Iron in PDB 2yyx: The Y65A Mutant of Tetraheme Cytochrome C3 From Desulfovibrio Vulgaris Miyazaki F

The structure of The Y65A Mutant of Tetraheme Cytochrome C3 From Desulfovibrio Vulgaris Miyazaki F, PDB code: 2yyx 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)	10.00 / 1.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	51.936, 67.592, 34.588, 90.00, 90.00, 90.00
R / Rfree (%)	12.5 / n/a

The binding sites of Iron atom in the The Y65A Mutant of Tetraheme Cytochrome C3 From Desulfovibrio Vulgaris Miyazaki F (pdb code 2yyx). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the The Y65A Mutant of Tetraheme Cytochrome C3 From Desulfovibrio Vulgaris Miyazaki F, PDB code: 2yyx:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the The Y65A 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 Y65A Mutant of Tetraheme Cytochrome C3 From Desulfovibrio Vulgaris Miyazaki F within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1004 b:6.1 occ:1.00 FE A:HEM1004 0.0 6.1 1.0 NE2 A:HIS106 2.0 6.2 1.0 NE2 A:HIS70 2.0 6.0 1.0 NC A:HEM1004 2.0 5.9 1.0 NA A:HEM1004 2.0 6.8 1.0 ND A:HEM1004 2.0 5.9 1.0 NB A:HEM1004 2.0 6.5 1.0 CE1 A:HIS106 2.9 6.9 1.0 CE1 A:HIS70 3.0 6.6 1.0 CD2 A:HIS106 3.0 6.7 1.0 C4C A:HEM1004 3.0 5.9 1.0 C4A A:HEM1004 3.0 7.5 1.0 C1D A:HEM1004 3.0 5.6 1.0 CD2 A:HIS70 3.0 6.3 1.0 C1B A:HEM1004 3.0 7.7 1.0 C1C A:HEM1004 3.0 6.4 1.0 C1A A:HEM1004 3.0 6.6 1.0 C4D A:HEM1004 3.1 6.0 1.0 C4B A:HEM1004 3.1 6.7 1.0 CHD A:HEM1004 3.4 6.0 1.0 CHB A:HEM1004 3.4 8.2 1.0 CHA A:HEM1004 3.4 6.9 1.0 CHC A:HEM1004 3.4 7.1 1.0 ND1 A:HIS106 4.1 7.7 1.0 ND1 A:HIS70 4.1 6.6 1.0 CG A:HIS106 4.2 7.2 1.0 CG A:HIS70 4.2 6.2 1.0 C2C A:HEM1004 4.2 6.3 1.0 C3D A:HEM1004 4.2 6.5 1.0 C2B A:HEM1004 4.2 8.8 1.0 C3A A:HEM1004 4.2 8.1 1.0 C2D A:HEM1004 4.2 6.3 1.0 C2A A:HEM1004 4.2 7.6 1.0 C3C A:HEM1004 4.3 6.3 1.0 C3B A:HEM1004 4.3 7.9 1.0 CE2 A:TYR66 4.7 9.5 1.0

Iron binding site 2 out of 4 in the The Y65A 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 Y65A Mutant of Tetraheme Cytochrome C3 From Desulfovibrio Vulgaris Miyazaki F within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1002 b:5.4 occ:1.00 FE A:HEM1002 0.0 5.4 1.0 NE2 A:HIS52 2.0 5.5 1.0 NE2 A:HIS35 2.0 5.4 1.0 NA A:HEM1002 2.0 5.5 1.0 NC A:HEM1002 2.0 5.7 1.0 NB A:HEM1002 2.0 5.4 1.0 ND A:HEM1002 2.0 5.6 1.0 CE1 A:HIS52 2.9 6.1 1.0 CE1 A:HIS35 2.9 6.0 1.0 C4A A:HEM1002 3.0 5.6 1.0 C1A A:HEM1002 3.0 5.9 1.0 C4D A:HEM1002 3.0 5.8 1.0 C1C A:HEM1002 3.0 5.7 1.0 CD2 A:HIS52 3.0 6.2 1.0 C4B A:HEM1002 3.0 5.3 1.0 C1B A:HEM1002 3.0 5.7 1.0 C1D A:HEM1002 3.0 6.0 1.0 C4C A:HEM1002 3.0 6.2 1.0 CD2 A:HIS35 3.0 5.6 1.0 CHD A:HEM1002 3.4 6.5 1.0 CHC A:HEM1002 3.4 6.2 1.0 CHA A:HEM1002 3.4 6.0 1.0 CHB A:HEM1002 3.4 6.3 1.0 ND1 A:HIS52 4.1 6.0 1.0 ND1 A:HIS35 4.1 6.0 1.0 CG A:HIS52 4.1 5.9 1.0 CG A:HIS35 4.2 5.6 1.0 C2A A:HEM1002 4.2 6.5 1.0 C2B A:HEM1002 4.2 5.9 1.0 C3D A:HEM1002 4.2 6.5 1.0 C3A A:HEM1002 4.2 6.2 1.0 C2C A:HEM1002 4.2 6.6 1.0 C2D A:HEM1002 4.2 6.2 1.0 C3C A:HEM1002 4.2 6.7 1.0 C3B A:HEM1002 4.3 5.9 1.0

Iron binding site 3 out of 4 in the The Y65A 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 Y65A Mutant of Tetraheme Cytochrome C3 From Desulfovibrio Vulgaris Miyazaki F within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1001 b:6.4 occ:1.00 FE A:HEM1001 0.0 6.4 1.0 NE2 A:HIS34 2.0 6.2 1.0 NE2 A:HIS22 2.0 6.7 1.0 ND A:HEM1001 2.0 5.9 1.0 NA A:HEM1001 2.0 6.7 1.0 NC A:HEM1001 2.0 6.7 1.0 NB A:HEM1001 2.0 7.5 1.0 CE1 A:HIS34 2.9 6.1 1.0 CE1 A:HIS22 3.0 6.7 1.0 CD2 A:HIS22 3.0 7.4 1.0 CD2 A:HIS34 3.0 6.0 1.0 C1A A:HEM1001 3.0 6.5 1.0 C1D A:HEM1001 3.0 6.1 1.0 C1C A:HEM1001 3.0 7.3 1.0 C4A A:HEM1001 3.0 7.2 1.0 C4C A:HEM1001 3.0 6.4 1.0 C4D A:HEM1001 3.0 5.9 1.0 C1B A:HEM1001 3.0 7.8 1.0 C4B A:HEM1001 3.1 7.5 1.0 CHD A:HEM1001 3.4 6.5 1.0 CHA A:HEM1001 3.4 6.6 1.0 CHB A:HEM1001 3.4 7.8 1.0 CHC A:HEM1001 3.4 8.0 1.0 ND1 A:HIS34 4.1 6.1 1.0 ND1 A:HIS22 4.1 7.5 1.0 CG A:HIS34 4.1 6.2 1.0 CG A:HIS22 4.2 7.3 1.0 C2C A:HEM1001 4.2 7.5 1.0 C2A A:HEM1001 4.2 7.6 1.0 C2D A:HEM1001 4.2 6.1 1.0 C3A A:HEM1001 4.2 7.9 1.0 C3D A:HEM1001 4.2 6.4 1.0 C3C A:HEM1001 4.3 7.1 1.0 C2B A:HEM1001 4.3 8.6 1.0 C3B A:HEM1001 4.3 8.4 1.0 CD A:PRO5 4.6 10.7 1.0 CE2 A:PHE20 4.7 7.4 1.0

Iron binding site 4 out of 4 in the The Y65A 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 Y65A Mutant of Tetraheme Cytochrome C3 From Desulfovibrio Vulgaris Miyazaki F within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1003 b:6.3 occ:1.00 FE A:HEM1003 0.0 6.3 1.0 NE2 A:HIS25 2.0 6.3 1.0 NE2 A:HIS83 2.0 6.6 1.0 ND A:HEM1003 2.0 7.0 1.0 NB A:HEM1003 2.0 5.8 1.0 NA A:HEM1003 2.0 6.6 1.0 NC A:HEM1003 2.0 6.5 1.0 CE1 A:HIS83 3.0 6.7 1.0 CE1 A:HIS25 3.0 7.4 1.0 CD2 A:HIS25 3.0 6.3 1.0 C1D A:HEM1003 3.0 7.1 1.0 C4B A:HEM1003 3.0 5.8 1.0 C4D A:HEM1003 3.0 7.2 1.0 C1C A:HEM1003 3.0 6.7 1.0 C1A A:HEM1003 3.0 7.3 1.0 C1B A:HEM1003 3.0 6.3 1.0 C4C A:HEM1003 3.0 7.3 1.0 C4A A:HEM1003 3.1 6.5 1.0 CD2 A:HIS83 3.1 7.0 1.0 CHA A:HEM1003 3.4 7.6 1.0 CHC A:HEM1003 3.4 6.4 1.0 CHD A:HEM1003 3.4 7.5 1.0 CHB A:HEM1003 3.4 6.8 1.0 ND1 A:HIS83 4.1 6.8 1.0 ND1 A:HIS25 4.1 7.6 1.0 CG A:HIS25 4.2 6.8 1.0 CG A:HIS83 4.2 6.8 1.0 C3D A:HEM1003 4.2 7.7 1.0 C2D A:HEM1003 4.2 8.6 1.0 C2A A:HEM1003 4.3 7.7 1.0 C2B A:HEM1003 4.3 6.2 1.0 C2C A:HEM1003 4.3 7.4 1.0 C3A A:HEM1003 4.3 7.5 1.0 C3B A:HEM1003 4.3 6.2 1.0 C3C A:HEM1003 4.3 8.0 1.0 O A:HOH1212 4.5 65.2 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.