Zinc in PDB 4cvr: Structure of Apobacterioferritin Y25F Variant

All present enzymatic activity of Structure of Apobacterioferritin Y25F Variant:
1.16.3.1;

The structure of Structure of Apobacterioferritin Y25F Variant, PDB code: 4cvr 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)	27.43 / 1.10
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	104.380, 27.950, 56.710, 90.00, 119.37, 90.00
R / Rfree (%)	13.373 / 16.544

The binding sites of Zinc atom in the Structure of Apobacterioferritin Y25F Variant (pdb code 4cvr). 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 Y25F Variant, PDB code: 4cvr:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Structure of Apobacterioferritin Y25F 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 Y25F Variant within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1157 b:10.9 occ:1.00 O A:HOH2102 2.1 12.7 1.0 OE2 A:GLU84 2.1 10.4 1.0 O A:HOH2104 2.1 12.2 1.0 CD A:GLU84 3.0 10.2 1.0 OE1 A:GLU84 3.3 11.4 1.0 O A:HOH2103 4.0 18.5 1.0 NH1 A:ARG88 4.1 13.5 1.0 OE1 A:GLN142 4.1 13.1 1.0 O A:HOH2168 4.1 23.5 1.0 O A:HOH2171 4.2 20.1 1.0 CG A:GLU84 4.4 8.2 1.0 CZ A:ARG88 4.9 11.6 1.0 NH2 A:ARG88 5.0 14.0 1.0

Zinc binding site 2 out of 4 in the Structure of Apobacterioferritin Y25F 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 Y25F Variant within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1158 b:8.2 occ:1.00 OE2 A:GLU44 2.0 10.4 1.0 OD2 A:ASP90 2.0 7.5 1.0 O A:HOH2038 2.0 10.5 1.0 ND1 A:HIS28 2.0 6.8 1.0 CG A:ASP90 2.6 7.0 1.0 OD1 A:ASP90 2.6 7.0 1.0 CD A:GLU44 2.9 16.6 1.0 CE1 A:HIS28 3.0 6.5 1.0 CG A:HIS28 3.1 6.7 1.0 OE1 A:GLU44 3.1 19.3 1.0 CB A:HIS28 3.4 7.2 1.0 O A:HOH2062 3.9 19.2 1.0 CB A:ASP90 4.1 6.8 1.0 NE2 A:HIS28 4.1 7.1 1.0 O A:HOH2032 4.1 17.0 1.0 CD2 A:HIS28 4.2 6.8 1.0 CG A:GLU44 4.3 17.0 1.0 O A:MET86 4.5 6.2 1.0 CG A:GLN24 4.6 8.4 1.0 CD1 A:PHE25 4.6 18.2 1.0 O A:GLN24 4.7 10.6 1.0 CE2 A:PHE32 4.8 10.7 1.0 CA A:HIS28 4.9 7.1 1.0 CA A:PHE25 4.9 12.7 1.0 CE1 A:PHE25 4.9 18.7 1.0 CD2 A:LEU87 5.0 9.2 1.0 NE2 A:GLN24 5.0 8.3 1.0

Zinc binding site 3 out of 4 in the Structure of Apobacterioferritin Y25F 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 Y25F Variant within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1159 b:9.3 occ:1.00 OE2 A:GLU127 1.9 12.9 1.0 ND1 A:HIS54 2.0 7.6 1.0 OE1 A:GLU51 2.0 10.3 1.0 OE1 A:GLU18 2.1 10.3 1.0 OE2 A:GLU18 2.3 10.3 1.0 CD A:GLU18 2.5 10.3 1.0 CE1 A:HIS54 2.9 8.8 1.0 CD A:GLU127 3.0 9.7 1.0 CD A:GLU51 3.0 11.1 1.0 CG A:HIS54 3.1 8.5 1.0 OE1 A:GLU127 3.5 12.5 1.0 CB A:HIS54 3.6 8.7 1.0 O A:HOH2070 3.6 21.6 1.0 OE2 A:GLU51 3.7 13.6 1.0 CA A:GLU51 3.9 10.0 1.0 CG A:GLU18 4.0 9.3 1.0 NE2 A:HIS54 4.1 7.8 1.0 CG A:GLU51 4.1 10.4 1.0 ZN A:ZN1160 4.1 9.9 1.0 CB A:GLU51 4.2 9.6 1.0 CG A:GLU127 4.2 8.4 1.0 CD2 A:HIS54 4.2 8.2 1.0 CG2 A:ILE123 4.3 7.8 1.0 O A:HOH2030 4.5 11.5 1.0 O A:HOH2150 4.5 23.7 1.0 N A:GLU51 4.7 9.8 1.0 O A:GLU51 4.7 10.6 1.0 O A:ASP50 4.7 10.5 0.5 O A:ASP50 4.7 10.3 0.5 C A:GLU51 4.8 9.9 1.0 CB A:GLU18 4.9 9.0 1.0 CE1 A:HIS130 4.9 10.7 1.0 C A:ASP50 5.0 11.2 0.5 C A:ASP50 5.0 10.9 0.5

Zinc binding site 4 out of 4 in the Structure of Apobacterioferritin Y25F 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 Y25F Variant within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1160 b:9.9 occ:1.00 O A:HOH2070 1.9 21.6 1.0 OE1 A:GLU127 2.0 12.5 1.0 OE2 A:GLU51 2.0 13.6 1.0 OE2 A:GLU94 2.0 19.6 1.0 ND1 A:HIS130 2.0 11.5 1.0 OE1 A:GLU94 2.5 19.5 1.0 CD A:GLU94 2.6 12.0 1.0 CD A:GLU51 2.9 11.1 1.0 CE1 A:HIS130 2.9 10.7 1.0 OE1 A:GLU51 3.1 10.3 1.0 CD A:GLU127 3.1 9.7 1.0 CG A:HIS130 3.2 9.5 1.0 OE2 A:GLU127 3.6 12.9 1.0 CB A:HIS130 3.6 8.2 1.0 CG A:GLU94 4.1 10.1 1.0 NE2 A:HIS130 4.1 11.4 1.0 ZN A:ZN1159 4.1 9.3 1.0 O A:HOH2017 4.1 40.4 1.0 CD2 A:HIS130 4.2 10.5 1.0 CG A:GLU51 4.3 10.4 1.0 O A:HOH2113 4.3 13.1 1.0 CG A:GLU127 4.3 8.4 1.0 CA A:GLU127 4.4 6.0 1.0 CB A:GLU127 4.5 6.8 1.0 CZ A:PHE25 4.8 18.8 1.0 O A:HOH2150 4.8 23.7 1.0 CE2 A:PHE25 4.9 19.6 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