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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:

Cobalt (Co) 1 atom
Sodium (Na) 1 atom

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

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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

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