Magnesium in PDB 5k2m: Bifunctional Lysx/Argx From Thermococcus Kodakarensis with Lysw-Gamma- Aaa
Protein crystallography data
The structure of Bifunctional Lysx/Argx From Thermococcus Kodakarensis with Lysw-Gamma- Aaa, PDB code: 5k2m
was solved by
A.Yoshida,
T.Tomita,
M.Nishiyama,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
50.00 /
2.18
|
|
Space group
|
P 1 21 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
76.150,
135.099,
136.977,
90.00,
97.49,
90.00
|
|
R / Rfree (%)
|
18 /
22
|
Other elements in 5k2m:
The structure of Bifunctional Lysx/Argx From Thermococcus Kodakarensis with Lysw-Gamma- Aaa also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Bifunctional Lysx/Argx From Thermococcus Kodakarensis with Lysw-Gamma- Aaa
(pdb code 5k2m). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 9 binding sites of Magnesium where determined in the
Bifunctional Lysx/Argx From Thermococcus Kodakarensis with Lysw-Gamma- Aaa, PDB code: 5k2m:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
Magnesium binding site 1 out
of 9 in 5k2m
Go back to
Magnesium Binding Sites List in 5k2m
Magnesium binding site 1 out
of 9 in the Bifunctional Lysx/Argx From Thermococcus Kodakarensis with Lysw-Gamma- Aaa
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Bifunctional Lysx/Argx From Thermococcus Kodakarensis with Lysw-Gamma- Aaa within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg303
b:37.0
occ:1.00
|
O1
|
A:PO4302
|
2.0
|
40.0
|
1.0
|
|
OD2
|
A:ASP229
|
2.0
|
45.0
|
1.0
|
|
O1A
|
A:ADP301
|
2.0
|
38.2
|
1.0
|
|
O
|
A:HOH413
|
2.2
|
42.7
|
1.0
|
|
O1B
|
A:ADP301
|
2.2
|
38.6
|
1.0
|
|
OE1
|
A:GLU241
|
2.3
|
51.4
|
1.0
|
|
CG
|
A:ASP229
|
3.2
|
43.2
|
1.0
|
|
P
|
A:PO4302
|
3.3
|
39.5
|
1.0
|
|
PB
|
A:ADP301
|
3.3
|
39.4
|
1.0
|
|
PA
|
A:ADP301
|
3.3
|
36.7
|
1.0
|
|
MG
|
A:MG304
|
3.5
|
42.0
|
1.0
|
|
O4
|
A:PO4302
|
3.5
|
44.3
|
1.0
|
|
CD
|
A:GLU241
|
3.5
|
50.9
|
1.0
|
|
O3A
|
A:ADP301
|
3.7
|
36.5
|
1.0
|
|
O3B
|
A:ADP301
|
3.7
|
37.3
|
1.0
|
|
OD1
|
A:ASP229
|
3.8
|
44.6
|
1.0
|
|
OD1
|
A:ASN195
|
3.9
|
48.8
|
1.0
|
|
C5'
|
A:ADP301
|
4.1
|
32.3
|
1.0
|
|
OE2
|
A:GLU241
|
4.1
|
53.7
|
1.0
|
|
NH2
|
A:ARG187
|
4.1
|
47.4
|
1.0
|
|
O5'
|
A:ADP301
|
4.2
|
33.4
|
1.0
|
|
O3
|
A:PO4302
|
4.2
|
43.0
|
1.0
|
|
ND2
|
A:ASN243
|
4.2
|
40.7
|
1.0
|
|
CB
|
A:ASP229
|
4.3
|
41.4
|
1.0
|
|
O3'
|
A:ADP301
|
4.3
|
32.7
|
1.0
|
|
O2
|
A:PO4302
|
4.3
|
43.4
|
1.0
|
|
NH1
|
A:ARG173
|
4.4
|
53.7
|
1.0
|
|
NH1
|
A:ARG187
|
4.5
|
47.3
|
1.0
|
|
O2A
|
A:ADP301
|
4.5
|
32.6
|
1.0
|
|
CB
|
A:GLU241
|
4.6
|
45.4
|
1.0
|
|
CG
|
A:GLU241
|
4.6
|
51.3
|
1.0
|
|
O2B
|
A:ADP301
|
4.6
|
35.2
|
1.0
|
|
OD1
|
A:ASN243
|
4.7
|
39.9
|
1.0
|
|
C3'
|
A:ADP301
|
4.7
|
32.9
|
1.0
|
|
ND2
|
A:ASN240
|
4.7
|
38.7
|
1.0
|
|
CZ
|
A:ARG187
|
4.8
|
47.2
|
1.0
|
|
CG
|
A:ASN195
|
4.8
|
48.7
|
1.0
|
|
CG
|
A:ASN243
|
4.9
|
39.9
|
1.0
|
|
C4'
|
A:ADP301
|
4.9
|
33.1
|
1.0
|
|
Magnesium binding site 2 out
of 9 in 5k2m
Go back to
Magnesium Binding Sites List in 5k2m
Magnesium binding site 2 out
of 9 in the Bifunctional Lysx/Argx From Thermococcus Kodakarensis with Lysw-Gamma- Aaa
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Bifunctional Lysx/Argx From Thermococcus Kodakarensis with Lysw-Gamma- Aaa within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg304
b:42.0
occ:1.00
|
O4
|
A:PO4302
|
1.9
|
44.3
|
1.0
|
|
OE2
|
A:GLU241
|
1.9
|
53.7
|
1.0
|
|
OD1
|
A:ASN243
|
2.0
|
39.9
|
1.0
|
|
O
|
A:HOH420
|
2.2
|
45.0
|
1.0
|
|
O3B
|
A:ADP301
|
2.3
|
37.3
|
1.0
|
|
CD
|
A:GLU241
|
2.5
|
50.9
|
1.0
|
|
OE1
|
A:GLU241
|
2.6
|
51.4
|
1.0
|
|
P
|
A:PO4302
|
3.0
|
39.5
|
1.0
|
|
CG
|
A:ASN243
|
3.0
|
39.9
|
1.0
|
|
PB
|
A:ADP301
|
3.4
|
39.4
|
1.0
|
|
O1
|
A:PO4302
|
3.4
|
40.0
|
1.0
|
|
ND2
|
A:ASN243
|
3.4
|
40.7
|
1.0
|
|
MG
|
A:MG303
|
3.5
|
37.0
|
1.0
|
|
O1B
|
A:ADP301
|
3.5
|
38.6
|
1.0
|
|
O3
|
A:PO4302
|
3.6
|
43.0
|
1.0
|
|
OG
|
A:SER127
|
3.8
|
45.7
|
1.0
|
|
O
|
A:HOH441
|
3.9
|
51.7
|
1.0
|
|
CG
|
A:GLU241
|
4.0
|
51.3
|
1.0
|
|
NZ
|
A:LYS83
|
4.1
|
43.3
|
1.0
|
|
CA
|
A:SER127
|
4.2
|
46.3
|
1.0
|
|
O
|
A:GLY126
|
4.3
|
42.5
|
1.0
|
|
O2
|
A:PO4302
|
4.3
|
43.4
|
1.0
|
|
O
|
E:HOH207
|
4.3
|
46.4
|
1.0
|
|
CB
|
A:SER127
|
4.3
|
47.3
|
1.0
|
|
CB
|
A:ASN243
|
4.4
|
37.5
|
1.0
|
|
O3A
|
A:ADP301
|
4.4
|
36.5
|
1.0
|
|
O2B
|
A:ADP301
|
4.5
|
35.2
|
1.0
|
|
O1A
|
A:ADP301
|
4.6
|
38.2
|
1.0
|
|
OD2
|
A:ASP229
|
4.8
|
45.0
|
1.0
|
|
CE
|
A:LYS83
|
4.8
|
45.3
|
1.0
|
|
O
|
A:HOH454
|
4.9
|
41.3
|
1.0
|
|
O
|
A:VAL242
|
4.9
|
42.7
|
1.0
|
|
N
|
A:TRP128
|
4.9
|
45.7
|
1.0
|
|
CB
|
A:GLU241
|
5.0
|
45.4
|
1.0
|
|
Magnesium binding site 3 out
of 9 in 5k2m
Go back to
Magnesium Binding Sites List in 5k2m
Magnesium binding site 3 out
of 9 in the Bifunctional Lysx/Argx From Thermococcus Kodakarensis with Lysw-Gamma- Aaa
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Bifunctional Lysx/Argx From Thermococcus Kodakarensis with Lysw-Gamma- Aaa within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg303
b:42.0
occ:1.00
|
O2A
|
B:ADP301
|
1.9
|
37.2
|
1.0
|
|
OD2
|
B:ASP229
|
2.0
|
43.8
|
1.0
|
|
O3B
|
B:ADP301
|
2.1
|
40.5
|
1.0
|
|
O3
|
B:PO4302
|
2.1
|
37.2
|
1.0
|
|
O
|
B:HOH418
|
2.1
|
43.4
|
1.0
|
|
OE1
|
B:GLU241
|
2.3
|
49.3
|
1.0
|
|
CG
|
B:ASP229
|
3.1
|
41.8
|
1.0
|
|
PB
|
B:ADP301
|
3.2
|
43.8
|
1.0
|
|
PA
|
B:ADP301
|
3.2
|
38.2
|
1.0
|
|
P
|
B:PO4302
|
3.4
|
37.9
|
1.0
|
|
MG
|
B:MG304
|
3.4
|
45.0
|
1.0
|
|
CD
|
B:GLU241
|
3.5
|
49.9
|
1.0
|
|
O3A
|
B:ADP301
|
3.6
|
38.0
|
1.0
|
|
O1B
|
B:ADP301
|
3.6
|
39.0
|
1.0
|
|
O1
|
B:PO4302
|
3.6
|
36.5
|
1.0
|
|
OD1
|
B:ASP229
|
3.7
|
40.9
|
1.0
|
|
OD1
|
B:ASN195
|
3.8
|
41.6
|
1.0
|
|
C5'
|
B:ADP301
|
4.0
|
34.3
|
1.0
|
|
OE2
|
B:GLU241
|
4.1
|
56.4
|
1.0
|
|
O5'
|
B:ADP301
|
4.1
|
34.7
|
1.0
|
|
NH2
|
B:ARG187
|
4.1
|
46.3
|
1.0
|
|
O3'
|
B:ADP301
|
4.1
|
37.8
|
1.0
|
|
CB
|
B:ASP229
|
4.2
|
39.8
|
1.0
|
|
O2
|
B:PO4302
|
4.3
|
39.5
|
1.0
|
|
O4
|
B:PO4302
|
4.3
|
41.8
|
1.0
|
|
ND2
|
B:ASN243
|
4.4
|
40.2
|
1.0
|
|
O1A
|
B:ADP301
|
4.4
|
38.3
|
1.0
|
|
NH1
|
B:ARG187
|
4.5
|
44.5
|
1.0
|
|
O2B
|
B:ADP301
|
4.5
|
37.0
|
1.0
|
|
NH1
|
B:ARG173
|
4.6
|
55.0
|
1.0
|
|
C3'
|
B:ADP301
|
4.6
|
34.4
|
1.0
|
|
CG
|
B:GLU241
|
4.6
|
51.3
|
1.0
|
|
CB
|
B:GLU241
|
4.7
|
45.7
|
1.0
|
|
OD1
|
B:ASN243
|
4.7
|
40.9
|
1.0
|
|
CG
|
B:ASN195
|
4.7
|
40.1
|
1.0
|
|
CZ
|
B:ARG187
|
4.8
|
45.4
|
1.0
|
|
ND2
|
B:ASN240
|
4.8
|
37.8
|
1.0
|
|
C4'
|
B:ADP301
|
4.8
|
33.7
|
1.0
|
|
Magnesium binding site 4 out
of 9 in 5k2m
Go back to
Magnesium Binding Sites List in 5k2m
Magnesium binding site 4 out
of 9 in the Bifunctional Lysx/Argx From Thermococcus Kodakarensis with Lysw-Gamma- Aaa
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Bifunctional Lysx/Argx From Thermococcus Kodakarensis with Lysw-Gamma- Aaa within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg304
b:45.0
occ:1.00
|
OE2
|
B:GLU241
|
1.8
|
56.4
|
1.0
|
|
O1
|
B:PO4302
|
1.9
|
36.5
|
1.0
|
|
O
|
B:HOH409
|
2.0
|
43.0
|
1.0
|
|
OD1
|
B:ASN243
|
2.1
|
40.9
|
1.0
|
|
O1B
|
B:ADP301
|
2.2
|
39.0
|
1.0
|
|
CD
|
B:GLU241
|
2.4
|
49.9
|
1.0
|
|
OE1
|
B:GLU241
|
2.5
|
49.3
|
1.0
|
|
P
|
B:PO4302
|
3.0
|
37.9
|
1.0
|
|
CG
|
B:ASN243
|
3.1
|
40.6
|
1.0
|
|
PB
|
B:ADP301
|
3.3
|
43.8
|
1.0
|
|
O3
|
B:PO4302
|
3.3
|
37.2
|
1.0
|
|
O3B
|
B:ADP301
|
3.3
|
40.5
|
1.0
|
|
MG
|
B:MG303
|
3.4
|
42.0
|
1.0
|
|
ND2
|
B:ASN243
|
3.5
|
40.2
|
1.0
|
|
O4
|
B:PO4302
|
3.6
|
41.8
|
1.0
|
|
OG
|
B:SER127
|
3.8
|
48.6
|
1.0
|
|
CG
|
B:GLU241
|
3.9
|
51.3
|
1.0
|
|
O
|
B:HOH439
|
4.1
|
48.8
|
1.0
|
|
NZ
|
B:LYS83
|
4.1
|
40.5
|
1.0
|
|
O2
|
B:PO4302
|
4.2
|
39.5
|
1.0
|
|
CA
|
B:SER127
|
4.3
|
47.1
|
1.0
|
|
CB
|
B:SER127
|
4.3
|
48.9
|
1.0
|
|
O3A
|
B:ADP301
|
4.3
|
38.0
|
1.0
|
|
O
|
B:GLY126
|
4.4
|
47.0
|
1.0
|
|
O
|
F:HOH403
|
4.4
|
43.7
|
1.0
|
|
CB
|
B:ASN243
|
4.4
|
38.6
|
1.0
|
|
O2B
|
B:ADP301
|
4.4
|
37.0
|
1.0
|
|
O2A
|
B:ADP301
|
4.4
|
37.2
|
1.0
|
|
OD2
|
B:ASP229
|
4.8
|
43.8
|
1.0
|
|
CE
|
B:LYS83
|
4.9
|
40.5
|
1.0
|
|
O
|
B:HOH459
|
4.9
|
46.7
|
1.0
|
|
CB
|
B:GLU241
|
4.9
|
45.7
|
1.0
|
|
N
|
B:TRP128
|
5.0
|
46.0
|
1.0
|
|
Magnesium binding site 5 out
of 9 in 5k2m
Go back to
Magnesium Binding Sites List in 5k2m
Magnesium binding site 5 out
of 9 in the Bifunctional Lysx/Argx From Thermococcus Kodakarensis with Lysw-Gamma- Aaa
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of Bifunctional Lysx/Argx From Thermococcus Kodakarensis with Lysw-Gamma- Aaa within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Mg303
b:58.7
occ:1.00
|
O4
|
G:PO4302
|
1.9
|
59.7
|
1.0
|
|
O2A
|
G:ADP301
|
2.3
|
49.1
|
1.0
|
|
O2B
|
G:ADP301
|
2.3
|
55.6
|
1.0
|
|
OD2
|
G:ASP229
|
2.4
|
63.8
|
1.0
|
|
OE1
|
G:GLU241
|
2.8
|
62.4
|
1.0
|
|
P
|
G:PO4302
|
3.1
|
62.6
|
1.0
|
|
CG
|
G:ASP229
|
3.1
|
55.2
|
1.0
|
|
O1
|
G:PO4302
|
3.3
|
64.2
|
1.0
|
|
OD1
|
G:ASP229
|
3.4
|
57.9
|
1.0
|
|
PB
|
G:ADP301
|
3.5
|
62.9
|
1.0
|
|
PA
|
G:ADP301
|
3.7
|
46.6
|
1.0
|
|
CD
|
G:GLU241
|
3.7
|
59.7
|
1.0
|
|
OD1
|
G:ASN195
|
3.8
|
59.4
|
1.0
|
|
O1B
|
G:ADP301
|
3.8
|
57.6
|
1.0
|
|
NH2
|
G:ARG187
|
3.9
|
65.7
|
1.0
|
|
O3
|
G:PO4302
|
4.0
|
62.7
|
1.0
|
|
O3'
|
G:ADP301
|
4.0
|
39.6
|
1.0
|
|
CG
|
G:GLU241
|
4.1
|
51.5
|
1.0
|
|
C5'
|
G:ADP301
|
4.1
|
40.7
|
1.0
|
|
O3A
|
G:ADP301
|
4.1
|
48.5
|
1.0
|
|
O2
|
G:PO4302
|
4.1
|
62.3
|
1.0
|
|
CB
|
G:ASP229
|
4.3
|
48.8
|
1.0
|
|
ND2
|
G:ASN243
|
4.3
|
52.0
|
1.0
|
|
NH1
|
G:ARG187
|
4.3
|
65.7
|
1.0
|
|
O5'
|
G:ADP301
|
4.4
|
43.8
|
1.0
|
|
NH1
|
G:ARG173
|
4.5
|
72.9
|
1.0
|
|
C3'
|
G:ADP301
|
4.5
|
39.3
|
1.0
|
|
CZ
|
G:ARG187
|
4.6
|
63.0
|
1.0
|
|
CG
|
G:ASN195
|
4.7
|
58.7
|
1.0
|
|
OE2
|
G:GLU241
|
4.7
|
60.4
|
1.0
|
|
ND2
|
G:ASN240
|
4.8
|
44.5
|
1.0
|
|
C4'
|
G:ADP301
|
4.8
|
39.9
|
1.0
|
|
O3B
|
G:ADP301
|
4.8
|
57.6
|
1.0
|
|
O1A
|
G:ADP301
|
4.8
|
46.6
|
1.0
|
|
OD1
|
G:ASN243
|
4.9
|
61.4
|
1.0
|
|
ND2
|
G:ASN195
|
4.9
|
56.6
|
1.0
|
|
Magnesium binding site 6 out
of 9 in 5k2m
Go back to
Magnesium Binding Sites List in 5k2m
Magnesium binding site 6 out
of 9 in the Bifunctional Lysx/Argx From Thermococcus Kodakarensis with Lysw-Gamma- Aaa
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 6 of Bifunctional Lysx/Argx From Thermococcus Kodakarensis with Lysw-Gamma- Aaa within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:Mg303
b:52.6
occ:1.00
|
O3A
|
H:ADP301
|
2.0
|
53.5
|
1.0
|
|
OD2
|
H:ASP229
|
2.1
|
59.1
|
1.0
|
|
O2
|
H:SO4302
|
2.3
|
61.0
|
1.0
|
|
O1B
|
H:ADP301
|
2.4
|
55.8
|
1.0
|
|
OE1
|
H:GLU241
|
2.5
|
46.7
|
1.0
|
|
PB
|
H:ADP301
|
2.8
|
56.0
|
1.0
|
|
CG
|
H:ASP229
|
3.2
|
52.4
|
1.0
|
|
CD
|
H:GLU241
|
3.3
|
49.8
|
1.0
|
|
O2B
|
H:ADP301
|
3.4
|
53.7
|
1.0
|
|
PA
|
H:ADP301
|
3.4
|
43.2
|
1.0
|
|
S
|
H:SO4302
|
3.5
|
59.5
|
1.0
|
|
CG
|
H:GLU241
|
3.7
|
45.5
|
1.0
|
|
O3
|
H:SO4302
|
3.8
|
58.2
|
1.0
|
|
OD1
|
H:ASP229
|
3.9
|
55.7
|
1.0
|
|
C5'
|
H:ADP301
|
4.0
|
36.7
|
1.0
|
|
NH2
|
H:ARG187
|
4.0
|
52.2
|
1.0
|
|
O5'
|
H:ADP301
|
4.0
|
40.2
|
1.0
|
|
O3'
|
H:ADP301
|
4.0
|
37.5
|
1.0
|
|
O1A
|
H:ADP301
|
4.0
|
43.5
|
1.0
|
|
ND2
|
H:ASN195
|
4.1
|
46.3
|
1.0
|
|
MG
|
H:MG304
|
4.1
|
64.5
|
1.0
|
|
O3B
|
H:ADP301
|
4.2
|
56.2
|
1.0
|
|
ND2
|
H:ASN243
|
4.3
|
44.1
|
1.0
|
|
CB
|
H:ASP229
|
4.3
|
45.3
|
1.0
|
|
OE2
|
H:GLU241
|
4.4
|
46.0
|
1.0
|
|
O1
|
H:SO4302
|
4.4
|
58.0
|
1.0
|
|
O2A
|
H:ADP301
|
4.4
|
52.0
|
1.0
|
|
C3'
|
H:ADP301
|
4.5
|
34.4
|
1.0
|
|
O4
|
H:SO4302
|
4.5
|
58.8
|
1.0
|
|
NH1
|
H:ARG173
|
4.6
|
57.9
|
1.0
|
|
ND2
|
H:ASN240
|
4.6
|
38.0
|
1.0
|
|
NH1
|
H:ARG187
|
4.6
|
53.8
|
1.0
|
|
CZ
|
H:ARG187
|
4.8
|
52.5
|
1.0
|
|
C4'
|
H:ADP301
|
4.8
|
34.3
|
1.0
|
|
OD1
|
H:ASN243
|
5.0
|
46.5
|
1.0
|
|
CG
|
H:ASN195
|
5.0
|
49.8
|
1.0
|
|
Magnesium binding site 7 out
of 9 in 5k2m
Go back to
Magnesium Binding Sites List in 5k2m
Magnesium binding site 7 out
of 9 in the Bifunctional Lysx/Argx From Thermococcus Kodakarensis with Lysw-Gamma- Aaa
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 7 of Bifunctional Lysx/Argx From Thermococcus Kodakarensis with Lysw-Gamma- Aaa within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:Mg304
b:64.5
occ:1.00
|
O2B
|
H:ADP301
|
2.0
|
53.7
|
1.0
|
|
O
|
H:HOH401
|
2.1
|
53.0
|
1.0
|
|
OD1
|
H:ASN243
|
2.2
|
46.5
|
1.0
|
|
O3
|
H:SO4302
|
2.3
|
58.2
|
1.0
|
|
OE1
|
H:GLU241
|
2.4
|
46.7
|
1.0
|
|
OE2
|
H:GLU241
|
2.6
|
46.0
|
1.0
|
|
CD
|
H:GLU241
|
2.8
|
49.8
|
1.0
|
|
CG
|
H:ASN243
|
3.3
|
43.8
|
1.0
|
|
PB
|
H:ADP301
|
3.3
|
56.0
|
1.0
|
|
S
|
H:SO4302
|
3.5
|
59.5
|
1.0
|
|
O
|
H:GLY126
|
3.7
|
54.0
|
1.0
|
|
NZ
|
H:LYS83
|
3.7
|
50.2
|
1.0
|
|
O
|
H:HOH434
|
3.7
|
59.6
|
1.0
|
|
ND2
|
H:ASN243
|
3.7
|
44.1
|
1.0
|
|
O1B
|
H:ADP301
|
3.8
|
55.8
|
1.0
|
|
OG
|
H:SER127
|
3.9
|
57.0
|
1.0
|
|
O2
|
H:SO4302
|
3.9
|
61.0
|
1.0
|
|
CA
|
H:SER127
|
4.0
|
54.4
|
1.0
|
|
O4
|
H:SO4302
|
4.0
|
58.8
|
1.0
|
|
O
|
L:HOH203
|
4.1
|
51.7
|
1.0
|
|
O3A
|
H:ADP301
|
4.1
|
53.5
|
1.0
|
|
CB
|
H:SER127
|
4.1
|
55.1
|
1.0
|
|
MG
|
H:MG303
|
4.1
|
52.6
|
1.0
|
|
CG
|
H:GLU241
|
4.3
|
45.5
|
1.0
|
|
O
|
H:HOH428
|
4.3
|
55.4
|
1.0
|
|
O3B
|
H:ADP301
|
4.4
|
56.2
|
1.0
|
|
CB
|
H:ASN243
|
4.6
|
40.6
|
1.0
|
|
C
|
H:GLY126
|
4.6
|
53.5
|
1.0
|
|
CE
|
H:LYS83
|
4.6
|
49.5
|
1.0
|
|
O1
|
H:SO4302
|
4.7
|
58.0
|
1.0
|
|
N
|
H:SER127
|
4.8
|
55.1
|
1.0
|
|
O
|
H:VAL242
|
5.0
|
44.1
|
1.0
|
|
Magnesium binding site 8 out
of 9 in 5k2m
Go back to
Magnesium Binding Sites List in 5k2m
Magnesium binding site 8 out
of 9 in the Bifunctional Lysx/Argx From Thermococcus Kodakarensis with Lysw-Gamma- Aaa
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 8 of Bifunctional Lysx/Argx From Thermococcus Kodakarensis with Lysw-Gamma- Aaa within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
J:Mg303
b:43.0
occ:1.00
|
O2A
|
J:ADP301
|
2.0
|
41.8
|
1.0
|
|
OD2
|
J:ASP229
|
2.0
|
46.8
|
1.0
|
|
O1
|
J:PO4302
|
2.1
|
44.0
|
1.0
|
|
O1B
|
J:ADP301
|
2.2
|
40.7
|
1.0
|
|
O
|
J:HOH408
|
2.3
|
45.9
|
1.0
|
|
OE1
|
J:GLU241
|
2.5
|
57.7
|
1.0
|
|
CG
|
J:ASP229
|
3.2
|
46.3
|
1.0
|
|
PB
|
J:ADP301
|
3.2
|
45.9
|
1.0
|
|
P
|
J:PO4302
|
3.3
|
41.6
|
1.0
|
|
MG
|
J:MG304
|
3.3
|
45.1
|
1.0
|
|
PA
|
J:ADP301
|
3.3
|
39.8
|
1.0
|
|
O3
|
J:PO4302
|
3.4
|
42.2
|
1.0
|
|
O2B
|
J:ADP301
|
3.5
|
44.5
|
1.0
|
|
CD
|
J:GLU241
|
3.7
|
55.0
|
1.0
|
|
O3A
|
J:ADP301
|
3.7
|
39.0
|
1.0
|
|
OD1
|
J:ASP229
|
3.7
|
48.0
|
1.0
|
|
ND2
|
J:ASN243
|
4.0
|
46.3
|
1.0
|
|
OD1
|
J:ASN195
|
4.0
|
44.2
|
1.0
|
|
O4
|
J:PO4302
|
4.2
|
42.6
|
1.0
|
|
C5'
|
J:ADP301
|
4.2
|
31.9
|
1.0
|
|
NH2
|
J:ARG187
|
4.2
|
52.1
|
1.0
|
|
O5'
|
J:ADP301
|
4.2
|
34.5
|
1.0
|
|
O2
|
J:PO4302
|
4.3
|
41.0
|
1.0
|
|
CB
|
J:ASP229
|
4.3
|
43.0
|
1.0
|
|
O3'
|
J:ADP301
|
4.3
|
33.5
|
1.0
|
|
NH2
|
J:ARG173
|
4.4
|
46.4
|
1.0
|
|
OE2
|
J:GLU241
|
4.4
|
56.3
|
1.0
|
|
O1A
|
J:ADP301
|
4.4
|
38.1
|
1.0
|
|
CB
|
J:GLU241
|
4.6
|
49.5
|
1.0
|
|
NH1
|
J:ARG187
|
4.6
|
50.6
|
1.0
|
|
O3B
|
J:ADP301
|
4.6
|
38.2
|
1.0
|
|
OD1
|
J:ASN243
|
4.7
|
45.9
|
1.0
|
|
CG
|
J:GLU241
|
4.7
|
54.1
|
1.0
|
|
ND2
|
J:ASN240
|
4.7
|
40.9
|
1.0
|
|
C3'
|
J:ADP301
|
4.7
|
33.1
|
1.0
|
|
CG
|
J:ASN243
|
4.8
|
46.6
|
1.0
|
|
CZ
|
J:ARG187
|
4.9
|
51.3
|
1.0
|
|
CG
|
J:ASN195
|
5.0
|
41.8
|
1.0
|
|
Magnesium binding site 9 out
of 9 in 5k2m
Go back to
Magnesium Binding Sites List in 5k2m
Magnesium binding site 9 out
of 9 in the Bifunctional Lysx/Argx From Thermococcus Kodakarensis with Lysw-Gamma- Aaa
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 9 of Bifunctional Lysx/Argx From Thermococcus Kodakarensis with Lysw-Gamma- Aaa within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
J:Mg304
b:45.1
occ:1.00
|
O3
|
J:PO4302
|
1.9
|
42.2
|
1.0
|
|
O2B
|
J:ADP301
|
2.1
|
44.5
|
1.0
|
|
OD1
|
J:ASN243
|
2.2
|
45.9
|
1.0
|
|
O
|
J:HOH405
|
2.2
|
39.9
|
1.0
|
|
OE2
|
J:GLU241
|
2.4
|
56.3
|
1.0
|
|
OE1
|
J:GLU241
|
2.5
|
57.7
|
1.0
|
|
CD
|
J:GLU241
|
2.8
|
55.0
|
1.0
|
|
P
|
J:PO4302
|
3.1
|
41.6
|
1.0
|
|
CG
|
J:ASN243
|
3.1
|
46.6
|
1.0
|
|
PB
|
J:ADP301
|
3.3
|
45.9
|
1.0
|
|
MG
|
J:MG303
|
3.3
|
43.0
|
1.0
|
|
ND2
|
J:ASN243
|
3.3
|
46.3
|
1.0
|
|
O1B
|
J:ADP301
|
3.4
|
40.7
|
1.0
|
|
O1
|
J:PO4302
|
3.4
|
44.0
|
1.0
|
|
O4
|
J:PO4302
|
3.6
|
42.6
|
1.0
|
|
NZ
|
J:LYS83
|
3.9
|
44.8
|
1.0
|
|
OG
|
J:SER127
|
4.0
|
48.7
|
1.0
|
|
O
|
J:HOH411
|
4.0
|
51.6
|
1.0
|
|
O
|
J:GLY126
|
4.2
|
45.7
|
1.0
|
|
CA
|
J:SER127
|
4.2
|
47.4
|
1.0
|
|
O2
|
J:PO4302
|
4.3
|
41.0
|
1.0
|
|
CG
|
J:GLU241
|
4.3
|
54.1
|
1.0
|
|
O3A
|
J:ADP301
|
4.3
|
39.0
|
1.0
|
|
CB
|
J:SER127
|
4.3
|
47.7
|
1.0
|
|
O3B
|
J:ADP301
|
4.4
|
38.2
|
1.0
|
|
O2A
|
J:ADP301
|
4.4
|
41.8
|
1.0
|
|
CB
|
J:ASN243
|
4.5
|
44.9
|
1.0
|
|
CE
|
J:LYS83
|
4.8
|
45.6
|
1.0
|
|
OD2
|
J:ASP229
|
4.9
|
46.8
|
1.0
|
|
O
|
J:VAL242
|
5.0
|
42.4
|
1.0
|
|
PA
|
J:ADP301
|
5.0
|
39.8
|
1.0
|
|
Reference:
A.Yoshida,
T.Tomita,
H.Atomi,
T.Kuzuyama,
M.Nishiyama.
Lysine Biosynthesis of Thermococcus Kodakarensis with the Capacity to Function As An Ornithine Biosynthetic System. J. Biol. Chem. V. 291 21630 2016.
ISSN: ESSN 1083-351X
PubMed: 27566549
DOI: 10.1074/JBC.M116.743021
Page generated: Sun Sep 29 18:49:53 2024
|
