Iron in PDB 8ed4: Structure of the Complex Between the Arsenite Oxidase and Its Native Electron Acceptor Cytochrome C552 From Pseudorhizobium Sp. Str. Nt-26

All present enzymatic activity of Structure of the Complex Between the Arsenite Oxidase and Its Native Electron Acceptor Cytochrome C552 From Pseudorhizobium Sp. Str. Nt-26:
1.20.98.1;

The structure of Structure of the Complex Between the Arsenite Oxidase and Its Native Electron Acceptor Cytochrome C552 From Pseudorhizobium Sp. Str. Nt-26, PDB code: 8ed4 was solved by M.J.Maher, N.Poddar, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.23 / 2.25
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	129.4, 126.56, 148.02, 90, 107.81, 90
R / Rfree (%)	18.1 / 23

The structure of Structure of the Complex Between the Arsenite Oxidase and Its Native Electron Acceptor Cytochrome C552 From Pseudorhizobium Sp. Str. Nt-26 also contains other interesting chemical elements:

Molybdenum

(Mo)

4 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 24;

Binding sites:

The binding sites of Iron atom in the Structure of the Complex Between the Arsenite Oxidase and Its Native Electron Acceptor Cytochrome C552 From Pseudorhizobium Sp. Str. Nt-26 (pdb code 8ed4). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 24 binding sites of Iron where determined in the Structure of the Complex Between the Arsenite Oxidase and Its Native Electron Acceptor Cytochrome C552 From Pseudorhizobium Sp. Str. Nt-26, PDB code: 8ed4:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 24 in the Structure of the Complex Between the Arsenite Oxidase and Its Native Electron Acceptor Cytochrome C552 From Pseudorhizobium Sp. Str. Nt-26


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structure of the Complex Between the Arsenite Oxidase and Its Native Electron Acceptor Cytochrome C552 From Pseudorhizobium Sp. Str. Nt-26 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe2004 b:2.2 occ:1.00 FE1 A:F3S2004 0.0 2.2 1.0 SG A:CYS24 2.2 5.8 1.0 S3 A:F3S2004 2.2 2.2 1.0 S2 A:F3S2004 2.2 2.2 1.0 S1 A:F3S2004 2.2 2.2 1.0 FE3 A:F3S2004 2.8 2.3 1.0 FE4 A:F3S2004 2.8 2.2 1.0 CB A:CYS24 3.1 5.8 1.0 OG A:SER102 3.7 5.5 1.0 S4 A:F3S2004 3.9 2.2 1.0 CA A:GLY105 4.0 4.7 1.0 N A:GLY105 4.0 4.8 1.0 N A:CYS27 4.5 4.0 1.0 CA A:CYS24 4.5 5.7 1.0 CB A:CYS31 4.6 4.7 1.0 SG A:CYS31 4.7 4.6 1.0 CB A:PHE26 4.7 4.5 1.0 CB A:SER102 4.9 5.5 1.0 SG A:CYS27 4.9 3.7 1.0 OH A:TYR33 4.9 5.3 1.0 CE1 A:TYR33 5.0 5.5 1.0 CD2 A:PHE26 5.0 4.5 1.0 N A:PHE26 5.0 4.7 1.0

Iron binding site 2 out of 24 in the Structure of the Complex Between the Arsenite Oxidase and Its Native Electron Acceptor Cytochrome C552 From Pseudorhizobium Sp. Str. Nt-26


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structure of the Complex Between the Arsenite Oxidase and Its Native Electron Acceptor Cytochrome C552 From Pseudorhizobium Sp. Str. Nt-26 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe2004 b:2.3 occ:1.00 FE3 A:F3S2004 0.0 2.3 1.0 S1 A:F3S2004 2.2 2.2 1.0 S3 A:F3S2004 2.2 2.2 1.0 S4 A:F3S2004 2.2 2.2 1.0 SG A:CYS31 2.2 4.6 1.0 FE1 A:F3S2004 2.8 2.2 1.0 FE4 A:F3S2004 2.8 2.2 1.0 CB A:CYS31 3.1 4.7 1.0 ND2 A:ASN245 3.4 2.1 1.0 S2 A:F3S2004 3.9 2.2 1.0 CB A:ASN245 4.0 2.1 1.0 CG A:ASN245 4.1 2.1 1.0 N A:CYS31 4.1 4.7 1.0 OG A:SER102 4.2 5.5 1.0 CA A:CYS31 4.2 4.8 1.0 CB A:VAL29 4.4 4.1 1.0 CG1 A:VAL29 4.4 4.0 1.0 CB A:SER102 4.5 5.5 1.0 N A:SER102 4.6 5.5 1.0 SG A:CYS24 4.7 5.8 1.0 CB A:CYS24 4.8 5.8 1.0 SG A:CYS27 4.8 3.7 1.0

Iron binding site 3 out of 24 in the Structure of the Complex Between the Arsenite Oxidase and Its Native Electron Acceptor Cytochrome C552 From Pseudorhizobium Sp. Str. Nt-26


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Structure of the Complex Between the Arsenite Oxidase and Its Native Electron Acceptor Cytochrome C552 From Pseudorhizobium Sp. Str. Nt-26 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe2004 b:2.2 occ:1.00 FE4 A:F3S2004 0.0 2.2 1.0 S3 A:F3S2004 2.2 2.2 1.0 S4 A:F3S2004 2.2 2.2 1.0 S2 A:F3S2004 2.2 2.2 1.0 SG A:CYS27 2.3 3.7 1.0 FE3 A:F3S2004 2.8 2.3 1.0 FE1 A:F3S2004 2.8 2.2 1.0 CB A:CYS27 3.4 3.9 1.0 NH1 A:ARG104 3.9 5.4 1.0 N A:CYS27 4.0 4.0 1.0 S1 A:F3S2004 4.0 2.2 1.0 CA A:CYS27 4.0 4.0 1.0 CB A:VAL29 4.1 4.1 1.0 O A:CYS27 4.2 3.9 1.0 C A:CYS27 4.2 4.0 1.0 OG A:SER102 4.3 5.5 1.0 CG2 A:VAL29 4.4 4.0 1.0 N A:VAL29 4.7 4.0 1.0 SG A:CYS24 4.7 5.8 1.0 SG A:CYS31 4.7 4.6 1.0 CA A:VAL29 4.9 4.1 1.0 N A:GLY30 4.9 4.4 1.0 CB A:SER102 5.0 5.5 1.0

Iron binding site 4 out of 24 in the Structure of the Complex Between the Arsenite Oxidase and Its Native Electron Acceptor Cytochrome C552 From Pseudorhizobium Sp. Str. Nt-26


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Structure of the Complex Between the Arsenite Oxidase and Its Native Electron Acceptor Cytochrome C552 From Pseudorhizobium Sp. Str. Nt-26 within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe201 b:10.1 occ:1.00 FE1 B:FES201 0.0 10.1 1.0 ND1 B:HIS105 2.0 8.4 1.0 ND1 B:HIS124 2.2 6.3 1.0 S2 B:FES201 2.2 9.9 1.0 S1 B:FES201 2.2 10.0 1.0 FE2 B:FES201 2.8 10.6 1.0 CG B:HIS105 2.9 9.1 1.0 CE1 B:HIS105 3.1 8.4 1.0 CG B:HIS124 3.1 6.3 1.0 CB B:HIS105 3.1 9.6 1.0 CE1 B:HIS124 3.2 6.2 1.0 CB B:HIS124 3.3 6.3 1.0 N B:HIS124 3.8 6.6 1.0 CD2 B:HIS105 4.1 8.7 1.0 NE2 B:HIS105 4.1 8.3 1.0 CA B:HIS124 4.1 6.4 1.0 N B:LYS106 4.2 11.4 1.0 CD2 B:HIS124 4.3 6.2 1.0 NE2 B:HIS124 4.3 6.1 1.0 SG B:CYS103 4.4 11.6 1.0 C B:GLY123 4.4 6.9 1.0 CB B:LYS106 4.4 12.0 1.0 CA B:HIS105 4.4 10.2 1.0 CG B:LYS106 4.5 12.0 1.0 SG B:CYS121 4.5 11.0 1.0 CA B:GLY123 4.6 7.3 1.0 C B:HIS105 4.7 11.1 1.0 CB B:GLN140 4.8 6.4 1.0 OG B:SER126 4.8 6.5 1.0 C B:HIS124 4.9 6.2 1.0 CA B:LYS106 4.9 11.8 1.0

Iron binding site 5 out of 24 in the Structure of the Complex Between the Arsenite Oxidase and Its Native Electron Acceptor Cytochrome C552 From Pseudorhizobium Sp. Str. Nt-26


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Structure of the Complex Between the Arsenite Oxidase and Its Native Electron Acceptor Cytochrome C552 From Pseudorhizobium Sp. Str. Nt-26 within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe201 b:10.6 occ:1.00 FE2 B:FES201 0.0 10.6 1.0 SG B:CYS121 2.1 11.0 1.0 S2 B:FES201 2.2 9.9 1.0 S1 B:FES201 2.2 10.0 1.0 SG B:CYS103 2.3 11.6 1.0 FE1 B:FES201 2.8 10.1 1.0 CB B:CYS103 3.0 11.4 1.0 CB B:CYS121 3.2 10.6 1.0 CB B:HIS105 4.0 9.6 1.0 N B:HIS124 4.3 6.6 1.0 OG B:SER126 4.4 6.5 1.0 ND1 B:HIS105 4.5 8.4 1.0 ND1 B:HIS124 4.5 6.3 1.0 CA B:CYS103 4.5 11.4 1.0 CA B:GLY123 4.5 7.3 1.0 CB B:SER126 4.6 6.6 1.0 CA B:CYS121 4.6 10.6 1.0 CB B:PHE108 4.6 12.5 1.0 CG B:HIS105 4.7 9.1 1.0 N B:LYS106 4.7 11.4 1.0 N B:GLY123 4.7 7.7 1.0 C B:GLY123 4.9 6.9 1.0 N B:HIS105 4.9 10.0 1.0 N B:PHE108 5.0 13.1 1.0 CA B:HIS105 5.0 10.2 1.0 CD2 B:LEU110 5.0 13.8 1.0 CD1 B:PHE108 5.0 12.1 1.0 C B:CYS121 5.0 10.1 1.0 C B:CYS103 5.0 10.8 1.0

Iron binding site 6 out of 24 in the Structure of the Complex Between the Arsenite Oxidase and Its Native Electron Acceptor Cytochrome C552 From Pseudorhizobium Sp. Str. Nt-26


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Structure of the Complex Between the Arsenite Oxidase and Its Native Electron Acceptor Cytochrome C552 From Pseudorhizobium Sp. Str. Nt-26 within 5.0Å range: probe atom residue distance (Å) B Occ I:Fe200 b:25.7 occ:1.00 FE I:HEM200 0.0 25.7 1.0 ND I:HEM200 1.9 26.8 1.0 NE2 I:HIS38 1.9 13.4 1.0 NA I:HEM200 2.0 27.9 1.0 NC I:HEM200 2.1 27.4 1.0 NB I:HEM200 2.1 27.3 1.0 SD I:MET103 2.2 28.0 1.0 CE1 I:HIS38 2.8 13.9 1.0 C4D I:HEM200 2.9 27.3 1.0 C1D I:HEM200 2.9 27.2 1.0 C1A I:HEM200 3.0 27.0 1.0 CD2 I:HIS38 3.0 14.1 1.0 C4C I:HEM200 3.0 27.3 1.0 C4A I:HEM200 3.1 27.4 1.0 C4B I:HEM200 3.1 28.4 1.0 C1B I:HEM200 3.1 28.2 1.0 C1C I:HEM200 3.1 28.2 1.0 CHA I:HEM200 3.4 26.7 1.0 CHD I:HEM200 3.4 27.0 1.0 CE I:MET103 3.4 27.6 1.0 CHB I:HEM200 3.5 27.7 1.0 CHC I:HEM200 3.5 28.0 1.0 CG I:MET103 3.5 30.2 1.0 ND1 I:HIS38 4.0 14.3 1.0 CG I:HIS38 4.1 14.7 1.0 C3D I:HEM200 4.1 27.3 1.0 C2D I:HEM200 4.2 26.7 1.0 C2A I:HEM200 4.2 27.8 1.0 C3A I:HEM200 4.2 28.3 1.0 C3C I:HEM200 4.3 27.7 1.0 C2C I:HEM200 4.3 28.2 1.0 C2B I:HEM200 4.3 29.5 1.0 C3B I:HEM200 4.3 29.1 1.0 CB I:MET103 4.5 31.4 1.0

Iron binding site 7 out of 24 in the Structure of the Complex Between the Arsenite Oxidase and Its Native Electron Acceptor Cytochrome C552 From Pseudorhizobium Sp. Str. Nt-26


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Structure of the Complex Between the Arsenite Oxidase and Its Native Electron Acceptor Cytochrome C552 From Pseudorhizobium Sp. Str. Nt-26 within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe2004 b:3.0 occ:1.00 FE1 C:F3S2004 0.0 3.0 1.0 S2 C:F3S2004 2.2 2.9 1.0 S3 C:F3S2004 2.2 3.0 1.0 SG C:CYS24 2.2 5.0 1.0 S1 C:F3S2004 2.2 3.0 1.0 FE3 C:F3S2004 2.8 3.1 1.0 FE4 C:F3S2004 2.9 2.9 1.0 CB C:CYS24 3.1 5.1 1.0 OG C:SER102 3.6 9.1 1.0 CA C:GLY105 3.9 9.8 1.0 S4 C:F3S2004 3.9 2.9 1.0 N C:GLY105 4.0 10.2 1.0 N C:CYS27 4.4 5.1 1.0 CB C:PHE26 4.5 5.0 1.0 NH1 C:ARG104 4.5 17.7 1.0 SG C:CYS31 4.5 5.9 1.0 CA C:CYS24 4.6 5.2 1.0 CB C:CYS31 4.7 5.8 1.0 CD2 C:PHE26 4.8 5.0 1.0 OH C:TYR33 4.8 5.8 1.0 CB C:SER102 4.8 9.1 1.0 SG C:CYS27 4.9 5.6 1.0 N C:PHE26 4.9 4.8 1.0 CE1 C:TYR33 5.0 5.9 1.0

Iron binding site 8 out of 24 in the Structure of the Complex Between the Arsenite Oxidase and Its Native Electron Acceptor Cytochrome C552 From Pseudorhizobium Sp. Str. Nt-26


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Structure of the Complex Between the Arsenite Oxidase and Its Native Electron Acceptor Cytochrome C552 From Pseudorhizobium Sp. Str. Nt-26 within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe2004 b:3.1 occ:1.00 FE3 C:F3S2004 0.0 3.1 1.0 SG C:CYS31 2.1 5.9 1.0 S4 C:F3S2004 2.2 2.9 1.0 S3 C:F3S2004 2.2 3.0 1.0 S1 C:F3S2004 2.2 3.0 1.0 FE1 C:F3S2004 2.8 3.0 1.0 FE4 C:F3S2004 2.8 2.9 1.0 CB C:CYS31 3.2 5.8 1.0 ND2 C:ASN245 3.6 8.6 1.0 S2 C:F3S2004 3.8 2.9 1.0 OG C:SER102 3.9 9.1 1.0 N C:CYS31 4.1 5.7 1.0 CG C:ASN245 4.2 8.6 1.0 CB C:ASN245 4.3 8.7 1.0 CA C:CYS31 4.3 5.8 1.0 CB C:VAL29 4.3 5.4 1.0 CG1 C:VAL29 4.4 5.3 1.0 CB C:SER102 4.4 9.1 1.0 N C:SER102 4.6 8.8 1.0 SG C:CYS24 4.7 5.0 1.0 CB C:CYS24 4.7 5.1 1.0 SG C:CYS27 4.7 5.6 1.0 N C:GLY30 5.0 5.5 1.0 N C:ASN245 5.0 8.6 1.0

Iron binding site 9 out of 24 in the Structure of the Complex Between the Arsenite Oxidase and Its Native Electron Acceptor Cytochrome C552 From Pseudorhizobium Sp. Str. Nt-26


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Structure of the Complex Between the Arsenite Oxidase and Its Native Electron Acceptor Cytochrome C552 From Pseudorhizobium Sp. Str. Nt-26 within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe2004 b:2.9 occ:1.00 FE4 C:F3S2004 0.0 2.9 1.0 S3 C:F3S2004 2.2 3.0 1.0 SG C:CYS27 2.2 5.6 1.0 S4 C:F3S2004 2.2 2.9 1.0 S2 C:F3S2004 2.2 2.9 1.0 FE3 C:F3S2004 2.8 3.1 1.0 FE1 C:F3S2004 2.9 3.0 1.0 CB C:CYS27 3.3 5.6 1.0 NH1 C:ARG104 3.5 17.7 1.0 N C:CYS27 3.8 5.1 1.0 CA C:CYS27 3.9 5.4 1.0 S1 C:F3S2004 4.1 3.0 1.0 CB C:VAL29 4.1 5.4 1.0 OG C:SER102 4.2 9.1 1.0 O C:CYS27 4.3 5.5 1.0 C C:CYS27 4.3 5.5 1.0 CG2 C:VAL29 4.4 5.4 1.0 CZ C:ARG104 4.5 16.4 1.0 NH2 C:ARG104 4.6 15.9 1.0 N C:VAL29 4.7 5.5 1.0 SG C:CYS31 4.7 5.9 1.0 SG C:CYS24 4.8 5.0 1.0 CB C:SER102 4.9 9.1 1.0 CA C:VAL29 4.9 5.4 1.0 N C:GLY30 5.0 5.5 1.0

Iron binding site 10 out of 24 in the Structure of the Complex Between the Arsenite Oxidase and Its Native Electron Acceptor Cytochrome C552 From Pseudorhizobium Sp. Str. Nt-26


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Structure of the Complex Between the Arsenite Oxidase and Its Native Electron Acceptor Cytochrome C552 From Pseudorhizobium Sp. Str. Nt-26 within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe201 b:13.6 occ:1.00 FE1 D:FES201 0.0 13.6 1.0 ND1 D:HIS105 2.2 18.9 1.0 ND1 D:HIS124 2.2 14.7 1.0 S1 D:FES201 2.2 11.9 1.0 S2 D:FES201 2.3 14.3 1.0 FE2 D:FES201 2.8 14.9 1.0 CE1 D:HIS105 3.1 19.5 1.0 CG D:HIS124 3.1 14.5 1.0 CG D:HIS105 3.2 18.9 1.0 CE1 D:HIS124 3.2 14.4 1.0 CB D:HIS124 3.4 14.6 1.0 CB D:HIS105 3.5 18.0 1.0 N D:HIS124 3.7 16.7 1.0 CA D:HIS124 4.1 15.2 1.0 CB D:LYS106 4.1 19.6 1.0 N D:LYS106 4.2 18.8 1.0 NE2 D:HIS105 4.2 19.7 1.0 CD2 D:HIS105 4.3 19.0 1.0 NE2 D:HIS124 4.3 14.4 1.0 C D:GLY123 4.3 17.9 1.0 CD2 D:HIS124 4.3 14.6 1.0 CG D:LYS106 4.4 20.2 1.0 SG D:CYS103 4.4 17.0 1.0 SG D:CYS121 4.6 17.3 1.0 CA D:GLY123 4.6 18.9 1.0 CA D:HIS105 4.6 17.6 1.0 C D:HIS105 4.7 17.9 1.0 CA D:LYS106 4.8 18.8 1.0 C D:HIS124 4.9 14.5 1.0 CB D:GLN140 5.0 13.3 1.0

N.Poddar, J.M.Santini, M.J.Maher. The Structure of the Complex Between the Arsenite Oxidase From Pseudorhizobium Banfieldiae Sp. Strain Nt-26 and Its Native Electron Acceptor Cytochrome C 552. Acta Crystallogr D Struct V. 79 345 2023BIOL.
ISSN: ISSN 2059-7983
PubMed: 36995233
DOI: 10.1107/S2059798323002103