Iron in PDB 1j0p: Three Dimensional Structure of the Y43L Mutant of Tetraheme Cytochrome C3 From Desulfovibrio Vulgaris Miyazaki F

The structure of Three Dimensional Structure of the Y43L Mutant of Tetraheme Cytochrome C3 From Desulfovibrio Vulgaris Miyazaki F, PDB code: 1j0p was solved by K.Ozawa, F.Yasukawa, J.Kumagai, T.Ohmura, M.A.Cusanvich, Y.Tomimoto, H.Ogata, Y.Higuchi, H.Akutsu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.00 / 0.91
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	51.868, 67.309, 34.328, 90.00, 90.00, 90.00
R / Rfree (%)	10.2 / 13.6

The binding sites of Iron atom in the Three Dimensional Structure of the Y43L Mutant of Tetraheme Cytochrome C3 From Desulfovibrio Vulgaris Miyazaki F (pdb code 1j0p). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Three Dimensional Structure of the Y43L Mutant of Tetraheme Cytochrome C3 From Desulfovibrio Vulgaris Miyazaki F, PDB code: 1j0p:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Three Dimensional Structure of the Y43L 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 Three Dimensional Structure of the Y43L Mutant of Tetraheme Cytochrome C3 From Desulfovibrio Vulgaris Miyazaki F within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1004 b:3.9 occ:1.00 FE A:HEM1004 0.0 3.9 1.0 NE2 A:HIS70 2.0 4.1 1.0 NE2 A:HIS106 2.0 4.2 1.0 NC A:HEM1004 2.0 4.2 1.0 NA A:HEM1004 2.0 4.2 1.0 NB A:HEM1004 2.0 4.8 1.0 ND A:HEM1004 2.0 4.3 1.0 CE1 A:HIS106 3.0 4.5 1.0 CE1 A:HIS70 3.0 4.3 1.0 C1B A:HEM1004 3.0 4.5 1.0 C1D A:HEM1004 3.0 3.9 1.0 C4C A:HEM1004 3.0 4.2 1.0 C1C A:HEM1004 3.0 4.1 1.0 C4A A:HEM1004 3.0 4.5 1.0 CD2 A:HIS70 3.0 4.0 1.0 CD2 A:HIS106 3.0 4.3 1.0 C1A A:HEM1004 3.0 4.4 1.0 C4B A:HEM1004 3.0 4.4 1.0 C4D A:HEM1004 3.0 4.0 1.0 CHB A:HEM1004 3.4 5.0 1.0 CHD A:HEM1004 3.4 4.1 1.0 CHC A:HEM1004 3.4 4.6 1.0 CHA A:HEM1004 3.4 4.3 1.0 ND1 A:HIS106 4.1 4.5 1.0 ND1 A:HIS70 4.1 4.2 1.0 CG A:HIS106 4.2 4.6 1.0 CG A:HIS70 4.2 4.2 1.0 C2B A:HEM1004 4.2 5.2 1.0 C2C A:HEM1004 4.2 4.7 1.0 C3A A:HEM1004 4.2 4.8 1.0 C2D A:HEM1004 4.3 4.2 1.0 C3C A:HEM1004 4.3 4.4 1.0 C2A A:HEM1004 4.3 4.9 1.0 C3B A:HEM1004 4.3 4.7 1.0 C3D A:HEM1004 4.3 4.3 1.0 CE2 A:TYR66 4.8 6.1 1.0 C2 A:EOH2003 4.9 12.2 1.0

Iron binding site 2 out of 4 in the Three Dimensional Structure of the Y43L 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 Three Dimensional Structure of the Y43L Mutant of Tetraheme Cytochrome C3 From Desulfovibrio Vulgaris Miyazaki F within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1002 b:4.3 occ:1.00 FE A:HEM1002 0.0 4.3 1.0 NE2 A:HIS52 2.0 4.4 1.0 NA A:HEM1002 2.0 4.3 1.0 NE2 A:HIS35 2.0 4.8 1.0 NC A:HEM1002 2.0 4.3 1.0 NB A:HEM1002 2.0 4.5 1.0 ND A:HEM1002 2.0 4.8 1.0 CE1 A:HIS52 2.9 4.4 1.0 CE1 A:HIS35 2.9 4.9 1.0 C4A A:HEM1002 3.0 4.3 1.0 C1C A:HEM1002 3.0 4.3 1.0 C1A A:HEM1002 3.0 4.7 1.0 C4C A:HEM1002 3.0 4.5 1.0 CD2 A:HIS35 3.0 4.8 1.0 C1B A:HEM1002 3.0 5.0 1.0 CD2 A:HIS52 3.0 4.7 1.0 C4B A:HEM1002 3.0 4.8 1.0 C4D A:HEM1002 3.0 5.2 1.0 C1D A:HEM1002 3.0 5.0 1.0 CHC A:HEM1002 3.4 4.7 1.0 CHB A:HEM1002 3.4 5.2 1.0 CHD A:HEM1002 3.4 4.7 1.0 CHA A:HEM1002 3.4 5.1 1.0 ND1 A:HIS52 4.1 4.2 1.0 ND1 A:HIS35 4.1 4.7 1.0 CG A:HIS52 4.2 4.3 1.0 CG A:HIS35 4.2 4.6 1.0 C2A A:HEM1002 4.2 4.8 1.0 C3A A:HEM1002 4.2 5.2 1.0 C2C A:HEM1002 4.2 4.8 1.0 C3C A:HEM1002 4.3 5.0 1.0 C3D A:HEM1002 4.3 5.9 1.0 C2D A:HEM1002 4.3 5.8 1.0 C3B A:HEM1002 4.3 4.8 1.0 C2B A:HEM1002 4.3 5.7 1.0

Iron binding site 3 out of 4 in the Three Dimensional Structure of the Y43L 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 Three Dimensional Structure of the Y43L Mutant of Tetraheme Cytochrome C3 From Desulfovibrio Vulgaris Miyazaki F within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1001 b:4.4 occ:1.00 FE A:HEM1001 0.0 4.4 1.0 NE2 A:HIS34 1.9 4.5 1.0 NE2 A:HIS22 2.0 4.6 1.0 ND A:HEM1001 2.0 4.5 1.0 NB A:HEM1001 2.0 4.5 1.0 NA A:HEM1001 2.0 5.0 1.0 NC A:HEM1001 2.0 4.3 1.0 CE1 A:HIS34 2.9 5.1 1.0 CE1 A:HIS22 3.0 4.7 1.0 C1D A:HEM1001 3.0 4.6 1.0 C4C A:HEM1001 3.0 4.0 1.0 CD2 A:HIS34 3.0 5.1 1.0 C4A A:HEM1001 3.0 5.3 1.0 C1B A:HEM1001 3.0 5.3 1.0 C1C A:HEM1001 3.0 4.5 1.0 C4D A:HEM1001 3.0 4.8 1.0 CD2 A:HIS22 3.0 5.2 1.0 C1A A:HEM1001 3.0 5.1 1.0 C4B A:HEM1001 3.0 4.6 1.0 CHB A:HEM1001 3.4 6.0 1.0 CHD A:HEM1001 3.4 4.3 1.0 CHC A:HEM1001 3.4 5.2 1.0 CHA A:HEM1001 3.4 5.2 1.0 ND1 A:HIS34 4.1 5.3 1.0 ND1 A:HIS22 4.1 5.3 1.0 CG A:HIS34 4.1 5.4 1.0 CG A:HIS22 4.2 5.1 1.0 C2A A:HEM1001 4.2 6.0 1.0 C3A A:HEM1001 4.2 6.6 1.0 C2D A:HEM1001 4.2 4.8 1.0 C3D A:HEM1001 4.2 5.5 1.0 C2B A:HEM1001 4.3 5.7 1.0 C3C A:HEM1001 4.3 4.6 1.0 C2C A:HEM1001 4.3 4.9 1.0 C3B A:HEM1001 4.3 5.6 1.0 CE2 A:PHE20 4.7 5.4 1.0 CD A:PRO5 4.8 7.3 1.0

Iron binding site 4 out of 4 in the Three Dimensional Structure of the Y43L 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 Three Dimensional Structure of the Y43L Mutant of Tetraheme Cytochrome C3 From Desulfovibrio Vulgaris Miyazaki F within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1003 b:4.3 occ:1.00 FE A:HEM1003 0.0 4.3 1.0 NE2 A:HIS83 2.0 4.3 1.0 NB A:HEM1003 2.0 4.5 1.0 ND A:HEM1003 2.0 5.2 1.0 NA A:HEM1003 2.0 4.9 1.0 NE2 A:HIS25 2.0 4.9 1.0 NC A:HEM1003 2.1 4.5 1.0 CE1 A:HIS83 3.0 5.0 1.0 CE1 A:HIS25 3.0 5.0 1.0 CD2 A:HIS25 3.0 4.5 1.0 C4D A:HEM1003 3.0 5.1 1.0 C1D A:HEM1003 3.0 5.3 1.0 C1A A:HEM1003 3.0 5.0 1.0 C4B A:HEM1003 3.0 4.3 1.0 C1B A:HEM1003 3.0 4.5 1.0 CD2 A:HIS83 3.0 4.5 1.0 C1C A:HEM1003 3.0 4.1 1.0 C4A A:HEM1003 3.1 4.9 1.0 C4C A:HEM1003 3.1 4.8 1.0 CHA A:HEM1003 3.4 5.0 1.0 CHC A:HEM1003 3.4 4.3 1.0 CHB A:HEM1003 3.4 5.2 1.0 CHD A:HEM1003 3.4 5.3 1.0 ND1 A:HIS25 4.1 5.0 1.0 ND1 A:HIS83 4.1 4.5 1.0 CG A:HIS25 4.1 4.9 1.0 CG A:HIS83 4.2 4.5 1.0 C3D A:HEM1003 4.2 5.5 1.0 C2A A:HEM1003 4.2 5.6 1.0 C2B A:HEM1003 4.3 4.3 1.0 C2D A:HEM1003 4.3 6.2 1.0 C3A A:HEM1003 4.3 5.2 1.0 C3B A:HEM1003 4.3 4.2 1.0 C2C A:HEM1003 4.3 4.5 1.0 C3C A:HEM1003 4.3 4.7 1.0

K.Ozawa, Y.Takayama, F.Yasukawa, T.Ohmura, M.A.Cusanovich, Y.Tomimoto, H.Ogata, Y.Higuchi, H.Akutsu. Role of the Aromatic Ring of TYR43 in Tetraheme Cytochrome C(3) From Desulfovibrio Vulgaris Miyazaki F. Biophys.J. V. 85 3367 2003.
ISSN: ISSN 0006-3495
PubMed: 14581238
DOI: 10.1016/S0006-3495(03)74756-0