Iron in PDB 6wte: Structure of Radical S-Adenosylmethionine Methyltransferase, Tsrm, From Kitasatospora Setae with Cobalamin and [4FE-4S] Cluster Bound

The structure of Structure of Radical S-Adenosylmethionine Methyltransferase, Tsrm, From Kitasatospora Setae with Cobalamin and [4FE-4S] Cluster Bound, PDB code: 6wte was solved by H.L.Knox, P.Y.-T.Chen, C.L.Drennan, S.J.Booker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.14 / 1.67
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	49.368, 103.759, 105.970, 90.00, 95.08, 90.00
R / Rfree (%)	19 / 21.5

The structure of Structure of Radical S-Adenosylmethionine Methyltransferase, Tsrm, From Kitasatospora Setae with Cobalamin and [4FE-4S] Cluster Bound also contains other interesting chemical elements:

Cobalt

(Co)

2 atoms

The binding sites of Iron atom in the Structure of Radical S-Adenosylmethionine Methyltransferase, Tsrm, From Kitasatospora Setae with Cobalamin and [4FE-4S] Cluster Bound (pdb code 6wte). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the Structure of Radical S-Adenosylmethionine Methyltransferase, Tsrm, From Kitasatospora Setae with Cobalamin and [4FE-4S] Cluster Bound, PDB code: 6wte:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in the Structure of Radical S-Adenosylmethionine Methyltransferase, Tsrm, From Kitasatospora Setae with Cobalamin and [4FE-4S] Cluster Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structure of Radical S-Adenosylmethionine Methyltransferase, Tsrm, From Kitasatospora Setae with Cobalamin and [4FE-4S] Cluster Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe801 b:12.9 occ:1.00 FE1 A:SF4801 0.0 12.9 1.0 S4 A:SF4801 2.3 13.1 1.0 SG A:CYS231 2.3 12.7 1.0 S2 A:SF4801 2.3 12.9 1.0 S3 A:SF4801 2.3 12.6 1.0 FE4 A:SF4801 2.7 12.9 1.0 FE2 A:SF4801 2.7 11.8 1.0 FE3 A:SF4801 2.8 13.0 1.0 CB A:CYS231 3.1 13.2 1.0 S1 A:SF4801 3.9 12.1 1.0 OH A:TYR354 4.0 13.9 1.0 N A:CYS231 4.1 9.8 1.0 CA A:CYS231 4.2 11.8 1.0 CE A:LYS346 4.4 14.3 1.0 CB A:TYR229 4.5 13.4 1.0 OE2 A:GLU273 4.6 14.3 1.0 CB A:CYS234 4.6 12.3 1.0 SG A:CYS227 4.7 10.8 1.0 SG A:CYS234 4.7 12.7 1.0 CE1 A:HIS233 4.8 13.5 1.0

Iron binding site 2 out of 8 in the Structure of Radical S-Adenosylmethionine Methyltransferase, Tsrm, From Kitasatospora Setae with Cobalamin and [4FE-4S] Cluster Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structure of Radical S-Adenosylmethionine Methyltransferase, Tsrm, From Kitasatospora Setae with Cobalamin and [4FE-4S] Cluster Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe801 b:11.8 occ:1.00 FE2 A:SF4801 0.0 11.8 1.0 SG A:CYS227 2.2 10.8 1.0 S3 A:SF4801 2.3 12.6 1.0 S4 A:SF4801 2.3 13.1 1.0 S1 A:SF4801 2.3 12.1 1.0 FE3 A:SF4801 2.7 13.0 1.0 FE4 A:SF4801 2.7 12.9 1.0 FE1 A:SF4801 2.7 12.9 1.0 CB A:CYS227 3.3 11.6 1.0 S2 A:SF4801 3.9 12.9 1.0 CB A:TYR229 4.2 13.4 1.0 CG A:GLU273 4.3 11.2 1.0 OE2 A:GLU273 4.3 14.3 1.0 O A:HOH992 4.5 17.3 1.0 CG A:PRO237 4.6 12.7 1.0 CD A:PRO237 4.7 12.9 1.0 CA A:CYS227 4.7 11.8 1.0 SG A:CYS234 4.7 12.7 1.0 N A:TYR229 4.8 11.5 1.0 SG A:CYS231 4.8 12.7 1.0 CD A:GLU273 4.8 13.8 1.0 CD1 A:LEU276 4.9 12.8 1.0 CA A:TYR229 4.9 12.3 1.0 C A:TYR229 5.0 14.2 1.0

Iron binding site 3 out of 8 in the Structure of Radical S-Adenosylmethionine Methyltransferase, Tsrm, From Kitasatospora Setae with Cobalamin and [4FE-4S] Cluster Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Structure of Radical S-Adenosylmethionine Methyltransferase, Tsrm, From Kitasatospora Setae with Cobalamin and [4FE-4S] Cluster Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe801 b:13.0 occ:1.00 FE3 A:SF4801 0.0 13.0 1.0 OE2 A:GLU273 1.9 14.3 1.0 S2 A:SF4801 2.3 12.9 1.0 S1 A:SF4801 2.3 12.1 1.0 S4 A:SF4801 2.3 13.1 1.0 FE4 A:SF4801 2.7 12.9 1.0 FE2 A:SF4801 2.7 11.8 1.0 FE1 A:SF4801 2.8 12.9 1.0 CD A:GLU273 2.9 13.8 1.0 CG A:GLU273 3.2 11.2 1.0 O A:HOH1215 3.7 25.5 1.0 S3 A:SF4801 3.9 12.6 1.0 NE2 A:GLN310 3.9 11.4 1.0 OE1 A:GLU273 4.0 16.4 1.0 CD A:GLN310 4.3 14.6 1.0 O A:HOH1102 4.4 17.2 1.0 CG A:GLN310 4.5 13.1 1.0 SG A:CYS227 4.6 10.8 1.0 O A:SER272 4.6 15.3 1.0 CB A:GLU273 4.8 13.9 1.0 SG A:CYS234 4.8 12.7 1.0 OE1 A:GLN310 4.9 14.7 1.0 SG A:CYS231 4.9 12.7 1.0

Iron binding site 4 out of 8 in the Structure of Radical S-Adenosylmethionine Methyltransferase, Tsrm, From Kitasatospora Setae with Cobalamin and [4FE-4S] Cluster Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Structure of Radical S-Adenosylmethionine Methyltransferase, Tsrm, From Kitasatospora Setae with Cobalamin and [4FE-4S] Cluster Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe801 b:12.9 occ:1.00 FE4 A:SF4801 0.0 12.9 1.0 S2 A:SF4801 2.3 12.9 1.0 S1 A:SF4801 2.3 12.1 1.0 SG A:CYS234 2.3 12.7 1.0 S3 A:SF4801 2.3 12.6 1.0 FE3 A:SF4801 2.7 13.0 1.0 FE2 A:SF4801 2.7 11.8 1.0 FE1 A:SF4801 2.7 12.9 1.0 CB A:CYS234 3.0 12.3 1.0 S4 A:SF4801 3.9 13.1 1.0 CD A:PRO237 4.3 12.9 1.0 OE2 A:GLU273 4.4 14.3 1.0 CB A:CYS231 4.5 13.2 1.0 CA A:CYS234 4.5 12.1 1.0 CB A:GLU236 4.6 11.0 1.0 O A:HOH1215 4.6 25.5 1.0 SG A:CYS231 4.6 12.7 1.0 SG A:CYS227 4.8 10.8 1.0 CG A:GLU236 4.8 13.0 1.0 CE1 A:HIS233 4.9 13.5 1.0 CG A:PRO237 4.9 12.7 1.0 CD A:GLU236 5.0 16.2 1.0

Iron binding site 5 out of 8 in the Structure of Radical S-Adenosylmethionine Methyltransferase, Tsrm, From Kitasatospora Setae with Cobalamin and [4FE-4S] Cluster Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Structure of Radical S-Adenosylmethionine Methyltransferase, Tsrm, From Kitasatospora Setae with Cobalamin and [4FE-4S] Cluster Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe801 b:14.1 occ:1.00 FE1 B:SF4801 0.0 14.1 1.0 S4 B:SF4801 2.3 14.7 1.0 S2 B:SF4801 2.3 15.7 1.0 SG B:CYS231 2.3 14.8 1.0 S3 B:SF4801 2.3 14.4 1.0 FE4 B:SF4801 2.7 14.5 1.0 FE2 B:SF4801 2.7 13.9 1.0 FE3 B:SF4801 2.8 14.6 1.0 CB B:CYS231 3.1 14.3 1.0 S1 B:SF4801 3.9 16.0 1.0 OH B:TYR354 4.0 16.0 1.0 N B:CYS231 4.1 13.1 1.0 CA B:CYS231 4.2 14.2 1.0 CE B:LYS346 4.4 15.0 1.0 CB B:TYR229 4.4 16.2 1.0 OE2 B:GLU273 4.5 16.8 1.0 CB B:CYS234 4.6 13.7 1.0 SG B:CYS227 4.7 14.2 1.0 SG B:CYS234 4.7 14.6 1.0 CE1 B:HIS233 4.8 16.4 1.0

Iron binding site 6 out of 8 in the Structure of Radical S-Adenosylmethionine Methyltransferase, Tsrm, From Kitasatospora Setae with Cobalamin and [4FE-4S] Cluster Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Structure of Radical S-Adenosylmethionine Methyltransferase, Tsrm, From Kitasatospora Setae with Cobalamin and [4FE-4S] Cluster Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe801 b:13.9 occ:1.00 FE2 B:SF4801 0.0 13.9 1.0 SG B:CYS227 2.2 14.2 1.0 S3 B:SF4801 2.3 14.4 1.0 S1 B:SF4801 2.3 16.0 1.0 S4 B:SF4801 2.3 14.7 1.0 FE3 B:SF4801 2.7 14.6 1.0 FE4 B:SF4801 2.7 14.5 1.0 FE1 B:SF4801 2.7 14.1 1.0 CB B:CYS227 3.3 12.4 1.0 S2 B:SF4801 3.9 15.7 1.0 CB B:TYR229 4.2 16.2 1.0 CG B:GLU273 4.3 11.5 1.0 OE2 B:GLU273 4.4 16.8 1.0 CG B:PRO237 4.6 16.6 1.0 O B:HOH950 4.6 20.6 1.0 CA B:CYS227 4.7 14.7 1.0 CD B:PRO237 4.7 15.1 1.0 SG B:CYS234 4.7 14.6 1.0 N B:TYR229 4.8 14.1 1.0 CD1 B:LEU276 4.8 16.3 1.0 SG B:CYS231 4.8 14.8 1.0 CD B:GLU273 4.8 14.2 1.0 CA B:TYR229 4.9 15.1 1.0 C B:TYR229 4.9 17.3 1.0 CB B:SER272 5.0 14.4 1.0

Iron binding site 7 out of 8 in the Structure of Radical S-Adenosylmethionine Methyltransferase, Tsrm, From Kitasatospora Setae with Cobalamin and [4FE-4S] Cluster Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Structure of Radical S-Adenosylmethionine Methyltransferase, Tsrm, From Kitasatospora Setae with Cobalamin and [4FE-4S] Cluster Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe801 b:14.6 occ:1.00 FE3 B:SF4801 0.0 14.6 1.0 OE2 B:GLU273 1.9 16.8 1.0 S2 B:SF4801 2.3 15.7 1.0 S1 B:SF4801 2.3 16.0 1.0 S4 B:SF4801 2.3 14.7 1.0 FE4 B:SF4801 2.7 14.5 1.0 FE2 B:SF4801 2.7 13.9 1.0 FE1 B:SF4801 2.8 14.1 1.0 CD B:GLU273 2.9 14.2 1.0 CG B:GLU273 3.2 11.5 1.0 S3 B:SF4801 3.9 14.4 1.0 NE2 B:GLN310 3.9 13.8 1.0 OE1 B:GLU273 4.0 17.5 1.0 CD B:GLN310 4.2 15.4 1.0 O B:HOH1093 4.4 21.8 1.0 CG B:GLN310 4.5 16.0 1.0 SG B:CYS227 4.6 14.2 1.0 O B:SER272 4.6 15.2 1.0 CB B:GLU273 4.7 15.4 1.0 SG B:CYS234 4.8 14.6 1.0 OE1 B:GLN310 4.9 16.0 1.0 SG B:CYS231 4.9 14.8 1.0

Iron binding site 8 out of 8 in the Structure of Radical S-Adenosylmethionine Methyltransferase, Tsrm, From Kitasatospora Setae with Cobalamin and [4FE-4S] Cluster Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Structure of Radical S-Adenosylmethionine Methyltransferase, Tsrm, From Kitasatospora Setae with Cobalamin and [4FE-4S] Cluster Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe801 b:14.5 occ:1.00 FE4 B:SF4801 0.0 14.5 1.0 SG B:CYS234 2.3 14.6 1.0 S2 B:SF4801 2.3 15.7 1.0 S1 B:SF4801 2.3 16.0 1.0 S3 B:SF4801 2.3 14.4 1.0 FE3 B:SF4801 2.7 14.6 1.0 FE1 B:SF4801 2.7 14.1 1.0 FE2 B:SF4801 2.7 13.9 1.0 CB B:CYS234 3.0 13.7 1.0 S4 B:SF4801 3.9 14.7 1.0 O B:HOH1164 4.1 28.6 1.0 CD B:PRO237 4.3 15.1 1.0 OE2 B:GLU273 4.4 16.8 1.0 CB B:CYS231 4.4 14.3 1.0 CA B:CYS234 4.5 15.7 1.0 CB B:GLU236 4.6 13.7 1.0 SG B:CYS231 4.6 14.8 1.0 SG B:CYS227 4.8 14.2 1.0 CG B:GLU236 4.8 13.0 1.0 CG B:PRO237 4.9 16.6 1.0 CE1 B:HIS233 4.9 16.4 1.0

H.L.Knox, P.Y.-T.Chen, A.J.Blaszczyk, A.Mukherjee, T.L.Grove, E.L.Schwalm, B.Wang, C.L.Drennan, S.J.Booker. Structural Basis For Non-Radical Catalysis By Tsrm, A Radical Sam Methylase Nat.Chem.Biol..
ISSN: ESSN 1552-4469
DOI: 10.1038/S41589-020-00717-Y