Zinc in PDB 2e84: Crystal Structure of High-Molecular Weight Cytochrome C From Desulfovibrio Vulgaris (Miyazaki F) in the Presence of Zinc Ion

The structure of Crystal Structure of High-Molecular Weight Cytochrome C From Desulfovibrio Vulgaris (Miyazaki F) in the Presence of Zinc Ion, PDB code: 2e84 was solved by N.Shibata, K.Suto, M.Sato, Y.Morimoto, M.Kitamura, Y.Higuchi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	27.20 / 2.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	60.090, 84.070, 142.670, 90.00, 90.00, 90.00
R / Rfree (%)	20.4 / 25.9

The structure of Crystal Structure of High-Molecular Weight Cytochrome C From Desulfovibrio Vulgaris (Miyazaki F) in the Presence of Zinc Ion also contains other interesting chemical elements:

Iron	(Fe)	16 atoms
Sodium	(Na)	4 atoms

The binding sites of Zinc atom in the Crystal Structure of High-Molecular Weight Cytochrome C From Desulfovibrio Vulgaris (Miyazaki F) in the Presence of Zinc Ion (pdb code 2e84). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of High-Molecular Weight Cytochrome C From Desulfovibrio Vulgaris (Miyazaki F) in the Presence of Zinc Ion, PDB code: 2e84:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of High-Molecular Weight Cytochrome C From Desulfovibrio Vulgaris (Miyazaki F) in the Presence of Zinc Ion


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of High-Molecular Weight Cytochrome C From Desulfovibrio Vulgaris (Miyazaki F) in the Presence of Zinc Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn557 b:28.5 occ:1.00 OD2 A:ASP419 1.8 36.9 1.0 OE1 A:GLU415 2.3 43.8 1.0 OE2 A:GLU415 2.7 38.0 1.0 CG A:ASP419 2.7 30.9 1.0 CD A:GLU415 2.8 41.4 1.0 OD1 A:ASP419 3.0 28.7 1.0 CB A:ASP419 4.1 27.4 1.0 CG A:GLU415 4.3 37.7 1.0 O A:GLU415 4.5 37.2 1.0 O A:HOH1456 4.8 44.8 1.0 CB A:GLU415 5.0 39.8 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of High-Molecular Weight Cytochrome C From Desulfovibrio Vulgaris (Miyazaki F) in the Presence of Zinc Ion


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of High-Molecular Weight Cytochrome C From Desulfovibrio Vulgaris (Miyazaki F) in the Presence of Zinc Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn558 b:28.2 occ:1.00 OE1 A:GLU540 1.8 52.5 1.0 OE1 A:GLU549 2.0 19.5 1.0 ND1 A:HIS534 2.0 25.6 1.0 CD A:GLU540 2.3 53.6 1.0 OE2 A:GLU540 2.4 56.5 1.0 CD A:GLU549 2.8 21.9 1.0 OE2 A:GLU549 2.9 30.3 1.0 CG A:HIS534 3.0 21.3 1.0 CE1 A:HIS534 3.0 31.1 1.0 CB A:HIS534 3.3 17.8 1.0 CG A:GLU540 3.8 58.0 1.0 NE2 A:HIS534 4.1 24.4 1.0 CD2 A:HIS534 4.1 26.2 1.0 CG A:GLU549 4.3 26.7 1.0 CBC A:HEM1316 4.3 21.7 1.0 CMC A:HEM1316 4.5 24.4 1.0 CB A:GLU540 4.8 63.0 1.0 CB A:GLU549 4.8 27.5 1.0 CA A:HIS534 4.8 22.3 1.0 CD1 A:LEU539 4.9 47.5 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of High-Molecular Weight Cytochrome C From Desulfovibrio Vulgaris (Miyazaki F) in the Presence of Zinc Ion


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of High-Molecular Weight Cytochrome C From Desulfovibrio Vulgaris (Miyazaki F) in the Presence of Zinc Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn559 b:28.9 occ:1.00 OE2 A:GLU442 1.8 15.3 1.0 CD A:GLU442 2.7 19.7 1.0 OE1 A:GLU442 3.0 22.9 1.0 O A:HOH1371 4.0 34.3 1.0 CG A:GLU442 4.0 22.1 1.0 CE1 A:PHE443 4.2 19.8 1.0 CZ A:PHE443 4.7 20.6 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of High-Molecular Weight Cytochrome C From Desulfovibrio Vulgaris (Miyazaki F) in the Presence of Zinc Ion


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of High-Molecular Weight Cytochrome C From Desulfovibrio Vulgaris (Miyazaki F) in the Presence of Zinc Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn560 b:53.6 occ:1.00 ND1 A:HIS320 2.2 35.8 1.0 N A:ASP325 2.5 33.7 1.0 O A:LYS323 2.6 30.7 1.0 O A:ASP325 2.8 38.5 1.0 O A:HOH1361 2.9 23.7 1.0 C A:ASP325 3.0 38.5 1.0 CG A:HIS320 3.2 33.3 1.0 CE1 A:HIS320 3.2 29.5 1.0 CA A:ASP325 3.2 39.0 1.0 CB A:HIS320 3.4 26.6 1.0 C A:ILE324 3.5 38.4 1.0 CA A:ILE324 3.6 35.6 1.0 C A:LYS323 3.7 29.5 1.0 N A:ASN326 3.8 37.0 1.0 CB A:ASP325 3.8 42.9 1.0 CA A:HIS320 3.9 25.1 1.0 N A:ILE324 4.1 31.6 1.0 CBB A:HEM1309 4.1 7.2 1.0 CMC A:HEM1309 4.2 29.7 1.0 CA A:ASN326 4.3 39.8 1.0 NE2 A:HIS320 4.3 33.4 1.0 CD2 A:HIS320 4.3 33.7 1.0 CAB A:HEM1309 4.6 17.7 1.0 O A:ILE324 4.6 42.5 1.0 C A:ASN326 4.6 36.6 1.0 C A:HIS320 4.7 28.0 1.0 CHC A:HEM1309 4.7 28.2 1.0 CB A:ILE324 4.9 32.6 1.0 N A:HIS320 5.0 27.2 1.0 CA A:LYS323 5.0 28.4 1.0

H.Osuka, K.Suto, M.Sato, N.Shibata, M.Kitamura, Y.Morimoto, K.Ozawa, H.Akutsu, Y.Higuchi, N.Yasuoka. Structure of High-Molecular Weight Cytochrome C From Desulfovibrio Vulgaris (Miyazaki F) To Be Published.