Iron in PDB 2bq4: Crystal Structure of Type I Cytochrome C3 From Desulfovibrio Africanus

The structure of Crystal Structure of Type I Cytochrome C3 From Desulfovibrio Africanus, PDB code: 2bq4 was solved by M.Czjzek, L.Pieulle, X.Morelli, F.Guerlesquin, E.C.Hatchikian, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.22 / 1.68
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	100.900, 46.300, 54.816, 90.00, 118.97, 90.00
R / Rfree (%)	20 / 24

The structure of Crystal Structure of Type I Cytochrome C3 From Desulfovibrio Africanus also contains other interesting chemical elements:

Calcium

(Ca)

2 atoms

The binding sites of Iron atom in the Crystal Structure of Type I Cytochrome C3 From Desulfovibrio Africanus (pdb code 2bq4). 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 Type I Cytochrome C3 From Desulfovibrio Africanus, PDB code: 2bq4:
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 Type I Cytochrome C3 From Desulfovibrio Africanus


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 Type I Cytochrome C3 From Desulfovibrio Africanus within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1115 b:6.7 occ:1.00 FE A:HEC1115 0.0 6.7 1.0 NC A:HEC1115 2.0 6.4 1.0 NE2 A:HIS44 2.0 6.8 1.0 NB A:HEC1115 2.0 6.7 1.0 NA A:HEC1115 2.0 7.1 1.0 ND A:HEC1115 2.1 7.1 1.0 NE2 A:HIS27 2.2 11.0 1.0 CE1 A:HIS27 3.0 11.7 1.0 CE1 A:HIS44 3.0 6.9 1.0 C4C A:HEC1115 3.0 6.3 1.0 C1B A:HEC1115 3.0 6.8 1.0 C4A A:HEC1115 3.0 6.7 1.0 C1D A:HEC1115 3.1 6.9 1.0 CD2 A:HIS44 3.1 7.5 1.0 C1C A:HEC1115 3.1 7.6 1.0 C4B A:HEC1115 3.1 6.6 1.0 C1A A:HEC1115 3.1 7.9 1.0 C4D A:HEC1115 3.1 8.1 1.0 CD2 A:HIS27 3.2 12.6 1.0 CHD A:HEC1115 3.4 6.2 1.0 CHB A:HEC1115 3.4 6.4 1.0 CHC A:HEC1115 3.5 6.4 1.0 CHA A:HEC1115 3.5 9.1 1.0 ND1 A:HIS27 4.1 12.7 1.0 ND1 A:HIS44 4.1 8.3 1.0 CG A:HIS44 4.2 7.2 1.0 C3C A:HEC1115 4.2 6.4 1.0 CG A:HIS27 4.2 11.2 1.0 C2B A:HEC1115 4.3 7.8 1.0 C2C A:HEC1115 4.3 6.8 1.0 C3A A:HEC1115 4.3 8.4 1.0 C3B A:HEC1115 4.3 7.6 1.0 C2A A:HEC1115 4.3 10.0 1.0 C2D A:HEC1115 4.3 8.6 1.0 C3D A:HEC1115 4.3 9.0 1.0

Iron binding site 2 out of 8 in the Crystal Structure of Type I Cytochrome C3 From Desulfovibrio Africanus


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 Type I Cytochrome C3 From Desulfovibrio Africanus within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1116 b:8.0 occ:1.00 FE A:HEC1116 0.0 8.0 1.0 NE2 A:HIS62 2.0 7.9 1.0 NA A:HEC1116 2.0 8.7 1.0 NB A:HEC1116 2.1 8.3 1.0 ND A:HEC1116 2.1 9.9 1.0 NC A:HEC1116 2.1 8.8 1.0 NE2 A:HIS45 2.1 7.8 1.0 CE1 A:HIS62 2.9 7.6 1.0 C4A A:HEC1116 3.0 8.0 1.0 CE1 A:HIS45 3.0 8.6 1.0 C4C A:HEC1116 3.0 9.2 1.0 C1D A:HEC1116 3.0 11.5 1.0 C1A A:HEC1116 3.0 10.1 1.0 C1B A:HEC1116 3.1 7.6 1.0 CD2 A:HIS62 3.1 6.8 1.0 C4D A:HEC1116 3.1 11.8 1.0 C4B A:HEC1116 3.1 7.9 1.0 CD2 A:HIS45 3.1 6.8 1.0 C1C A:HEC1116 3.1 8.7 1.0 CHD A:HEC1116 3.4 9.8 1.0 CHB A:HEC1116 3.4 7.2 1.0 CHA A:HEC1116 3.4 10.6 1.0 CHC A:HEC1116 3.5 7.8 1.0 ND1 A:HIS62 4.0 8.8 1.0 CG A:HIS62 4.2 8.4 1.0 ND1 A:HIS45 4.2 7.9 1.0 CG A:HIS45 4.2 8.0 1.0 C3A A:HEC1116 4.3 9.3 1.0 C2A A:HEC1116 4.3 10.8 1.0 C3C A:HEC1116 4.3 9.4 1.0 C2B A:HEC1116 4.3 7.8 1.0 C2D A:HEC1116 4.3 13.0 1.0 C3B A:HEC1116 4.3 7.3 1.0 C3D A:HEC1116 4.3 13.2 1.0 C2C A:HEC1116 4.3 8.8 1.0 CE A:MET88 5.0 15.1 1.0

Iron binding site 3 out of 8 in the Crystal Structure of Type I Cytochrome C3 From Desulfovibrio Africanus


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 Type I Cytochrome C3 From Desulfovibrio Africanus within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1117 b:7.1 occ:1.00 FE A:HEC1117 0.0 7.1 1.0 NC A:HEC1117 2.0 5.9 1.0 NA A:HEC1117 2.0 6.4 1.0 NB A:HEC1117 2.0 5.5 1.0 ND A:HEC1117 2.1 7.1 1.0 NE2 A:HIS94 2.1 6.0 1.0 NE2 A:HIS30 2.1 10.5 1.0 CE1 A:HIS30 3.0 12.3 1.0 C4B A:HEC1117 3.0 6.0 1.0 C1C A:HEC1117 3.0 6.3 1.0 CE1 A:HIS94 3.0 7.9 1.0 C1A A:HEC1117 3.1 8.3 1.0 C4C A:HEC1117 3.1 7.1 1.0 C4D A:HEC1117 3.1 8.6 1.0 C4A A:HEC1117 3.1 6.7 1.0 C1D A:HEC1117 3.1 8.4 1.0 C1B A:HEC1117 3.1 5.6 1.0 CD2 A:HIS30 3.1 12.0 1.0 CD2 A:HIS94 3.2 7.7 1.0 CHC A:HEC1117 3.4 5.9 1.0 CHA A:HEC1117 3.4 8.6 1.0 CHD A:HEC1117 3.4 7.2 1.0 CHB A:HEC1117 3.5 4.7 1.0 ND1 A:HIS30 4.1 13.2 1.0 CG A:HIS30 4.2 11.2 1.0 ND1 A:HIS94 4.2 7.9 1.0 C3B A:HEC1117 4.2 5.2 1.0 C2C A:HEC1117 4.3 7.6 1.0 C3C A:HEC1117 4.3 8.2 1.0 C2A A:HEC1117 4.3 8.9 1.0 C2B A:HEC1117 4.3 4.9 1.0 C3A A:HEC1117 4.3 8.0 1.0 CG A:HIS94 4.3 8.2 1.0 C3D A:HEC1117 4.3 8.8 1.0 C2D A:HEC1117 4.3 8.2 1.0 CA A:GLY105 4.6 10.1 1.0 N A:GLY105 4.8 10.5 1.0 CE1 A:PHE25 5.0 7.3 1.0

Iron binding site 4 out of 8 in the Crystal Structure of Type I Cytochrome C3 From Desulfovibrio Africanus


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 Type I Cytochrome C3 From Desulfovibrio Africanus within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1118 b:8.7 occ:1.00 FE A:HEC1118 0.0 8.7 1.0 NA A:HEC1118 2.0 9.1 1.0 NE2 A:HIS83 2.0 4.6 1.0 NB A:HEC1118 2.0 9.7 1.0 NC A:HEC1118 2.0 8.7 1.0 ND A:HEC1118 2.1 9.0 1.0 NE2 A:HIS113 2.1 5.3 1.0 CE1 A:HIS113 3.0 7.5 1.0 CD2 A:HIS83 3.0 5.3 1.0 CE1 A:HIS83 3.0 5.0 1.0 C1A A:HEC1118 3.0 9.4 1.0 C4B A:HEC1118 3.0 10.8 1.0 C1C A:HEC1118 3.1 8.9 1.0 C4A A:HEC1118 3.1 9.4 1.0 C1B A:HEC1118 3.1 10.0 1.0 C4D A:HEC1118 3.1 8.0 1.0 C4C A:HEC1118 3.1 7.3 1.0 C1D A:HEC1118 3.1 7.6 1.0 CD2 A:HIS113 3.2 7.6 1.0 CHC A:HEC1118 3.4 9.2 1.0 CHA A:HEC1118 3.4 8.5 1.0 CHB A:HEC1118 3.4 9.4 1.0 CHD A:HEC1118 3.5 8.7 1.0 ND1 A:HIS83 4.1 6.7 1.0 ND1 A:HIS113 4.1 6.6 1.0 CG A:HIS83 4.1 5.1 1.0 CG A:HIS113 4.3 7.7 1.0 C2A A:HEC1118 4.3 9.4 1.0 C3B A:HEC1118 4.3 9.0 1.0 C2B A:HEC1118 4.3 10.6 1.0 C3A A:HEC1118 4.3 10.1 1.0 C2C A:HEC1118 4.3 9.7 1.0 C3C A:HEC1118 4.3 8.6 1.0 C3D A:HEC1118 4.3 8.3 1.0 C2D A:HEC1118 4.3 7.4 1.0 CD1 A:TYR21 4.9 3.8 1.0

Iron binding site 5 out of 8 in the Crystal Structure of Type I Cytochrome C3 From Desulfovibrio Africanus


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 Type I Cytochrome C3 From Desulfovibrio Africanus within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe1116 b:2.0 occ:1.00 FE B:HEC1116 0.0 2.0 1.0 NB B:HEC1116 2.0 2.0 1.0 NC B:HEC1116 2.0 2.0 1.0 ND B:HEC1116 2.1 2.0 1.0 NA B:HEC1116 2.1 2.1 1.0 NE2 B:HIS27 2.1 2.7 1.0 NE2 B:HIS44 2.1 6.3 1.0 CE1 B:HIS44 2.9 9.0 1.0 CE1 B:HIS27 3.0 4.8 1.0 CD2 B:HIS27 3.0 3.5 1.0 C4C B:HEC1116 3.0 2.4 1.0 C1B B:HEC1116 3.0 2.0 1.0 C4B B:HEC1116 3.1 2.1 1.0 C1C B:HEC1116 3.1 3.1 1.0 C1D B:HEC1116 3.1 2.2 1.0 C4A B:HEC1116 3.1 2.8 1.0 C4D B:HEC1116 3.1 2.4 1.0 C1A B:HEC1116 3.1 4.2 1.0 CD2 B:HIS44 3.2 8.6 1.0 CHD B:HEC1116 3.4 2.5 1.0 CHB B:HEC1116 3.4 2.0 1.0 CHC B:HEC1116 3.4 2.1 1.0 CHA B:HEC1116 3.4 3.4 1.0 ND1 B:HIS44 4.1 9.2 1.0 ND1 B:HIS27 4.1 5.0 1.0 CG B:HIS27 4.2 4.1 1.0 CG B:HIS44 4.2 5.6 1.0 C3C B:HEC1116 4.3 2.3 1.0 C2B B:HEC1116 4.3 2.2 1.0 C2C B:HEC1116 4.3 2.8 1.0 C3B B:HEC1116 4.3 2.6 1.0 C3A B:HEC1116 4.3 4.9 1.0 C2D B:HEC1116 4.3 2.1 1.0 C3D B:HEC1116 4.3 3.0 1.0 C2A B:HEC1116 4.3 5.8 1.0 CG2 B:ILE53 5.0 11.0 1.0

Iron binding site 6 out of 8 in the Crystal Structure of Type I Cytochrome C3 From Desulfovibrio Africanus


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 Type I Cytochrome C3 From Desulfovibrio Africanus within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe1117 b:7.0 occ:1.00 FE B:HEC1117 0.0 7.0 1.0 NA B:HEC1117 2.0 7.7 1.0 NC B:HEC1117 2.0 8.0 1.0 NB B:HEC1117 2.0 5.0 1.0 NE2 B:HIS62 2.0 7.2 1.0 ND B:HEC1117 2.1 8.3 1.0 NE2 B:HIS45 2.1 9.2 1.0 CE1 B:HIS62 2.9 5.6 1.0 CE1 B:HIS45 3.0 10.3 1.0 C4C B:HEC1117 3.0 8.8 1.0 C4A B:HEC1117 3.0 6.4 1.0 C1B B:HEC1117 3.0 4.8 1.0 C1D B:HEC1117 3.1 10.5 1.0 C1C B:HEC1117 3.1 6.4 1.0 C1A B:HEC1117 3.1 7.8 1.0 C4B B:HEC1117 3.1 5.5 1.0 CD2 B:HIS62 3.1 7.2 1.0 C4D B:HEC1117 3.1 10.6 1.0 CD2 B:HIS45 3.2 8.5 1.0 CHD B:HEC1117 3.4 9.5 1.0 CHB B:HEC1117 3.4 5.6 1.0 CHC B:HEC1117 3.5 5.7 1.0 CHA B:HEC1117 3.5 9.4 1.0 ND1 B:HIS62 4.1 6.7 1.0 ND1 B:HIS45 4.1 10.2 1.0 CG B:HIS62 4.2 7.5 1.0 C3C B:HEC1117 4.2 9.5 1.0 C2B B:HEC1117 4.3 3.3 1.0 C3A B:HEC1117 4.3 8.0 1.0 C2C B:HEC1117 4.3 7.6 1.0 C2A B:HEC1117 4.3 10.1 1.0 CG B:HIS45 4.3 8.1 1.0 C3B B:HEC1117 4.3 3.4 1.0 C2D B:HEC1117 4.3 12.0 1.0 C3D B:HEC1117 4.4 13.0 1.0

Iron binding site 7 out of 8 in the Crystal Structure of Type I Cytochrome C3 From Desulfovibrio Africanus


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 Type I Cytochrome C3 From Desulfovibrio Africanus within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe1118 b:2.2 occ:1.00 FE B:HEC1118 0.0 2.2 1.0 ND B:HEC1118 2.0 2.5 1.0 NA B:HEC1118 2.0 2.0 1.0 NC B:HEC1118 2.1 2.5 1.0 NB B:HEC1118 2.1 2.0 1.0 NE2 B:HIS30 2.1 2.0 1.0 NE2 B:HIS94 2.1 3.1 1.0 CE1 B:HIS94 3.0 3.5 1.0 CE1 B:HIS30 3.0 3.0 1.0 C1D B:HEC1118 3.0 3.2 1.0 C1A B:HEC1118 3.0 3.2 1.0 C4D B:HEC1118 3.0 3.9 1.0 CD2 B:HIS30 3.1 3.0 1.0 C4B B:HEC1118 3.1 2.0 1.0 C1C B:HEC1118 3.1 2.0 1.0 C4C B:HEC1118 3.1 3.0 1.0 C4A B:HEC1118 3.1 2.4 1.0 C1B B:HEC1118 3.1 2.2 1.0 CD2 B:HIS94 3.2 4.6 1.0 CHA B:HEC1118 3.4 4.1 1.0 CHC B:HEC1118 3.4 2.0 1.0 CHD B:HEC1118 3.4 3.2 1.0 CHB B:HEC1118 3.5 2.0 1.0 ND1 B:HIS30 4.1 4.0 1.0 ND1 B:HIS94 4.1 3.5 1.0 CG B:HIS30 4.2 3.4 1.0 CG B:HIS94 4.3 4.8 1.0 C2D B:HEC1118 4.3 5.0 1.0 C3D B:HEC1118 4.3 5.8 1.0 C2A B:HEC1118 4.3 5.2 1.0 C3B B:HEC1118 4.3 2.0 1.0 C3A B:HEC1118 4.3 3.4 1.0 C2C B:HEC1118 4.3 3.4 1.0 C3C B:HEC1118 4.3 4.2 1.0 C2B B:HEC1118 4.3 2.0 1.0 CA B:GLY105 4.6 8.3 1.0 N B:GLY105 4.7 9.1 1.0 CE1 B:PHE25 5.0 3.2 1.0

Iron binding site 8 out of 8 in the Crystal Structure of Type I Cytochrome C3 From Desulfovibrio Africanus


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 Type I Cytochrome C3 From Desulfovibrio Africanus within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe1119 b:8.5 occ:1.00 FE B:HEC1119 0.0 8.5 1.0 NA B:HEC1119 2.0 8.6 1.0 NB B:HEC1119 2.0 8.3 1.0 ND B:HEC1119 2.0 7.9 1.0 NE2 B:HIS83 2.0 4.5 1.0 NE2 B:HIS113 2.0 2.5 1.0 NC B:HEC1119 2.0 7.6 1.0 CE1 B:HIS113 2.9 5.4 1.0 CE1 B:HIS83 3.0 6.1 1.0 C4D B:HEC1119 3.0 8.3 1.0 C1A B:HEC1119 3.0 8.3 1.0 C4A B:HEC1119 3.0 7.6 1.0 C1C B:HEC1119 3.0 8.2 1.0 C4B B:HEC1119 3.0 9.6 1.0 C1B B:HEC1119 3.1 8.9 1.0 C1D B:HEC1119 3.1 7.6 1.0 CD2 B:HIS83 3.1 5.9 1.0 C4C B:HEC1119 3.1 7.5 1.0 CD2 B:HIS113 3.1 4.2 1.0 CHA B:HEC1119 3.4 9.3 1.0 CHC B:HEC1119 3.4 8.4 1.0 CHB B:HEC1119 3.4 8.2 1.0 CHD B:HEC1119 3.5 7.6 1.0 ND1 B:HIS113 4.1 5.8 1.0 ND1 B:HIS83 4.1 5.6 1.0 CG B:HIS83 4.2 4.5 1.0 CG B:HIS113 4.2 4.9 1.0 C3D B:HEC1119 4.3 7.1 1.0 C3A B:HEC1119 4.3 8.8 1.0 C2A B:HEC1119 4.3 8.7 1.0 C3B B:HEC1119 4.3 8.8 1.0 C2B B:HEC1119 4.3 9.7 1.0 C2C B:HEC1119 4.3 8.1 1.0 C2D B:HEC1119 4.3 7.6 1.0 C3C B:HEC1119 4.3 8.5 1.0

L.Pieulle, X.Morelli, P.Gallice, E.Lojou, P.Barbier, M.Czjzek, P.Bianco, F.Guerlesquin, E.C.Hatchikian. The Type I / Type II Cytochrome C(3) Complex: An Electron Transfer Link in the Hydrogen-Sulfate Reduction Pathway. J.Mol.Biol. V. 354 73 2005.
ISSN: ISSN 0022-2836
PubMed: 16226767
DOI: 10.1016/J.JMB.2005.09.036