Zinc in PDB 4cvt: Structure of Apobacterioferritin Y58F Variant

The structure of Structure of Apobacterioferritin Y58F Variant, PDB code: 4cvt was solved by K.Hingorani, R.Pace, S.Whitney, J.W.Murray, T.Wydrzynski, M.H.Cheah, P.Smith, W.Hillier, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.817 / 1.79
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	104.460, 28.070, 56.810, 90.00, 119.18, 90.00
R / Rfree (%)	16.72 / 21.42

The binding sites of Zinc atom in the Structure of Apobacterioferritin Y58F Variant (pdb code 4cvt). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Structure of Apobacterioferritin Y58F Variant, PDB code: 4cvt:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Structure of Apobacterioferritin Y58F Variant


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Apobacterioferritin Y58F Variant within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1157 b:16.9 occ:1.00 O A:HOH2080 2.1 21.6 1.0 OE2 A:GLU84 2.1 11.5 1.0 O A:HOH2082 2.1 18.8 1.0 CD A:GLU84 3.0 12.0 1.0 OE1 A:GLU84 3.3 13.8 1.0 OE1 A:GLN142 3.8 16.9 1.0 NH1 A:ARG88 3.9 17.9 1.0 O A:HOH2081 4.0 25.4 1.0 O A:HOH2129 4.1 20.4 1.0 O A:HOH2086 4.2 29.0 1.0 CG A:GLU84 4.4 10.5 1.0 CZ A:ARG88 4.8 14.7 1.0 NH2 A:ARG88 4.9 16.3 1.0

Zinc binding site 2 out of 4 in the Structure of Apobacterioferritin Y58F Variant


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Apobacterioferritin Y58F Variant within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1158 b:13.3 occ:1.00 OE2 A:GLU44 1.9 13.0 1.0 O A:HOH2021 1.9 11.3 1.0 OD2 A:ASP90 2.0 8.3 1.0 ND1 A:HIS28 2.1 8.5 1.0 CG A:ASP90 2.6 7.7 1.0 OD1 A:ASP90 2.7 7.3 1.0 CD A:GLU44 2.8 19.1 1.0 OE1 A:GLU44 3.0 24.6 1.0 CG A:HIS28 3.1 8.8 1.0 CE1 A:HIS28 3.1 8.6 1.0 CB A:HIS28 3.4 10.7 1.0 O A:HOH2023 3.8 30.6 1.0 CB A:ASP90 4.1 7.2 1.0 O A:HOH2018 4.2 16.8 1.0 CG A:GLU44 4.2 19.1 1.0 NE2 A:HIS28 4.2 8.8 1.0 CD2 A:HIS28 4.2 8.7 1.0 O A:MET86 4.5 6.3 1.0 O A:GLN24 4.7 16.0 1.0 CE2 A:PHE32 4.7 14.4 1.0 CG A:GLN24 4.7 10.7 1.0 CD1 A:TYR25 4.8 34.6 1.0 CA A:TYR25 4.8 20.3 1.0 CA A:HIS28 4.9 11.5 1.0 NE2 A:GLN24 5.0 10.8 1.0

Zinc binding site 3 out of 4 in the Structure of Apobacterioferritin Y58F Variant


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Apobacterioferritin Y58F Variant within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1159 b:11.6 occ:1.00 ND1 A:HIS54 2.0 8.4 1.0 OE2 A:GLU127 2.0 11.7 1.0 OE1 A:GLU51 2.0 14.9 1.0 OE1 A:GLU18 2.2 15.6 1.0 OE2 A:GLU18 2.2 16.2 1.0 CD A:GLU18 2.5 13.8 1.0 CE1 A:HIS54 2.8 8.5 1.0 CD A:GLU127 3.0 11.6 1.0 CG A:HIS54 3.1 8.6 1.0 CD A:GLU51 3.1 15.6 1.0 OE1 A:GLU127 3.4 12.7 1.0 CB A:HIS54 3.5 9.6 1.0 O A:HOH2053 3.6 16.0 1.0 OE2 A:GLU51 3.9 18.4 1.0 CA A:GLU51 3.9 13.2 1.0 NE2 A:HIS54 4.0 9.2 1.0 CG A:GLU18 4.0 14.2 1.0 ZN A:ZN1160 4.1 14.1 1.0 CD2 A:HIS54 4.1 8.5 1.0 CG A:GLU51 4.2 14.5 1.0 CB A:GLU51 4.2 13.5 1.0 CG A:GLU127 4.2 10.4 1.0 O A:HOH2116 4.3 35.9 1.0 CG2 A:ILE123 4.3 8.2 1.0 N A:GLU51 4.7 13.0 1.0 O A:GLU51 4.7 10.7 1.0 C A:GLU51 4.8 11.8 1.0 CB A:GLU18 4.9 12.7 1.0 O A:ASP50 4.9 13.4 1.0 CE1 A:HIS130 5.0 11.7 1.0

Zinc binding site 4 out of 4 in the Structure of Apobacterioferritin Y58F Variant


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Apobacterioferritin Y58F Variant within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1160 b:14.1 occ:1.00 O A:HOH2053 1.9 16.0 1.0 OE1 A:GLU127 2.0 12.7 1.0 OE2 A:GLU51 2.1 18.4 1.0 ND1 A:HIS130 2.1 10.8 1.0 OE2 A:GLU94 2.1 20.1 1.0 OE1 A:GLU94 2.4 17.3 1.0 CD A:GLU94 2.6 14.8 1.0 CD A:GLU51 2.9 15.6 1.0 CE1 A:HIS130 2.9 11.7 1.0 OE1 A:GLU51 3.0 14.9 1.0 CD A:GLU127 3.1 11.6 1.0 CG A:HIS130 3.2 9.8 1.0 OE2 A:GLU127 3.7 11.7 1.0 CB A:HIS130 3.7 9.5 1.0 OH A:TYR25 3.9 54.9 1.0 ZN A:ZN1159 4.1 11.6 1.0 CG A:GLU94 4.1 11.8 1.0 NE2 A:HIS130 4.1 12.2 1.0 CG A:GLU51 4.3 14.5 1.0 CD2 A:HIS130 4.3 10.8 1.0 CG A:GLU127 4.3 10.4 1.0 O A:HOH2090 4.3 14.8 1.0 CA A:GLU127 4.4 9.3 1.0 CB A:GLU127 4.4 9.5 1.0 O A:HOH2116 4.6 35.9 1.0 O A:HOH2024 4.8 31.2 1.0 CZ A:TYR25 5.0 42.6 1.0

K.Hingorani, R.Pace, S.Whitney, J.W.Murray, P.Smith, M.H.Cheah, T.Wydrzynski, W.Hillier. Photo-Oxidation of Tyrosine in A Bio-Engineered Bacterioferritin 'Reaction Centre'-A Protein Model For Artificial Photosynthesis. Biochim.Biophys.Acta V.1837 1821 2014.
ISSN: ISSN 0006-3002
PubMed: 25107631
DOI: 10.1016/J.BBABIO.2014.07.019