Iron in PDB 7qbs: B12-Dependent Radical Sam Methyltransferase, MMP10 with [4FE-4S] Cluster, Cobalamin, S-Adenosyl-L-Methionine, and Peptide Bound.
Protein crystallography data
The structure of B12-Dependent Radical Sam Methyltransferase, MMP10 with [4FE-4S] Cluster, Cobalamin, S-Adenosyl-L-Methionine, and Peptide Bound., PDB code: 7qbs
was solved by
N.Bernardo-Garcia,
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)
|
45.00 /
2.33
|
Space group
|
P 63
|
Cell size a, b, c (Å), α, β, γ (°)
|
119.29,
119.29,
68.56,
90,
90,
120
|
R / Rfree (%)
|
18.2 /
23.5
|
Other elements in 7qbs:
The structure of B12-Dependent Radical Sam Methyltransferase, MMP10 with [4FE-4S] Cluster, Cobalamin, S-Adenosyl-L-Methionine, and Peptide Bound. also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the B12-Dependent Radical Sam Methyltransferase, MMP10 with [4FE-4S] Cluster, Cobalamin, S-Adenosyl-L-Methionine, and Peptide Bound.
(pdb code 7qbs). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 5 binding sites of Iron where determined in the
B12-Dependent Radical Sam Methyltransferase, MMP10 with [4FE-4S] Cluster, Cobalamin, S-Adenosyl-L-Methionine, and Peptide Bound., PDB code: 7qbs:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
Iron binding site 1 out
of 5 in 7qbs
Go back to
Iron Binding Sites List in 7qbs
Iron binding site 1 out
of 5 in the B12-Dependent Radical Sam Methyltransferase, MMP10 with [4FE-4S] Cluster, Cobalamin, S-Adenosyl-L-Methionine, and Peptide Bound.
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of B12-Dependent Radical Sam Methyltransferase, MMP10 with [4FE-4S] Cluster, Cobalamin, S-Adenosyl-L-Methionine, and Peptide Bound. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe501
b:57.2
occ:1.00
|
FE1
|
A:SF4501
|
0.0
|
57.2
|
1.0
|
SG
|
A:CYS22
|
2.3
|
55.2
|
1.0
|
S4
|
A:SF4501
|
2.3
|
57.9
|
1.0
|
S3
|
A:SF4501
|
2.3
|
57.3
|
1.0
|
S2
|
A:SF4501
|
2.3
|
57.8
|
1.0
|
FE2
|
A:SF4501
|
2.7
|
57.8
|
1.0
|
FE3
|
A:SF4501
|
2.8
|
59.7
|
1.0
|
FE4
|
A:SF4501
|
2.8
|
57.4
|
1.0
|
CB
|
A:CYS22
|
3.0
|
54.1
|
1.0
|
S1
|
A:SF4501
|
3.9
|
58.1
|
1.0
|
CA
|
A:CYS22
|
4.1
|
54.2
|
1.0
|
CE
|
A:SAM503
|
4.3
|
74.8
|
1.0
|
CB
|
A:PRO11
|
4.6
|
54.0
|
1.0
|
SG
|
A:CYS15
|
4.8
|
50.5
|
1.0
|
SD
|
A:SAM503
|
4.8
|
74.4
|
1.0
|
CD1
|
A:PHE18
|
4.8
|
51.6
|
1.0
|
SG
|
A:CYS19
|
4.9
|
52.9
|
1.0
|
CD2
|
A:PHE24
|
4.9
|
63.6
|
1.0
|
N
|
A:CYS19
|
4.9
|
52.1
|
1.0
|
N
|
A:GLY12
|
4.9
|
54.1
|
1.0
|
C
|
A:CYS22
|
5.0
|
55.2
|
1.0
|
OXT
|
A:SAM503
|
5.0
|
73.7
|
1.0
|
|
Iron binding site 2 out
of 5 in 7qbs
Go back to
Iron Binding Sites List in 7qbs
Iron binding site 2 out
of 5 in the B12-Dependent Radical Sam Methyltransferase, MMP10 with [4FE-4S] Cluster, Cobalamin, S-Adenosyl-L-Methionine, and Peptide Bound.
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of B12-Dependent Radical Sam Methyltransferase, MMP10 with [4FE-4S] Cluster, Cobalamin, S-Adenosyl-L-Methionine, and Peptide Bound. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe501
b:57.8
occ:1.00
|
FE2
|
A:SF4501
|
0.0
|
57.8
|
1.0
|
S3
|
A:SF4501
|
2.3
|
57.3
|
1.0
|
S4
|
A:SF4501
|
2.3
|
57.9
|
1.0
|
S1
|
A:SF4501
|
2.3
|
58.1
|
1.0
|
SG
|
A:CYS19
|
2.4
|
52.9
|
1.0
|
FE1
|
A:SF4501
|
2.7
|
57.2
|
1.0
|
FE3
|
A:SF4501
|
2.8
|
59.7
|
1.0
|
FE4
|
A:SF4501
|
2.8
|
57.4
|
1.0
|
CB
|
A:CYS19
|
3.3
|
52.0
|
1.0
|
O
|
A:HOH651
|
3.6
|
63.1
|
1.0
|
N
|
A:CYS19
|
3.8
|
52.1
|
1.0
|
S2
|
A:SF4501
|
3.9
|
57.8
|
1.0
|
NZ
|
A:LYS119
|
4.1
|
55.7
|
1.0
|
CA
|
A:CYS19
|
4.2
|
52.0
|
1.0
|
OXT
|
A:SAM503
|
4.2
|
73.7
|
1.0
|
CE
|
A:LYS119
|
4.2
|
56.8
|
1.0
|
CB
|
A:CYS22
|
4.3
|
54.1
|
1.0
|
SG
|
A:CYS22
|
4.6
|
55.2
|
1.0
|
CB
|
A:CYS15
|
4.7
|
54.5
|
1.0
|
SG
|
A:CYS15
|
4.8
|
50.5
|
1.0
|
C
|
A:PHE18
|
4.8
|
52.4
|
1.0
|
|
Iron binding site 3 out
of 5 in 7qbs
Go back to
Iron Binding Sites List in 7qbs
Iron binding site 3 out
of 5 in the B12-Dependent Radical Sam Methyltransferase, MMP10 with [4FE-4S] Cluster, Cobalamin, S-Adenosyl-L-Methionine, and Peptide Bound.
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of B12-Dependent Radical Sam Methyltransferase, MMP10 with [4FE-4S] Cluster, Cobalamin, S-Adenosyl-L-Methionine, and Peptide Bound. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe501
b:59.7
occ:1.00
|
FE3
|
A:SF4501
|
0.0
|
59.7
|
1.0
|
S1
|
A:SF4501
|
2.3
|
58.1
|
1.0
|
S4
|
A:SF4501
|
2.3
|
57.9
|
1.0
|
S2
|
A:SF4501
|
2.3
|
57.8
|
1.0
|
OXT
|
A:SAM503
|
2.3
|
73.7
|
1.0
|
N
|
A:SAM503
|
2.7
|
72.8
|
1.0
|
FE4
|
A:SF4501
|
2.7
|
57.4
|
1.0
|
FE2
|
A:SF4501
|
2.8
|
57.8
|
1.0
|
FE1
|
A:SF4501
|
2.8
|
57.2
|
1.0
|
C
|
A:SAM503
|
3.2
|
73.4
|
1.0
|
SD
|
A:SAM503
|
3.3
|
74.4
|
1.0
|
CA
|
A:SAM503
|
3.4
|
73.3
|
1.0
|
CG
|
A:SAM503
|
3.7
|
74.4
|
1.0
|
CE
|
A:SAM503
|
3.9
|
74.8
|
1.0
|
S3
|
A:SF4501
|
3.9
|
57.3
|
1.0
|
O
|
A:HOH651
|
4.0
|
63.1
|
1.0
|
CB
|
A:SAM503
|
4.1
|
73.8
|
1.0
|
O
|
A:SAM503
|
4.4
|
73.2
|
1.0
|
SG
|
A:CYS15
|
4.7
|
50.5
|
1.0
|
OD1
|
A:ASP90
|
4.7
|
72.0
|
1.0
|
C2'
|
A:SAM503
|
4.8
|
69.2
|
1.0
|
SG
|
A:CYS19
|
4.8
|
52.9
|
1.0
|
SG
|
A:CYS22
|
4.9
|
55.2
|
1.0
|
CB
|
A:SER117
|
5.0
|
56.6
|
1.0
|
|
Iron binding site 4 out
of 5 in 7qbs
Go back to
Iron Binding Sites List in 7qbs
Iron binding site 4 out
of 5 in the B12-Dependent Radical Sam Methyltransferase, MMP10 with [4FE-4S] Cluster, Cobalamin, S-Adenosyl-L-Methionine, and Peptide Bound.
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of B12-Dependent Radical Sam Methyltransferase, MMP10 with [4FE-4S] Cluster, Cobalamin, S-Adenosyl-L-Methionine, and Peptide Bound. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe501
b:57.4
occ:1.00
|
FE4
|
A:SF4501
|
0.0
|
57.4
|
1.0
|
SG
|
A:CYS15
|
2.2
|
50.5
|
1.0
|
S1
|
A:SF4501
|
2.3
|
58.1
|
1.0
|
S2
|
A:SF4501
|
2.3
|
57.8
|
1.0
|
S3
|
A:SF4501
|
2.3
|
57.3
|
1.0
|
FE3
|
A:SF4501
|
2.7
|
59.7
|
1.0
|
FE2
|
A:SF4501
|
2.8
|
57.8
|
1.0
|
FE1
|
A:SF4501
|
2.8
|
57.2
|
1.0
|
CB
|
A:CYS15
|
3.0
|
54.5
|
1.0
|
N
|
A:SAM503
|
3.9
|
72.8
|
1.0
|
N
|
A:GLY12
|
3.9
|
54.1
|
1.0
|
S4
|
A:SF4501
|
3.9
|
57.9
|
1.0
|
CA
|
A:CYS15
|
4.4
|
55.8
|
1.0
|
CA
|
A:PRO11
|
4.5
|
53.5
|
1.0
|
CB
|
A:ASP90
|
4.7
|
65.3
|
1.0
|
N
|
A:ASP90
|
4.7
|
64.7
|
1.0
|
CA
|
A:GLY12
|
4.7
|
54.5
|
1.0
|
C
|
A:PRO11
|
4.8
|
53.9
|
1.0
|
CB
|
A:PRO11
|
4.8
|
54.0
|
1.0
|
OXT
|
A:SAM503
|
4.8
|
73.7
|
1.0
|
NZ
|
A:LYS119
|
4.8
|
55.7
|
1.0
|
SG
|
A:CYS22
|
4.8
|
55.2
|
1.0
|
CE
|
A:LYS119
|
4.9
|
56.8
|
1.0
|
SG
|
A:CYS19
|
4.9
|
52.9
|
1.0
|
|
Iron binding site 5 out
of 5 in 7qbs
Go back to
Iron Binding Sites List in 7qbs
Iron binding site 5 out
of 5 in the B12-Dependent Radical Sam Methyltransferase, MMP10 with [4FE-4S] Cluster, Cobalamin, S-Adenosyl-L-Methionine, and Peptide Bound.
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 5 of B12-Dependent Radical Sam Methyltransferase, MMP10 with [4FE-4S] Cluster, Cobalamin, S-Adenosyl-L-Methionine, and Peptide Bound. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe502
b:64.3
occ:1.00
|
SG
|
A:CYS38
|
2.3
|
62.7
|
1.0
|
SG
|
A:CYS48
|
2.4
|
67.0
|
1.0
|
SG
|
A:CYS35
|
2.4
|
57.2
|
1.0
|
SG
|
A:CYS45
|
2.5
|
66.3
|
1.0
|
CB
|
A:CYS48
|
3.4
|
64.9
|
1.0
|
CB
|
A:CYS45
|
3.4
|
65.0
|
1.0
|
N
|
A:CYS35
|
3.5
|
57.4
|
1.0
|
CB
|
A:CYS38
|
3.5
|
62.2
|
1.0
|
N
|
A:CYS38
|
3.5
|
61.2
|
1.0
|
CB
|
A:CYS35
|
3.6
|
56.9
|
1.0
|
N
|
A:CYS45
|
3.6
|
65.0
|
1.0
|
CA
|
A:CYS38
|
3.7
|
62.6
|
1.0
|
N
|
A:CYS48
|
3.9
|
63.8
|
1.0
|
CA
|
A:CYS35
|
4.0
|
56.8
|
1.0
|
CA
|
A:CYS45
|
4.0
|
65.2
|
1.0
|
C
|
A:GLY34
|
4.2
|
59.0
|
1.0
|
C
|
A:GLY44
|
4.2
|
65.5
|
1.0
|
CA
|
A:CYS48
|
4.3
|
64.9
|
1.0
|
C
|
A:TYR37
|
4.3
|
60.9
|
1.0
|
O
|
A:CYS35
|
4.4
|
55.7
|
1.0
|
C
|
A:CYS35
|
4.4
|
56.2
|
1.0
|
CA
|
A:GLY34
|
4.4
|
61.3
|
1.0
|
CA
|
A:GLY44
|
4.5
|
66.0
|
1.0
|
C
|
A:CYS45
|
4.5
|
66.2
|
1.0
|
O
|
A:CYS45
|
4.7
|
66.5
|
1.0
|
CB
|
A:TYR47
|
4.7
|
62.3
|
1.0
|
N
|
A:GLY44
|
4.7
|
66.5
|
1.0
|
N
|
A:TYR37
|
4.8
|
58.7
|
1.0
|
N
|
A:GLY34
|
4.8
|
63.2
|
1.0
|
CA
|
A:TYR37
|
4.9
|
59.5
|
1.0
|
C
|
A:TYR47
|
4.9
|
63.7
|
1.0
|
CB
|
A:TYR37
|
4.9
|
59.0
|
1.0
|
N
|
A:TYR47
|
4.9
|
65.0
|
1.0
|
O
|
A:GLY44
|
4.9
|
65.4
|
1.0
|
O
|
A:TYR37
|
5.0
|
61.5
|
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: Thu Aug 8 18:10:31 2024
|