Iron in PDB 8dbx: Cryoem Structure of Partially Oxidized Mofe-Protein on Ultrathin Carbon

All present enzymatic activity of Cryoem Structure of Partially Oxidized Mofe-Protein on Ultrathin Carbon:
1.18.6.1;

The structure of Cryoem Structure of Partially Oxidized Mofe-Protein on Ultrathin Carbon also contains other interesting chemical elements:

Molybdenum

(Mo)

2 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 48;

Binding sites:

The binding sites of Iron atom in the Cryoem Structure of Partially Oxidized Mofe-Protein on Ultrathin Carbon (pdb code 8dbx). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 48 binding sites of Iron where determined in the Cryoem Structure of Partially Oxidized Mofe-Protein on Ultrathin Carbon, PDB code: 8dbx:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 48 in the Cryoem Structure of Partially Oxidized Mofe-Protein on Ultrathin Carbon


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Cryoem Structure of Partially Oxidized Mofe-Protein on Ultrathin Carbon within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe600 b:39.3 occ:1.00 FE1 A:ICS600 0.0 39.3 1.0 SG A:CYS275 2.1 26.6 1.0 S2A A:ICS600 2.3 25.8 1.0 S4A A:ICS600 2.3 25.3 1.0 S1A A:ICS600 2.3 26.5 1.0 FE4 A:ICS600 2.7 34.3 1.0 FE2 A:ICS600 2.7 30.2 1.0 FE3 A:ICS600 2.7 31.2 1.0 CB A:CYS275 3.3 20.0 1.0 CX A:ICS600 3.5 23.6 1.0 OG A:SER278 3.7 24.1 1.0 CB A:SER278 4.0 19.9 1.0 CB A:LEU358 4.3 28.6 1.0 CE1 A:TYR229 4.4 16.6 1.0 CA A:CYS275 4.6 22.2 1.0 N A:SER278 4.6 26.3 1.0 CE1 A:HIS195 4.6 20.9 1.0 S2B A:ICS600 4.8 22.4 1.0 N A:LEU358 4.8 22.3 1.0 S5A A:ICS600 4.8 20.5 1.0 S3A A:ICS600 4.8 29.0 1.0 NE2 A:HIS195 4.9 20.6 1.0 CB A:ARG277 5.0 17.7 1.0 CA A:SER278 5.0 23.0 1.0 CD2 A:LEU358 5.0 28.4 1.0 FE6 A:ICS600 5.0 29.9 1.0

Iron binding site 2 out of 48 in the Cryoem Structure of Partially Oxidized Mofe-Protein on Ultrathin Carbon


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Cryoem Structure of Partially Oxidized Mofe-Protein on Ultrathin Carbon within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe600 b:30.2 occ:1.00 FE2 A:ICS600 0.0 30.2 1.0 CX A:ICS600 2.0 23.6 1.0 S2B A:ICS600 2.2 22.4 1.0 S2A A:ICS600 2.2 25.8 1.0 S1A A:ICS600 2.3 26.5 1.0 FE6 A:ICS600 2.6 29.9 1.0 FE4 A:ICS600 2.7 34.3 1.0 FE1 A:ICS600 2.7 39.3 1.0 FE3 A:ICS600 2.7 31.2 1.0 CE1 A:HIS195 3.5 20.9 1.0 NE2 A:HIS195 3.5 20.6 1.0 FE5 A:ICS600 3.7 39.5 1.0 FE7 A:ICS600 3.7 30.4 1.0 S4A A:ICS600 3.9 25.3 1.0 CZ A:PHE381 3.9 18.4 1.0 S1B A:ICS600 4.2 20.2 1.0 S3B A:ICS600 4.2 17.1 1.0 CE1 A:PHE381 4.3 19.2 1.0 CG1 A:VAL70 4.5 20.0 1.0 S3A A:ICS600 4.5 29.0 1.0 S5A A:ICS600 4.5 20.5 1.0 SG A:CYS275 4.7 26.6 1.0 ND1 A:HIS195 4.7 20.5 1.0 CD2 A:HIS195 4.7 22.1 1.0 CG2 A:VAL70 4.8 17.3 1.0 N A:GLY357 4.9 28.4 1.0 CB A:SER278 4.9 19.9 1.0

Iron binding site 3 out of 48 in the Cryoem Structure of Partially Oxidized Mofe-Protein on Ultrathin Carbon


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Cryoem Structure of Partially Oxidized Mofe-Protein on Ultrathin Carbon within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe600 b:31.2 occ:1.00 FE3 A:ICS600 0.0 31.2 1.0 CX A:ICS600 2.0 23.6 1.0 S5A A:ICS600 2.2 20.5 1.0 S4A A:ICS600 2.2 25.3 1.0 S2A A:ICS600 2.3 25.8 1.0 FE7 A:ICS600 2.6 30.4 1.0 FE4 A:ICS600 2.6 34.3 1.0 FE2 A:ICS600 2.7 30.2 1.0 FE1 A:ICS600 2.7 39.3 1.0 FE6 A:ICS600 3.7 29.9 1.0 O A:HOH824 3.7 32.5 1.0 NH2 A:ARG96 3.7 25.0 1.0 FE5 A:ICS600 3.7 39.5 1.0 S1A A:ICS600 3.9 26.5 1.0 CD1 A:TYR229 4.1 17.2 1.0 S3B A:ICS600 4.2 17.1 1.0 S4B A:ICS600 4.3 18.0 1.0 CE1 A:TYR229 4.3 16.6 1.0 S2B A:ICS600 4.5 22.4 1.0 S3A A:ICS600 4.5 29.0 1.0 SG A:CYS275 4.6 26.6 1.0 CZ A:ARG96 4.9 20.9 1.0 NH2 A:ARG359 4.9 22.6 1.0

Iron binding site 4 out of 48 in the Cryoem Structure of Partially Oxidized Mofe-Protein on Ultrathin Carbon


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Cryoem Structure of Partially Oxidized Mofe-Protein on Ultrathin Carbon within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe600 b:34.3 occ:1.00 FE4 A:ICS600 0.0 34.3 1.0 CX A:ICS600 2.0 23.6 1.0 S3A A:ICS600 2.2 29.0 1.0 S1A A:ICS600 2.3 26.5 1.0 S4A A:ICS600 2.3 25.3 1.0 FE5 A:ICS600 2.6 39.5 1.0 FE3 A:ICS600 2.6 31.2 1.0 FE2 A:ICS600 2.7 30.2 1.0 FE1 A:ICS600 2.7 39.3 1.0 FE7 A:ICS600 3.7 30.4 1.0 FE6 A:ICS600 3.7 29.9 1.0 N A:GLY357 3.8 28.4 1.0 S2A A:ICS600 3.8 25.8 1.0 N A:LEU358 3.8 22.3 1.0 CB A:LEU358 4.2 28.6 1.0 S1B A:ICS600 4.3 20.2 1.0 S4B A:ICS600 4.3 18.0 1.0 SG A:CYS275 4.5 26.6 1.0 S5A A:ICS600 4.5 20.5 1.0 S2B A:ICS600 4.5 22.4 1.0 CA A:GLY357 4.5 25.1 1.0 CA A:LEU358 4.6 26.7 1.0 N A:ARG359 4.6 21.9 1.0 C A:GLY357 4.6 28.6 1.0 C A:GLY356 4.6 24.8 1.0 CZ A:PHE381 4.7 18.4 1.0 CA A:GLY356 4.7 17.6 1.0 CG A:ARG359 4.8 22.6 1.0

Iron binding site 5 out of 48 in the Cryoem Structure of Partially Oxidized Mofe-Protein on Ultrathin Carbon


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Cryoem Structure of Partially Oxidized Mofe-Protein on Ultrathin Carbon within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe600 b:39.5 occ:1.00 FE5 A:ICS600 0.0 39.5 1.0 CX A:ICS600 2.0 23.6 1.0 S4B A:ICS600 2.3 18.0 1.0 S3A A:ICS600 2.3 29.0 1.0 S1B A:ICS600 2.3 20.2 1.0 FE4 A:ICS600 2.6 34.3 1.0 FE7 A:ICS600 2.6 30.4 1.0 FE6 A:ICS600 2.6 29.9 1.0 MO1 A:ICS600 2.8 37.8 1.0 FE2 A:ICS600 3.7 30.2 1.0 FE3 A:ICS600 3.7 31.2 1.0 S3B A:ICS600 3.9 17.1 1.0 ND1 A:HIS442 3.9 19.9 1.0 N A:GLY356 3.9 26.8 1.0 CA A:GLY356 4.0 17.6 1.0 CE1 A:HIS442 4.1 17.9 1.0 CG2 A:ILE355 4.2 27.8 1.0 S1A A:ICS600 4.3 26.5 1.0 S4A A:ICS600 4.3 25.3 1.0 S5A A:ICS600 4.5 20.5 1.0 S2B A:ICS600 4.5 22.4 1.0 O7 A:HCA601 4.6 28.0 1.0 N A:GLY357 4.6 28.4 1.0 CZ A:PHE381 4.7 18.4 1.0 O6 A:HCA601 4.8 24.8 1.0 C A:GLY356 4.8 24.8 1.0 CG A:HIS442 4.8 15.1 1.0 CD A:ARG359 4.9 19.1 1.0 NE A:ARG359 4.9 36.2 1.0

Iron binding site 6 out of 48 in the Cryoem Structure of Partially Oxidized Mofe-Protein on Ultrathin Carbon


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Cryoem Structure of Partially Oxidized Mofe-Protein on Ultrathin Carbon within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe600 b:29.9 occ:1.00 FE6 A:ICS600 0.0 29.9 1.0 CX A:ICS600 2.0 23.6 1.0 S2B A:ICS600 2.2 22.4 1.0 S3B A:ICS600 2.2 17.1 1.0 S1B A:ICS600 2.2 20.2 1.0 FE2 A:ICS600 2.6 30.2 1.0 FE7 A:ICS600 2.6 30.4 1.0 FE5 A:ICS600 2.6 39.5 1.0 MO1 A:ICS600 2.7 37.8 1.0 O7 A:HCA601 3.5 28.0 1.0 FE3 A:ICS600 3.7 31.2 1.0 FE4 A:ICS600 3.7 34.3 1.0 S4B A:ICS600 3.8 18.0 1.0 CZ A:PHE381 4.0 18.4 1.0 S2A A:ICS600 4.2 25.8 1.0 S1A A:ICS600 4.3 26.5 1.0 CG2 A:VAL70 4.3 17.3 1.0 S5A A:ICS600 4.5 20.5 1.0 O2 A:HCA601 4.5 37.8 1.0 O6 A:HCA601 4.5 24.8 1.0 S3A A:ICS600 4.5 29.0 1.0 CE2 A:PHE381 4.5 14.4 1.0 C3 A:HCA601 4.7 25.6 1.0 ND1 A:HIS442 4.7 19.9 1.0 C7 A:HCA601 4.9 27.8 1.0 CE1 A:HIS442 4.9 17.9 1.0 NE2 A:HIS195 4.9 20.6 1.0 FE1 A:ICS600 5.0 39.3 1.0 C1 A:HCA601 5.0 29.3 1.0

Iron binding site 7 out of 48 in the Cryoem Structure of Partially Oxidized Mofe-Protein on Ultrathin Carbon


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Cryoem Structure of Partially Oxidized Mofe-Protein on Ultrathin Carbon within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe600 b:30.4 occ:1.00 FE7 A:ICS600 0.0 30.4 1.0 CX A:ICS600 2.0 23.6 1.0 S5A A:ICS600 2.2 20.5 1.0 S4B A:ICS600 2.2 18.0 1.0 S3B A:ICS600 2.3 17.1 1.0 FE3 A:ICS600 2.6 31.2 1.0 FE6 A:ICS600 2.6 29.9 1.0 FE5 A:ICS600 2.6 39.5 1.0 MO1 A:ICS600 2.7 37.8 1.0 O A:HOH759 3.7 15.3 1.0 FE4 A:ICS600 3.7 34.3 1.0 FE2 A:ICS600 3.7 30.2 1.0 S1B A:ICS600 3.8 20.2 1.0 NH2 A:ARG96 3.8 25.0 1.0 O6 A:HCA601 3.9 24.8 1.0 NE A:ARG96 4.0 23.3 1.0 S2A A:ICS600 4.3 25.8 1.0 S4A A:ICS600 4.3 25.3 1.0 CZ A:ARG96 4.4 20.9 1.0 S2B A:ICS600 4.4 22.4 1.0 S3A A:ICS600 4.5 29.0 1.0 NH2 A:ARG359 4.5 22.6 1.0 O7 A:HCA601 4.5 28.0 1.0 CZ A:ARG359 4.6 28.3 1.0 C7 A:HCA601 4.7 27.8 1.0 ND1 A:HIS442 4.8 19.9 1.0 NE A:ARG359 4.9 36.2 1.0 NH1 A:ARG359 4.9 13.6 1.0 O A:HOH824 4.9 32.5 1.0

Iron binding site 8 out of 48 in the Cryoem Structure of Partially Oxidized Mofe-Protein on Ultrathin Carbon


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Cryoem Structure of Partially Oxidized Mofe-Protein on Ultrathin Carbon within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe600 b:34.3 occ:0.50 FE1 B:CLF600 0.0 34.3 0.5 FE1 B:1CL601 0.1 37.2 0.5 S3A B:1CL601 2.3 19.3 0.5 SG A:CYS154 2.3 28.4 1.0 S2A B:CLF600 2.3 16.5 0.5 S3A B:CLF600 2.3 19.2 0.5 S1 B:1CL601 2.3 21.0 0.5 S1 B:CLF600 2.4 20.8 0.5 S2A B:1CL601 2.4 16.4 0.5 FE2 B:CLF600 2.5 42.4 0.5 FE2 B:1CL601 2.6 40.8 0.5 FE4 B:1CL601 2.6 40.2 0.5 FE4 B:CLF600 2.6 38.5 0.5 FE3 B:CLF600 2.8 28.2 0.5 FE3 B:1CL601 2.9 27.5 0.5 CB A:CYS154 3.6 18.5 1.0 O B:HOH816 3.7 27.4 1.0 OG B:SER92 3.7 35.4 1.0 S4A B:CLF600 3.8 16.6 0.5 S4A B:1CL601 3.9 16.0 0.5 SG B:CYS95 3.9 31.7 1.0 CA A:GLY185 3.9 19.2 1.0 N A:CYS154 4.0 25.9 1.0 N A:GLY185 4.1 22.7 1.0 FE8 B:CLF600 4.4 36.3 0.5 CA A:CYS154 4.4 19.4 1.0 FE8 B:1CL601 4.4 38.3 0.5 FE5 B:CLF600 4.6 35.8 0.5 SG A:CYS88 4.7 23.5 1.0 CB B:SER92 4.7 27.4 1.0 C A:GLY185 4.7 20.2 1.0 SG B:CYS153 4.8 31.2 1.0 FE6 B:CLF600 4.9 26.7 0.5 SG A:CYS62 4.9 21.7 1.0

Iron binding site 9 out of 48 in the Cryoem Structure of Partially Oxidized Mofe-Protein on Ultrathin Carbon


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Cryoem Structure of Partially Oxidized Mofe-Protein on Ultrathin Carbon within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe600 b:42.4 occ:0.50 FE2 B:CLF600 0.0 42.4 0.5 FE2 B:1CL601 0.2 40.8 0.5 SG B:CYS95 2.1 31.7 1.0 S4A B:CLF600 2.3 16.6 0.5 S2A B:CLF600 2.3 16.5 0.5 S4A B:1CL601 2.3 16.0 0.5 S1 B:1CL601 2.3 21.0 0.5 S2A B:1CL601 2.4 16.4 0.5 FE4 B:1CL601 2.5 40.2 0.5 FE1 B:1CL601 2.5 37.2 0.5 S1 B:CLF600 2.5 20.8 0.5 FE1 B:CLF600 2.5 34.3 0.5 FE4 B:CLF600 2.5 38.5 0.5 FE3 B:CLF600 2.8 28.2 0.5 FE3 B:1CL601 2.8 27.5 0.5 FE8 B:1CL601 2.9 38.3 0.5 FE8 B:CLF600 3.0 36.3 0.5 N B:CYS95 3.1 24.0 1.0 CB B:CYS95 3.2 9.7 1.0 CA B:CYS95 3.3 28.4 1.0 S3A B:1CL601 3.7 19.3 0.5 S3A B:CLF600 3.8 19.2 0.5 C B:GLY94 3.8 23.6 1.0 FE5 B:CLF600 3.8 35.8 0.5 S4B B:1CL601 3.9 27.6 0.5 S4B B:CLF600 3.9 26.1 0.5 OG B:SER92 4.0 35.4 1.0 O B:HOH816 4.4 27.4 1.0 FE5 B:1CL601 4.4 37.5 0.5 CA B:GLY94 4.4 11.9 1.0 O B:GLY94 4.5 22.9 1.0 SG A:CYS154 4.6 28.4 1.0 SG A:CYS88 4.6 23.5 1.0 FE6 B:CLF600 4.6 26.7 0.5 C B:CYS95 4.8 18.1 1.0 N B:GLY94 4.8 21.8 1.0 SG A:CYS62 4.9 21.7 1.0 O B:SER92 4.9 34.7 1.0 CB B:SER92 5.0 27.4 1.0

Iron binding site 10 out of 48 in the Cryoem Structure of Partially Oxidized Mofe-Protein on Ultrathin Carbon


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Cryoem Structure of Partially Oxidized Mofe-Protein on Ultrathin Carbon within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe600 b:28.2 occ:0.50 FE3 B:CLF600 0.0 28.2 0.5 FE3 B:1CL601 0.1 27.5 0.5 S4A B:1CL601 2.2 16.0 0.5 S4A B:CLF600 2.3 16.6 0.5 S3A B:1CL601 2.3 19.3 0.5 S2A B:CLF600 2.3 16.5 0.5 S2A B:1CL601 2.3 16.4 0.5 SG A:CYS62 2.3 21.7 1.0 S3A B:CLF600 2.3 19.2 0.5 FE4 B:1CL601 2.7 40.2 0.5 FE2 B:1CL601 2.7 40.8 0.5 FE4 B:CLF600 2.7 38.5 0.5 FE1 B:1CL601 2.8 37.2 0.5 FE2 B:CLF600 2.8 42.4 0.5 FE1 B:CLF600 2.8 34.3 0.5 CB A:CYS62 3.2 19.9 1.0 CA A:GLY185 3.8 19.2 1.0 CB A:TYR64 4.1 11.9 1.0 S1 B:1CL601 4.2 21.0 0.5 CA B:GLY94 4.2 11.9 1.0 S1 B:CLF600 4.3 20.8 0.5 C B:GLY94 4.3 23.6 1.0 N B:CYS95 4.4 24.0 1.0 N A:GLY185 4.5 22.7 1.0 CD1 A:TYR64 4.6 18.4 1.0 CA A:CYS62 4.6 21.6 1.0 CG A:TYR64 4.7 17.2 1.0 SG A:CYS154 4.7 28.4 1.0 SG B:CYS95 4.8 31.7 1.0 O B:GLY94 4.9 22.9 1.0 C A:GLY185 4.9 20.2 1.0 N B:GLY94 4.9 21.8 1.0 N A:TYR64 5.0 25.2 1.0 SG A:CYS88 5.0 23.5 1.0

R.A.Warmack, A.O.Maggiolo, A.Orta, B.B.Wenke, J.B.Howard, D.C.Rees. Structural Consequences of Turnover-Induced Homocitrate Loss in Nitrogenase. Nat Commun V. 14 1091 2023.
ISSN: ESSN 2041-1723
PubMed: 36841829
DOI: 10.1038/S41467-023-36636-4