Zinc in PDB 2v08: Structure of Wild-Type Phormidium Laminosum Cytochrome C6

The structure of Structure of Wild-Type Phormidium Laminosum Cytochrome C6, PDB code: 2v08 was solved by J.A.R.Worrall, B.G.Schlarb-Ridley, T.Reda, M.J.Marcaida, R.J.Moorlen, J.Wastl, J.Hirst, D.S.Bendall, B.F.Luisi, C.J.Howe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.59 / 2.00
Space group	P 63
Cell size a, b, c (Å), α, β, γ (°)	57.364, 57.364, 89.553, 90.00, 90.00, 120.00
R / Rfree (%)	18.4 / 25.5

The structure of Structure of Wild-Type Phormidium Laminosum Cytochrome C6 also contains other interesting chemical elements:

Iron	(Fe)	2 atoms
Chlorine	(Cl)	3 atoms

The binding sites of Zinc atom in the Structure of Wild-Type Phormidium Laminosum Cytochrome C6 (pdb code 2v08). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 9 binding sites of Zinc where determined in the Structure of Wild-Type Phormidium Laminosum Cytochrome C6, PDB code: 2v08:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Zinc binding site 1 out of 9 in the Structure of Wild-Type Phormidium Laminosum Cytochrome C6


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Wild-Type Phormidium Laminosum Cytochrome C6 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1090 b:31.6 occ:1.00 OE1 A:GLU29 1.9 18.5 1.0 OD1 A:ASN27 2.2 19.7 1.0 O A:HOH2066 2.2 7.2 1.0 O A:HOH2065 2.3 10.6 1.0 CD A:GLU29 2.7 20.3 1.0 OE2 A:GLU29 3.0 20.1 1.0 CG A:ASN27 3.1 17.7 1.0 ND2 A:ASN27 3.5 17.5 1.0 O A:HOH2019 3.7 48.6 1.0 CG A:GLU29 4.0 16.3 1.0 CB A:GLU29 4.2 13.7 1.0 N A:GLU29 4.3 12.3 1.0 CB A:ASN27 4.5 13.4 1.0 C A:ASN27 4.6 11.6 1.0 N A:ALA28 4.7 12.2 1.0 CA A:ASN27 4.7 11.8 1.0 CA A:GLU29 4.8 13.6 1.0 CD A:LYS30 4.9 19.4 1.0 O A:HOH2001 4.9 32.0 1.0 O A:ASN27 5.0 11.6 1.0

Zinc binding site 2 out of 9 in the Structure of Wild-Type Phormidium Laminosum Cytochrome C6


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Wild-Type Phormidium Laminosum Cytochrome C6 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1091 b:36.3 occ:0.33 N1 A:IMD1088 2.0 20.1 1.0 O A:HOH2067 2.7 22.6 0.3 C5 A:IMD1088 3.0 19.8 1.0 C2 A:IMD1088 3.0 20.6 1.0 N3 A:IMD1088 4.2 21.0 1.0 C4 A:IMD1088 4.2 21.8 1.0 O A:HOH2009 4.4 39.9 0.3 CD2 A:LEU25 4.6 24.2 1.0 CD1 A:ILE23 4.8 15.7 1.0

Zinc binding site 3 out of 9 in the Structure of Wild-Type Phormidium Laminosum Cytochrome C6


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Wild-Type Phormidium Laminosum Cytochrome C6 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1092 b:16.8 occ:0.33 O A:HOH2068 1.6 11.0 0.3 OD2 A:ASP68 2.1 24.9 1.0 CG A:ASP68 2.8 27.5 1.0 OD1 A:ASP68 2.9 36.5 1.0 O A:HOH2054 3.3 8.8 1.0 OD2 A:ASP69 3.9 31.1 1.0 OD1 A:ASP69 4.0 21.1 1.0 CG A:ASP69 4.1 22.7 1.0 CB A:ASP68 4.3 24.9 1.0 O A:HOH2052 4.4 27.3 1.0 N A:ASP69 4.5 20.9 1.0 N A:ASP68 4.7 23.8 1.0 CA A:ASP68 5.0 23.6 1.0

Zinc binding site 4 out of 9 in the Structure of Wild-Type Phormidium Laminosum Cytochrome C6


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Wild-Type Phormidium Laminosum Cytochrome C6 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1093 b:16.8 occ:1.00 N1 A:IMD1089 1.9 16.6 1.0 CL A:CL1095 2.3 16.0 1.0 CL A:CL1096 2.3 20.8 1.0 CL A:CL1097 2.3 16.4 1.0 C2 A:IMD1089 2.8 15.4 1.0 C5 A:IMD1089 3.0 17.9 1.0 O A:HOH2021 3.8 15.7 1.0 O A:HOH2030 4.0 16.6 1.0 N3 A:IMD1089 4.0 17.2 1.0 C4 A:IMD1089 4.1 14.3 1.0 CB A:GLU35 4.4 16.0 1.0 N A:ALA36 4.5 13.2 1.0 CB A:ALA36 4.6 14.7 1.0 NZ A:LYS39 4.8 16.9 1.0 CA A:ALA36 4.8 13.8 1.0 C A:GLU35 4.9 13.7 1.0

Zinc binding site 5 out of 9 in the Structure of Wild-Type Phormidium Laminosum Cytochrome C6


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of Wild-Type Phormidium Laminosum Cytochrome C6 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1094 b:49.8 occ:1.00 O A:HOH2069 2.5 33.0 1.0 OE1 A:GLU35 3.0 22.5 1.0 OE2 A:GLU35 3.4 30.9 1.0 CD A:GLU35 3.6 23.1 1.0 O A:HOH2058 3.7 18.5 1.0 CD A:LYS33 4.5 26.4 1.0 C4 A:IMD1089 4.5 14.3 1.0 C5 A:IMD1089 4.8 17.9 1.0 NZ A:LYS33 4.8 23.2 1.0 CE A:LYS33 4.8 25.1 1.0 CA A:GLY85 4.9 21.5 1.0

Zinc binding site 6 out of 9 in the Structure of Wild-Type Phormidium Laminosum Cytochrome C6


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of Wild-Type Phormidium Laminosum Cytochrome C6 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1090 b:36.4 occ:0.33 N1 B:IMD1088 1.8 20.6 1.0 O B:HOH2041 2.6 23.2 0.3 C5 B:IMD1088 2.8 19.5 1.0 C2 B:IMD1088 2.8 22.7 1.0 C4 B:IMD1088 3.9 18.4 1.0 N3 B:IMD1088 3.9 22.9 1.0 CD2 B:LEU25 4.3 23.0 1.0 CD1 B:ILE23 4.9 22.8 1.0

Zinc binding site 7 out of 9 in the Structure of Wild-Type Phormidium Laminosum Cytochrome C6


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structure of Wild-Type Phormidium Laminosum Cytochrome C6 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1091 b:29.7 occ:1.00 N3 B:IMD1089 1.9 24.9 1.0 O B:HOH2042 2.3 9.8 1.0 O B:HOH2044 2.3 12.0 1.0 O B:HOH2043 2.3 8.0 1.0 C4 B:IMD1089 2.9 28.0 1.0 C2 B:IMD1089 2.9 28.1 1.0 N B:GLY21 4.0 20.8 1.0 C5 B:IMD1089 4.1 27.9 1.0 N1 B:IMD1089 4.1 30.6 1.0 CA B:GLY21 4.2 21.2 1.0

Zinc binding site 8 out of 9 in the Structure of Wild-Type Phormidium Laminosum Cytochrome C6


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structure of Wild-Type Phormidium Laminosum Cytochrome C6 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1092 b:30.2 occ:1.00 OD1 B:ASN27 2.0 22.5 1.0 O B:HOH2045 2.2 10.6 1.0 O B:HOH2046 2.3 6.1 1.0 OE1 B:GLU29 2.9 24.7 1.0 CG B:ASN27 3.1 19.1 1.0 ND2 B:ASN27 3.5 17.5 1.0 CD B:GLU29 3.7 30.3 1.0 O B:HOH2011 4.0 34.0 1.0 CG B:GLU29 4.0 22.3 1.0 CB B:GLU29 4.2 19.3 1.0 N B:GLU29 4.3 16.6 1.0 CB B:ASN27 4.4 16.0 1.0 C B:ASN27 4.5 13.6 1.0 OE2 B:GLU29 4.6 36.4 1.0 CA B:ASN27 4.7 15.1 1.0 N B:ALA28 4.7 13.9 1.0 O B:ASN27 4.8 13.7 1.0 CA B:GLU29 4.9 18.7 1.0

Zinc binding site 9 out of 9 in the Structure of Wild-Type Phormidium Laminosum Cytochrome C6


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Structure of Wild-Type Phormidium Laminosum Cytochrome C6 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1093 b:61.3 occ:1.00 OE2 B:GLU35 2.4 41.6 1.0 OE1 B:GLU35 3.0 36.4 1.0 CD B:GLU35 3.1 38.2 1.0 O B:HOH2047 3.3 36.0 1.0 O B:HOH2036 3.9 39.3 1.0 O B:GLY85 4.5 38.4 1.0 CG B:GLU35 4.7 33.5 1.0 CB B:LYS33 4.9 26.4 1.0 CG B:LYS33 4.9 26.7 1.0

J.A.Worrall, B.G.Schlarb-Ridley, T.Reda, M.J.Marcaida, R.J.Moorlen, J.Wastl, J.Hirst, D.S.Bendall, B.F.Luisi, C.J.Howe. Modulation of Heme Redox Potential in the Cytochrome C6 Family. J. Am. Chem. Soc. V. 129 9468 2007.
ISSN: ISSN 0002-7863
PubMed: 17625855
DOI: 10.1021/JA072346G