Iron in PDB 7qbv: B12-Dependent Radical Sam Methyltransferase, MMP10 with [4FE-4S] Cluster, Cobalamin, and S-Adenosyl-L-Homocysteine Bound.

The structure of B12-Dependent Radical Sam Methyltransferase, MMP10 with [4FE-4S] Cluster, Cobalamin, and S-Adenosyl-L-Homocysteine Bound., PDB code: 7qbv 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)	49.40 / 2.70
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	155.498, 163, 77.328, 90, 90, 90
R / Rfree (%)	21.4 / 23.5

The structure of B12-Dependent Radical Sam Methyltransferase, MMP10 with [4FE-4S] Cluster, Cobalamin, and S-Adenosyl-L-Homocysteine 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-Adenosyl-L-Homocysteine Bound. (pdb code 7qbv). 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-Adenosyl-L-Homocysteine Bound., PDB code: 7qbv:
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-Adenosyl-L-Homocysteine 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-Adenosyl-L-Homocysteine Bound. within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:43.3 occ:1.00 FE1 A:SF4501 0.0 43.3 1.0 SG A:CYS22 2.2 46.4 1.0 S2 A:SF4501 2.3 42.8 1.0 S4 A:SF4501 2.3 42.8 1.0 S3 A:SF4501 2.3 42.7 1.0 FE3 A:SF4501 2.8 42.3 1.0 FE2 A:SF4501 2.8 42.7 1.0 FE4 A:SF4501 2.8 42.7 1.0 CB A:CYS22 3.1 43.3 1.0 S1 A:SF4501 3.9 42.6 1.0 CB A:PRO11 4.1 49.2 1.0 OH A:TYR115 4.2 53.4 1.0 CA A:CYS22 4.2 42.7 1.0 N A:GLY12 4.6 46.0 1.0 CD1 A:PHE18 4.7 44.8 1.0 SG A:CYS15 4.8 44.3 1.0 SG A:CYS19 4.8 43.5 1.0 CA A:PRO11 4.8 48.2 1.0 N A:CYS19 4.9 42.2 1.0 CB A:CYS19 5.0 42.3 1.0

Iron binding site 2 out of 20 in the B12-Dependent Radical Sam Methyltransferase, MMP10 with [4FE-4S] Cluster, Cobalamin, and S-Adenosyl-L-Homocysteine 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-Adenosyl-L-Homocysteine Bound. within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:42.7 occ:1.00 FE2 A:SF4501 0.0 42.7 1.0 SG A:CYS19 2.3 43.5 1.0 S3 A:SF4501 2.3 42.7 1.0 S1 A:SF4501 2.3 42.6 1.0 S4 A:SF4501 2.3 42.8 1.0 FE4 A:SF4501 2.8 42.7 1.0 FE1 A:SF4501 2.8 43.3 1.0 FE3 A:SF4501 2.8 42.3 1.0 CB A:CYS19 3.2 42.3 1.0 O A:HOH606 3.8 47.5 1.0 N A:CYS19 3.8 42.2 1.0 OH A:TYR115 3.9 53.4 1.0 S2 A:SF4501 3.9 42.8 1.0 NZ A:LYS119 4.0 59.3 1.0 CA A:CYS19 4.1 42.2 1.0 CE A:LYS119 4.3 57.4 1.0 CB A:CYS22 4.4 43.3 1.0 SG A:CYS22 4.5 46.4 1.0 SG A:CYS15 4.9 44.3 1.0 CB A:CYS15 4.9 43.0 1.0 OG A:SER117 4.9 49.4 1.0 C A:PHE18 4.9 42.7 1.0

Iron binding site 3 out of 20 in the B12-Dependent Radical Sam Methyltransferase, MMP10 with [4FE-4S] Cluster, Cobalamin, and S-Adenosyl-L-Homocysteine 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-Adenosyl-L-Homocysteine Bound. within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:42.3 occ:1.00 FE3 A:SF4501 0.0 42.3 1.0 OH A:TYR115 1.6 53.4 1.0 S2 A:SF4501 2.3 42.8 1.0 S4 A:SF4501 2.3 42.8 1.0 S1 A:SF4501 2.3 42.6 1.0 CZ A:TYR115 2.6 52.2 1.0 FE1 A:SF4501 2.8 43.3 1.0 FE4 A:SF4501 2.8 42.7 1.0 FE2 A:SF4501 2.8 42.7 1.0 CE2 A:TYR115 3.0 51.2 1.0 O A:HOH606 3.4 47.5 1.0 CE1 A:TYR115 3.9 51.4 1.0 S3 A:SF4501 3.9 42.7 1.0 OG A:SER117 4.3 49.4 1.0 C5' A:SAH503 4.4 51.0 0.9 CD2 A:TYR115 4.4 50.1 1.0 CG A:SAH503 4.6 53.5 0.9 C3' A:SAH503 4.7 49.0 0.9 C2' A:SAH503 4.7 48.6 0.9 SG A:CYS15 4.7 44.3 1.0 SG A:CYS22 4.9 46.4 1.0 SG A:CYS19 4.9 43.5 1.0

Iron binding site 4 out of 20 in the B12-Dependent Radical Sam Methyltransferase, MMP10 with [4FE-4S] Cluster, Cobalamin, and S-Adenosyl-L-Homocysteine 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-Adenosyl-L-Homocysteine Bound. within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:42.7 occ:1.00 FE4 A:SF4501 0.0 42.7 1.0 SG A:CYS15 2.3 44.3 1.0 S1 A:SF4501 2.3 42.6 1.0 S3 A:SF4501 2.3 42.7 1.0 S2 A:SF4501 2.3 42.8 1.0 FE2 A:SF4501 2.8 42.7 1.0 FE1 A:SF4501 2.8 43.3 1.0 FE3 A:SF4501 2.8 42.3 1.0 CB A:CYS15 3.1 43.0 1.0 N A:GLY12 3.8 46.0 1.0 S4 A:SF4501 3.9 42.8 1.0 OH A:TYR115 4.2 53.4 1.0 CA A:PRO11 4.3 48.2 1.0 N A:ASP90 4.5 50.2 1.0 CB A:PRO11 4.5 49.2 1.0 CA A:CYS15 4.5 43.0 1.0 CE2 A:TYR115 4.5 51.2 1.0 C A:PRO11 4.6 47.1 1.0 CA A:GLY12 4.6 45.8 1.0 NZ A:LYS119 4.7 59.3 1.0 SG A:CYS19 4.8 43.5 1.0 CE A:LYS119 4.8 57.4 1.0 CA A:GLY89 4.8 51.5 1.0 SG A:CYS22 4.8 46.4 1.0 CZ A:TYR115 4.9 52.2 1.0 CB A:ASP90 4.9 50.2 1.0 O A:GLY17 5.0 43.8 1.0

Iron binding site 5 out of 20 in the B12-Dependent Radical Sam Methyltransferase, MMP10 with [4FE-4S] Cluster, Cobalamin, and S-Adenosyl-L-Homocysteine 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-Adenosyl-L-Homocysteine Bound. within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe502 b:42.8 occ:1.00 SG A:CYS35 2.3 57.0 1.0 SG A:CYS45 2.3 56.8 1.0 SG A:CYS38 2.3 54.6 1.0 SG A:CYS48 2.4 63.1 1.0 CB A:CYS48 3.3 59.8 1.0 CB A:CYS35 3.4 54.1 1.0 N A:CYS35 3.5 54.2 1.0 CB A:CYS45 3.5 55.8 1.0 N A:CYS38 3.5 52.5 1.0 CB A:CYS38 3.6 53.4 1.0 N A:CYS45 3.7 56.0 1.0 CA A:CYS38 3.7 53.3 1.0 CA A:CYS35 3.9 53.6 1.0 N A:CYS48 3.9 57.8 1.0 CA A:CYS45 4.1 55.9 1.0 C A:GLY34 4.1 55.1 1.0 CA A:CYS48 4.2 59.1 1.0 O A:CYS35 4.2 53.3 1.0 C A:TYR37 4.3 52.0 1.0 C A:CYS35 4.3 52.9 1.0 C A:GLY44 4.3 56.7 1.0 CA A:GLY34 4.4 56.2 1.0 CA A:GLY44 4.6 57.3 1.0 C A:CYS45 4.6 56.5 1.0 O A:CYS45 4.7 56.9 1.0 N A:TYR37 4.7 51.1 1.0 CB A:TYR47 4.8 55.3 1.0 N A:GLY34 4.8 57.0 1.0 CA A:TYR37 4.8 51.4 1.0 N A:GLY44 4.8 57.5 1.0 CB A:TYR37 4.8 50.9 1.0 O A:GLY34 4.9 55.0 1.0 C A:TYR47 4.9 56.8 1.0 O A:TYR37 5.0 51.9 1.0

Iron binding site 6 out of 20 in the B12-Dependent Radical Sam Methyltransferase, MMP10 with [4FE-4S] Cluster, Cobalamin, and S-Adenosyl-L-Homocysteine 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-Adenosyl-L-Homocysteine Bound. within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe501 b:40.7 occ:1.00 FE1 B:SF4501 0.0 40.7 1.0 SG B:CYS22 2.2 43.0 1.0 S3 B:SF4501 2.3 40.6 1.0 S4 B:SF4501 2.3 40.6 1.0 S2 B:SF4501 2.3 40.5 1.0 FE2 B:SF4501 2.7 40.8 1.0 FE3 B:SF4501 2.8 40.6 1.0 FE4 B:SF4501 2.8 40.6 1.0 CB B:CYS22 3.0 41.6 1.0 S1 B:SF4501 3.9 40.6 1.0 CA B:CYS22 4.1 41.3 1.0 CB B:PRO11 4.2 42.5 1.0 OH B:TYR115 4.3 45.7 1.0 CD1 B:PHE18 4.6 40.6 1.0 N B:GLY12 4.6 40.2 1.0 N B:CYS19 4.7 39.5 1.0 SG B:CYS19 4.7 43.2 1.0 CB B:CYS19 4.7 40.2 1.0 SG B:CYS15 4.7 40.6 1.0 CA B:PRO11 4.9 41.7 1.0 CD2 B:PHE24 4.9 47.4 1.0 CE1 B:PHE18 5.0 41.1 1.0

Iron binding site 7 out of 20 in the B12-Dependent Radical Sam Methyltransferase, MMP10 with [4FE-4S] Cluster, Cobalamin, and S-Adenosyl-L-Homocysteine 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-Adenosyl-L-Homocysteine Bound. within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe501 b:40.8 occ:1.00 FE2 B:SF4501 0.0 40.8 1.0 SG B:CYS19 2.3 43.2 1.0 S4 B:SF4501 2.3 40.6 1.0 S3 B:SF4501 2.3 40.6 1.0 S1 B:SF4501 2.3 40.6 1.0 FE1 B:SF4501 2.7 40.7 1.0 FE3 B:SF4501 2.8 40.6 1.0 FE4 B:SF4501 2.8 40.6 1.0 CB B:CYS19 3.2 40.2 1.0 N B:CYS19 3.8 39.5 1.0 NZ B:LYS119 3.8 55.3 1.0 S2 B:SF4501 3.9 40.5 1.0 O B:HOH605 3.9 36.2 1.0 OH B:TYR115 4.0 45.7 1.0 CA B:CYS19 4.1 39.8 1.0 CE B:LYS119 4.1 53.6 1.0 CB B:CYS22 4.4 41.6 1.0 SG B:CYS22 4.6 43.0 1.0 SG B:CYS15 4.8 40.6 1.0 CB B:CYS15 4.8 39.4 1.0 C B:PHE18 4.9 39.7 1.0 OG B:SER117 4.9 42.9 1.0

Iron binding site 8 out of 20 in the B12-Dependent Radical Sam Methyltransferase, MMP10 with [4FE-4S] Cluster, Cobalamin, and S-Adenosyl-L-Homocysteine 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-Adenosyl-L-Homocysteine Bound. within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe501 b:40.6 occ:1.00 FE3 B:SF4501 0.0 40.6 1.0 OH B:TYR115 1.6 45.7 1.0 S1 B:SF4501 2.3 40.6 1.0 S2 B:SF4501 2.3 40.5 1.0 S4 B:SF4501 2.3 40.6 1.0 CZ B:TYR115 2.7 44.3 1.0 FE4 B:SF4501 2.8 40.6 1.0 FE1 B:SF4501 2.8 40.7 1.0 FE2 B:SF4501 2.8 40.8 1.0 O B:HOH605 3.2 36.2 1.0 CE2 B:TYR115 3.2 43.5 1.0 S3 B:SF4501 3.9 40.6 1.0 CE1 B:TYR115 3.9 43.2 1.0 OG B:SER117 4.3 42.9 1.0 C5' B:SAH503 4.3 49.7 0.9 C2' B:SAH503 4.5 48.1 0.9 CD2 B:TYR115 4.6 42.6 1.0 CG B:SAH503 4.6 51.4 0.9 C3' B:SAH503 4.7 48.7 0.9 SG B:CYS19 4.7 43.2 1.0 SG B:CYS22 4.8 43.0 1.0 SG B:CYS15 4.8 40.6 1.0

Iron binding site 9 out of 20 in the B12-Dependent Radical Sam Methyltransferase, MMP10 with [4FE-4S] Cluster, Cobalamin, and S-Adenosyl-L-Homocysteine 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-Adenosyl-L-Homocysteine Bound. within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe501 b:40.6 occ:1.00 FE4 B:SF4501 0.0 40.6 1.0 SG B:CYS15 2.3 40.6 1.0 S1 B:SF4501 2.3 40.6 1.0 S2 B:SF4501 2.3 40.5 1.0 S3 B:SF4501 2.3 40.6 1.0 FE3 B:SF4501 2.8 40.6 1.0 FE1 B:SF4501 2.8 40.7 1.0 FE2 B:SF4501 2.8 40.8 1.0 CB B:CYS15 3.1 39.4 1.0 N B:GLY12 3.9 40.2 1.0 S4 B:SF4501 3.9 40.6 1.0 OH B:TYR115 4.1 45.7 1.0 N B:ASP90 4.4 43.8 1.0 CE2 B:TYR115 4.4 43.5 1.0 CA B:PRO11 4.4 41.7 1.0 CB B:PRO11 4.5 42.5 1.0 CA B:CYS15 4.6 39.6 1.0 C B:PRO11 4.7 41.5 1.0 NZ B:LYS119 4.7 55.3 1.0 CA B:GLY89 4.7 44.9 1.0 CZ B:TYR115 4.7 44.3 1.0 CA B:GLY12 4.7 40.0 1.0 CE B:LYS119 4.8 53.6 1.0 CB B:ASP90 4.8 44.1 1.0 SG B:CYS22 4.8 43.0 1.0 C B:GLY89 4.9 44.9 1.0 SG B:CYS19 4.9 43.2 1.0

Iron binding site 10 out of 20 in the B12-Dependent Radical Sam Methyltransferase, MMP10 with [4FE-4S] Cluster, Cobalamin, and S-Adenosyl-L-Homocysteine 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-Adenosyl-L-Homocysteine Bound. within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe502 b:47.3 occ:1.00 SG B:CYS38 2.2 52.9 1.0 SG B:CYS45 2.3 56.8 1.0 SG B:CYS35 2.3 53.3 1.0 SG B:CYS48 2.5 58.8 1.0 N B:CYS38 3.4 52.1 1.0 CB B:CYS38 3.4 52.1 1.0 CB B:CYS48 3.4 56.5 1.0 N B:CYS35 3.5 52.0 1.0 CB B:CYS45 3.5 54.7 1.0 CB B:CYS35 3.5 51.8 1.0 CA B:CYS38 3.6 52.2 1.0 N B:CYS45 3.8 54.9 1.0 CA B:CYS35 3.9 51.7 1.0 N B:CYS48 4.0 54.8 1.0 C B:TYR37 4.1 52.5 1.0 C B:GLY34 4.1 52.8 1.0 CA B:CYS45 4.2 54.8 1.0 O B:CYS35 4.2 52.2 1.0 C B:CYS35 4.3 51.8 1.0 CA B:CYS48 4.3 55.9 1.0 C B:GLY44 4.3 55.6 1.0 CA B:GLY34 4.5 53.6 1.0 N B:TYR37 4.6 51.5 1.0 CA B:GLY44 4.7 56.0 1.0 CA B:TYR37 4.7 52.1 1.0 C B:CYS45 4.7 55.3 1.0 O B:CYS45 4.8 55.5 1.0 CB B:TYR37 4.8 52.2 1.0 N B:GLY44 4.8 56.3 1.0 CB B:TYR47 4.8 53.3 1.0 N B:GLY34 4.8 54.3 1.0 O B:TYR37 4.8 53.0 1.0 O B:GLY34 4.9 53.0 1.0 C B:TYR47 5.0 54.3 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