Iron in PDB 2cym: Effects of Amino Acid Substitution on Three-Dimensional Structure: An X-Ray Analysis of Cytochrome C3 From Desulfovibrio Vulgaris Hildenborough at 2 Angstroms Resolution

The structure of Effects of Amino Acid Substitution on Three-Dimensional Structure: An X-Ray Analysis of Cytochrome C3 From Desulfovibrio Vulgaris Hildenborough at 2 Angstroms Resolution, PDB code: 2cym was solved by Y.Morimoto, T.Tani, H.Okumura, Y.Higuchi, N.Yasuoka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	N/A / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	43.170, 62.910, 41.170, 90.00, 90.00, 90.00
R / Rfree (%)	n/a / n/a

The binding sites of Iron atom in the Effects of Amino Acid Substitution on Three-Dimensional Structure: An X-Ray Analysis of Cytochrome C3 From Desulfovibrio Vulgaris Hildenborough at 2 Angstroms Resolution (pdb code 2cym). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Effects of Amino Acid Substitution on Three-Dimensional Structure: An X-Ray Analysis of Cytochrome C3 From Desulfovibrio Vulgaris Hildenborough at 2 Angstroms Resolution, PDB code: 2cym:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Effects of Amino Acid Substitution on Three-Dimensional Structure: An X-Ray Analysis of Cytochrome C3 From Desulfovibrio Vulgaris Hildenborough at 2 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Effects of Amino Acid Substitution on Three-Dimensional Structure: An X-Ray Analysis of Cytochrome C3 From Desulfovibrio Vulgaris Hildenborough at 2 Angstroms Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe108 b:8.1 occ:1.00 FE A:HEM108 0.0 8.1 1.0 NA A:HEM108 2.0 8.1 1.0 ND A:HEM108 2.0 7.1 1.0 NB A:HEM108 2.0 8.0 1.0 NC A:HEM108 2.0 6.8 1.0 NE2 A:HIS106 2.1 5.8 1.0 NE2 A:HIS70 2.2 5.7 1.0 C4B A:HEM108 3.0 7.7 1.0 C1D A:HEM108 3.0 7.2 1.0 C4A A:HEM108 3.0 8.9 1.0 C1B A:HEM108 3.0 8.5 1.0 C4D A:HEM108 3.1 7.0 1.0 C4C A:HEM108 3.1 6.9 1.0 C1A A:HEM108 3.1 7.6 1.0 CD2 A:HIS106 3.1 5.6 1.0 C1C A:HEM108 3.1 6.7 1.0 CD2 A:HIS70 3.1 4.2 1.0 CE1 A:HIS106 3.2 4.6 1.0 CE1 A:HIS70 3.3 5.0 1.0 CHC A:HEM108 3.4 7.0 1.0 CHD A:HEM108 3.4 7.2 1.0 CHA A:HEM108 3.4 7.6 1.0 CHB A:HEM108 3.4 8.3 1.0 C3B A:HEM108 4.2 9.7 1.0 C2B A:HEM108 4.2 8.6 1.0 ND1 A:HIS106 4.2 6.5 1.0 CG A:HIS106 4.2 6.5 1.0 C3A A:HEM108 4.2 8.6 1.0 C2D A:HEM108 4.3 7.3 1.0 C3D A:HEM108 4.3 7.2 1.0 C2A A:HEM108 4.3 8.9 1.0 C2C A:HEM108 4.3 6.7 1.0 CG A:HIS70 4.3 5.0 1.0 C3C A:HEM108 4.3 6.2 1.0 ND1 A:HIS70 4.3 4.4 1.0

Iron binding site 2 out of 4 in the Effects of Amino Acid Substitution on Three-Dimensional Structure: An X-Ray Analysis of Cytochrome C3 From Desulfovibrio Vulgaris Hildenborough at 2 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Effects of Amino Acid Substitution on Three-Dimensional Structure: An X-Ray Analysis of Cytochrome C3 From Desulfovibrio Vulgaris Hildenborough at 2 Angstroms Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe109 b:14.7 occ:1.00 FE A:HEM109 0.0 14.7 1.0 NB A:HEM109 2.0 15.2 1.0 NC A:HEM109 2.0 16.2 1.0 ND A:HEM109 2.0 16.6 1.0 NA A:HEM109 2.0 14.5 1.0 NE2 A:HIS52 2.0 14.9 1.0 NE2 A:HIS35 2.1 7.8 1.0 CE1 A:HIS52 2.8 17.0 1.0 CE1 A:HIS35 2.8 9.4 1.0 C4C A:HEM109 3.0 16.2 1.0 C1B A:HEM109 3.0 15.1 1.0 C4B A:HEM109 3.0 16.1 1.0 C1C A:HEM109 3.0 16.1 1.0 C1D A:HEM109 3.0 16.4 1.0 C4D A:HEM109 3.1 16.2 1.0 C1A A:HEM109 3.1 14.3 1.0 C4A A:HEM109 3.1 14.2 1.0 CD2 A:HIS52 3.3 15.3 1.0 CD2 A:HIS35 3.3 8.4 1.0 CHC A:HEM109 3.4 16.1 1.0 CHB A:HEM109 3.4 14.5 1.0 CHD A:HEM109 3.4 16.5 1.0 CHA A:HEM109 3.5 15.7 1.0 ND1 A:HIS52 4.0 15.6 1.0 ND1 A:HIS35 4.0 8.6 1.0 C2C A:HEM109 4.2 16.1 1.0 C3C A:HEM109 4.2 16.5 1.0 CG A:HIS52 4.3 14.1 1.0 C3D A:HEM109 4.3 17.1 1.0 C2B A:HEM109 4.3 16.0 1.0 C2D A:HEM109 4.3 16.6 1.0 C3B A:HEM109 4.3 16.1 1.0 CG A:HIS35 4.3 9.0 1.0 C2A A:HEM109 4.3 13.9 1.0 C3A A:HEM109 4.3 13.5 1.0

Iron binding site 3 out of 4 in the Effects of Amino Acid Substitution on Three-Dimensional Structure: An X-Ray Analysis of Cytochrome C3 From Desulfovibrio Vulgaris Hildenborough at 2 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Effects of Amino Acid Substitution on Three-Dimensional Structure: An X-Ray Analysis of Cytochrome C3 From Desulfovibrio Vulgaris Hildenborough at 2 Angstroms Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe110 b:15.7 occ:1.00 FE A:HEM110 0.0 15.7 1.0 ND A:HEM110 2.0 14.6 1.0 NB A:HEM110 2.0 14.7 1.0 NE2 A:HIS34 2.0 5.8 1.0 NC A:HEM110 2.0 13.9 1.0 NA A:HEM110 2.0 16.5 1.0 NE2 A:HIS22 2.2 14.5 1.0 CE1 A:HIS34 3.0 6.5 1.0 CD2 A:HIS34 3.0 5.2 1.0 C1D A:HEM110 3.0 14.0 1.0 C1B A:HEM110 3.0 14.2 1.0 C4D A:HEM110 3.0 14.7 1.0 C4A A:HEM110 3.0 16.7 1.0 C4C A:HEM110 3.0 13.0 1.0 C1A A:HEM110 3.1 16.9 1.0 C1C A:HEM110 3.1 13.6 1.0 C4B A:HEM110 3.1 14.7 1.0 CE1 A:HIS22 3.2 14.2 1.0 CD2 A:HIS22 3.2 13.1 1.0 CHA A:HEM110 3.4 15.6 1.0 CHB A:HEM110 3.4 15.5 1.0 CHD A:HEM110 3.4 12.9 1.0 CHC A:HEM110 3.5 13.8 1.0 CG A:HIS34 4.1 7.6 1.0 ND1 A:HIS34 4.1 7.5 1.0 C2B A:HEM110 4.2 14.2 1.0 C2D A:HEM110 4.2 13.8 1.0 C3D A:HEM110 4.2 14.5 1.0 C2A A:HEM110 4.2 17.8 1.0 C3B A:HEM110 4.3 14.5 1.0 C3A A:HEM110 4.3 17.0 1.0 C2C A:HEM110 4.3 13.7 1.0 ND1 A:HIS22 4.3 12.5 1.0 C3C A:HEM110 4.3 13.4 1.0 CG A:HIS22 4.3 13.5 1.0 CD A:PRO5 4.8 29.0 1.0 CE2 A:PHE20 5.0 10.1 1.0

Iron binding site 4 out of 4 in the Effects of Amino Acid Substitution on Three-Dimensional Structure: An X-Ray Analysis of Cytochrome C3 From Desulfovibrio Vulgaris Hildenborough at 2 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Effects of Amino Acid Substitution on Three-Dimensional Structure: An X-Ray Analysis of Cytochrome C3 From Desulfovibrio Vulgaris Hildenborough at 2 Angstroms Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe111 b:8.3 occ:1.00 FE A:HEM111 0.0 8.3 1.0 NA A:HEM111 2.0 8.8 1.0 NB A:HEM111 2.0 8.2 1.0 ND A:HEM111 2.0 9.6 1.0 NC A:HEM111 2.0 8.9 1.0 NE2 A:HIS25 2.1 11.2 1.0 NE2 A:HIS83 2.2 5.6 1.0 CE1 A:HIS25 3.0 12.4 1.0 C4B A:HEM111 3.0 7.7 1.0 C1A A:HEM111 3.0 8.6 1.0 C4D A:HEM111 3.0 10.4 1.0 C1C A:HEM111 3.0 8.5 1.0 C4A A:HEM111 3.0 8.6 1.0 CE1 A:HIS83 3.1 4.2 1.0 C1D A:HEM111 3.1 9.5 1.0 C1B A:HEM111 3.1 7.7 1.0 C4C A:HEM111 3.1 9.3 1.0 CD2 A:HIS25 3.1 12.4 1.0 CD2 A:HIS83 3.2 5.9 1.0 CHC A:HEM111 3.3 8.1 1.0 CHA A:HEM111 3.4 9.8 1.0 CHD A:HEM111 3.4 8.8 1.0 CHB A:HEM111 3.5 7.8 1.0 ND1 A:HIS25 4.1 13.2 1.0 CG A:HIS25 4.2 12.3 1.0 C3A A:HEM111 4.2 8.7 1.0 C2A A:HEM111 4.2 9.2 1.0 ND1 A:HIS83 4.2 4.8 1.0 C3B A:HEM111 4.3 8.0 1.0 C2C A:HEM111 4.3 9.2 1.0 C3D A:HEM111 4.3 11.0 1.0 C2B A:HEM111 4.3 7.9 1.0 C2D A:HEM111 4.3 9.7 1.0 C3C A:HEM111 4.3 9.7 1.0 CG A:HIS83 4.3 6.1 1.0

Y.Morimoto, T.Tani, H.Okumura, Y.Higuchi, N.Yasuoka. Effects of Amino Acid Substitution on Three-Dimensional Structure: An X-Ray Analysis of Cytochrome C3 From Desulfovibrio Vulgaris Hildenborough at 2 A Resolution. J.Biochem.(Tokyo) V. 110 532 1991.
ISSN: ISSN 0021-924X
PubMed: 1663945