Iron in PDB 7qbu: 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: 7qbu
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)
|
44.84 /
2.30
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
77.779,
79.493,
151.659,
90,
90,
90
|
R / Rfree (%)
|
19.1 /
22.5
|
Other elements in 7qbu:
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:
Iron Binding Sites:
The binding sites of Iron atom in the B12-Dependent Radical Sam Methyltransferase, MMP10 with [4FE-4S] Cluster, Cobalamin, and S-Methyl-5'-Thioadenosine Bound.
(pdb code 7qbu). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 10 binding sites of Iron where determined in the
B12-Dependent Radical Sam Methyltransferase, MMP10 with [4FE-4S] Cluster, Cobalamin, and S-Methyl-5'-Thioadenosine Bound., PDB code: 7qbu:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Iron binding site 1 out
of 10 in 7qbu
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Iron Binding Sites List in 7qbu
Iron binding site 1 out
of 10 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 Iron with other atoms in the Fe 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:Fe501
b:41.8
occ:1.00
|
FE1
|
A:SF4501
|
0.0
|
41.8
|
1.0
|
S4
|
A:SF4501
|
2.3
|
42.5
|
1.0
|
S3
|
A:SF4501
|
2.3
|
42.0
|
1.0
|
S2
|
A:SF4501
|
2.3
|
42.2
|
1.0
|
SG
|
A:CYS22
|
2.4
|
39.8
|
1.0
|
FE2
|
A:SF4501
|
2.7
|
42.8
|
1.0
|
FE4
|
A:SF4501
|
2.8
|
41.8
|
1.0
|
FE3
|
A:SF4501
|
2.8
|
42.9
|
1.0
|
CB
|
A:CYS22
|
3.2
|
38.2
|
1.0
|
S1
|
A:SF4501
|
3.9
|
42.7
|
1.0
|
CB
|
A:PRO11
|
4.0
|
41.1
|
1.0
|
CA
|
A:CYS22
|
4.1
|
39.2
|
1.0
|
OH
|
A:TYR115
|
4.3
|
44.6
|
1.0
|
CE1
|
A:TYR23
|
4.5
|
53.2
|
1.0
|
N
|
A:GLY12
|
4.6
|
42.1
|
1.0
|
CD1
|
A:PHE18
|
4.6
|
40.8
|
1.0
|
CD1
|
A:TYR23
|
4.7
|
51.3
|
1.0
|
CA
|
A:PRO11
|
4.7
|
41.4
|
1.0
|
N
|
A:CYS19
|
4.8
|
40.2
|
1.0
|
SG
|
A:CYS15
|
4.8
|
37.0
|
1.0
|
SG
|
A:CYS19
|
4.8
|
43.0
|
1.0
|
CB
|
A:CYS19
|
4.9
|
40.9
|
1.0
|
CG
|
A:PRO11
|
4.9
|
41.0
|
1.0
|
C
|
A:CYS22
|
5.0
|
40.4
|
1.0
|
C
|
A:PRO11
|
5.0
|
42.4
|
1.0
|
|
Iron binding site 2 out
of 10 in 7qbu
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Iron Binding Sites List in 7qbu
Iron binding site 2 out
of 10 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 Iron with other atoms in the Fe 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
|
A:Fe501
b:42.8
occ:1.00
|
FE2
|
A:SF4501
|
0.0
|
42.8
|
1.0
|
S4
|
A:SF4501
|
2.3
|
42.5
|
1.0
|
S3
|
A:SF4501
|
2.3
|
42.0
|
1.0
|
SG
|
A:CYS19
|
2.3
|
43.0
|
1.0
|
S1
|
A:SF4501
|
2.3
|
42.7
|
1.0
|
FE3
|
A:SF4501
|
2.7
|
42.9
|
1.0
|
FE1
|
A:SF4501
|
2.7
|
41.8
|
1.0
|
FE4
|
A:SF4501
|
2.8
|
41.8
|
1.0
|
CB
|
A:CYS19
|
3.2
|
40.9
|
1.0
|
O
|
A:HOH640
|
3.6
|
47.9
|
1.0
|
N
|
A:CYS19
|
3.8
|
40.2
|
1.0
|
S2
|
A:SF4501
|
3.9
|
42.2
|
1.0
|
CA
|
A:CYS19
|
4.1
|
40.7
|
1.0
|
NZ
|
A:LYS119
|
4.1
|
47.4
|
1.0
|
OH
|
A:TYR115
|
4.2
|
44.6
|
1.0
|
CE
|
A:LYS119
|
4.3
|
45.8
|
1.0
|
CB
|
A:CYS22
|
4.5
|
38.2
|
1.0
|
SG
|
A:CYS22
|
4.7
|
39.8
|
1.0
|
SG
|
A:CYS15
|
4.9
|
37.0
|
1.0
|
CB
|
A:CYS15
|
4.9
|
39.6
|
1.0
|
C
|
A:PHE18
|
4.9
|
41.1
|
1.0
|
|
Iron binding site 3 out
of 10 in 7qbu
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Iron Binding Sites List in 7qbu
Iron binding site 3 out
of 10 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 Iron with other atoms in the Fe 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
|
A:Fe501
b:42.9
occ:1.00
|
FE3
|
A:SF4501
|
0.0
|
42.9
|
1.0
|
OH
|
A:TYR115
|
1.7
|
44.6
|
1.0
|
S1
|
A:SF4501
|
2.3
|
42.7
|
1.0
|
S4
|
A:SF4501
|
2.3
|
42.5
|
1.0
|
S2
|
A:SF4501
|
2.3
|
42.2
|
1.0
|
FE4
|
A:SF4501
|
2.7
|
41.8
|
1.0
|
FE2
|
A:SF4501
|
2.7
|
42.8
|
1.0
|
FE1
|
A:SF4501
|
2.8
|
41.8
|
1.0
|
CZ
|
A:TYR115
|
2.8
|
43.3
|
1.0
|
CE2
|
A:TYR115
|
3.2
|
42.5
|
1.0
|
O
|
A:HOH640
|
3.6
|
47.9
|
1.0
|
S3
|
A:SF4501
|
3.9
|
42.0
|
1.0
|
O2'
|
A:MTA503
|
4.0
|
51.4
|
1.0
|
CE1
|
A:TYR115
|
4.0
|
42.4
|
1.0
|
C2'
|
A:MTA503
|
4.3
|
51.2
|
1.0
|
OG
|
A:SER117
|
4.4
|
44.4
|
1.0
|
CD2
|
A:TYR115
|
4.6
|
41.9
|
1.0
|
SG
|
A:CYS15
|
4.8
|
37.0
|
1.0
|
SG
|
A:CYS19
|
4.8
|
43.0
|
1.0
|
|
Iron binding site 4 out
of 10 in 7qbu
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Iron Binding Sites List in 7qbu
Iron binding site 4 out
of 10 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 Iron with other atoms in the Fe 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
|
A:Fe501
b:41.8
occ:1.00
|
FE4
|
A:SF4501
|
0.0
|
41.8
|
1.0
|
S2
|
A:SF4501
|
2.3
|
42.2
|
1.0
|
S1
|
A:SF4501
|
2.3
|
42.7
|
1.0
|
SG
|
A:CYS15
|
2.3
|
37.0
|
1.0
|
S3
|
A:SF4501
|
2.3
|
42.0
|
1.0
|
FE3
|
A:SF4501
|
2.7
|
42.9
|
1.0
|
FE1
|
A:SF4501
|
2.8
|
41.8
|
1.0
|
FE2
|
A:SF4501
|
2.8
|
42.8
|
1.0
|
CB
|
A:CYS15
|
3.1
|
39.6
|
1.0
|
N
|
A:GLY12
|
3.8
|
42.1
|
1.0
|
S4
|
A:SF4501
|
3.9
|
42.5
|
1.0
|
OH
|
A:TYR115
|
4.2
|
44.6
|
1.0
|
N
|
A:ASP90
|
4.3
|
40.0
|
1.0
|
CA
|
A:PRO11
|
4.3
|
41.4
|
1.0
|
CE2
|
A:TYR115
|
4.5
|
42.5
|
1.0
|
CB
|
A:PRO11
|
4.6
|
41.1
|
1.0
|
CA
|
A:CYS15
|
4.6
|
41.0
|
1.0
|
C
|
A:PRO11
|
4.6
|
42.4
|
1.0
|
CA
|
A:GLY12
|
4.7
|
43.1
|
1.0
|
CB
|
A:ASP90
|
4.8
|
39.5
|
1.0
|
CE
|
A:LYS119
|
4.8
|
45.8
|
1.0
|
CA
|
A:GLY89
|
4.8
|
42.8
|
1.0
|
SG
|
A:CYS19
|
4.8
|
43.0
|
1.0
|
CZ
|
A:TYR115
|
4.9
|
43.3
|
1.0
|
SG
|
A:CYS22
|
4.9
|
39.8
|
1.0
|
NZ
|
A:LYS119
|
4.9
|
47.4
|
1.0
|
|
Iron binding site 5 out
of 10 in 7qbu
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Iron Binding Sites List in 7qbu
Iron binding site 5 out
of 10 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 Iron with other atoms in the Fe binding
site number 5 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:Fe502
b:46.8
occ:1.00
|
SG
|
A:CYS38
|
2.3
|
50.9
|
1.0
|
SG
|
A:CYS45
|
2.3
|
56.8
|
1.0
|
SG
|
A:CYS48
|
2.4
|
54.4
|
1.0
|
SG
|
A:CYS35
|
2.4
|
50.2
|
1.0
|
CB
|
A:CYS45
|
3.4
|
53.6
|
1.0
|
CB
|
A:CYS48
|
3.4
|
54.5
|
1.0
|
CB
|
A:CYS35
|
3.5
|
49.5
|
1.0
|
N
|
A:CYS38
|
3.5
|
49.3
|
1.0
|
N
|
A:CYS35
|
3.5
|
49.8
|
1.0
|
CB
|
A:CYS38
|
3.6
|
49.8
|
1.0
|
N
|
A:CYS45
|
3.6
|
54.0
|
1.0
|
CA
|
A:CYS38
|
3.7
|
50.0
|
1.0
|
N
|
A:CYS48
|
3.9
|
53.6
|
1.0
|
CA
|
A:CYS45
|
4.0
|
53.6
|
1.0
|
CA
|
A:CYS35
|
4.0
|
50.2
|
1.0
|
C
|
A:GLY44
|
4.1
|
55.1
|
1.0
|
C
|
A:GLY34
|
4.2
|
50.2
|
1.0
|
C
|
A:TYR37
|
4.3
|
48.9
|
1.0
|
CA
|
A:CYS48
|
4.3
|
55.2
|
1.0
|
C
|
A:CYS35
|
4.4
|
51.0
|
1.0
|
CA
|
A:GLY34
|
4.5
|
50.9
|
1.0
|
O
|
A:CYS35
|
4.5
|
51.6
|
1.0
|
CA
|
A:GLY44
|
4.5
|
55.5
|
1.0
|
C
|
A:CYS45
|
4.5
|
53.9
|
1.0
|
O
|
A:CYS45
|
4.6
|
54.0
|
1.0
|
N
|
A:GLY44
|
4.7
|
56.0
|
1.0
|
N
|
A:TYR37
|
4.7
|
48.0
|
1.0
|
CB
|
A:TYR37
|
4.7
|
46.7
|
1.0
|
N
|
A:GLY34
|
4.7
|
51.2
|
1.0
|
CA
|
A:TYR37
|
4.8
|
47.7
|
1.0
|
O
|
A:GLY44
|
4.8
|
55.6
|
1.0
|
CB
|
A:TYR47
|
4.9
|
50.0
|
1.0
|
C
|
A:TYR47
|
4.9
|
52.5
|
1.0
|
O
|
A:GLY34
|
4.9
|
49.9
|
1.0
|
O
|
A:TYR37
|
5.0
|
49.2
|
1.0
|
|
Iron binding site 6 out
of 10 in 7qbu
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Iron Binding Sites List in 7qbu
Iron binding site 6 out
of 10 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 Iron with other atoms in the Fe binding
site number 6 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:Fe501
b:47.9
occ:1.00
|
FE1
|
B:SF4501
|
0.0
|
47.9
|
1.0
|
SG
|
B:CYS22
|
2.3
|
40.5
|
1.0
|
S3
|
B:SF4501
|
2.3
|
48.5
|
1.0
|
S2
|
B:SF4501
|
2.3
|
48.8
|
1.0
|
S4
|
B:SF4501
|
2.3
|
48.5
|
1.0
|
FE4
|
B:SF4501
|
2.8
|
48.2
|
1.0
|
FE2
|
B:SF4501
|
2.8
|
48.7
|
1.0
|
FE3
|
B:SF4501
|
2.8
|
48.4
|
1.0
|
CB
|
B:CYS22
|
3.2
|
39.8
|
1.0
|
CB
|
B:PRO11
|
3.9
|
52.7
|
1.0
|
S1
|
B:SF4501
|
3.9
|
48.4
|
1.0
|
CA
|
B:CYS22
|
4.1
|
40.2
|
1.0
|
OH
|
B:TYR115
|
4.3
|
42.1
|
1.0
|
CE1
|
B:TYR23
|
4.5
|
51.3
|
1.0
|
N
|
B:GLY12
|
4.5
|
51.6
|
1.0
|
CA
|
B:PRO11
|
4.6
|
52.5
|
1.0
|
CD1
|
B:TYR23
|
4.6
|
49.8
|
1.0
|
CD1
|
B:PHE18
|
4.6
|
42.1
|
1.0
|
N
|
B:CYS19
|
4.8
|
41.3
|
1.0
|
SG
|
B:CYS15
|
4.8
|
50.0
|
1.0
|
SG
|
B:CYS19
|
4.8
|
43.1
|
1.0
|
CB
|
B:CYS19
|
4.9
|
41.1
|
1.0
|
CG
|
B:PRO11
|
4.9
|
52.9
|
1.0
|
C
|
B:CYS22
|
4.9
|
41.8
|
1.0
|
C
|
B:PRO11
|
5.0
|
52.1
|
1.0
|
|
Iron binding site 7 out
of 10 in 7qbu
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Iron Binding Sites List in 7qbu
Iron binding site 7 out
of 10 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 Iron with other atoms in the Fe binding
site number 7 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:Fe501
b:48.7
occ:1.00
|
FE2
|
B:SF4501
|
0.0
|
48.7
|
1.0
|
S4
|
B:SF4501
|
2.3
|
48.5
|
1.0
|
S1
|
B:SF4501
|
2.3
|
48.4
|
1.0
|
S3
|
B:SF4501
|
2.3
|
48.5
|
1.0
|
SG
|
B:CYS19
|
2.3
|
43.1
|
1.0
|
FE3
|
B:SF4501
|
2.7
|
48.4
|
1.0
|
FE1
|
B:SF4501
|
2.8
|
47.9
|
1.0
|
FE4
|
B:SF4501
|
2.8
|
48.2
|
1.0
|
CB
|
B:CYS19
|
3.1
|
41.1
|
1.0
|
O
|
B:HOH649
|
3.6
|
56.3
|
1.0
|
N
|
B:CYS19
|
3.8
|
41.3
|
1.0
|
S2
|
B:SF4501
|
3.9
|
48.8
|
1.0
|
NZ
|
B:LYS119
|
3.9
|
48.5
|
1.0
|
CA
|
B:CYS19
|
4.1
|
41.1
|
1.0
|
OH
|
B:TYR115
|
4.1
|
42.1
|
1.0
|
CE
|
B:LYS119
|
4.3
|
47.3
|
1.0
|
CB
|
B:CYS22
|
4.5
|
39.8
|
1.0
|
SG
|
B:CYS22
|
4.6
|
40.5
|
1.0
|
SG
|
B:CYS15
|
4.9
|
50.0
|
1.0
|
CB
|
B:CYS15
|
4.9
|
46.3
|
1.0
|
C
|
B:PHE18
|
5.0
|
42.2
|
1.0
|
|
Iron binding site 8 out
of 10 in 7qbu
Go back to
Iron Binding Sites List in 7qbu
Iron binding site 8 out
of 10 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 Iron with other atoms in the Fe binding
site number 8 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:Fe501
b:48.4
occ:1.00
|
FE3
|
B:SF4501
|
0.0
|
48.4
|
1.0
|
OH
|
B:TYR115
|
1.7
|
42.1
|
1.0
|
S1
|
B:SF4501
|
2.3
|
48.4
|
1.0
|
S2
|
B:SF4501
|
2.3
|
48.8
|
1.0
|
S4
|
B:SF4501
|
2.3
|
48.5
|
1.0
|
FE4
|
B:SF4501
|
2.7
|
48.2
|
1.0
|
FE2
|
B:SF4501
|
2.7
|
48.7
|
1.0
|
CZ
|
B:TYR115
|
2.8
|
41.9
|
1.0
|
FE1
|
B:SF4501
|
2.8
|
47.9
|
1.0
|
CE2
|
B:TYR115
|
3.2
|
41.3
|
1.0
|
O
|
B:HOH649
|
3.5
|
56.3
|
1.0
|
O2'
|
B:MTA503
|
3.8
|
48.7
|
1.0
|
S3
|
B:SF4501
|
3.9
|
48.5
|
1.0
|
CE1
|
B:TYR115
|
4.0
|
41.4
|
1.0
|
C2'
|
B:MTA503
|
4.4
|
48.8
|
1.0
|
OG
|
B:SER117
|
4.5
|
47.4
|
1.0
|
CD2
|
B:TYR115
|
4.5
|
40.7
|
1.0
|
O
|
B:HOH676
|
4.6
|
48.6
|
1.0
|
SG
|
B:CYS15
|
4.8
|
50.0
|
1.0
|
SG
|
B:CYS19
|
4.8
|
43.1
|
1.0
|
SG
|
B:CYS22
|
4.9
|
40.5
|
1.0
|
|
Iron binding site 9 out
of 10 in 7qbu
Go back to
Iron Binding Sites List in 7qbu
Iron binding site 9 out
of 10 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 Iron with other atoms in the Fe binding
site number 9 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:Fe501
b:48.2
occ:1.00
|
FE4
|
B:SF4501
|
0.0
|
48.2
|
1.0
|
S2
|
B:SF4501
|
2.3
|
48.8
|
1.0
|
S1
|
B:SF4501
|
2.3
|
48.4
|
1.0
|
SG
|
B:CYS15
|
2.3
|
50.0
|
1.0
|
S3
|
B:SF4501
|
2.3
|
48.5
|
1.0
|
FE3
|
B:SF4501
|
2.7
|
48.4
|
1.0
|
FE1
|
B:SF4501
|
2.8
|
47.9
|
1.0
|
FE2
|
B:SF4501
|
2.8
|
48.7
|
1.0
|
CB
|
B:CYS15
|
3.2
|
46.3
|
1.0
|
N
|
B:GLY12
|
3.9
|
51.6
|
1.0
|
S4
|
B:SF4501
|
3.9
|
48.5
|
1.0
|
OH
|
B:TYR115
|
4.2
|
42.1
|
1.0
|
CA
|
B:PRO11
|
4.3
|
52.5
|
1.0
|
N
|
B:ASP90
|
4.3
|
46.6
|
1.0
|
CE2
|
B:TYR115
|
4.5
|
41.3
|
1.0
|
CB
|
B:PRO11
|
4.5
|
52.7
|
1.0
|
CA
|
B:CYS15
|
4.6
|
45.7
|
1.0
|
C
|
B:PRO11
|
4.6
|
52.1
|
1.0
|
NZ
|
B:LYS119
|
4.7
|
48.5
|
1.0
|
CA
|
B:GLY12
|
4.7
|
51.6
|
1.0
|
CA
|
B:GLY89
|
4.8
|
49.1
|
1.0
|
SG
|
B:CYS22
|
4.8
|
40.5
|
1.0
|
CZ
|
B:TYR115
|
4.8
|
41.9
|
1.0
|
SG
|
B:CYS19
|
4.8
|
43.1
|
1.0
|
CB
|
B:ASP90
|
4.9
|
45.7
|
1.0
|
CE
|
B:LYS119
|
4.9
|
47.3
|
1.0
|
|
Iron binding site 10 out
of 10 in 7qbu
Go back to
Iron Binding Sites List in 7qbu
Iron binding site 10 out
of 10 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 Iron with other atoms in the Fe binding
site number 10 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:Fe502
b:45.3
occ:1.00
|
SG
|
B:CYS48
|
2.2
|
51.3
|
1.0
|
SG
|
B:CYS38
|
2.3
|
59.0
|
1.0
|
SG
|
B:CYS35
|
2.4
|
45.5
|
1.0
|
SG
|
B:CYS45
|
2.4
|
53.7
|
1.0
|
CB
|
B:CYS48
|
3.1
|
54.5
|
1.0
|
CB
|
B:CYS35
|
3.4
|
45.2
|
1.0
|
CB
|
B:CYS45
|
3.5
|
54.0
|
1.0
|
N
|
B:CYS35
|
3.5
|
45.8
|
1.0
|
N
|
B:CYS45
|
3.6
|
55.7
|
1.0
|
N
|
B:CYS48
|
3.6
|
54.4
|
1.0
|
CB
|
B:CYS38
|
3.7
|
55.6
|
1.0
|
N
|
B:CYS38
|
3.8
|
53.0
|
1.0
|
CA
|
B:CYS35
|
4.0
|
45.2
|
1.0
|
CA
|
B:CYS38
|
4.0
|
55.2
|
1.0
|
CA
|
B:CYS45
|
4.0
|
54.7
|
1.0
|
CA
|
B:CYS48
|
4.0
|
55.5
|
1.0
|
C
|
B:GLY34
|
4.1
|
47.3
|
1.0
|
C
|
B:GLY44
|
4.2
|
56.6
|
1.0
|
CA
|
B:GLY34
|
4.4
|
49.7
|
1.0
|
C
|
B:TYR37
|
4.5
|
51.5
|
1.0
|
CA
|
B:GLY44
|
4.5
|
57.3
|
1.0
|
C
|
B:CYS35
|
4.5
|
44.6
|
1.0
|
C
|
B:CYS45
|
4.5
|
53.9
|
1.0
|
O
|
B:CYS45
|
4.6
|
53.8
|
1.0
|
O
|
B:CYS35
|
4.6
|
45.2
|
1.0
|
N
|
B:GLY34
|
4.6
|
51.0
|
1.0
|
N
|
B:GLY44
|
4.7
|
57.7
|
1.0
|
C
|
B:TYR47
|
4.7
|
53.8
|
1.0
|
CB
|
B:TYR47
|
4.8
|
51.0
|
1.0
|
O
|
B:GLY34
|
4.8
|
46.6
|
1.0
|
CB
|
B:TYR37
|
4.8
|
47.2
|
1.0
|
N
|
B:TYR37
|
4.8
|
47.0
|
1.0
|
O
|
B:GLY44
|
4.9
|
56.8
|
1.0
|
CA
|
B:TYR37
|
4.9
|
48.3
|
1.0
|
N
|
B:TYR47
|
5.0
|
52.4
|
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: Thu Aug 8 18:10:40 2024
|