Sodium in PDB 7qbv: B12-Dependent Radical Sam Methyltransferase, MMP10 with [4FE-4S] Cluster, Cobalamin, and S-Adenosyl-L-Homocysteine Bound.
Protein crystallography data
The structure of B12-Dependent Radical Sam Methyltransferase, MMP10 with [4FE-4S] Cluster, Cobalamin, and S-Adenosyl-L-Homocysteine Bound., PDB code: 7qbv
was solved by
C.D.Fyfe,
L.M.G.Chavas,
P.Legrand,
A.Benjdia,
O.Berteau,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
49.40 /
2.70
|
Space group
|
P 21 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
155.498,
163,
77.328,
90,
90,
90
|
R / Rfree (%)
|
21.4 /
23.5
|
Other elements in 7qbv:
The structure of B12-Dependent Radical Sam Methyltransferase, MMP10 with [4FE-4S] Cluster, Cobalamin, and S-Adenosyl-L-Homocysteine Bound. also contains other interesting chemical elements:
Sodium Binding Sites:
The binding sites of Sodium atom in the B12-Dependent Radical Sam Methyltransferase, MMP10 with [4FE-4S] Cluster, Cobalamin, and S-Adenosyl-L-Homocysteine Bound.
(pdb code 7qbv). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the
B12-Dependent Radical Sam Methyltransferase, MMP10 with [4FE-4S] Cluster, Cobalamin, and S-Adenosyl-L-Homocysteine Bound., PDB code: 7qbv:
Jump to Sodium binding site number:
1;
2;
3;
4;
Sodium binding site 1 out
of 4 in 7qbv
Go back to
Sodium Binding Sites List in 7qbv
Sodium binding site 1 out
of 4 in the B12-Dependent Radical Sam Methyltransferase, MMP10 with [4FE-4S] Cluster, Cobalamin, and S-Adenosyl-L-Homocysteine Bound.
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 1 of B12-Dependent Radical Sam Methyltransferase, MMP10 with [4FE-4S] Cluster, Cobalamin, and S-Adenosyl-L-Homocysteine Bound. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na505
b:42.0
occ:1.00
|
OD1
|
A:ASP156
|
2.5
|
46.6
|
1.0
|
O
|
A:PHE121
|
2.7
|
45.2
|
1.0
|
O
|
A:GLU158
|
2.9
|
45.0
|
1.0
|
O
|
A:GLY118
|
3.1
|
45.8
|
1.0
|
OG
|
A:SER162
|
3.1
|
43.7
|
1.0
|
N
|
A:GLU158
|
3.3
|
44.5
|
1.0
|
CB
|
A:GLU158
|
3.4
|
48.7
|
1.0
|
C
|
A:GLU158
|
3.4
|
44.8
|
1.0
|
C
|
A:PHE121
|
3.5
|
45.2
|
1.0
|
O
|
A:LYS119
|
3.5
|
45.5
|
1.0
|
CA
|
A:GLU158
|
3.6
|
45.2
|
1.0
|
CG
|
A:ASP156
|
3.7
|
46.1
|
1.0
|
C
|
A:LYS119
|
3.8
|
45.4
|
1.0
|
CA
|
A:LYS119
|
3.9
|
45.4
|
1.0
|
CD
|
A:PRO157
|
4.1
|
42.6
|
1.0
|
CG
|
A:PRO157
|
4.1
|
44.3
|
1.0
|
C
|
A:GLY118
|
4.1
|
45.6
|
1.0
|
OD2
|
A:ASP156
|
4.2
|
47.4
|
1.0
|
CA
|
A:SER122
|
4.2
|
45.9
|
1.0
|
N
|
A:SER122
|
4.2
|
45.4
|
1.0
|
N
|
A:PHE121
|
4.2
|
44.5
|
1.0
|
OG
|
A:SER122
|
4.3
|
50.6
|
1.0
|
CG
|
A:GLU158
|
4.4
|
57.4
|
1.0
|
N
|
A:PRO157
|
4.4
|
43.1
|
1.0
|
CA
|
A:PHE121
|
4.4
|
44.6
|
1.0
|
C
|
A:PRO157
|
4.5
|
44.2
|
1.0
|
N
|
A:PRO159
|
4.5
|
44.2
|
1.0
|
N
|
A:LYS119
|
4.5
|
45.1
|
1.0
|
CB
|
A:SER162
|
4.5
|
42.0
|
1.0
|
N
|
A:GLY120
|
4.7
|
45.1
|
1.0
|
N
|
A:SER162
|
4.8
|
41.2
|
1.0
|
C
|
A:ASP156
|
4.8
|
43.3
|
1.0
|
CA
|
A:PRO157
|
4.9
|
43.4
|
1.0
|
CB
|
A:SER122
|
4.9
|
47.5
|
1.0
|
CB
|
A:ASP156
|
4.9
|
43.6
|
1.0
|
CB
|
A:PHE121
|
4.9
|
44.0
|
1.0
|
C
|
A:GLY120
|
4.9
|
44.9
|
1.0
|
|
Sodium binding site 2 out
of 4 in 7qbv
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Sodium Binding Sites List in 7qbv
Sodium binding site 2 out
of 4 in the B12-Dependent Radical Sam Methyltransferase, MMP10 with [4FE-4S] Cluster, Cobalamin, and S-Adenosyl-L-Homocysteine Bound.
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 2 of B12-Dependent Radical Sam Methyltransferase, MMP10 with [4FE-4S] Cluster, Cobalamin, and S-Adenosyl-L-Homocysteine Bound. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na505
b:39.7
occ:1.00
|
OD1
|
B:ASP156
|
2.5
|
52.7
|
1.0
|
O
|
B:PHE121
|
2.6
|
42.6
|
1.0
|
O
|
B:GLY118
|
2.9
|
40.3
|
1.0
|
O
|
B:GLU158
|
3.0
|
50.0
|
1.0
|
OG
|
B:SER162
|
3.1
|
46.8
|
1.0
|
N
|
B:GLU158
|
3.4
|
50.1
|
1.0
|
O
|
B:LYS119
|
3.5
|
40.8
|
1.0
|
C
|
B:PHE121
|
3.5
|
42.5
|
1.0
|
C
|
B:GLU158
|
3.6
|
49.8
|
1.0
|
CB
|
B:GLU158
|
3.6
|
53.9
|
1.0
|
CG
|
B:ASP156
|
3.7
|
52.2
|
1.0
|
C
|
B:LYS119
|
3.7
|
40.6
|
1.0
|
CA
|
B:GLU158
|
3.7
|
50.5
|
1.0
|
CA
|
B:LYS119
|
3.8
|
40.1
|
1.0
|
C
|
B:GLY118
|
4.0
|
40.1
|
1.0
|
CD
|
B:PRO157
|
4.1
|
49.1
|
1.0
|
N
|
B:PHE121
|
4.1
|
40.9
|
1.0
|
OD2
|
B:ASP156
|
4.1
|
53.5
|
1.0
|
CG
|
B:PRO157
|
4.1
|
50.7
|
1.0
|
N
|
B:SER122
|
4.2
|
43.1
|
1.0
|
CA
|
B:SER122
|
4.2
|
44.0
|
1.0
|
OG
|
B:SER122
|
4.3
|
48.9
|
1.0
|
CA
|
B:PHE121
|
4.3
|
41.4
|
1.0
|
N
|
B:LYS119
|
4.4
|
39.8
|
1.0
|
N
|
B:PRO157
|
4.5
|
49.8
|
1.0
|
CB
|
B:SER162
|
4.5
|
45.0
|
1.0
|
CG
|
B:GLU158
|
4.5
|
61.5
|
1.0
|
N
|
B:GLY120
|
4.5
|
40.4
|
1.0
|
C
|
B:PRO157
|
4.6
|
50.4
|
1.0
|
N
|
B:PRO159
|
4.7
|
48.9
|
1.0
|
CB
|
B:PHE121
|
4.8
|
40.9
|
1.0
|
C
|
B:GLY120
|
4.8
|
40.9
|
1.0
|
N
|
B:SER162
|
4.8
|
44.4
|
1.0
|
C
|
B:ASP156
|
4.9
|
49.8
|
1.0
|
CB
|
B:ASP156
|
4.9
|
49.7
|
1.0
|
CB
|
B:SER122
|
4.9
|
45.8
|
1.0
|
CA
|
B:PRO157
|
5.0
|
49.9
|
1.0
|
|
Sodium binding site 3 out
of 4 in 7qbv
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Sodium Binding Sites List in 7qbv
Sodium binding site 3 out
of 4 in the B12-Dependent Radical Sam Methyltransferase, MMP10 with [4FE-4S] Cluster, Cobalamin, and S-Adenosyl-L-Homocysteine Bound.
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 3 of B12-Dependent Radical Sam Methyltransferase, MMP10 with [4FE-4S] Cluster, Cobalamin, and S-Adenosyl-L-Homocysteine Bound. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Na505
b:42.7
occ:1.00
|
OD1
|
C:ASP156
|
2.5
|
51.8
|
1.0
|
O
|
C:PHE121
|
2.5
|
47.2
|
1.0
|
O
|
C:GLY118
|
2.6
|
46.5
|
1.0
|
OG
|
C:SER162
|
2.7
|
47.9
|
1.0
|
O
|
C:GLU158
|
2.9
|
49.9
|
1.0
|
C
|
C:PHE121
|
3.5
|
47.3
|
1.0
|
CG
|
C:ASP156
|
3.6
|
51.8
|
1.0
|
C
|
C:GLU158
|
3.6
|
49.9
|
1.0
|
O
|
C:LYS119
|
3.7
|
47.0
|
1.0
|
N
|
C:GLU158
|
3.7
|
50.3
|
1.0
|
C
|
C:GLY118
|
3.7
|
46.5
|
1.0
|
CA
|
C:LYS119
|
3.8
|
46.5
|
1.0
|
C
|
C:LYS119
|
3.8
|
46.9
|
1.0
|
CB
|
C:GLU158
|
3.8
|
53.6
|
1.0
|
CA
|
C:GLU158
|
3.9
|
50.5
|
1.0
|
OD2
|
C:ASP156
|
3.9
|
53.2
|
1.0
|
N
|
C:PHE121
|
4.1
|
46.6
|
1.0
|
CB
|
C:SER162
|
4.1
|
46.3
|
1.0
|
N
|
C:LYS119
|
4.2
|
46.3
|
1.0
|
CA
|
C:PHE121
|
4.3
|
46.9
|
1.0
|
N
|
C:SER122
|
4.3
|
47.7
|
1.0
|
CA
|
C:SER122
|
4.4
|
48.3
|
1.0
|
CD
|
C:PRO157
|
4.4
|
49.3
|
1.0
|
N
|
C:SER162
|
4.5
|
45.8
|
1.0
|
CG
|
C:PRO157
|
4.5
|
50.9
|
1.0
|
N
|
C:GLY120
|
4.6
|
46.9
|
1.0
|
CB
|
C:PHE121
|
4.6
|
46.5
|
1.0
|
N
|
C:PRO159
|
4.6
|
49.2
|
1.0
|
OG
|
C:SER122
|
4.6
|
52.6
|
1.0
|
N
|
C:PRO157
|
4.7
|
50.0
|
1.0
|
CA
|
C:SER162
|
4.7
|
45.4
|
1.0
|
CG
|
C:GLU158
|
4.8
|
59.9
|
1.0
|
C
|
C:GLY120
|
4.9
|
46.9
|
1.0
|
CB
|
C:ASP156
|
4.9
|
50.0
|
1.0
|
C
|
C:PRO157
|
4.9
|
50.5
|
1.0
|
CA
|
C:GLY118
|
5.0
|
46.5
|
1.0
|
|
Sodium binding site 4 out
of 4 in 7qbv
Go back to
Sodium Binding Sites List in 7qbv
Sodium binding site 4 out
of 4 in the B12-Dependent Radical Sam Methyltransferase, MMP10 with [4FE-4S] Cluster, Cobalamin, and S-Adenosyl-L-Homocysteine Bound.
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 4 of B12-Dependent Radical Sam Methyltransferase, MMP10 with [4FE-4S] Cluster, Cobalamin, and S-Adenosyl-L-Homocysteine Bound. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Na505
b:36.7
occ:1.00
|
O
|
D:PHE121
|
2.4
|
54.7
|
1.0
|
OD1
|
D:ASP156
|
2.6
|
60.3
|
1.0
|
OG
|
D:SER162
|
2.6
|
52.0
|
1.0
|
O
|
D:GLY118
|
2.7
|
52.2
|
1.0
|
O
|
D:GLU158
|
2.7
|
55.8
|
1.0
|
C
|
D:PHE121
|
3.4
|
54.5
|
1.0
|
C
|
D:GLU158
|
3.5
|
55.9
|
1.0
|
CG
|
D:ASP156
|
3.7
|
60.0
|
1.0
|
CB
|
D:GLU158
|
3.7
|
60.1
|
1.0
|
N
|
D:GLU158
|
3.7
|
56.5
|
1.0
|
CA
|
D:GLU158
|
3.8
|
56.8
|
1.0
|
C
|
D:GLY118
|
3.8
|
51.8
|
1.0
|
O
|
D:LYS119
|
3.8
|
52.6
|
1.0
|
CA
|
D:LYS119
|
4.0
|
51.7
|
1.0
|
C
|
D:LYS119
|
4.0
|
52.4
|
1.0
|
OD2
|
D:ASP156
|
4.0
|
61.4
|
1.0
|
CB
|
D:SER162
|
4.0
|
50.7
|
1.0
|
N
|
D:PHE121
|
4.1
|
53.3
|
1.0
|
N
|
D:SER122
|
4.2
|
55.2
|
1.0
|
CA
|
D:PHE121
|
4.2
|
53.6
|
1.0
|
CA
|
D:SER122
|
4.3
|
56.4
|
1.0
|
N
|
D:SER162
|
4.3
|
51.4
|
1.0
|
N
|
D:LYS119
|
4.4
|
51.5
|
1.0
|
CB
|
D:PHE121
|
4.5
|
52.9
|
1.0
|
CD
|
D:PRO157
|
4.6
|
56.3
|
1.0
|
N
|
D:PRO159
|
4.6
|
55.0
|
1.0
|
CA
|
D:SER162
|
4.6
|
50.5
|
1.0
|
OG
|
D:SER122
|
4.6
|
61.6
|
1.0
|
CG
|
D:PRO157
|
4.7
|
57.9
|
1.0
|
N
|
D:GLY120
|
4.7
|
52.4
|
1.0
|
CG
|
D:GLU158
|
4.7
|
67.3
|
1.0
|
CB
|
D:ALA161
|
4.8
|
53.0
|
1.0
|
N
|
D:PRO157
|
4.8
|
56.8
|
1.0
|
C
|
D:GLY120
|
4.9
|
53.6
|
1.0
|
C
|
D:PRO157
|
4.9
|
56.9
|
1.0
|
CB
|
D:ASP156
|
5.0
|
57.5
|
1.0
|
|
Reference:
C.D.Fyfe,
N.Bernardo-Garcia,
L.Fradale,
S.Grimaldi,
A.Guillot,
C.Brewee,
L.M.G.Chavas,
P.Legrand,
A.Benjdia,
O.Berteau.
Crystallographic Snapshots of A B 12 -Dependent Radical Sam Methyltransferase. Nature V. 602 336 2022.
ISSN: ESSN 1476-4687
PubMed: 35110733
DOI: 10.1038/S41586-021-04355-9
Page generated: Wed Oct 9 08:20:34 2024
|