Iron in PDB 2yxc: The H25M Mutant of Tetraheme Cytochrome C3 From Desulfovibrio Vulgaris Miyazaki F

The structure of The H25M Mutant of Tetraheme Cytochrome C3 From Desulfovibrio Vulgaris Miyazaki F, PDB code: 2yxc 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)	12.23 / 1.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	51.942, 67.156, 34.574, 90.00, 90.00, 90.00
R / Rfree (%)	17.8 / 19.5

The binding sites of Iron atom in the The H25M Mutant of Tetraheme Cytochrome C3 From Desulfovibrio Vulgaris Miyazaki F (pdb code 2yxc). 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 H25M Mutant of Tetraheme Cytochrome C3 From Desulfovibrio Vulgaris Miyazaki F, PDB code: 2yxc:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the The H25M 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 H25M Mutant of Tetraheme Cytochrome C3 From Desulfovibrio Vulgaris Miyazaki F within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1004 b:8.0 occ:1.00 FE A:HEM1004 0.0 8.0 1.0 NE2 A:HIS70 2.0 6.8 1.0 NE2 A:HIS106 2.0 7.0 1.0 NA A:HEM1004 2.1 6.6 1.0 NC A:HEM1004 2.1 6.6 1.0 NB A:HEM1004 2.1 7.9 1.0 ND A:HEM1004 2.1 7.0 1.0 CE1 A:HIS70 2.9 8.1 1.0 CD2 A:HIS106 2.9 7.5 1.0 CE1 A:HIS106 3.0 8.2 1.0 CD2 A:HIS70 3.0 7.8 1.0 C4A A:HEM1004 3.1 7.7 1.0 C1B A:HEM1004 3.1 8.1 1.0 C1A A:HEM1004 3.1 7.7 1.0 C1C A:HEM1004 3.1 7.4 1.0 C4C A:HEM1004 3.1 6.5 1.0 C1D A:HEM1004 3.1 7.2 1.0 C4D A:HEM1004 3.1 6.5 1.0 C4B A:HEM1004 3.1 6.7 1.0 CHB A:HEM1004 3.4 8.0 1.0 CHD A:HEM1004 3.4 6.9 1.0 CHA A:HEM1004 3.4 6.8 1.0 CHC A:HEM1004 3.4 7.9 1.0 ND1 A:HIS70 4.0 6.6 1.0 ND1 A:HIS106 4.1 8.3 1.0 CG A:HIS106 4.1 7.8 1.0 CG A:HIS70 4.1 6.0 1.0 C3A A:HEM1004 4.2 8.3 1.0 C2A A:HEM1004 4.2 7.5 1.0 C2B A:HEM1004 4.2 8.9 1.0 C2C A:HEM1004 4.2 7.2 1.0 C3C A:HEM1004 4.3 7.6 1.0 C2D A:HEM1004 4.3 6.2 1.0 C3B A:HEM1004 4.3 7.3 1.0 C3D A:HEM1004 4.3 7.2 1.0 CE2 A:TYR66 4.8 9.3 1.0

Iron binding site 2 out of 4 in the The H25M 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 H25M Mutant of Tetraheme Cytochrome C3 From Desulfovibrio Vulgaris Miyazaki F within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1002 b:8.2 occ:1.00 FE A:HEM1002 0.0 8.2 1.0 NE2 A:HIS52 2.0 7.0 1.0 NE2 A:HIS35 2.0 7.0 1.0 ND A:HEM1002 2.1 7.8 1.0 NA A:HEM1002 2.1 7.5 1.0 NC A:HEM1002 2.1 7.2 1.0 NB A:HEM1002 2.1 6.6 1.0 CE1 A:HIS35 2.9 8.2 1.0 CE1 A:HIS52 3.0 7.9 1.0 CD2 A:HIS52 3.0 8.1 1.0 CD2 A:HIS35 3.0 7.9 1.0 C4D A:HEM1002 3.0 6.8 1.0 C1A A:HEM1002 3.1 7.5 1.0 C1C A:HEM1002 3.1 8.5 1.0 C1D A:HEM1002 3.1 7.8 1.0 C4A A:HEM1002 3.1 7.2 1.0 C1B A:HEM1002 3.1 6.4 1.0 C4C A:HEM1002 3.1 7.9 1.0 C4B A:HEM1002 3.1 6.9 1.0 CHA A:HEM1002 3.4 8.2 1.0 CHB A:HEM1002 3.4 6.8 1.0 CHC A:HEM1002 3.4 8.6 1.0 CHD A:HEM1002 3.4 8.0 1.0 ND1 A:HIS35 4.0 8.5 1.0 ND1 A:HIS52 4.1 6.8 1.0 CG A:HIS52 4.1 6.6 1.0 CG A:HIS35 4.1 7.3 1.0 C3D A:HEM1002 4.2 8.6 1.0 C2D A:HEM1002 4.2 7.2 1.0 C2A A:HEM1002 4.2 7.4 1.0 C3A A:HEM1002 4.3 7.1 1.0 C2C A:HEM1002 4.3 7.8 1.0 C3C A:HEM1002 4.3 8.2 1.0 C2B A:HEM1002 4.3 6.3 1.0 C3B A:HEM1002 4.3 7.1 1.0

Iron binding site 3 out of 4 in the The H25M 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 H25M Mutant of Tetraheme Cytochrome C3 From Desulfovibrio Vulgaris Miyazaki F within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1001 b:8.3 occ:1.00 FE A:HEM1001 0.0 8.3 1.0 NE2 A:HIS34 2.0 6.6 1.0 NE2 A:HIS22 2.0 7.1 1.0 NA A:HEM1001 2.1 8.2 1.0 ND A:HEM1001 2.1 6.6 1.0 NB A:HEM1001 2.1 7.3 1.0 NC A:HEM1001 2.1 7.5 1.0 CE1 A:HIS34 2.9 6.0 1.0 CE1 A:HIS22 3.0 6.9 1.0 CD2 A:HIS22 3.0 7.5 1.0 C4A A:HEM1001 3.0 7.3 1.0 CD2 A:HIS34 3.0 7.3 1.0 C1D A:HEM1001 3.1 6.7 1.0 C1B A:HEM1001 3.1 7.9 1.0 C1A A:HEM1001 3.1 8.2 1.0 C4D A:HEM1001 3.1 6.1 1.0 C1C A:HEM1001 3.1 6.8 1.0 C4C A:HEM1001 3.1 7.2 1.0 C4B A:HEM1001 3.1 7.7 1.0 CHB A:HEM1001 3.4 8.3 1.0 CHD A:HEM1001 3.4 7.2 1.0 CHC A:HEM1001 3.4 7.7 1.0 CHA A:HEM1001 3.4 7.2 1.0 ND1 A:HIS34 4.0 7.8 1.0 ND1 A:HIS22 4.1 7.5 1.0 CG A:HIS22 4.1 6.0 1.0 CG A:HIS34 4.1 6.8 1.0 C3A A:HEM1001 4.2 8.0 1.0 C2D A:HEM1001 4.2 6.7 1.0 C2A A:HEM1001 4.2 8.4 1.0 C3D A:HEM1001 4.2 6.8 1.0 C2C A:HEM1001 4.3 8.4 1.0 C2B A:HEM1001 4.3 9.5 1.0 C3B A:HEM1001 4.3 9.6 1.0 C3C A:HEM1001 4.3 7.7 1.0 CD A:PRO5 4.7 12.0 1.0 CE2 A:PHE20 4.8 8.4 1.0

Iron binding site 4 out of 4 in the The H25M 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 H25M Mutant of Tetraheme Cytochrome C3 From Desulfovibrio Vulgaris Miyazaki F within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1003 b:8.1 occ:1.00 FE A:HEM1003 0.0 8.1 1.0 NE2 A:HIS83 2.0 8.4 1.0 ND A:HEM1003 2.1 7.6 1.0 NA A:HEM1003 2.1 8.1 1.0 NC A:HEM1003 2.1 7.8 1.0 NB A:HEM1003 2.1 7.0 1.0 SD A:MET25 2.3 7.9 1.0 CE1 A:HIS83 2.9 7.2 1.0 C1A A:HEM1003 3.0 7.2 1.0 C4D A:HEM1003 3.1 8.3 1.0 C1C A:HEM1003 3.1 7.7 1.0 C1D A:HEM1003 3.1 8.4 1.0 C4B A:HEM1003 3.1 7.9 1.0 CD2 A:HIS83 3.1 7.5 1.0 C4A A:HEM1003 3.1 7.6 1.0 C4C A:HEM1003 3.1 8.7 1.0 C1B A:HEM1003 3.1 7.6 1.0 CG A:MET25 3.3 7.2 1.0 CHA A:HEM1003 3.4 7.9 1.0 CHC A:HEM1003 3.4 7.6 1.0 CHD A:HEM1003 3.4 7.8 1.0 CE A:MET25 3.4 8.6 1.0 CHB A:HEM1003 3.4 6.9 1.0 ND1 A:HIS83 4.1 6.6 1.0 CG A:HIS83 4.2 8.4 1.0 C2A A:HEM1003 4.2 8.3 1.0 C3D A:HEM1003 4.2 10.1 1.0 C2D A:HEM1003 4.3 9.0 1.0 C3A A:HEM1003 4.3 8.0 1.0 C2C A:HEM1003 4.3 8.9 1.0 C3C A:HEM1003 4.3 9.1 1.0 C3B A:HEM1003 4.3 7.2 1.0 C2B A:HEM1003 4.3 6.4 1.0 CB A:MET25 4.7 9.3 1.0

Y.Takayama, N.D.Werbeck, H.Komori, K.Morita, K.Ozawa, Y.Higuchi, H.Akutsu. Strategic Roles of Axial Histidines in Structure Formation and Redox Regulation of Tetraheme Cytochrome C3. Biochemistry V. 47 9405 2008.
ISSN: ISSN 0006-2960
PubMed: 18702516
DOI: 10.1021/BI8005708