.0
|
|
O
|
D:HOH415
|
2.1
|
56.4
|
1.0
|
|
O
|
D:HOH416
|
2.1
|
58.0
|
1.0
|
|
OG1
|
D:THR17
|
2.1
|
53.7
|
1.0
|
|
HB
|
D:THR17
|
3.1
|
53.5
|
1.0
|
|
CB
|
D:THR17
|
3.2
|
54.5
|
1.0
|
|
H
|
D:THR17
|
3.5
|
53.5
|
1.0
|
|
HOP3
|
D:AMP301
|
3.6
|
53.5
|
1.0
|
|
HH12
|
D:ARG138
|
3.6
|
53.5
|
1.0
|
|
HOP2
|
D:AMP302
|
3.7
|
53.5
|
1.0
|
|
HG21
|
D:THR17
|
3.9
|
53.5
|
1.0
|
|
O2P
|
D:AMP301
|
4.0
|
54.2
|
1.0
|
|
O3P
|
D:AMP302
|
4.0
|
54.7
|
1.0
|
|
O3P
|
D:AMP301
|
4.1
|
58.1
|
1.0
|
|
HD21
|
D:ASN38
|
4.1
|
53.5
|
1.0
|
|
CG2
|
D:THR17
|
4.1
|
56.3
|
1.0
|
|
N
|
D:THR17
|
4.1
|
52.9
|
1.0
|
|
O1P
|
D:AMP301
|
4.2
|
55.3
|
1.0
|
|
P
|
D:AMP301
|
4.2
|
54.9
|
1.0
|
|
CA
|
D:THR17
|
4.2
|
54.6
|
1.0
|
|
HH21
|
D:ARG140
|
4.3
|
53.5
|
1.0
|
|
O2P
|
D:AMP302
|
4.3
|
52.5
|
1.0
|
|
NH1
|
D:ARG138
|
4.3
|
65.4
|
1.0
|
|
HH22
|
D:ARG140
|
4.4
|
53.5
|
1.0
|
|
OD2
|
D:ASP90
|
4.4
|
52.6
|
1.0
|
|
HOP2
|
D:AMP301
|
4.5
|
53.5
|
1.0
|
|
HD22
|
D:ASN38
|
4.5
|
53.5
|
1.0
|
|
HA
|
D:THR17
|
4.5
|
53.5
|
1.0
|
|
OD1
|
D:ASP90
|
4.6
|
49.9
|
1.0
|
|
HH22
|
D:ARG138
|
4.6
|
53.5
|
1.0
|
|
P
|
D:AMP302
|
4.6
|
54.2
|
1.0
|
|
ND2
|
D:ASN38
|
4.7
|
55.0
|
1.0
|
|
HH11
|
D:ARG138
|
4.7
|
53.5
|
1.0
|
|
NH2
|
D:ARG140
|
4.7
|
65.9
|
1.0
|
|
HOP3
|
D:AMP302
|
4.7
|
53.5
|
1.0
|
|
HG23
|
D:THR17
|
4.7
|
53.5
|
1.0
|
|
HG22
|
D:THR17
|
4.8
|
53.5
|
1.0
|
|
HE1
|
D:HIS92
|
4.9
|
53.5
|
1.0
|
|
CG
|
D:ASP90
|
4.9
|
51.2
|
1.0
|
|
Magnesium binding site 5 out
of 12 in 6pjw
Go back to
Magnesium Binding Sites List in 6pjw
Magnesium binding site 5 out
of 12 in the Adenylate Kinase From Methanococcus Igneus - Amp Bound Form
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of Adenylate Kinase From Methanococcus Igneus - Amp Bound Form within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Mg303
b:55.7
occ:1.00
|
O
|
E:HOH402
|
2.0
|
58.6
|
1.0
|
|
O
|
E:HOH417
|
2.0
|
54.4
|
1.0
|
|
O
|
E:HOH406
|
2.0
|
53.2
|
1.0
|
|
O
|
E:HOH412
|
2.1
|
57.7
|
1.0
|
|
O
|
E:HOH409
|
2.1
|
56.3
|
1.0
|
|
OG1
|
E:THR17
|
2.2
|
53.8
|
1.0
|
|
HB
|
E:THR17
|
3.2
|
53.5
|
1.0
|
|
CB
|
E:THR17
|
3.3
|
54.5
|
1.0
|
|
H
|
E:THR17
|
3.4
|
53.5
|
1.0
|
|
HOP3
|
E:AMP301
|
3.7
|
53.5
|
1.0
|
|
HH21
|
E:ARG140
|
3.8
|
53.5
|
1.0
|
|
HH22
|
E:ARG140
|
3.8
|
53.5
|
1.0
|
|
HH12
|
E:ARG138
|
3.8
|
53.5
|
1.0
|
|
HD21
|
E:ASN38
|
3.9
|
53.5
|
1.0
|
|
O2P
|
E:AMP301
|
3.9
|
47.8
|
1.0
|
|
O3P
|
E:AMP302
|
4.0
|
53.2
|
1.0
|
|
O1P
|
E:AMP301
|
4.0
|
50.2
|
1.0
|
|
N
|
E:THR17
|
4.1
|
52.8
|
1.0
|
|
HG21
|
E:THR17
|
4.1
|
53.5
|
1.0
|
|
NH2
|
E:ARG140
|
4.1
|
64.7
|
1.0
|
|
OD1
|
E:ASP90
|
4.1
|
50.9
|
1.0
|
|
HOP2
|
E:AMP302
|
4.2
|
53.5
|
1.0
|
|
P
|
E:AMP301
|
4.2
|
49.8
|
1.0
|
|
O3P
|
E:AMP301
|
4.3
|
52.6
|
1.0
|
|
CA
|
E:THR17
|
4.3
|
54.2
|
1.0
|
|
OD2
|
E:ASP90
|
4.3
|
53.5
|
1.0
|
|
CG2
|
E:THR17
|
4.3
|
56.4
|
1.0
|
|
HD22
|
E:ASN38
|
4.4
|
53.5
|
1.0
|
|
NH1
|
E:ARG138
|
4.4
|
66.7
|
1.0
|
|
O2P
|
E:AMP302
|
4.4
|
52.3
|
1.0
|
|
ND2
|
E:ASN38
|
4.5
|
51.6
|
1.0
|
|
HH11
|
E:ARG138
|
4.5
|
53.5
|
1.0
|
|
HOP3
|
E:AMP302
|
4.5
|
53.5
|
1.0
|
|
HA
|
E:THR17
|
4.6
|
53.5
|
1.0
|
|
P
|
E:AMP302
|
4.6
|
53.5
|
1.0
|
|
CG
|
E:ASP90
|
4.7
|
51.8
|
1.0
|
|
HOP2
|
E:AMP301
|
4.8
|
53.5
|
1.0
|
|
HG23
|
E:THR17
|
4.9
|
53.5
|
1.0
|
|
O1P
|
E:AMP302
|
4.9
|
52.6
|
1.0
|
|
HG22
|
E:THR17
|
4.9
|
53.5
|
1.0
|
|
Magnesium binding site 6 out
of 12 in 6pjw
Go back to
Magnesium Binding Sites List in 6pjw
Magnesium binding site 6 out
of 12 in the Adenylate Kinase From Methanococcus Igneus - Amp Bound Form
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 6 of Adenylate Kinase From Methanococcus Igneus - Amp Bound Form within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Mg303
b:49.4
occ:1.00
|
O
|
F:HOH408
|
2.0
|
50.6
|
1.0
|
|
O
|
F:HOH402
|
2.0
|
48.6
|
1.0
|
|
O
|
F:HOH410
|
2.1
|
49.1
|
1.0
|
|
O
|
F:HOH416
|
2.1
|
47.4
|
1.0
|
|
O
|
F:HOH413
|
2.1
|
51.9
|
1.0
|
|
OG1
|
F:THR17
|
2.1
|
52.3
|
1.0
|
|
HB
|
F:THR17
|
3.1
|
53.5
|
1.0
|
|
CB
|
F:THR17
|
3.2
|
52.6
|
1.0
|
|
H
|
F:THR17
|
3.4
|
53.5
|
1.0
|
|
HH22
|
F:ARG140
|
3.6
|
53.5
|
1.0
|
|
HH12
|
F:ARG138
|
3.7
|
53.5
|
1.0
|
|
O2P
|
F:AMP301
|
3.8
|
51.7
|
1.0
|
|
HOP2
|
F:AMP302
|
3.8
|
53.5
|
1.0
|
|
OD2
|
F:ASP90
|
4.0
|
54.8
|
1.0
|
|
OD1
|
F:ASP90
|
4.0
|
52.2
|
1.0
|
|
N
|
F:THR17
|
4.0
|
52.2
|
1.0
|
|
HG21
|
F:THR17
|
4.0
|
53.5
|
1.0
|
|
CA
|
F:THR17
|
4.1
|
54.0
|
1.0
|
|
HH12
|
F:ARG140
|
4.2
|
53.5
|
1.0
|
|
HD21
|
F:ASN38
|
4.2
|
53.5
|
1.0
|
|
CG2
|
F:THR17
|
4.2
|
54.6
|
1.0
|
|
O3P
|
F:AMP301
|
4.3
|
51.3
|
1.0
|
|
P
|
F:AMP301
|
4.3
|
52.6
|
1.0
|
|
O1P
|
F:AMP301
|
4.4
|
51.8
|
1.0
|
|
HA
|
F:THR17
|
4.4
|
53.5
|
1.0
|
|
O3P
|
F:AMP302
|
4.4
|
51.7
|
1.0
|
|
O2P
|
F:AMP302
|
4.4
|
51.8
|
1.0
|
|
NH2
|
F:ARG140
|
4.4
|
70.6
|
1.0
|
|
CG
|
F:ASP90
|
4.5
|
53.8
|
1.0
|
|
NH1
|
F:ARG138
|
4.5
|
75.6
|
1.0
|
|
HOP2
|
F:AMP301
|
4.5
|
53.5
|
1.0
|
|
HD22
|
F:ASN38
|
4.6
|
53.5
|
1.0
|
|
O
|
F:HOH411
|
4.7
|
50.3
|
1.0
|
|
ND2
|
F:ASN38
|
4.8
|
55.0
|
1.0
|
|
P
|
F:AMP302
|
4.8
|
53.1
|
1.0
|
|
HH11
|
F:ARG138
|
4.8
|
53.5
|
1.0
|
|
HG23
|
F:THR17
|
4.8
|
53.5
|
1.0
|
|
HOP3
|
F:AMP301
|
4.8
|
53.5
|
1.0
|
|
HG22
|
F:THR17
|
4.9
|
53.5
|
1.0
|
|
HH22
|
F:ARG138
|
4.9
|
53.5
|
1.0
|
|
HOP3
|
F:AMP302
|
4.9
|
53.5
|
1.0
|
|
HE1
|
F:HIS92
|
4.9
|
53.5
|
1.0
|
|
O1P
|
F:AMP302
|
4.9
|
53.4
|
1.0
|
|
NH1
|
F:ARG140
|
4.9
|
69.1
|
1.0
|
|
HH21
|
F:ARG140
|
4.9
|
53.5
|
1.0
|
|
Magnesium binding site 7 out
of 12 in 6pjw
Go back to
Magnesium Binding Sites List in 6pjw
Magnesium binding site 7 out
of 12 in the Adenylate Kinase From Methanococcus Igneus - Amp Bound Form
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 7 of Adenylate Kinase From Methanococcus Igneus - Amp Bound Form within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Mg303
b:70.8
occ:1.00
|
O
|
G:HOH405
|
2.0
|
69.3
|
1.0
|
|
O
|
G:HOH402
|
2.0
|
73.2
|
1.0
|
|
O
|
G:HOH404
|
2.0
|
74.2
|
1.0
|
|
O
|
G:HOH409
|
2.1
|
67.7
|
1.0
|
|
O
|
G:HOH408
|
2.1
|
69.9
|
1.0
|
|
OG1
|
G:THR17
|
2.1
|
75.8
|
1.0
|
|
HB
|
G:THR17
|
3.0
|
53.5
|
1.0
|
|
CB
|
G:THR17
|
3.1
|
77.3
|
1.0
|
|
HH12
|
G:ARG138
|
3.3
|
53.5
|
1.0
|
|
H
|
G:THR17
|
3.5
|
53.5
|
1.0
|
|
HOP3
|
G:AMP301
|
3.7
|
53.5
|
1.0
|
|
O
|
G:HOH401
|
3.7
|
53.5
|
1.0
|
|
O3P
|
G:AMP302
|
3.7
|
72.6
|
1.0
|
|
O2P
|
G:AMP301
|
3.8
|
69.2
|
1.0
|
|
HD21
|
G:ASN38
|
3.8
|
53.5
|
1.0
|
|
OD2
|
G:ASP90
|
3.8
|
77.8
|
1.0
|
|
O3P
|
G:AMP301
|
3.9
|
73.1
|
1.0
|
|
HG21
|
G:THR17
|
3.9
|
53.5
|
1.0
|
|
NH1
|
G:ARG138
|
4.0
|
79.8
|
1.0
|
|
O1P
|
G:AMP301
|
4.0
|
69.1
|
1.0
|
|
N
|
G:THR17
|
4.1
|
74.9
|
1.0
|
|
P
|
G:AMP301
|
4.1
|
70.5
|
1.0
|
|
HH11
|
G:ARG138
|
4.1
|
53.5
|
1.0
|
|
CG2
|
G:THR17
|
4.1
|
81.2
|
1.0
|
|
CA
|
G:THR17
|
4.2
|
78.3
|
1.0
|
|
OD1
|
G:ASP90
|
4.2
|
73.5
|
1.0
|
|
HOP3
|
G:AMP302
|
4.2
|
53.5
|
1.0
|
|
O2P
|
G:AMP302
|
4.3
|
69.5
|
1.0
|
|
HOP2
|
G:AMP302
|
4.3
|
53.5
|
1.0
|
|
HD22
|
G:ASN38
|
4.3
|
53.5
|
1.0
|
|
ND2
|
G:ASN38
|
4.4
|
75.7
|
1.0
|
|
CG
|
G:ASP90
|
4.5
|
75.8
|
1.0
|
|
HH22
|
G:ARG140
|
4.5
|
53.5
|
1.0
|
|
HA
|
G:THR17
|
4.5
|
53.5
|
1.0
|
|
P
|
G:AMP302
|
4.6
|
72.8
|
1.0
|
|
HOP2
|
G:AMP301
|
4.7
|
53.5
|
1.0
|
|
HG23
|
G:THR17
|
4.7
|
53.5
|
1.0
|
|
HH21
|
G:ARG140
|
4.7
|
53.5
|
1.0
|
|
HE1
|
G:HIS92
|
4.8
|
53.5
|
1.0
|
|
HG22
|
G:THR17
|
4.8
|
53.5
|
1.0
|
|
HH22
|
G:ARG138
|
4.9
|
53.5
|
1.0
|
|
NH2
|
G:ARG140
|
4.9
|
79.6
|
1.0
|
|
Magnesium binding site 8 out
of 12 in 6pjw
Go back to
Magnesium Binding Sites List in 6pjw
Magnesium binding site 8 out
of 12 in the Adenylate Kinase From Methanococcus Igneus - Amp Bound Form
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 8 of Adenylate Kinase From Methanococcus Igneus - Amp Bound Form within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:Mg303
b:72.5
occ:1.00
|
O
|
H:HOH406
|
2.0
|
72.3
|
1.0
|
|
O
|
H:HOH410
|
2.0
|
69.7
|
1.0
|
|
O
|
H:HOH403
|
2.0
|
73.0
|
1.0
|
|
O
|
H:HOH412
|
2.1
|
69.7
|
1.0
|
|
O
|
H:HOH402
|
2.1
|
75.9
|
1.0
|
|
OG1
|
H:THR17
|
2.2
|
66.0
|
1.0
|
|
HOP2
|
H:AMP301
|
3.0
|
53.5
|
1.0
|
|
HB
|
H:THR17
|
3.1
|
53.5
|
1.0
|
|
CB
|
H:THR17
|
3.2
|
68.7
|
1.0
|
|
HH12
|
H:ARG138
|
3.4
|
53.5
|
1.0
|
|
H
|
H:THR17
|
3.4
|
53.5
|
1.0
|
|
HOP3
|
H:AMP301
|
3.5
|
53.5
|
1.0
|
|
O3P
|
H:AMP302
|
3.6
|
62.0
|
1.0
|
|
HH22
|
H:ARG140
|
3.7
|
53.5
|
1.0
|
|
O2P
|
H:AMP301
|
3.8
|
68.9
|
1.0
|
|
OD2
|
H:ASP90
|
3.9
|
70.2
|
1.0
|
|
HG21
|
H:THR17
|
4.0
|
53.5
|
1.0
|
|
HOP3
|
H:AMP302
|
4.0
|
53.5
|
1.0
|
|
N
|
H:THR17
|
4.1
|
67.1
|
1.0
|
|
O3P
|
H:AMP301
|
4.1
|
72.8
|
1.0
|
|
HD21
|
H:ASN38
|
4.1
|
53.5
|
1.0
|
|
HH21
|
H:ARG140
|
4.2
|
53.5
|
1.0
|
|
HOP2
|
H:AMP302
|
4.2
|
53.5
|
1.0
|
|
CG2
|
H:THR17
|
4.2
|
71.4
|
1.0
|
|
O1P
|
H:AMP301
|
4.2
|
68.3
|
1.0
|
|
NH1
|
H:ARG138
|
4.2
|
86.0
|
1.0
|
|
P
|
H:AMP301
|
4.2
|
69.1
|
1.0
|
|
CA
|
H:THR17
|
4.3
|
69.3
|
1.0
|
|
NH2
|
H:ARG140
|
4.3
|
79.6
|
1.0
|
|
O2P
|
H:AMP302
|
4.4
|
64.0
|
1.0
|
|
HH11
|
H:ARG138
|
4.4
|
53.5
|
1.0
|
|
HD22
|
H:ASN38
|
4.5
|
53.5
|
1.0
|
|
P
|
H:AMP302
|
4.6
|
67.5
|
1.0
|
|
HA
|
H:THR17
|
4.6
|
53.5
|
1.0
|
|
OD1
|
H:ASP90
|
4.6
|
66.3
|
1.0
|
|
ND2
|
H:ASN38
|
4.6
|
68.1
|
1.0
|
|
CG
|
H:ASP90
|
4.7
|
68.4
|
1.0
|
|
HE1
|
H:HIS92
|
4.8
|
53.5
|
1.0
|
|
HG22
|
H:THR17
|
4.8
|
53.5
|
1.0
|
|
HG23
|
H:THR17
|
4.8
|
53.5
|
1.0
|
|
HH22
|
H:ARG138
|
4.9
|
53.5
|
1.0
|
|
Magnesium binding site 9 out
of 12 in 6pjw
Go back to
Magnesium Binding Sites List in 6pjw
Magnesium binding site 9 out
of 12 in the Adenylate Kinase From Methanococcus Igneus - Amp Bound Form
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 9 of Adenylate Kinase From Methanococcus Igneus - Amp Bound Form within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
I:Mg303
b:88.7
occ:1.00
|
OG1
|
I:THR17
|
1.9
|
73.7
|
1.0
|
|
O
|
I:HOH407
|
2.0
|
94.2
|
1.0
|
|
O
|
I:HOH408
|
2.0
|
82.6
|
1.0
|
|
O
|
I:HOH402
|
2.0
|
92.1
|
1.0
|
|
O
|
I:HOH405
|
2.0
|
83.5
|
1.0
|
|
O
|
I:HOH409
|
2.0
|
85.5
|
1.0
|
|
HB
|
I:THR17
|
3.0
|
53.5
|
1.0
|
|
CB
|
I:THR17
|
3.0
|
74.3
|
1.0
|
|
O
|
I:HOH401
|
3.1
|
53.5
|
1.0
|
|
H
|
I:THR17
|
3.3
|
53.5
|
1.0
|
|
HG21
|
I:THR17
|
3.9
|
53.5
|
1.0
|
|
N
|
I:THR17
|
3.9
|
68.8
|
1.0
|
|
CA
|
I:THR17
|
4.0
|
74.5
|
1.0
|
|
HH12
|
I:ARG138
|
4.0
|
53.5
|
1.0
|
|
O1P
|
I:AMP301
|
4.0
|
75.4
|
1.0
|
|
CG2
|
I:THR17
|
4.1
|
78.8
|
1.0
|
|
OD2
|
I:ASP90
|
4.1
|
77.3
|
1.0
|
|
O3P
|
I:AMP302
|
4.1
|
78.9
|
1.0
|
|
OD1
|
I:ASP90
|
4.1
|
67.4
|
1.0
|
|
HD21
|
I:ASN38
|
4.2
|
53.5
|
1.0
|
|
O2P
|
I:AMP301
|
4.2
|
83.5
|
1.0
|
|
HA
|
I:THR17
|
4.3
|
53.5
|
1.0
|
|
HOP2
|
I:AMP301
|
4.3
|
53.5
|
1.0
|
|
O3P
|
I:AMP301
|
4.4
|
83.5
|
1.0
|
|
P
|
I:AMP301
|
4.4
|
78.8
|
1.0
|
|
HOP2
|
I:AMP302
|
4.4
|
53.5
|
1.0
|
|
O2P
|
I:AMP302
|
4.4
|
69.4
|
1.0
|
|
HH11
|
I:ARG138
|
4.5
|
53.5
|
1.0
|
|
CG
|
I:ASP90
|
4.5
|
72.0
|
1.0
|
|
HD22
|
I:ASN38
|
4.5
|
53.5
|
1.0
|
|
P
|
I:AMP302
|
4.6
|
73.3
|
1.0
|
|
HH22
|
I:ARG140
|
4.6
|
53.5
|
1.0
|
|
NH1
|
I:ARG138
|
4.6
|
93.2
|
1.0
|
|
HOP3
|
I:AMP301
|
4.6
|
53.5
|
1.0
|
|
HG23
|
I:THR17
|
4.7
|
53.5
|
1.0
|
|
HG22
|
I:THR17
|
4.7
|
53.5
|
1.0
|
|
ND2
|
I:ASN38
|
4.7
|
76.4
|
1.0
|
|
HE2
|
I:HIS92
|
4.7
|
53.5
|
1.0
|
|
O1P
|
I:AMP302
|
4.7
|
73.9
|
1.0
|
|
HOP3
|
I:AMP302
|
4.8
|
53.5
|
1.0
|
|
Magnesium binding site 10 out
of 12 in 6pjw
Go back to
Magnesium Binding Sites List in 6pjw
Magnesium binding site 10 out
of 12 in the Adenylate Kinase From Methanococcus Igneus - Amp Bound Form
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 10 of Adenylate Kinase From Methanococcus Igneus - Amp Bound Form within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
J:Mg303
b:55.0
occ:1.00
|
O
|
J:HOH409
|
2.0
|
54.0
|
1.0
|
|
O
|
J:HOH413
|
2.0
|
52.3
|
1.0
|
|
O
|
J:HOH404
|
2.0
|
56.8
|
1.0
|
|
OG1
|
J:THR17
|
2.0
|
59.0
|
1.0
|
|
O
|
J:HOH415
|
2.1
|
54.8
|
1.0
|
|
O
|
J:HOH410
|
2.1
|
58.5
|
1.0
|
|
HB
|
J:THR17
|
3.1
|
53.5
|
1.0
|
|
CB
|
J:THR17
|
3.1
|
59.5
|
1.0
|
|
H
|
J:THR17
|
3.4
|
53.5
|
1.0
|
|
HH12
|
J:ARG138
|
3.8
|
53.5
|
1.0
|
|
HOP3
|
J:AMP301
|
3.8
|
53.5
|
1.0
|
|
HD21
|
J:ASN38
|
3.9
|
53.5
|
1.0
|
|
HG21
|
J:THR17
|
3.9
|
53.5
|
1.0
|
|
HH22
|
J:ARG140
|
3.9
|
53.5
|
1.0
|
|
O3P
|
J:AMP302
|
4.0
|
58.7
|
1.0
|
|
HOP2
|
J:AMP302
|
4.1
|
53.5
|
1.0
|
|
N
|
J:THR17
|
4.1
|
56.3
|
1.0
|
|
CG2
|
J:THR17
|
4.1
|
62.4
|
1.0
|
|
OD2
|
J:ASP90
|
4.1
|
62.3
|
1.0
|
|
CA
|
J:THR17
|
4.2
|
58.9
|
1.0
|
|
O2P
|
J:AMP301
|
4.2
|
61.3
|
1.0
|
|
O3P
|
J:AMP301
|
4.2
|
64.5
|
1.0
|
|
OD1
|
J:ASP90
|
4.2
|
58.8
|
1.0
|
|
HOP2
|
J:AMP301
|
4.3
|
53.5
|
1.0
|
|
HD22
|
J:ASN38
|
4.3
|
53.5
|
1.0
|
|
HH21
|
J:ARG140
|
4.3
|
53.5
|
1.0
|
|
O1P
|
J:AMP301
|
4.3
|
62.0
|
1.0
|
|
P
|
J:AMP301
|
4.3
|
62.8
|
1.0
|
|
O2P
|
J:AMP302
|
4.4
|
53.5
|
1.0
|
|
ND2
|
J:ASN38
|
4.4
|
63.2
|
1.0
|
|
NH2
|
J:ARG140
|
4.5
|
71.8
|
1.0
|
|
HA
|
J:THR17
|
4.5
|
53.5
|
1.0
|
|
NH1
|
J:ARG138
|
4.6
|
78.0
|
1.0
|
|
HOP3
|
J:AMP302
|
4.6
|
53.5
|
1.0
|
|
CG
|
J:ASP90
|
4.6
|
60.7
|
1.0
|
|
HG23
|
J:THR17
|
4.6
|
53.5
|
1.0
|
|
P
|
J:AMP302
|
4.7
|
55.6
|
1.0
|
|
HH11
|
J:ARG138
|
4.8
|
53.5
|
1.0
|
|
HG22
|
J:THR17
|
4.8
|
53.5
|
1.0
|
|
O1P
|
J:AMP302
|
5.0
|
56.4
|
1.0
|
|
Reference:
E.Bae,
S.Moon,
J.Kim,
J.L.Olmos,
E.Bae,
G.N.Phillips.
N/A N/A.
Page generated: Mon Dec 14 23:49:02 2020
|
