Iron in PDB 2z47: The Y66L Mutant of Tetraheme Cytochrome C3 From Desulfovibrio Vulgaris Miyazaki F

The structure of The Y66L Mutant of Tetraheme Cytochrome C3 From Desulfovibrio Vulgaris Miyazaki F, PDB code: 2z47 was solved by Y.Higuchi, H.Komori, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.83 / 1.60
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	34.424, 69.558, 53.749, 90.00, 92.73, 90.00
R / Rfree (%)	18.4 / 21.6

The binding sites of Iron atom in the The Y66L Mutant of Tetraheme Cytochrome C3 From Desulfovibrio Vulgaris Miyazaki F (pdb code 2z47). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the The Y66L Mutant of Tetraheme Cytochrome C3 From Desulfovibrio Vulgaris Miyazaki F, PDB code: 2z47:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in the The Y66L Mutant of Tetraheme Cytochrome C3 From Desulfovibrio Vulgaris Miyazaki F


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of The Y66L Mutant of Tetraheme Cytochrome C3 From Desulfovibrio Vulgaris Miyazaki F within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1004 b:10.7 occ:1.00 FE A:HEC1004 0.0 10.7 1.0 NE2 A:HIS70 2.0 9.4 1.0 NE2 A:HIS106 2.0 10.2 1.0 ND A:HEC1004 2.1 10.5 1.0 NA A:HEC1004 2.1 10.6 1.0 NC A:HEC1004 2.1 8.9 1.0 NB A:HEC1004 2.1 10.5 1.0 CD2 A:HIS70 2.9 9.6 1.0 CE1 A:HIS70 3.0 8.9 1.0 CE1 A:HIS106 3.0 11.7 1.0 CD2 A:HIS106 3.0 12.4 1.0 C4D A:HEC1004 3.0 10.7 1.0 C1B A:HEC1004 3.1 11.8 1.0 C4A A:HEC1004 3.1 11.6 1.0 C1A A:HEC1004 3.1 11.8 1.0 C1C A:HEC1004 3.1 9.5 1.0 C4C A:HEC1004 3.1 8.9 1.0 C1D A:HEC1004 3.1 9.0 1.0 C4B A:HEC1004 3.1 10.0 1.0 CHB A:HEC1004 3.4 12.9 1.0 CHA A:HEC1004 3.4 11.7 1.0 CHD A:HEC1004 3.4 9.1 1.0 CHC A:HEC1004 3.4 9.3 1.0 ND1 A:HIS70 4.1 9.1 1.0 CG A:HIS70 4.1 9.4 1.0 ND1 A:HIS106 4.1 12.7 1.0 CG A:HIS106 4.1 10.3 1.0 C3D A:HEC1004 4.2 10.7 1.0 C2C A:HEC1004 4.2 9.7 1.0 C3C A:HEC1004 4.2 9.0 1.0 C3A A:HEC1004 4.3 13.3 1.0 C2B A:HEC1004 4.3 12.3 1.0 C2D A:HEC1004 4.3 9.1 1.0 C2A A:HEC1004 4.3 13.2 1.0 C3B A:HEC1004 4.3 10.5 1.0

Iron binding site 2 out of 8 in the The Y66L Mutant of Tetraheme Cytochrome C3 From Desulfovibrio Vulgaris Miyazaki F


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of The Y66L Mutant of Tetraheme Cytochrome C3 From Desulfovibrio Vulgaris Miyazaki F within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1002 b:11.8 occ:1.00 FE A:HEC1002 0.0 11.8 1.0 NE2 A:HIS35 2.0 12.5 1.0 NE2 A:HIS52 2.0 10.6 1.0 NA A:HEC1002 2.1 9.5 1.0 ND A:HEC1002 2.1 11.6 1.0 NC A:HEC1002 2.1 10.6 1.0 NB A:HEC1002 2.1 11.0 1.0 CE1 A:HIS35 2.9 12.4 1.0 CE1 A:HIS52 2.9 11.3 1.0 CD2 A:HIS52 3.0 9.3 1.0 C4D A:HEC1002 3.0 12.8 1.0 CD2 A:HIS35 3.0 11.2 1.0 C1A A:HEC1002 3.0 12.0 1.0 C1C A:HEC1002 3.1 12.1 1.0 C1D A:HEC1002 3.1 13.0 1.0 C4A A:HEC1002 3.1 10.2 1.0 C4B A:HEC1002 3.1 9.6 1.0 C4C A:HEC1002 3.1 13.0 1.0 C1B A:HEC1002 3.1 9.3 1.0 CHA A:HEC1002 3.4 12.3 1.0 CHC A:HEC1002 3.4 11.0 1.0 CHD A:HEC1002 3.4 13.4 1.0 CHB A:HEC1002 3.4 10.3 1.0 ND1 A:HIS35 4.0 12.3 1.0 ND1 A:HIS52 4.1 10.4 1.0 CG A:HIS52 4.1 10.8 1.0 CG A:HIS35 4.1 11.8 1.0 C3D A:HEC1002 4.2 14.3 1.0 C3A A:HEC1002 4.2 12.2 1.0 C2A A:HEC1002 4.2 11.8 1.0 C2D A:HEC1002 4.2 13.7 1.0 C2C A:HEC1002 4.3 12.8 1.0 C3C A:HEC1002 4.3 12.5 1.0 C3B A:HEC1002 4.3 11.0 1.0 C2B A:HEC1002 4.3 9.8 1.0 O A:HOH1034 4.6 29.5 1.0

Iron binding site 3 out of 8 in the The Y66L Mutant of Tetraheme Cytochrome C3 From Desulfovibrio Vulgaris Miyazaki F


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of The Y66L Mutant of Tetraheme Cytochrome C3 From Desulfovibrio Vulgaris Miyazaki F within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1001 b:13.6 occ:1.00 FE A:HEC1001 0.0 13.6 1.0 NE2 A:HIS34 2.0 12.6 1.0 NE2 A:HIS22 2.0 15.1 1.0 NA A:HEC1001 2.1 13.6 1.0 ND A:HEC1001 2.1 14.7 1.0 NB A:HEC1001 2.1 13.8 1.0 NC A:HEC1001 2.1 13.6 1.0 CE1 A:HIS34 2.9 12.1 1.0 CE1 A:HIS22 3.0 14.7 1.0 CD2 A:HIS22 3.0 15.9 1.0 C4A A:HEC1001 3.0 14.3 1.0 C4D A:HEC1001 3.1 13.0 1.0 C1A A:HEC1001 3.1 12.8 1.0 CD2 A:HIS34 3.1 11.4 1.0 C1B A:HEC1001 3.1 14.7 1.0 C1D A:HEC1001 3.1 13.2 1.0 C4B A:HEC1001 3.1 14.1 1.0 C4C A:HEC1001 3.1 14.5 1.0 C1C A:HEC1001 3.1 15.1 1.0 CHA A:HEC1001 3.4 14.4 1.0 CHB A:HEC1001 3.4 14.8 1.0 CHC A:HEC1001 3.4 15.2 1.0 CHD A:HEC1001 3.4 11.7 1.0 ND1 A:HIS34 4.1 11.8 1.0 ND1 A:HIS22 4.1 16.8 1.0 CG A:HIS22 4.1 16.0 1.0 CG A:HIS34 4.2 11.8 1.0 C3A A:HEC1001 4.2 13.2 1.0 C2A A:HEC1001 4.2 12.7 1.0 C3D A:HEC1001 4.2 13.6 1.0 C2D A:HEC1001 4.3 14.4 1.0 C2B A:HEC1001 4.3 15.7 1.0 C3B A:HEC1001 4.3 16.7 1.0 C3C A:HEC1001 4.3 14.2 1.0 C2C A:HEC1001 4.3 14.0 1.0 CE2 A:PHE20 4.7 11.9 1.0 CD A:PRO5 4.7 29.0 1.0

Iron binding site 4 out of 8 in the The Y66L Mutant of Tetraheme Cytochrome C3 From Desulfovibrio Vulgaris Miyazaki F


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of The Y66L Mutant of Tetraheme Cytochrome C3 From Desulfovibrio Vulgaris Miyazaki F within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1003 b:11.8 occ:1.00 FE A:HEC1003 0.0 11.8 1.0 NE2 A:HIS25 2.0 12.2 1.0 NE2 A:HIS83 2.0 11.2 1.0 ND A:HEC1003 2.1 14.1 1.0 NB A:HEC1003 2.1 11.7 1.0 NC A:HEC1003 2.1 12.2 1.0 NA A:HEC1003 2.1 12.6 1.0 CE1 A:HIS83 2.9 10.9 1.0 CD2 A:HIS25 2.9 13.9 1.0 CE1 A:HIS25 3.0 13.3 1.0 C4D A:HEC1003 3.0 14.2 1.0 C1D A:HEC1003 3.1 13.6 1.0 C4B A:HEC1003 3.1 11.9 1.0 C1C A:HEC1003 3.1 11.2 1.0 C1B A:HEC1003 3.1 11.2 1.0 C4C A:HEC1003 3.1 11.4 1.0 C1A A:HEC1003 3.1 14.1 1.0 C4A A:HEC1003 3.1 12.7 1.0 CD2 A:HIS83 3.1 11.0 1.0 CHC A:HEC1003 3.4 10.8 1.0 CHD A:HEC1003 3.4 13.1 1.0 CHA A:HEC1003 3.4 14.8 1.0 CHB A:HEC1003 3.4 12.5 1.0 ND1 A:HIS83 4.1 11.3 1.0 ND1 A:HIS25 4.1 14.3 1.0 CG A:HIS25 4.1 14.4 1.0 CG A:HIS83 4.2 10.4 1.0 C3D A:HEC1003 4.2 16.0 1.0 C2D A:HEC1003 4.2 14.3 1.0 C3B A:HEC1003 4.3 10.4 1.0 C3C A:HEC1003 4.3 12.7 1.0 C2B A:HEC1003 4.3 11.8 1.0 C2C A:HEC1003 4.3 11.1 1.0 C2A A:HEC1003 4.3 13.2 1.0 C3A A:HEC1003 4.3 13.9 1.0

Iron binding site 5 out of 8 in the The Y66L Mutant of Tetraheme Cytochrome C3 From Desulfovibrio Vulgaris Miyazaki F


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of The Y66L Mutant of Tetraheme Cytochrome C3 From Desulfovibrio Vulgaris Miyazaki F within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe3004 b:9.5 occ:1.00 FE B:HEC3004 0.0 9.5 1.0 NE2 B:HIS2070 2.0 7.5 1.0 NE2 B:HIS2106 2.0 8.4 1.0 ND B:HEC3004 2.1 7.6 1.0 NA B:HEC3004 2.1 8.0 1.0 NB B:HEC3004 2.1 8.1 1.0 NC B:HEC3004 2.1 7.6 1.0 CD2 B:HIS2070 2.9 9.4 1.0 CD2 B:HIS2106 3.0 10.4 1.0 CE1 B:HIS2070 3.0 9.6 1.0 CE1 B:HIS2106 3.0 10.9 1.0 C1D B:HEC3004 3.0 7.6 1.0 C4A B:HEC3004 3.0 10.4 1.0 C1B B:HEC3004 3.0 10.9 1.0 C4D B:HEC3004 3.0 7.4 1.0 C4C B:HEC3004 3.1 8.1 1.0 C1A B:HEC3004 3.1 9.4 1.0 C1C B:HEC3004 3.1 8.8 1.0 C4B B:HEC3004 3.1 9.1 1.0 CHB B:HEC3004 3.4 10.3 1.0 CHD B:HEC3004 3.4 8.1 1.0 CHA B:HEC3004 3.4 8.6 1.0 CHC B:HEC3004 3.4 8.8 1.0 ND1 B:HIS2070 4.1 9.4 1.0 CG B:HIS2070 4.1 9.5 1.0 ND1 B:HIS2106 4.1 10.8 1.0 CG B:HIS2106 4.1 10.4 1.0 C2D B:HEC3004 4.2 8.2 1.0 C3D B:HEC3004 4.2 8.2 1.0 C3A B:HEC3004 4.2 11.3 1.0 C2B B:HEC3004 4.2 10.5 1.0 C3B B:HEC3004 4.3 8.9 1.0 C2A B:HEC3004 4.3 10.4 1.0 C3C B:HEC3004 4.3 8.6 1.0 C2C B:HEC3004 4.3 8.5 1.0 OE1 B:GLN2016 4.8 24.2 1.0 O B:HOH3100 4.9 29.3 1.0

Iron binding site 6 out of 8 in the The Y66L Mutant of Tetraheme Cytochrome C3 From Desulfovibrio Vulgaris Miyazaki F


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of The Y66L Mutant of Tetraheme Cytochrome C3 From Desulfovibrio Vulgaris Miyazaki F within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe3002 b:10.2 occ:1.00 FE B:HEC3002 0.0 10.2 1.0 NE2 B:HIS2035 2.0 10.3 1.0 NE2 B:HIS2052 2.0 10.9 1.0 ND B:HEC3002 2.1 8.8 1.0 NA B:HEC3002 2.1 9.4 1.0 NC B:HEC3002 2.1 9.1 1.0 NB B:HEC3002 2.1 9.5 1.0 CE1 B:HIS2035 2.9 11.6 1.0 CE1 B:HIS2052 3.0 8.4 1.0 CD2 B:HIS2035 3.0 10.8 1.0 CD2 B:HIS2052 3.0 8.5 1.0 C4D B:HEC3002 3.0 11.4 1.0 C1A B:HEC3002 3.1 10.5 1.0 C1D B:HEC3002 3.1 10.9 1.0 C4A B:HEC3002 3.1 10.0 1.0 C4C B:HEC3002 3.1 10.6 1.0 C1C B:HEC3002 3.1 11.3 1.0 C1B B:HEC3002 3.1 9.2 1.0 C4B B:HEC3002 3.1 10.3 1.0 CHA B:HEC3002 3.4 11.2 1.0 CHD B:HEC3002 3.4 10.6 1.0 CHB B:HEC3002 3.4 10.1 1.0 CHC B:HEC3002 3.4 11.2 1.0 ND1 B:HIS2035 4.0 13.0 1.0 ND1 B:HIS2052 4.1 10.3 1.0 CG B:HIS2035 4.1 12.2 1.0 CG B:HIS2052 4.1 9.6 1.0 C3D B:HEC3002 4.2 11.8 1.0 C2D B:HEC3002 4.2 12.1 1.0 C3A B:HEC3002 4.3 9.7 1.0 C2A B:HEC3002 4.3 9.9 1.0 C3C B:HEC3002 4.3 10.4 1.0 C2C B:HEC3002 4.3 11.2 1.0 C2B B:HEC3002 4.3 11.2 1.0 C3B B:HEC3002 4.3 10.4 1.0 O B:HOH3054 4.7 21.7 1.0

Iron binding site 7 out of 8 in the The Y66L Mutant of Tetraheme Cytochrome C3 From Desulfovibrio Vulgaris Miyazaki F


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of The Y66L Mutant of Tetraheme Cytochrome C3 From Desulfovibrio Vulgaris Miyazaki F within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe3001 b:10.7 occ:1.00 FE B:HEC3001 0.0 10.7 1.0 NE2 B:HIS2034 2.0 10.7 1.0 NE2 B:HIS2022 2.0 11.3 1.0 NB B:HEC3001 2.1 10.9 1.0 NA B:HEC3001 2.1 10.6 1.0 NC B:HEC3001 2.1 9.7 1.0 ND B:HEC3001 2.1 11.5 1.0 CE1 B:HIS2034 2.9 10.0 1.0 CE1 B:HIS2022 3.0 11.2 1.0 CD2 B:HIS2022 3.0 10.9 1.0 CD2 B:HIS2034 3.0 10.4 1.0 C4B B:HEC3001 3.0 10.7 1.0 C1C B:HEC3001 3.1 10.0 1.0 C1A B:HEC3001 3.1 10.1 1.0 C4A B:HEC3001 3.1 11.4 1.0 C4D B:HEC3001 3.1 11.0 1.0 C1B B:HEC3001 3.1 11.3 1.0 C1D B:HEC3001 3.1 11.2 1.0 C4C B:HEC3001 3.1 10.6 1.0 CHC B:HEC3001 3.4 11.0 1.0 CHB B:HEC3001 3.4 10.8 1.0 CHA B:HEC3001 3.4 12.1 1.0 CHD B:HEC3001 3.4 10.3 1.0 ND1 B:HIS2034 4.0 10.4 1.0 ND1 B:HIS2022 4.1 12.3 1.0 CG B:HIS2034 4.1 10.5 1.0 CG B:HIS2022 4.1 11.7 1.0 C3B B:HEC3001 4.2 12.9 1.0 C3A B:HEC3001 4.2 11.3 1.0 C2B B:HEC3001 4.2 11.5 1.0 C2A B:HEC3001 4.2 12.1 1.0 C2D B:HEC3001 4.3 12.4 1.0 C3D B:HEC3001 4.3 12.7 1.0 C2C B:HEC3001 4.3 9.6 1.0 C3C B:HEC3001 4.3 11.1 1.0 CE2 B:PHE2020 4.7 10.2 1.0 CD B:PRO2005 4.7 18.4 1.0

Iron binding site 8 out of 8 in the The Y66L Mutant of Tetraheme Cytochrome C3 From Desulfovibrio Vulgaris Miyazaki F


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of The Y66L Mutant of Tetraheme Cytochrome C3 From Desulfovibrio Vulgaris Miyazaki F within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe3003 b:10.5 occ:1.00 FE B:HEC3003 0.0 10.5 1.0 NE2 B:HIS2025 2.0 9.9 1.0 NE2 B:HIS2083 2.0 10.3 1.0 ND B:HEC3003 2.1 11.1 1.0 NC B:HEC3003 2.1 9.6 1.0 NA B:HEC3003 2.1 10.3 1.0 NB B:HEC3003 2.1 9.2 1.0 CE1 B:HIS2083 2.9 10.2 1.0 CD2 B:HIS2025 3.0 11.7 1.0 CE1 B:HIS2025 3.0 12.4 1.0 C4D B:HEC3003 3.0 10.9 1.0 C1A B:HEC3003 3.1 12.1 1.0 C1C B:HEC3003 3.1 9.7 1.0 C1D B:HEC3003 3.1 10.8 1.0 C4C B:HEC3003 3.1 11.2 1.0 C4B B:HEC3003 3.1 9.6 1.0 C4A B:HEC3003 3.1 10.3 1.0 C1B B:HEC3003 3.1 8.6 1.0 CD2 B:HIS2083 3.1 10.9 1.0 CHA B:HEC3003 3.3 11.9 1.0 CHC B:HEC3003 3.4 9.4 1.0 CHD B:HEC3003 3.4 10.6 1.0 CHB B:HEC3003 3.4 11.8 1.0 ND1 B:HIS2083 4.0 9.9 1.0 ND1 B:HIS2025 4.1 12.3 1.0 CG B:HIS2025 4.1 12.6 1.0 CG B:HIS2083 4.2 9.8 1.0 C3D B:HEC3003 4.2 12.8 1.0 C2D B:HEC3003 4.3 12.9 1.0 C2A B:HEC3003 4.3 11.0 1.0 C3C B:HEC3003 4.3 10.1 1.0 C2C B:HEC3003 4.3 9.8 1.0 C3A B:HEC3003 4.3 11.0 1.0 C3B B:HEC3003 4.3 8.9 1.0 C2B B:HEC3003 4.3 8.8 1.0

Y.Takayama, H.Komori, K.Morita, Y.Higuchi, H.Akutsu. Structures of Noncoordinated Aromatic Residue Mutants in Tetraheme Cytochrome C3 From Desulfovibrio Vulgaris Miyazaki F To Be Published.