Iron in PDB 7qbt: B12-Dependent Radical Sam Methyltransferase, MMP10 with [4FE-4S] Cluster, Cobalamin, and S-Methyl-5'-Thioadenosine Bound.

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

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:

Sodium	(Na)	4 atoms
Cobalt	(Co)	4 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20;

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 7qbt). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 20 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: 7qbt:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 20 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:26.8 occ:1.00 FE1 A:SF4501 0.0 26.8 1.0 S4 A:SF4501 2.3 29.0 1.0 SG A:CYS22 2.3 26.2 1.0 S2 A:SF4501 2.4 27.8 1.0 S3 A:SF4501 2.4 27.9 1.0 FE2 A:SF4501 2.8 28.2 1.0 FE3 A:SF4501 2.8 29.1 1.0 FE4 A:SF4501 2.8 27.4 1.0 CB A:CYS22 3.0 26.3 1.0 S1 A:SF4501 4.0 29.3 1.0 CS A:MTA503 4.0 42.9 1.0 CA A:CYS22 4.1 27.0 1.0 CB A:PRO11 4.3 28.5 1.0 OH A:TYR115 4.4 35.0 1.0 S5' A:MTA503 4.5 43.3 1.0 N A:GLY12 4.7 27.1 1.0 CD1 A:PHE18 4.8 30.9 1.0 SG A:CYS19 4.8 29.1 1.0 N A:CYS19 4.8 29.8 1.0 SG A:CYS15 4.9 26.4 1.0 CB A:CYS19 4.9 29.0 1.0 CA A:PRO11 4.9 27.6 1.0

Iron binding site 2 out of 20 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:28.2 occ:1.00 FE2 A:SF4501 0.0 28.2 1.0 SG A:CYS19 2.2 29.1 1.0 S3 A:SF4501 2.3 27.9 1.0 S1 A:SF4501 2.3 29.3 1.0 S4 A:SF4501 2.3 29.0 1.0 FE3 A:SF4501 2.8 29.1 1.0 FE1 A:SF4501 2.8 26.8 1.0 FE4 A:SF4501 2.8 27.4 1.0 CB A:CYS19 3.2 29.0 1.0 N A:CYS19 3.8 29.8 1.0 O A:HOH736 3.9 59.0 1.0 S2 A:SF4501 3.9 27.8 1.0 NZ A:LYS119 4.0 38.1 1.0 CA A:CYS19 4.1 29.1 1.0 CE A:LYS119 4.2 38.3 1.0 OH A:TYR115 4.2 35.0 1.0 CB A:CYS22 4.4 26.3 1.0 SG A:CYS22 4.7 26.2 1.0 CB A:CYS15 4.9 25.8 1.0 C A:PHE18 4.9 30.3 1.0 SG A:CYS15 4.9 26.4 1.0

Iron binding site 3 out of 20 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:29.1 occ:1.00 FE3 A:SF4501 0.0 29.1 1.0 OH A:TYR115 1.8 35.0 1.0 S2 A:SF4501 2.3 27.8 1.0 S1 A:SF4501 2.3 29.3 1.0 S4 A:SF4501 2.3 29.0 1.0 FE4 A:SF4501 2.7 27.4 1.0 FE2 A:SF4501 2.8 28.2 1.0 FE1 A:SF4501 2.8 26.8 1.0 CZ A:TYR115 2.8 34.5 1.0 CE2 A:TYR115 3.2 33.2 1.0 O A:HOH736 3.4 59.0 1.0 S5' A:MTA503 3.7 43.3 1.0 S3 A:SF4501 3.9 27.9 1.0 CE1 A:TYR115 4.1 34.1 1.0 OG A:SER117 4.3 29.6 1.0 CS A:MTA503 4.4 42.9 1.0 C2' A:MTA503 4.5 36.2 1.0 CD2 A:TYR115 4.6 31.9 1.0 SG A:CYS19 4.7 29.1 1.0 O2' A:MTA503 4.8 38.2 1.0 SG A:CYS15 4.8 26.4 1.0 C3' A:MTA503 4.9 36.8 1.0 O A:HOH708 5.0 47.4 1.0 SG A:CYS22 5.0 26.2 1.0

Iron binding site 4 out of 20 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:27.4 occ:1.00 FE4 A:SF4501 0.0 27.4 1.0 S1 A:SF4501 2.3 29.3 1.0 SG A:CYS15 2.3 26.4 1.0 S2 A:SF4501 2.3 27.8 1.0 S3 A:SF4501 2.4 27.9 1.0 FE3 A:SF4501 2.7 29.1 1.0 FE2 A:SF4501 2.8 28.2 1.0 FE1 A:SF4501 2.8 26.8 1.0 CB A:CYS15 3.1 25.8 1.0 N A:GLY12 3.9 27.1 1.0 S4 A:SF4501 4.0 29.0 1.0 N A:ASP90 4.3 27.2 1.0 OH A:TYR115 4.3 35.0 1.0 CA A:PRO11 4.5 27.6 1.0 CA A:CYS15 4.6 28.0 1.0 CE2 A:TYR115 4.6 33.2 1.0 CA A:GLY89 4.7 30.6 1.0 CB A:ASP90 4.7 24.8 1.0 C A:PRO11 4.7 27.2 1.0 CB A:PRO11 4.7 28.5 1.0 CA A:GLY12 4.8 27.8 1.0 CE A:LYS119 4.8 38.3 1.0 SG A:CYS19 4.8 29.1 1.0 NZ A:LYS119 4.8 38.1 1.0 C A:GLY89 4.9 29.7 1.0 CZ A:TYR115 4.9 34.5 1.0 SG A:CYS22 5.0 26.2 1.0

Iron binding site 5 out of 20 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:32.5 occ:1.00 SG A:CYS35 2.3 32.3 1.0 SG A:CYS38 2.3 34.8 1.0 SG A:CYS45 2.3 38.5 1.0 SG A:CYS48 2.4 35.7 1.0 CB A:CYS48 3.4 35.8 1.0 CB A:CYS35 3.5 31.9 1.0 CB A:CYS45 3.5 38.5 1.0 N A:CYS35 3.5 32.3 1.0 N A:CYS38 3.5 33.8 1.0 CB A:CYS38 3.5 34.3 1.0 N A:CYS45 3.7 39.2 1.0 CA A:CYS38 3.7 34.3 1.0 CA A:CYS35 3.9 31.9 1.0 N A:CYS48 4.0 35.9 1.0 CA A:CYS45 4.1 39.2 1.0 C A:GLY34 4.1 33.9 1.0 O A:CYS35 4.1 31.9 1.0 C A:GLY44 4.2 39.7 1.0 C A:TYR37 4.2 34.9 1.0 CA A:CYS48 4.3 36.4 1.0 C A:CYS35 4.3 32.4 1.0 CA A:GLY34 4.4 35.2 1.0 CA A:GLY44 4.5 40.0 1.0 C A:CYS45 4.6 40.4 1.0 N A:TYR37 4.6 34.5 1.0 O A:CYS45 4.7 40.4 1.0 N A:GLY44 4.7 40.6 1.0 N A:GLY34 4.7 36.1 1.0 CA A:TYR37 4.8 34.8 1.0 CB A:TYR37 4.8 34.9 1.0 CB A:TYR47 4.8 35.2 1.0 O A:TYR37 4.9 35.6 1.0 O A:GLY44 4.9 39.9 1.0 O A:GLY34 4.9 33.4 1.0

Iron binding site 6 out of 20 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:29.3 occ:1.00 FE1 B:SF4501 0.0 29.3 1.0 SG B:CYS22 2.3 29.2 1.0 S2 B:SF4501 2.3 29.9 1.0 S4 B:SF4501 2.3 29.5 1.0 S3 B:SF4501 2.4 30.3 1.0 FE2 B:SF4501 2.8 29.4 1.0 FE3 B:SF4501 2.8 30.1 1.0 FE4 B:SF4501 2.8 29.3 1.0 CB B:CYS22 3.1 27.2 1.0 CS B:MTA503 3.9 44.3 1.0 S1 B:SF4501 4.0 30.6 1.0 CA B:CYS22 4.2 28.1 1.0 CB B:PRO11 4.3 32.9 1.0 OH B:TYR115 4.4 38.0 1.0 S5' B:MTA503 4.4 44.6 1.0 N B:GLY12 4.7 32.3 1.0 CD1 B:PHE18 4.7 33.4 1.0 SG B:CYS19 4.8 29.6 1.0 N B:CYS19 4.8 30.0 1.0 CA B:PRO11 4.9 32.3 1.0 SG B:CYS15 4.9 30.3 1.0 CB B:CYS19 4.9 29.4 1.0

Iron binding site 7 out of 20 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:29.4 occ:1.00 FE2 B:SF4501 0.0 29.4 1.0 SG B:CYS19 2.3 29.6 1.0 S3 B:SF4501 2.3 30.3 1.0 S1 B:SF4501 2.3 30.6 1.0 S4 B:SF4501 2.3 29.5 1.0 FE4 B:SF4501 2.8 29.3 1.0 FE3 B:SF4501 2.8 30.1 1.0 FE1 B:SF4501 2.8 29.3 1.0 CB B:CYS19 3.2 29.4 1.0 O B:HOH631 3.4 37.2 1.0 N B:CYS19 3.8 30.0 1.0 S2 B:SF4501 3.9 29.9 1.0 NZ B:LYS119 4.0 40.6 1.0 CA B:CYS19 4.1 29.0 1.0 OH B:TYR115 4.2 38.0 1.0 CE B:LYS119 4.3 39.8 1.0 CB B:CYS22 4.4 27.2 1.0 SG B:CYS22 4.7 29.2 1.0 CB B:CYS15 4.8 29.8 1.0 SG B:CYS15 4.9 30.3 1.0 C B:PHE18 4.9 30.9 1.0

Iron binding site 8 out of 20 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:30.1 occ:1.00 FE3 B:SF4501 0.0 30.1 1.0 OH B:TYR115 1.7 38.0 1.0 S2 B:SF4501 2.3 29.9 1.0 S4 B:SF4501 2.3 29.5 1.0 S1 B:SF4501 2.4 30.6 1.0 FE4 B:SF4501 2.8 29.3 1.0 FE2 B:SF4501 2.8 29.4 1.0 FE1 B:SF4501 2.8 29.3 1.0 CZ B:TYR115 2.8 36.4 1.0 CE2 B:TYR115 3.2 34.9 1.0 S5' B:MTA503 3.6 44.6 1.0 S3 B:SF4501 3.9 30.3 1.0 O B:HOH631 4.1 37.2 1.0 CE1 B:TYR115 4.1 36.1 1.0 CS B:MTA503 4.3 44.3 1.0 OG B:SER117 4.4 34.2 1.0 C2' B:MTA503 4.5 37.0 1.0 CD2 B:TYR115 4.6 34.2 1.0 O2' B:MTA503 4.7 37.6 1.0 O B:HOH613 4.7 61.1 1.0 C3' B:MTA503 4.8 37.9 1.0 SG B:CYS19 4.8 29.6 1.0 SG B:CYS15 4.8 30.3 1.0 SG B:CYS22 4.9 29.2 1.0

Iron binding site 9 out of 20 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:29.3 occ:1.00 FE4 B:SF4501 0.0 29.3 1.0 S1 B:SF4501 2.3 30.6 1.0 S3 B:SF4501 2.3 30.3 1.0 S2 B:SF4501 2.3 29.9 1.0 SG B:CYS15 2.3 30.3 1.0 FE3 B:SF4501 2.8 30.1 1.0 FE2 B:SF4501 2.8 29.4 1.0 FE1 B:SF4501 2.8 29.3 1.0 CB B:CYS15 3.1 29.8 1.0 N B:GLY12 3.9 32.3 1.0 S4 B:SF4501 4.0 29.5 1.0 OH B:TYR115 4.3 38.0 1.0 N B:ASP90 4.4 29.9 1.0 CA B:PRO11 4.4 32.3 1.0 CA B:CYS15 4.6 30.4 1.0 CE2 B:TYR115 4.6 34.9 1.0 C B:PRO11 4.7 32.6 1.0 CA B:GLY12 4.7 32.5 1.0 CB B:PRO11 4.7 32.9 1.0 CB B:ASP90 4.8 27.1 1.0 SG B:CYS19 4.8 29.6 1.0 NZ B:LYS119 4.8 40.6 1.0 CE B:LYS119 4.9 39.8 1.0 CA B:GLY89 4.9 33.6 1.0 SG B:CYS22 4.9 29.2 1.0 CZ B:TYR115 4.9 36.4 1.0

Iron binding site 10 out of 20 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:46.1 occ:1.00 SG B:CYS45 2.3 52.0 1.0 SG B:CYS38 2.3 51.1 1.0 SG B:CYS35 2.3 43.9 1.0 SG B:CYS48 2.3 50.4 1.0 CB B:CYS48 3.3 50.7 1.0 CB B:CYS45 3.4 54.3 1.0 CB B:CYS35 3.5 45.2 1.0 N B:CYS35 3.5 46.9 1.0 N B:CYS45 3.6 55.9 1.0 N B:CYS38 3.6 54.0 1.0 CB B:CYS38 3.7 54.4 1.0 CA B:CYS38 3.8 55.8 1.0 N B:CYS48 3.9 50.7 1.0 CA B:CYS35 4.0 46.4 1.0 CA B:CYS45 4.0 54.8 1.0 C B:GLY34 4.1 48.5 1.0 C B:GLY44 4.1 58.0 1.0 CA B:CYS48 4.2 51.1 1.0 O B:CYS35 4.3 48.3 1.0 C B:TYR37 4.3 53.1 1.0 C B:CYS35 4.4 47.7 1.0 CA B:GLY34 4.4 49.6 1.0 CA B:GLY44 4.5 60.1 1.0 C B:CYS45 4.5 54.5 1.0 O B:CYS45 4.5 53.8 1.0 N B:GLY44 4.7 62.0 1.0 N B:GLY34 4.7 50.3 1.0 N B:TYR37 4.7 50.8 1.0 CB B:TYR47 4.8 50.5 1.0 CA B:TYR37 4.8 51.1 1.0 CB B:TYR37 4.9 50.1 1.0 C B:TYR47 4.9 51.0 1.0 O B:GLY44 4.9 58.6 1.0 O B:GLY34 4.9 48.5 1.0 O B:TYR37 5.0 53.4 1.0

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