Iron in PDB 1gyo: Crystal Structure of the Di-Tetraheme Cytochrome C3 From Desulfovibrio Gigas at 1.2 Angstrom Resolution

The structure of Crystal Structure of the Di-Tetraheme Cytochrome C3 From Desulfovibrio Gigas at 1.2 Angstrom Resolution, PDB code: 1gyo was solved by D.Aragao, C.Frazao, L.Sieker, G.M.Sheldrick, J.Legall, M.A.Carrondo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	26.50 / 1.20
Space group	P 31
Cell size a, b, c (Å), α, β, γ (°)	56.670, 56.670, 94.170, 90.00, 90.00, 120.00
R / Rfree (%)	13 / 15.7

The binding sites of Iron atom in the Crystal Structure of the Di-Tetraheme Cytochrome C3 From Desulfovibrio Gigas at 1.2 Angstrom Resolution (pdb code 1gyo). 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 the Di-Tetraheme Cytochrome C3 From Desulfovibrio Gigas at 1.2 Angstrom Resolution, PDB code: 1gyo:
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 the Di-Tetraheme Cytochrome C3 From Desulfovibrio Gigas at 1.2 Angstrom Resolution


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 the Di-Tetraheme Cytochrome C3 From Desulfovibrio Gigas at 1.2 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe111 b:11.0 occ:1.00 FE A:HEC111 0.0 11.0 1.0 NE2 A:HIS40 2.0 11.8 1.0 NC A:HEC111 2.0 11.4 1.0 ND A:HEC111 2.0 11.6 1.0 NB A:HEC111 2.0 12.4 1.0 NA A:HEC111 2.0 12.3 1.0 NE2 A:HIS28 2.0 11.3 1.0 CE1 A:HIS40 2.9 11.9 1.0 CE1 A:HIS28 3.0 11.8 1.0 C1C A:HEC111 3.0 11.6 1.0 C1D A:HEC111 3.0 11.4 1.0 C4C A:HEC111 3.0 11.3 1.0 CD2 A:HIS40 3.0 12.1 1.0 C4B A:HEC111 3.0 12.5 1.0 C1B A:HEC111 3.0 13.2 1.0 C4A A:HEC111 3.0 13.0 1.0 C4D A:HEC111 3.0 12.1 1.0 C1A A:HEC111 3.0 12.8 1.0 CD2 A:HIS28 3.1 11.9 1.0 CHD A:HEC111 3.3 11.3 1.0 CHC A:HEC111 3.4 12.3 1.0 CHB A:HEC111 3.4 13.2 1.0 CHA A:HEC111 3.4 12.6 1.0 ND1 A:HIS40 4.1 12.5 1.0 ND1 A:HIS28 4.1 12.7 1.0 CG A:HIS40 4.2 12.5 1.0 CG A:HIS28 4.2 11.6 1.0 C3C A:HEC111 4.2 11.4 1.0 C2D A:HEC111 4.2 12.5 1.0 C2C A:HEC111 4.3 12.1 1.0 C3D A:HEC111 4.3 12.6 1.0 C3A A:HEC111 4.3 13.9 1.0 C2B A:HEC111 4.3 13.8 1.0 C2A A:HEC111 4.3 14.2 1.0 C3B A:HEC111 4.3 13.1 1.0

Iron binding site 2 out of 8 in the Crystal Structure of the Di-Tetraheme Cytochrome C3 From Desulfovibrio Gigas at 1.2 Angstrom Resolution


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 the Di-Tetraheme Cytochrome C3 From Desulfovibrio Gigas at 1.2 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe112 b:11.5 occ:1.00 FE A:HEC112 0.0 11.5 1.0 ND A:HEC112 2.0 13.2 1.0 NE2 A:HIS41 2.0 12.3 1.0 NA A:HEC112 2.0 12.0 1.0 NE2 A:HIS56 2.0 12.0 1.0 NC A:HEC112 2.0 12.7 1.0 NB A:HEC112 2.0 11.8 1.0 CE1 A:HIS41 3.0 14.1 1.0 CE1 A:HIS56 3.0 12.3 1.0 C1D A:HEC112 3.0 14.2 1.0 C4D A:HEC112 3.0 14.3 1.0 C1A A:HEC112 3.0 12.2 1.0 CD2 A:HIS56 3.0 12.0 1.0 CD2 A:HIS41 3.0 12.3 1.0 C4A A:HEC112 3.0 11.6 1.0 C4C A:HEC112 3.0 13.2 1.0 C1B A:HEC112 3.0 11.1 1.0 C1C A:HEC112 3.0 12.3 1.0 C4B A:HEC112 3.1 11.7 1.0 CHD A:HEC112 3.4 14.3 1.0 CHB A:HEC112 3.4 11.4 1.0 CHA A:HEC112 3.4 13.6 1.0 CHC A:HEC112 3.4 12.1 1.0 ND1 A:HIS41 4.1 13.6 1.0 ND1 A:HIS56 4.1 12.5 1.0 CG A:HIS56 4.2 12.3 1.0 CG A:HIS41 4.2 12.3 1.0 C2D A:HEC112 4.2 15.1 1.0 C3D A:HEC112 4.2 15.7 1.0 C2A A:HEC112 4.3 12.2 1.0 C3A A:HEC112 4.3 11.5 1.0 C3C A:HEC112 4.3 13.4 1.0 C2C A:HEC112 4.3 13.6 1.0 C2B A:HEC112 4.3 11.5 1.0 C3B A:HEC112 4.3 11.6 1.0 O A:HOH2086 4.7 17.4 1.0

Iron binding site 3 out of 8 in the Crystal Structure of the Di-Tetraheme Cytochrome C3 From Desulfovibrio Gigas at 1.2 Angstrom Resolution


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 the Di-Tetraheme Cytochrome C3 From Desulfovibrio Gigas at 1.2 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe113 b:11.9 occ:1.00 FE A:HEC113 0.0 11.9 1.0 NC A:HEC113 2.0 12.4 1.0 NE2 A:HIS31 2.0 12.7 1.0 ND A:HEC113 2.0 13.7 1.0 NB A:HEC113 2.0 11.9 1.0 NA A:HEC113 2.0 13.8 1.0 NE2 A:HIS84 2.0 12.4 1.0 CE1 A:HIS84 2.9 12.3 1.0 CE1 A:HIS31 3.0 13.7 1.0 C1C A:HEC113 3.0 11.7 1.0 C1D A:HEC113 3.0 13.4 1.0 CD2 A:HIS31 3.0 12.7 1.0 C4C A:HEC113 3.0 12.7 1.0 C4B A:HEC113 3.0 11.6 1.0 C4D A:HEC113 3.0 14.5 1.0 C1A A:HEC113 3.1 14.4 1.0 C1B A:HEC113 3.1 12.4 1.0 C4A A:HEC113 3.1 14.0 1.0 CD2 A:HIS84 3.1 12.8 1.0 CHC A:HEC113 3.3 11.7 1.0 CHD A:HEC113 3.4 13.5 1.0 CHA A:HEC113 3.4 15.0 1.0 CHB A:HEC113 3.4 13.4 1.0 ND1 A:HIS84 4.1 12.7 1.0 ND1 A:HIS31 4.1 14.1 1.0 CG A:HIS31 4.2 13.0 1.0 CG A:HIS84 4.2 13.1 1.0 C2C A:HEC113 4.3 11.8 1.0 C2D A:HEC113 4.3 15.6 1.0 C3D A:HEC113 4.3 16.2 1.0 C3C A:HEC113 4.3 12.6 1.0 C3B A:HEC113 4.3 11.4 1.0 C2B A:HEC113 4.3 12.3 1.0 C2A A:HEC113 4.3 16.1 1.0 C3A A:HEC113 4.3 15.9 1.0 CA A:GLY95 4.6 15.4 1.0 N A:GLY95 4.8 15.8 1.0 CBC A:HEC111 5.0 13.1 1.0

Iron binding site 4 out of 8 in the Crystal Structure of the Di-Tetraheme Cytochrome C3 From Desulfovibrio Gigas at 1.2 Angstrom Resolution


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 the Di-Tetraheme Cytochrome C3 From Desulfovibrio Gigas at 1.2 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe114 b:10.4 occ:1.00 FE A:HEC114 0.0 10.4 1.0 NE2 A:HIS73 2.0 10.6 1.0 NE2 A:HIS104 2.0 12.0 1.0 NA A:HEC114 2.0 11.8 1.0 NC A:HEC114 2.0 11.3 1.0 ND A:HEC114 2.0 10.7 1.0 NB A:HEC114 2.0 11.3 1.0 CE1 A:HIS73 2.9 10.8 1.0 CE1 A:HIS104 2.9 12.3 1.0 C4A A:HEC114 3.0 11.5 1.0 C1B A:HEC114 3.0 11.5 1.0 CD2 A:HIS73 3.0 11.1 1.0 C4C A:HEC114 3.0 10.7 1.0 CD2 A:HIS104 3.0 12.3 1.0 C1D A:HEC114 3.0 10.6 1.0 C4B A:HEC114 3.1 11.3 1.0 C1C A:HEC114 3.1 11.3 1.0 C1A A:HEC114 3.1 11.2 1.0 C4D A:HEC114 3.1 11.1 1.0 CHB A:HEC114 3.4 11.4 1.0 CHD A:HEC114 3.4 11.1 1.0 CHC A:HEC114 3.4 11.7 1.0 CHA A:HEC114 3.4 11.5 1.0 ND1 A:HIS73 4.1 11.0 1.0 ND1 A:HIS104 4.1 13.1 1.0 CG A:HIS73 4.2 10.9 1.0 CG A:HIS104 4.2 12.4 1.0 C3A A:HEC114 4.3 11.9 1.0 C2D A:HEC114 4.3 10.8 1.0 C2B A:HEC114 4.3 12.2 1.0 C3B A:HEC114 4.3 11.5 1.0 C3C A:HEC114 4.3 10.9 1.0 C2A A:HEC114 4.3 11.9 1.0 C2C A:HEC114 4.3 11.3 1.0 C3D A:HEC114 4.3 10.4 1.0

Iron binding site 5 out of 8 in the Crystal Structure of the Di-Tetraheme Cytochrome C3 From Desulfovibrio Gigas at 1.2 Angstrom Resolution


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 the Di-Tetraheme Cytochrome C3 From Desulfovibrio Gigas at 1.2 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe111 b:12.0 occ:1.00 FE B:HEC111 0.0 12.0 1.0 NC B:HEC111 2.0 13.2 1.0 NB B:HEC111 2.0 12.6 1.0 NE2 B:HIS28 2.0 12.9 1.0 ND B:HEC111 2.0 12.3 1.0 NA B:HEC111 2.0 12.2 1.0 NE2 B:HIS40 2.0 11.8 1.0 CE1 B:HIS28 3.0 15.2 1.0 CE1 B:HIS40 3.0 12.4 1.0 C4B B:HEC111 3.0 12.7 1.0 C1C B:HEC111 3.0 13.4 1.0 CD2 B:HIS28 3.0 13.7 1.0 C1D B:HEC111 3.0 12.5 1.0 C1B B:HEC111 3.0 12.1 1.0 C4C B:HEC111 3.0 13.3 1.0 CD2 B:HIS40 3.0 12.4 1.0 C4A B:HEC111 3.0 12.1 1.0 C4D B:HEC111 3.1 12.0 1.0 C1A B:HEC111 3.1 12.2 1.0 CHB B:HEC111 3.4 12.8 1.0 CHC B:HEC111 3.4 13.8 1.0 CHD B:HEC111 3.4 12.5 1.0 CHA B:HEC111 3.4 12.9 1.0 ND1 B:HIS40 4.1 12.7 1.0 ND1 B:HIS28 4.1 15.6 1.0 CG B:HIS28 4.2 13.3 1.0 CG B:HIS40 4.2 12.6 1.0 C2B B:HEC111 4.3 12.9 1.0 C2C B:HEC111 4.3 13.8 1.0 C3C B:HEC111 4.3 13.1 1.0 C3B B:HEC111 4.3 13.3 1.0 C2D B:HEC111 4.3 12.8 1.0 C3D B:HEC111 4.3 12.1 1.0 C3A B:HEC111 4.3 12.7 1.0 C2A B:HEC111 4.3 12.2 1.0 CE B:MET26 5.0 18.0 1.0

Iron binding site 6 out of 8 in the Crystal Structure of the Di-Tetraheme Cytochrome C3 From Desulfovibrio Gigas at 1.2 Angstrom Resolution


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 the Di-Tetraheme Cytochrome C3 From Desulfovibrio Gigas at 1.2 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe112 b:12.2 occ:1.00 FE B:HEC112 0.0 12.2 1.0 NA B:HEC112 2.0 13.6 1.0 NE2 B:HIS56 2.0 12.8 1.0 NE2 B:HIS41 2.0 13.3 1.0 ND B:HEC112 2.0 13.3 1.0 NB B:HEC112 2.0 12.9 1.0 NC B:HEC112 2.0 12.8 1.0 CE1 B:HIS41 3.0 14.5 1.0 CE1 B:HIS56 3.0 13.2 1.0 CD2 B:HIS41 3.0 12.6 1.0 C4A B:HEC112 3.0 13.2 1.0 C1A B:HEC112 3.0 13.8 1.0 C1D B:HEC112 3.0 13.4 1.0 CD2 B:HIS56 3.0 12.6 1.0 C1B B:HEC112 3.0 12.8 1.0 C4D B:HEC112 3.0 14.2 1.0 C4C B:HEC112 3.0 13.1 1.0 C1C B:HEC112 3.0 12.8 1.0 C4B B:HEC112 3.0 12.2 1.0 CHB B:HEC112 3.4 12.8 1.0 CHD B:HEC112 3.4 14.1 1.0 CHC B:HEC112 3.4 12.4 1.0 CHA B:HEC112 3.4 14.5 1.0 ND1 B:HIS41 4.1 14.3 1.0 ND1 B:HIS56 4.1 13.1 1.0 CG B:HIS41 4.2 13.5 1.0 CG B:HIS56 4.2 12.7 1.0 C2A B:HEC112 4.3 14.2 1.0 C3A B:HEC112 4.3 13.2 1.0 C2D B:HEC112 4.3 15.2 1.0 C3D B:HEC112 4.3 15.5 1.0 C2B B:HEC112 4.3 12.7 1.0 C3C B:HEC112 4.3 12.9 1.0 C2C B:HEC112 4.3 12.3 1.0 C3B B:HEC112 4.3 12.1 1.0 CG B:MET42 4.9 14.7 1.0

Iron binding site 7 out of 8 in the Crystal Structure of the Di-Tetraheme Cytochrome C3 From Desulfovibrio Gigas at 1.2 Angstrom Resolution


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 the Di-Tetraheme Cytochrome C3 From Desulfovibrio Gigas at 1.2 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe113 b:15.0 occ:1.00 FE B:HEC113 0.0 15.0 1.0 ND B:HEC113 2.0 16.0 1.0 NA B:HEC113 2.0 16.2 1.0 NC B:HEC113 2.0 15.9 1.0 NB B:HEC113 2.0 14.8 1.0 NE2 B:HIS31 2.0 14.5 1.0 NE2 B:HIS84 2.0 15.2 1.0 CE1 B:HIS84 2.9 15.8 1.0 CE1 B:HIS31 3.0 15.4 1.0 C1D B:HEC113 3.0 16.5 1.0 C4D B:HEC113 3.0 17.7 1.0 C1A B:HEC113 3.0 17.8 1.0 C4B B:HEC113 3.0 14.3 1.0 C1C B:HEC113 3.0 14.6 1.0 CD2 B:HIS31 3.0 14.9 1.0 C4C B:HEC113 3.0 16.1 1.0 C4A B:HEC113 3.0 16.4 1.0 C1B B:HEC113 3.1 15.6 1.0 CD2 B:HIS84 3.1 15.6 1.0 CHC B:HEC113 3.4 14.3 1.0 CHD B:HEC113 3.4 16.8 1.0 CHA B:HEC113 3.4 18.7 1.0 CHB B:HEC113 3.4 16.4 1.0 ND1 B:HIS84 4.1 15.9 1.0 ND1 B:HIS31 4.1 15.9 1.0 CG B:HIS31 4.2 14.7 1.0 CG B:HIS84 4.2 17.4 1.0 C2D B:HEC113 4.3 18.6 1.0 C3D B:HEC113 4.3 19.5 1.0 C3B B:HEC113 4.3 13.7 1.0 C2A B:HEC113 4.3 19.9 1.0 C2C B:HEC113 4.3 14.9 1.0 C3C B:HEC113 4.3 15.4 1.0 C3A B:HEC113 4.3 18.7 1.0 C2B B:HEC113 4.3 15.1 1.0 CA B:GLY95 4.6 19.4 1.0 N B:GLY95 4.8 19.6 1.0 CBC B:HEC111 5.0 14.8 1.0

Iron binding site 8 out of 8 in the Crystal Structure of the Di-Tetraheme Cytochrome C3 From Desulfovibrio Gigas at 1.2 Angstrom Resolution


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 the Di-Tetraheme Cytochrome C3 From Desulfovibrio Gigas at 1.2 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe114 b:12.9 occ:1.00 FE B:HEC114 0.0 12.9 1.0 NE2 B:HIS104 1.9 13.7 1.0 NC B:HEC114 2.0 14.3 1.0 ND B:HEC114 2.0 13.1 1.0 NB B:HEC114 2.0 14.2 1.0 NE2 B:HIS73 2.0 13.4 1.0 NA B:HEC114 2.0 13.6 1.0 CE1 B:HIS104 2.9 14.9 1.0 CE1 B:HIS73 2.9 13.3 1.0 CD2 B:HIS104 3.0 14.5 1.0 C1D B:HEC114 3.0 12.8 1.0 C1C B:HEC114 3.0 14.4 1.0 C4C B:HEC114 3.0 13.3 1.0 C4A B:HEC114 3.0 14.4 1.0 C1B B:HEC114 3.0 15.4 1.0 C4B B:HEC114 3.0 14.4 1.0 CD2 B:HIS73 3.0 14.0 1.0 C4D B:HEC114 3.1 13.3 1.0 C1A B:HEC114 3.1 13.5 1.0 CHD B:HEC114 3.3 13.1 1.0 CHB B:HEC114 3.4 14.5 1.0 CHC B:HEC114 3.4 14.7 1.0 CHA B:HEC114 3.4 13.2 1.0 ND1 B:HIS104 4.1 14.7 1.0 ND1 B:HIS73 4.1 13.4 1.0 CG B:HIS104 4.1 14.4 1.0 CG B:HIS73 4.2 14.0 1.0 C3C B:HEC114 4.2 13.9 1.0 C2C B:HEC114 4.3 14.8 1.0 C2D B:HEC114 4.3 12.9 1.0 C3B B:HEC114 4.3 14.9 1.0 C2B B:HEC114 4.3 15.3 1.0 C3A B:HEC114 4.3 14.5 1.0 C3D B:HEC114 4.3 13.5 1.0 C2A B:HEC114 4.3 13.3 1.0 CD2 B:PHE21 4.9 16.6 1.0

D.Aragao, C.Frazao, L.Sieker, G.M.Sheldrick, J.Legall, M.A.Carrondo. Structure of Dimeric Cytochrome C3 From Desulfovibrio Gigas at 1.2 A Resolution Acta Crystallogr.,Sect.D V. 59 644 2003.
ISSN: ISSN 0907-4449
PubMed: 12657783
DOI: 10.1107/S090744490300194X