Cobalt in PDB 7qbt: B12-Dependent Radical Sam Methyltransferase, MMP10 with [4FE-4S] Cluster, Cobalamin, and S-Methyl-5'-Thioadenosine Bound.
Protein crystallography data
The structure of B12-Dependent Radical Sam Methyltransferase, MMP10 with [4FE-4S] Cluster, Cobalamin, and S-Methyl-5'-Thioadenosine Bound., PDB code: 7qbt
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)
|
44.71 /
1.90
|
Space group
|
P 21 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
156.064,
163.915,
77.805,
90,
90,
90
|
R / Rfree (%)
|
20.3 /
22.9
|
Other elements in 7qbt:
The structure of B12-Dependent Radical Sam Methyltransferase, MMP10 with [4FE-4S] Cluster, Cobalamin, and S-Methyl-5'-Thioadenosine 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-Methyl-5'-Thioadenosine Bound.
(pdb code 7qbt). 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-Methyl-5'-Thioadenosine Bound., PDB code: 7qbt:
Jump to Cobalt binding site number:
1;
2;
3;
4;
Cobalt binding site 1 out
of 4 in 7qbt
Go back to
Cobalt Binding Sites List in 7qbt
Cobalt binding site 1 out
of 4 in the B12-Dependent Radical Sam Methyltransferase, MMP10 with [4FE-4S] Cluster, Cobalamin, and S-Methyl-5'-Thioadenosine 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-Methyl-5'-Thioadenosine Bound. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Co504
b:26.6
occ:1.00
|
CO
|
A:COB504
|
0.0
|
26.6
|
1.0
|
N21
|
A:COB504
|
1.8
|
26.2
|
1.0
|
N24
|
A:COB504
|
1.9
|
26.8
|
1.0
|
N22
|
A:COB504
|
1.9
|
26.5
|
1.0
|
N23
|
A:COB504
|
1.9
|
27.1
|
1.0
|
C1A
|
A:COB504
|
2.0
|
27.2
|
1.0
|
C19
|
A:COB504
|
2.7
|
27.8
|
1.0
|
C9
|
A:COB504
|
2.8
|
26.8
|
1.0
|
C4
|
A:COB504
|
2.8
|
25.9
|
1.0
|
C11
|
A:COB504
|
2.8
|
27.1
|
1.0
|
C1
|
A:COB504
|
2.8
|
26.8
|
1.0
|
C6
|
A:COB504
|
2.9
|
26.4
|
1.0
|
C14
|
A:COB504
|
2.9
|
26.4
|
1.0
|
C16
|
A:COB504
|
2.9
|
26.6
|
1.0
|
C10
|
A:COB504
|
3.2
|
26.9
|
1.0
|
C5
|
A:COB504
|
3.3
|
25.9
|
1.0
|
C15
|
A:COB504
|
3.4
|
25.9
|
1.0
|
C20
|
A:COB504
|
3.5
|
24.6
|
1.0
|
CD1
|
A:LEU322
|
3.9
|
26.1
|
1.0
|
C2
|
A:COB504
|
4.1
|
27.5
|
1.0
|
C8
|
A:COB504
|
4.1
|
26.6
|
1.0
|
C3
|
A:COB504
|
4.1
|
26.6
|
1.0
|
C18
|
A:COB504
|
4.1
|
28.1
|
1.0
|
C17
|
A:COB504
|
4.2
|
26.6
|
1.0
|
C12
|
A:COB504
|
4.2
|
27.2
|
1.0
|
C7
|
A:COB504
|
4.2
|
26.7
|
1.0
|
C13
|
A:COB504
|
4.3
|
27.3
|
1.0
|
O
|
A:HOH880
|
4.4
|
37.3
|
1.0
|
CD2
|
A:LEU322
|
4.4
|
26.5
|
1.0
|
C26
|
A:COB504
|
4.5
|
29.7
|
1.0
|
N40
|
A:COB504
|
4.6
|
25.6
|
1.0
|
CG
|
A:LEU322
|
4.6
|
26.3
|
1.0
|
OH
|
A:TYR23
|
4.8
|
41.5
|
1.0
|
C35
|
A:COB504
|
4.8
|
25.9
|
1.0
|
C53
|
A:COB504
|
4.9
|
25.6
|
1.0
|
C54
|
A:COB504
|
4.9
|
25.6
|
1.0
|
|
Cobalt binding site 2 out
of 4 in 7qbt
Go back to
Cobalt Binding Sites List in 7qbt
Cobalt binding site 2 out
of 4 in the B12-Dependent Radical Sam Methyltransferase, MMP10 with [4FE-4S] Cluster, Cobalamin, and S-Methyl-5'-Thioadenosine 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-Methyl-5'-Thioadenosine Bound. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Co504
b:27.1
occ:1.00
|
CO
|
B:COB504
|
0.0
|
27.1
|
1.0
|
N21
|
B:COB504
|
1.8
|
27.4
|
1.0
|
N24
|
B:COB504
|
1.9
|
26.9
|
1.0
|
N22
|
B:COB504
|
1.9
|
28.6
|
1.0
|
N23
|
B:COB504
|
1.9
|
27.7
|
1.0
|
C1A
|
B:COB504
|
2.0
|
28.0
|
1.0
|
C19
|
B:COB504
|
2.7
|
27.4
|
1.0
|
C9
|
B:COB504
|
2.8
|
28.6
|
1.0
|
C4
|
B:COB504
|
2.8
|
27.6
|
1.0
|
C11
|
B:COB504
|
2.9
|
27.5
|
1.0
|
C1
|
B:COB504
|
2.9
|
26.8
|
1.0
|
C14
|
B:COB504
|
2.9
|
27.6
|
1.0
|
C6
|
B:COB504
|
2.9
|
28.6
|
1.0
|
C16
|
B:COB504
|
2.9
|
26.6
|
1.0
|
C10
|
B:COB504
|
3.2
|
27.9
|
1.0
|
C5
|
B:COB504
|
3.3
|
28.1
|
1.0
|
C15
|
B:COB504
|
3.3
|
26.9
|
1.0
|
C20
|
B:COB504
|
3.5
|
24.1
|
1.0
|
CD1
|
B:LEU322
|
3.9
|
25.6
|
1.0
|
C2
|
B:COB504
|
4.1
|
27.9
|
1.0
|
C8
|
B:COB504
|
4.1
|
29.3
|
1.0
|
C3
|
B:COB504
|
4.1
|
27.5
|
1.0
|
C18
|
B:COB504
|
4.2
|
27.2
|
1.0
|
C17
|
B:COB504
|
4.2
|
26.1
|
1.0
|
C7
|
B:COB504
|
4.2
|
29.6
|
1.0
|
C12
|
B:COB504
|
4.2
|
27.9
|
1.0
|
C13
|
B:COB504
|
4.2
|
28.1
|
1.0
|
CD2
|
B:LEU322
|
4.4
|
27.0
|
1.0
|
O
|
B:HOH853
|
4.5
|
41.1
|
1.0
|
C26
|
B:COB504
|
4.5
|
30.1
|
1.0
|
CG
|
B:LEU322
|
4.6
|
26.4
|
1.0
|
N40
|
B:COB504
|
4.6
|
32.0
|
1.0
|
C35
|
B:COB504
|
4.8
|
27.9
|
1.0
|
C53
|
B:COB504
|
4.8
|
26.2
|
1.0
|
OH
|
B:TYR23
|
4.8
|
38.5
|
1.0
|
C54
|
B:COB504
|
4.9
|
24.8
|
1.0
|
|
Cobalt binding site 3 out
of 4 in 7qbt
Go back to
Cobalt Binding Sites List in 7qbt
Cobalt binding site 3 out
of 4 in the B12-Dependent Radical Sam Methyltransferase, MMP10 with [4FE-4S] Cluster, Cobalamin, and S-Methyl-5'-Thioadenosine 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-Methyl-5'-Thioadenosine Bound. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Co504
b:32.7
occ:1.00
|
CO
|
C:COB504
|
0.0
|
32.7
|
1.0
|
N21
|
C:COB504
|
1.8
|
33.0
|
1.0
|
N24
|
C:COB504
|
1.9
|
32.8
|
1.0
|
N22
|
C:COB504
|
1.9
|
33.4
|
1.0
|
N23
|
C:COB504
|
1.9
|
33.9
|
1.0
|
C1A
|
C:COB504
|
2.0
|
32.7
|
1.0
|
C19
|
C:COB504
|
2.7
|
33.7
|
1.0
|
C9
|
C:COB504
|
2.8
|
33.6
|
1.0
|
C4
|
C:COB504
|
2.8
|
33.0
|
1.0
|
C11
|
C:COB504
|
2.8
|
34.0
|
1.0
|
C1
|
C:COB504
|
2.8
|
33.2
|
1.0
|
C14
|
C:COB504
|
2.9
|
34.2
|
1.0
|
C6
|
C:COB504
|
2.9
|
33.4
|
1.0
|
C16
|
C:COB504
|
2.9
|
32.9
|
1.0
|
C10
|
C:COB504
|
3.2
|
33.6
|
1.0
|
C5
|
C:COB504
|
3.3
|
32.8
|
1.0
|
C15
|
C:COB504
|
3.3
|
33.5
|
1.0
|
C20
|
C:COB504
|
3.5
|
32.4
|
1.0
|
CD1
|
C:LEU322
|
4.0
|
36.8
|
1.0
|
C2
|
C:COB504
|
4.1
|
33.4
|
1.0
|
C8
|
C:COB504
|
4.1
|
34.2
|
1.0
|
C18
|
C:COB504
|
4.1
|
34.0
|
1.0
|
C3
|
C:COB504
|
4.1
|
32.6
|
1.0
|
C17
|
C:COB504
|
4.2
|
32.6
|
1.0
|
C7
|
C:COB504
|
4.2
|
34.4
|
1.0
|
C13
|
C:COB504
|
4.2
|
34.5
|
1.0
|
C12
|
C:COB504
|
4.2
|
34.4
|
1.0
|
CD2
|
C:LEU322
|
4.5
|
37.7
|
1.0
|
C26
|
C:COB504
|
4.5
|
34.8
|
1.0
|
N40
|
C:COB504
|
4.6
|
34.7
|
1.0
|
O
|
C:HOH767
|
4.6
|
47.6
|
1.0
|
CG
|
C:LEU322
|
4.6
|
36.8
|
1.0
|
OH
|
C:TYR23
|
4.8
|
47.2
|
1.0
|
C35
|
C:COB504
|
4.8
|
31.9
|
1.0
|
C54
|
C:COB504
|
4.8
|
31.9
|
1.0
|
C53
|
C:COB504
|
4.8
|
32.9
|
1.0
|
|
Cobalt binding site 4 out
of 4 in 7qbt
Go back to
Cobalt Binding Sites List in 7qbt
Cobalt binding site 4 out
of 4 in the B12-Dependent Radical Sam Methyltransferase, MMP10 with [4FE-4S] Cluster, Cobalamin, and S-Methyl-5'-Thioadenosine 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-Methyl-5'-Thioadenosine Bound. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Co504
b:26.6
occ:1.00
|
CO
|
D:COB504
|
0.0
|
26.6
|
1.0
|
N22
|
D:COB504
|
1.9
|
26.7
|
1.0
|
N21
|
D:COB504
|
1.9
|
26.9
|
1.0
|
N23
|
D:COB504
|
1.9
|
27.0
|
1.0
|
N24
|
D:COB504
|
1.9
|
26.9
|
1.0
|
C1A
|
D:COB504
|
2.0
|
26.8
|
1.0
|
C19
|
D:COB504
|
2.8
|
27.6
|
1.0
|
C9
|
D:COB504
|
2.8
|
26.6
|
1.0
|
C11
|
D:COB504
|
2.8
|
27.1
|
1.0
|
C4
|
D:COB504
|
2.8
|
26.9
|
1.0
|
C1
|
D:COB504
|
2.9
|
26.8
|
1.0
|
C14
|
D:COB504
|
2.9
|
27.0
|
1.0
|
C6
|
D:COB504
|
2.9
|
26.8
|
1.0
|
C16
|
D:COB504
|
2.9
|
27.1
|
1.0
|
C10
|
D:COB504
|
3.1
|
26.8
|
1.0
|
C5
|
D:COB504
|
3.3
|
26.9
|
1.0
|
C15
|
D:COB504
|
3.3
|
27.2
|
1.0
|
C20
|
D:COB504
|
3.5
|
24.8
|
1.0
|
CD1
|
D:LEU322
|
4.0
|
26.8
|
1.0
|
C2
|
D:COB504
|
4.1
|
27.9
|
1.0
|
C8
|
D:COB504
|
4.1
|
26.4
|
1.0
|
C3
|
D:COB504
|
4.2
|
26.7
|
1.0
|
C18
|
D:COB504
|
4.2
|
28.0
|
1.0
|
C12
|
D:COB504
|
4.2
|
27.6
|
1.0
|
C7
|
D:COB504
|
4.2
|
26.6
|
1.0
|
C13
|
D:COB504
|
4.2
|
27.1
|
1.0
|
C17
|
D:COB504
|
4.2
|
27.1
|
1.0
|
CD2
|
D:LEU322
|
4.4
|
28.4
|
1.0
|
O
|
D:HOH874
|
4.5
|
41.7
|
1.0
|
N40
|
D:COB504
|
4.5
|
26.9
|
1.0
|
C26
|
D:COB504
|
4.5
|
30.2
|
1.0
|
CG
|
D:LEU322
|
4.7
|
27.5
|
1.0
|
C35
|
D:COB504
|
4.8
|
27.6
|
1.0
|
C53
|
D:COB504
|
4.9
|
27.2
|
1.0
|
OH
|
D:TYR23
|
4.9
|
41.1
|
1.0
|
C54
|
D:COB504
|
4.9
|
25.4
|
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 19:26:00 2024
|