Cobalt 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:
Cobalt Binding Sites:
The binding sites of Cobalt 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 Cobalt atom.
In total 4 binding sites of Cobalt 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 Cobalt binding site number:
1;
2;
3;
4;
Cobalt binding site 1 out
of 4 in 7qbv
Go back to
Cobalt Binding Sites List in 7qbv
Cobalt 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 Cobalt with other atoms in the Co 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:Co504
b:40.0
occ:1.00
|
CO
|
A:COB504
|
0.0
|
40.0
|
1.0
|
N21
|
A:COB504
|
1.8
|
40.2
|
1.0
|
N22
|
A:COB504
|
1.8
|
39.4
|
1.0
|
N23
|
A:COB504
|
1.9
|
40.1
|
1.0
|
N24
|
A:COB504
|
1.9
|
40.5
|
1.0
|
C1A
|
A:COB504
|
2.0
|
40.3
|
1.0
|
C19
|
A:COB504
|
2.7
|
41.0
|
1.0
|
C9
|
A:COB504
|
2.8
|
39.3
|
1.0
|
C4
|
A:COB504
|
2.8
|
39.8
|
1.0
|
C11
|
A:COB504
|
2.8
|
40.1
|
1.0
|
C1
|
A:COB504
|
2.8
|
40.6
|
1.0
|
C14
|
A:COB504
|
2.9
|
40.2
|
1.0
|
C6
|
A:COB504
|
2.9
|
39.1
|
1.0
|
C16
|
A:COB504
|
2.9
|
40.5
|
1.0
|
C10
|
A:COB504
|
3.1
|
39.7
|
1.0
|
C5
|
A:COB504
|
3.2
|
39.0
|
1.0
|
C15
|
A:COB504
|
3.3
|
40.2
|
1.0
|
C20
|
A:COB504
|
3.7
|
40.5
|
1.0
|
C2
|
A:COB504
|
4.0
|
40.5
|
1.0
|
C3
|
A:COB504
|
4.1
|
40.1
|
1.0
|
C8
|
A:COB504
|
4.1
|
38.9
|
1.0
|
C18
|
A:COB504
|
4.1
|
41.4
|
1.0
|
CD1
|
A:LEU322
|
4.1
|
42.1
|
1.0
|
C12
|
A:COB504
|
4.2
|
40.2
|
1.0
|
C17
|
A:COB504
|
4.2
|
40.7
|
1.0
|
C13
|
A:COB504
|
4.2
|
40.2
|
1.0
|
C26
|
A:COB504
|
4.2
|
40.9
|
1.0
|
C7
|
A:COB504
|
4.2
|
38.8
|
1.0
|
O39
|
A:COB504
|
4.4
|
38.2
|
1.0
|
CD2
|
A:LEU322
|
4.5
|
42.6
|
1.0
|
OH
|
A:TYR23
|
4.7
|
48.5
|
1.0
|
C35
|
A:COB504
|
4.7
|
38.3
|
1.0
|
CG
|
A:LEU322
|
4.7
|
41.8
|
1.0
|
C54
|
A:COB504
|
4.8
|
40.5
|
1.0
|
C53
|
A:COB504
|
4.9
|
39.7
|
1.0
|
|
Cobalt binding site 2 out
of 4 in 7qbv
Go back to
Cobalt Binding Sites List in 7qbv
Cobalt 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 Cobalt with other atoms in the Co 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:Co504
b:39.7
occ:1.00
|
CO
|
B:COB504
|
0.0
|
39.7
|
1.0
|
N21
|
B:COB504
|
1.8
|
40.0
|
1.0
|
N22
|
B:COB504
|
1.8
|
39.6
|
1.0
|
N23
|
B:COB504
|
1.9
|
39.7
|
1.0
|
N24
|
B:COB504
|
1.9
|
40.1
|
1.0
|
C1A
|
B:COB504
|
2.0
|
39.8
|
1.0
|
C19
|
B:COB504
|
2.7
|
40.3
|
1.0
|
C9
|
B:COB504
|
2.7
|
39.5
|
1.0
|
C4
|
B:COB504
|
2.8
|
40.0
|
1.0
|
C11
|
B:COB504
|
2.8
|
39.7
|
1.0
|
C1
|
B:COB504
|
2.8
|
40.4
|
1.0
|
C6
|
B:COB504
|
2.9
|
39.7
|
1.0
|
C14
|
B:COB504
|
2.9
|
39.6
|
1.0
|
C16
|
B:COB504
|
2.9
|
40.0
|
1.0
|
C10
|
B:COB504
|
3.1
|
39.5
|
1.0
|
C5
|
B:COB504
|
3.2
|
39.6
|
1.0
|
C15
|
B:COB504
|
3.4
|
39.4
|
1.0
|
C20
|
B:COB504
|
3.7
|
40.6
|
1.0
|
C2
|
B:COB504
|
3.9
|
40.7
|
1.0
|
C3
|
B:COB504
|
4.0
|
40.4
|
1.0
|
C8
|
B:COB504
|
4.1
|
39.5
|
1.0
|
C18
|
B:COB504
|
4.1
|
40.4
|
1.0
|
CD1
|
B:LEU322
|
4.2
|
45.0
|
1.0
|
C26
|
B:COB504
|
4.2
|
41.1
|
1.0
|
C12
|
B:COB504
|
4.2
|
39.9
|
1.0
|
C13
|
B:COB504
|
4.2
|
39.6
|
1.0
|
C7
|
B:COB504
|
4.2
|
39.6
|
1.0
|
C17
|
B:COB504
|
4.2
|
40.5
|
1.0
|
CD2
|
B:LEU322
|
4.4
|
45.0
|
1.0
|
O39
|
B:COB504
|
4.4
|
40.2
|
1.0
|
OH
|
B:TYR23
|
4.6
|
48.0
|
1.0
|
CG
|
B:LEU322
|
4.7
|
44.7
|
1.0
|
C35
|
B:COB504
|
4.7
|
39.2
|
1.0
|
C54
|
B:COB504
|
4.8
|
40.6
|
1.0
|
C53
|
B:COB504
|
4.9
|
39.0
|
1.0
|
|
Cobalt binding site 3 out
of 4 in 7qbv
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Cobalt Binding Sites List in 7qbv
Cobalt 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 Cobalt with other atoms in the Co 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:Co504
b:42.3
occ:1.00
|
CO
|
C:COB504
|
0.0
|
42.3
|
1.0
|
N21
|
C:COB504
|
1.8
|
42.7
|
1.0
|
N22
|
C:COB504
|
1.8
|
42.2
|
1.0
|
N23
|
C:COB504
|
1.9
|
42.5
|
1.0
|
N24
|
C:COB504
|
1.9
|
42.6
|
1.0
|
C1A
|
C:COB504
|
2.0
|
42.4
|
1.0
|
C19
|
C:COB504
|
2.7
|
42.9
|
1.0
|
C9
|
C:COB504
|
2.7
|
42.3
|
1.0
|
C4
|
C:COB504
|
2.8
|
42.5
|
1.0
|
C11
|
C:COB504
|
2.8
|
42.5
|
1.0
|
C1
|
C:COB504
|
2.8
|
43.1
|
1.0
|
C14
|
C:COB504
|
2.9
|
42.4
|
1.0
|
C6
|
C:COB504
|
2.9
|
42.3
|
1.0
|
C16
|
C:COB504
|
2.9
|
42.4
|
1.0
|
C10
|
C:COB504
|
3.1
|
42.2
|
1.0
|
C5
|
C:COB504
|
3.2
|
41.9
|
1.0
|
C15
|
C:COB504
|
3.4
|
41.9
|
1.0
|
C20
|
C:COB504
|
3.7
|
43.3
|
1.0
|
C2
|
C:COB504
|
3.9
|
43.5
|
1.0
|
C3
|
C:COB504
|
4.1
|
43.1
|
1.0
|
C8
|
C:COB504
|
4.1
|
42.6
|
1.0
|
C18
|
C:COB504
|
4.1
|
42.9
|
1.0
|
CD1
|
C:LEU322
|
4.1
|
44.4
|
1.0
|
C26
|
C:COB504
|
4.2
|
44.3
|
1.0
|
C12
|
C:COB504
|
4.2
|
42.8
|
1.0
|
C13
|
C:COB504
|
4.2
|
42.8
|
1.0
|
C17
|
C:COB504
|
4.2
|
42.4
|
1.0
|
C7
|
C:COB504
|
4.2
|
42.6
|
1.0
|
O39
|
C:COB504
|
4.4
|
43.9
|
1.0
|
CD2
|
C:LEU322
|
4.4
|
44.7
|
1.0
|
OH
|
C:TYR23
|
4.5
|
51.4
|
1.0
|
CG
|
C:LEU322
|
4.7
|
44.2
|
1.0
|
C35
|
C:COB504
|
4.7
|
41.1
|
1.0
|
C54
|
C:COB504
|
4.8
|
42.3
|
1.0
|
C53
|
C:COB504
|
4.9
|
41.1
|
1.0
|
|
Cobalt binding site 4 out
of 4 in 7qbv
Go back to
Cobalt Binding Sites List in 7qbv
Cobalt 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 Cobalt with other atoms in the Co 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:Co504
b:49.2
occ:1.00
|
CO
|
D:COB504
|
0.0
|
49.2
|
1.0
|
N21
|
D:COB504
|
1.8
|
49.0
|
1.0
|
N22
|
D:COB504
|
1.8
|
48.9
|
1.0
|
N24
|
D:COB504
|
1.9
|
49.0
|
1.0
|
N23
|
D:COB504
|
1.9
|
49.0
|
1.0
|
C1A
|
D:COB504
|
2.0
|
49.3
|
1.0
|
C19
|
D:COB504
|
2.7
|
49.0
|
1.0
|
C9
|
D:COB504
|
2.8
|
48.6
|
1.0
|
C4
|
D:COB504
|
2.8
|
48.9
|
1.0
|
C11
|
D:COB504
|
2.8
|
48.9
|
1.0
|
C1
|
D:COB504
|
2.8
|
49.0
|
1.0
|
C14
|
D:COB504
|
2.9
|
49.0
|
1.0
|
C6
|
D:COB504
|
2.9
|
48.7
|
1.0
|
C16
|
D:COB504
|
2.9
|
48.7
|
1.0
|
C10
|
D:COB504
|
3.1
|
48.5
|
1.0
|
C5
|
D:COB504
|
3.2
|
48.5
|
1.0
|
C15
|
D:COB504
|
3.4
|
48.6
|
1.0
|
C20
|
D:COB504
|
3.7
|
48.9
|
1.0
|
C2
|
D:COB504
|
3.9
|
49.2
|
1.0
|
C3
|
D:COB504
|
4.1
|
49.2
|
1.0
|
C18
|
D:COB504
|
4.1
|
48.8
|
1.0
|
C8
|
D:COB504
|
4.1
|
48.6
|
1.0
|
C26
|
D:COB504
|
4.2
|
49.6
|
1.0
|
C17
|
D:COB504
|
4.2
|
48.6
|
1.0
|
C12
|
D:COB504
|
4.2
|
49.0
|
1.0
|
C13
|
D:COB504
|
4.2
|
49.1
|
1.0
|
C7
|
D:COB504
|
4.2
|
48.6
|
1.0
|
CD1
|
D:LEU322
|
4.2
|
58.0
|
1.0
|
O39
|
D:COB504
|
4.4
|
49.3
|
1.0
|
CD2
|
D:LEU322
|
4.5
|
58.0
|
1.0
|
OH
|
D:TYR23
|
4.7
|
62.5
|
1.0
|
C35
|
D:COB504
|
4.7
|
48.1
|
1.0
|
CG
|
D:LEU322
|
4.8
|
57.5
|
1.0
|
C54
|
D:COB504
|
4.8
|
48.8
|
1.0
|
C53
|
D:COB504
|
4.9
|
48.1
|
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: Tue Jul 30 19:26:30 2024
|