Iron in PDB 6bxm: Crystal Structure of Candidatus Methanoperedens Nitroreducens DPH2 with 4FE-4S Cluster and Sam/Cleaved Sam

The structure of Crystal Structure of Candidatus Methanoperedens Nitroreducens DPH2 with 4FE-4S Cluster and Sam/Cleaved Sam, PDB code: 6bxm was solved by M.K.Fenwick, A.T.Torelli, Y.Zhang, M.Dong, V.Kathiresan, J.D.Carantoa, B.Dzikovski, K.M.Lancaster, J.H.Freed, B.M.Hoffman, H.Lin, S.E.Ealick, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.81 / 2.25
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	61.887, 64.080, 158.368, 90.00, 90.00, 90.00
R / Rfree (%)	17.5 / 22.7

The binding sites of Iron atom in the Crystal Structure of Candidatus Methanoperedens Nitroreducens DPH2 with 4FE-4S Cluster and Sam/Cleaved Sam (pdb code 6bxm). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the Crystal Structure of Candidatus Methanoperedens Nitroreducens DPH2 with 4FE-4S Cluster and Sam/Cleaved Sam, PDB code: 6bxm:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in the Crystal Structure of Candidatus Methanoperedens Nitroreducens DPH2 with 4FE-4S Cluster and Sam/Cleaved Sam


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of Candidatus Methanoperedens Nitroreducens DPH2 with 4FE-4S Cluster and Sam/Cleaved Sam within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:22.1 occ:1.00 FE1 A:SF4401 0.0 22.1 1.0 S4 A:SF4401 2.2 20.4 1.0 S2 A:SF4401 2.3 22.4 1.0 SG A:CYS61 2.3 25.0 1.0 S3 A:SF4401 2.3 22.1 1.0 FE3 A:SF4401 2.7 21.0 1.0 FE4 A:SF4401 2.7 32.6 1.0 FE2 A:SF4401 2.7 24.2 1.0 CB A:CYS61 3.2 19.8 1.0 S1 A:SF4401 3.8 26.2 1.0 NE2 A:GLN237 3.9 20.2 1.0 N A:SAM402 4.3 42.7 1.0 CA A:CYS61 4.5 18.5 1.0 N A:CYS61 4.6 20.6 1.0 SG A:CYS283 4.6 23.6 1.0 CD A:GLN237 4.7 22.5 1.0 SG A:CYS159 4.7 28.6 1.0 O A:PHE58 4.8 29.6 1.0 CG A:GLN237 4.8 22.9 1.0 CB A:CYS283 4.9 18.0 1.0

Iron binding site 2 out of 8 in the Crystal Structure of Candidatus Methanoperedens Nitroreducens DPH2 with 4FE-4S Cluster and Sam/Cleaved Sam


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of Candidatus Methanoperedens Nitroreducens DPH2 with 4FE-4S Cluster and Sam/Cleaved Sam within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:24.2 occ:1.00 FE2 A:SF4401 0.0 24.2 1.0 SG A:CYS159 2.2 28.6 1.0 S3 A:SF4401 2.2 22.1 1.0 S1 A:SF4401 2.3 26.2 1.0 S4 A:SF4401 2.3 20.4 1.0 FE4 A:SF4401 2.7 32.6 1.0 FE1 A:SF4401 2.7 22.1 1.0 FE3 A:SF4401 2.8 21.0 1.0 CB A:CYS159 3.2 30.5 1.0 N A:CYS159 3.9 22.4 1.0 S2 A:SF4401 3.9 22.4 1.0 CA A:CYS159 4.2 25.0 1.0 CB A:LEU157 4.6 29.9 1.0 C A:GLY158 4.7 27.7 1.0 N A:GLY158 4.8 30.8 1.0 SG A:CYS61 4.8 25.0 1.0 CD A:PRO284 4.8 23.4 1.0 N A:SAM402 4.8 42.7 1.0 CB A:CYS61 4.9 19.8 1.0 SG A:CYS283 4.9 23.6 1.0 CG A:MET321 4.9 34.9 1.0

Iron binding site 3 out of 8 in the Crystal Structure of Candidatus Methanoperedens Nitroreducens DPH2 with 4FE-4S Cluster and Sam/Cleaved Sam


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of Candidatus Methanoperedens Nitroreducens DPH2 with 4FE-4S Cluster and Sam/Cleaved Sam within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:21.0 occ:1.00 FE3 A:SF4401 0.0 21.0 1.0 S2 A:SF4401 2.2 22.4 1.0 SG A:CYS283 2.3 23.6 1.0 S4 A:SF4401 2.3 20.4 1.0 S1 A:SF4401 2.3 26.2 1.0 FE1 A:SF4401 2.7 22.1 1.0 FE4 A:SF4401 2.8 32.6 1.0 FE2 A:SF4401 2.8 24.2 1.0 CB A:CYS283 3.2 18.0 1.0 CA A:CYS283 3.8 21.4 1.0 S3 A:SF4401 3.9 22.1 1.0 C A:CYS283 4.4 23.1 1.0 CD A:PRO284 4.4 23.4 1.0 C8 A:SAM402 4.5 20.2 1.0 N A:PRO284 4.5 23.4 1.0 CG A:ARG285 4.6 40.2 1.0 CB A:ARG285 4.6 27.2 1.0 NE2 A:GLN237 4.6 20.2 1.0 N A:ARG285 4.7 21.4 1.0 SG A:CYS61 4.7 25.0 1.0 CG A:SAM402 4.7 42.1 1.0 SG A:CYS159 4.8 28.6 1.0 N A:SAM402 4.8 42.7 1.0 N7 A:SAM402 4.9 25.3 1.0 C5' A:SAM402 4.9 40.9 1.0 CD A:ARG285 5.0 37.1 1.0

Iron binding site 4 out of 8 in the Crystal Structure of Candidatus Methanoperedens Nitroreducens DPH2 with 4FE-4S Cluster and Sam/Cleaved Sam


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of Candidatus Methanoperedens Nitroreducens DPH2 with 4FE-4S Cluster and Sam/Cleaved Sam within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:32.6 occ:1.00 FE4 A:SF4401 0.0 32.6 1.0 N A:SAM402 2.3 42.7 1.0 S1 A:SF4401 2.3 26.2 1.0 S3 A:SF4401 2.3 22.1 1.0 S2 A:SF4401 2.3 22.4 1.0 FE2 A:SF4401 2.7 24.2 1.0 FE1 A:SF4401 2.7 22.1 1.0 FE3 A:SF4401 2.8 21.0 1.0 CA A:SAM402 3.2 48.6 1.0 C A:SAM402 3.3 42.1 1.0 CG A:SAM402 3.4 42.1 1.0 OXT A:SAM402 3.5 49.1 1.0 O A:SAM402 3.9 41.2 1.0 S4 A:SF4401 3.9 20.4 1.0 CB A:SAM402 4.0 39.7 1.0 O A:PHE58 4.6 29.6 1.0 N A:GLY158 4.7 30.8 1.0 SG A:CYS159 4.7 28.6 1.0 O A:HOH572 4.8 35.2 1.0 SG A:CYS61 4.8 25.0 1.0 SD A:SAM402 4.8 59.8 1.0 SG A:CYS283 4.8 23.6 1.0 CD A:ARG285 4.8 37.1 1.0 CB A:LEU157 5.0 29.9 1.0

Iron binding site 5 out of 8 in the Crystal Structure of Candidatus Methanoperedens Nitroreducens DPH2 with 4FE-4S Cluster and Sam/Cleaved Sam


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Crystal Structure of Candidatus Methanoperedens Nitroreducens DPH2 with 4FE-4S Cluster and Sam/Cleaved Sam within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe401 b:24.7 occ:1.00 FE1 B:SF4401 0.0 24.7 1.0 S2 B:SF4401 2.2 24.8 1.0 S4 B:SF4401 2.2 17.2 1.0 SG B:CYS61 2.3 26.0 1.0 S3 B:SF4401 2.3 24.5 1.0 FE3 B:SF4401 2.6 19.3 1.0 FE4 B:SF4401 2.7 35.1 1.0 FE2 B:SF4401 2.8 21.1 1.0 CB B:CYS61 3.2 24.7 1.0 S1 B:SF4401 3.8 24.1 1.0 NE2 B:GLN237 3.9 19.5 1.0 CA B:CYS61 4.5 23.7 1.0 N B:CYS61 4.6 22.0 1.0 NH1 B:ARG149 4.7 42.1 1.0 SG B:CYS283 4.7 21.3 1.0 CD B:GLN237 4.8 20.4 1.0 SG B:CYS159 4.8 24.8 1.0 CG B:GLN237 4.8 20.4 1.0 O B:HOH577 4.8 40.2 1.0 O B:PHE58 5.0 25.9 1.0 CB B:CYS283 5.0 21.1 1.0 N B:ABA402 5.0 51.3 1.0

Iron binding site 6 out of 8 in the Crystal Structure of Candidatus Methanoperedens Nitroreducens DPH2 with 4FE-4S Cluster and Sam/Cleaved Sam


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Crystal Structure of Candidatus Methanoperedens Nitroreducens DPH2 with 4FE-4S Cluster and Sam/Cleaved Sam within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe401 b:21.1 occ:1.00 FE2 B:SF4401 0.0 21.1 1.0 S3 B:SF4401 2.3 24.5 1.0 SG B:CYS159 2.3 24.8 1.0 S1 B:SF4401 2.3 24.1 1.0 S4 B:SF4401 2.3 17.2 1.0 FE4 B:SF4401 2.7 35.1 1.0 FE3 B:SF4401 2.7 19.3 1.0 FE1 B:SF4401 2.8 24.7 1.0 CB B:CYS159 3.2 29.9 1.0 S2 B:SF4401 3.9 24.8 1.0 N B:CYS159 3.9 27.8 1.0 CA B:CYS159 4.2 28.1 1.0 NH1 B:ARG149 4.3 42.1 1.0 N B:ABA402 4.5 51.3 1.0 C B:GLY158 4.7 25.9 1.0 N B:GLY158 4.7 27.1 1.0 CB B:LEU157 4.7 23.1 1.0 CD B:PRO284 4.7 20.3 1.0 NE B:ARG149 4.8 52.6 1.0 SG B:CYS61 4.8 26.0 1.0 SG B:CYS283 4.8 21.3 1.0 CA B:GLY158 4.9 27.7 1.0

Iron binding site 7 out of 8 in the Crystal Structure of Candidatus Methanoperedens Nitroreducens DPH2 with 4FE-4S Cluster and Sam/Cleaved Sam


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Crystal Structure of Candidatus Methanoperedens Nitroreducens DPH2 with 4FE-4S Cluster and Sam/Cleaved Sam within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe401 b:19.3 occ:1.00 FE3 B:SF4401 0.0 19.3 1.0 S2 B:SF4401 2.2 24.8 1.0 S1 B:SF4401 2.2 24.1 1.0 S4 B:SF4401 2.3 17.2 1.0 SG B:CYS283 2.3 21.3 1.0 FE1 B:SF4401 2.6 24.7 1.0 FE2 B:SF4401 2.7 21.1 1.0 FE4 B:SF4401 2.8 35.1 1.0 CB B:CYS283 3.2 21.1 1.0 S3 B:SF4401 3.9 24.5 1.0 CA B:CYS283 3.9 21.8 1.0 CD B:PRO284 4.2 20.3 1.0 NE2 B:GLN237 4.4 19.5 1.0 C B:CYS283 4.6 19.7 1.0 CG B:ARG285 4.6 28.5 1.0 C5' B:MTA403 4.6 44.6 1.0 SG B:CYS61 4.6 26.0 1.0 C8 B:MTA403 4.6 19.9 1.0 N B:PRO284 4.7 24.6 1.0 CB B:ARG285 4.7 25.5 1.0 N B:ARG285 4.8 22.6 1.0 SG B:CYS159 4.8 24.8 1.0 N7 B:MTA403 4.9 16.9 1.0

Iron binding site 8 out of 8 in the Crystal Structure of Candidatus Methanoperedens Nitroreducens DPH2 with 4FE-4S Cluster and Sam/Cleaved Sam


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Crystal Structure of Candidatus Methanoperedens Nitroreducens DPH2 with 4FE-4S Cluster and Sam/Cleaved Sam within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe401 b:35.1 occ:1.00 FE4 B:SF4401 0.0 35.1 1.0 S3 B:SF4401 2.3 24.5 1.0 S1 B:SF4401 2.3 24.1 1.0 S2 B:SF4401 2.3 24.8 1.0 N B:ABA402 2.7 51.3 1.0 FE2 B:SF4401 2.7 21.1 1.0 FE1 B:SF4401 2.7 24.7 1.0 FE3 B:SF4401 2.8 19.3 1.0 CB B:ABA402 3.0 41.6 1.0 CA B:ABA402 3.3 45.3 1.0 CG B:ABA402 3.4 46.5 1.0 C B:ABA402 3.8 38.5 1.0 S4 B:SF4401 3.9 17.2 1.0 O B:ABA402 4.1 42.3 1.0 OXT B:ABA402 4.4 45.6 1.0 O B:HOH577 4.5 40.2 1.0 SG B:CYS61 4.7 26.0 1.0 SG B:CYS159 4.7 24.8 1.0 S5' B:MTA403 4.7 63.5 1.0 N B:GLY158 4.8 27.1 1.0 SG B:CYS283 4.8 21.3 1.0 C5' B:MTA403 4.8 44.6 1.0 O B:PHE58 4.9 25.9 1.0 CD B:ARG285 5.0 38.5 1.0

M.Dong, V.Kathiresan, M.K.Fenwick, A.T.Torelli, Y.Zhang, J.D.Caranto, B.Dzikovski, A.Sharma, K.M.Lancaster, J.H.Freed, S.E.Ealick, B.M.Hoffman, H.Lin. Organometallic and Radical Intermediates Reveal Mechanism of Diphthamide Biosynthesis. Science V. 359 1247 2018.
ISSN: ESSN 1095-9203
PubMed: 29590073
DOI: 10.1126/SCIENCE.AAO6595