Zinc in PDB 2boq: Crystal Structure of Versatile Peroxidase

The structure of Crystal Structure of Versatile Peroxidase, PDB code: 2boq was solved by T.Choinowski, K.Piontek, A.T.Martinez, M.Perez-Boada, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	63.25 / 1.33
Space group	P 43
Cell size a, b, c (Å), α, β, γ (°)	62.799, 62.799, 98.222, 90.00, 90.00, 90.00
R / Rfree (%)	15.9 / 18.2

The structure of Crystal Structure of Versatile Peroxidase also contains other interesting chemical elements:

Arsenic	(As)	1 atom
Manganese	(Mn)	1 atom
Iron	(Fe)	1 atom
Calcium	(Ca)	2 atoms

The binding sites of Zinc atom in the Crystal Structure of Versatile Peroxidase (pdb code 2boq). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of Versatile Peroxidase, PDB code: 2boq:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in the Crystal Structure of Versatile Peroxidase


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 Versatile Peroxidase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1323 b:15.8 occ:1.00 OD2 A:ASP30 1.9 15.3 1.0 OE2 A:GLU37 1.9 18.1 1.0 O A:HOH2376 2.0 19.5 1.0 OD1 A:ASP30 2.7 18.1 1.0 CD A:GLU37 2.7 17.8 1.0 CG A:ASP30 2.7 13.4 1.0 OE1 A:GLU37 2.8 16.7 1.0 O A:HOH2062 3.8 49.5 1.0 CG A:GLU37 4.1 14.3 1.0 CB A:ASP30 4.1 13.3 1.0 O A:HOH2047 4.2 25.7 1.0 O A:LEU28 4.9 15.2 1.0

Zinc binding site 2 out of 8 in the Crystal Structure of Versatile Peroxidase


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 Versatile Peroxidase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1324 b:20.1 occ:1.00 OD2 A:ASP237 2.0 15.7 1.0 O A:HOH2377 2.0 28.2 1.0 O A:HOH2378 2.1 24.5 1.0 CG A:ASP237 2.7 16.3 1.0 OD1 A:ASP237 2.8 17.4 1.0 OD1 A:ASP146 4.1 20.6 1.0 CB A:ASP237 4.2 15.8 1.0 NE2 A:GLN239 4.2 24.3 1.0 O A:HOH2209 4.5 16.5 1.0 CD A:PRO238 4.6 16.1 1.0 CG1 A:VAL145 4.6 14.8 1.0 CB A:VAL145 4.7 13.0 1.0 CG A:GLN239 4.7 23.0 1.0 O A:HOH2077 4.9 30.9 1.0 CG A:ASP146 4.9 18.5 1.0

Zinc binding site 3 out of 8 in the Crystal Structure of Versatile Peroxidase


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 Versatile Peroxidase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1325 b:32.0 occ:1.00 O1 A:CAC1329 1.9 24.7 1.0 ND1 A:HIS136 2.1 27.3 1.0 CE1 A:HIS136 3.0 31.6 1.0 CG A:HIS136 3.1 24.1 1.0 AS A:CAC1329 3.2 13.1 1.0 ZN A:ZN1326 3.3 40.4 1.0 CB A:HIS136 3.5 19.1 1.0 OE1 A:GLU140 3.7 23.7 1.0 CA A:HIS136 3.7 16.4 1.0 O2 A:CAC1329 3.8 24.1 1.0 O A:HOH2195 3.9 22.3 1.0 ZN A:ZN1327 4.0 24.6 1.0 NE2 A:HIS136 4.2 30.3 1.0 C1 A:CAC1329 4.2 25.2 1.0 CD2 A:HIS136 4.2 27.7 1.0 CD A:GLU140 4.4 23.0 1.0 OE2 A:GLU140 4.5 22.0 1.0 C A:HIS136 4.7 14.6 1.0 O A:HOH2198 4.7 39.8 1.0 N A:HIS136 4.7 15.5 1.0 O A:HIS136 4.8 16.2 1.0 C2 A:CAC1329 4.8 22.8 1.0 O A:HOH2188 4.9 22.0 1.0

Zinc binding site 4 out of 8 in the Crystal Structure of Versatile Peroxidase


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 Versatile Peroxidase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1326 b:40.4 occ:1.00 ZN A:ZN1327 3.2 24.6 1.0 ZN A:ZN1325 3.3 32.0 1.0 OE1 A:GLU140 3.5 23.7 1.0 O2 A:CAC1329 3.9 24.1 1.0 O A:HOH2198 4.1 39.8 1.0 O A:HOH2268 4.3 42.6 1.0 O1 A:CAC1329 4.3 24.7 1.0 CE1 A:PHE142 4.4 16.8 1.0 CD A:GLU140 4.5 23.0 1.0 OD1 A:ASP143 4.7 15.8 1.0 OE2 A:GLU140 4.7 22.0 1.0 AS A:CAC1329 4.8 13.1 1.0 ND1 A:HIS136 4.8 27.3 1.0

Zinc binding site 5 out of 8 in the Crystal Structure of Versatile Peroxidase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Versatile Peroxidase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1327 b:24.6 occ:1.00 OE1 A:GLU140 1.9 23.7 1.0 O2 A:CAC1329 1.9 24.1 1.0 OD1 A:ASP143 2.0 15.8 1.0 CG A:ASP143 2.7 14.8 1.0 OD2 A:ASP143 2.7 15.2 1.0 CD A:GLU140 3.1 23.0 1.0 ZN A:ZN1326 3.2 40.4 1.0 AS A:CAC1329 3.2 13.1 1.0 O1 A:CAC1329 3.5 24.7 1.0 CG A:GLU140 3.8 17.8 1.0 CB A:GLU140 4.0 12.8 1.0 CE1 A:PHE142 4.0 16.8 1.0 ZN A:ZN1325 4.0 32.0 1.0 OE2 A:GLU140 4.1 22.0 1.0 CB A:ASP143 4.1 13.4 1.0 C2 A:CAC1329 4.4 22.8 1.0 CD1 A:PHE142 4.5 16.4 1.0 N A:GLU140 4.7 12.2 1.0 CA A:ASP143 4.7 12.9 1.0 CZ A:PHE142 4.8 16.9 1.0 C1 A:CAC1329 4.8 25.2 1.0 CA A:GLU140 4.9 12.5 1.0 O A:HOH2203 5.0 18.5 1.0

Zinc binding site 6 out of 8 in the Crystal Structure of Versatile Peroxidase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Versatile Peroxidase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1358 b:15.6 occ:1.00 O A:HOH2379 1.9 31.8 1.0 O A:HOH2380 2.1 45.3 1.0 NE2 A:HIS293 2.2 31.7 1.0 OD2 A:ASP318 2.9 42.9 1.0 CD2 A:HIS293 3.1 30.7 1.0 CE1 A:HIS293 3.1 30.2 1.0 O A:HOH2001 3.8 44.2 1.0 CG A:ASP318 3.8 46.9 1.0 OG A:SER188 4.2 17.6 1.0 ND1 A:HIS293 4.2 31.2 1.0 CG A:HIS293 4.3 28.2 1.0 CB A:ASP318 4.3 46.0 1.0 OD1 A:ASP318 4.7 49.8 1.0 CB A:SER188 4.8 14.7 1.0 CA A:PRO295 4.9 25.4 1.0

Zinc binding site 7 out of 8 in the Crystal Structure of Versatile Peroxidase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of Versatile Peroxidase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1359 b:23.6 occ:1.00 O A:HOH2381 2.0 32.4 1.0 ND1 A:HIS95 2.3 21.2 1.0 O A:HOH2024 3.1 31.8 1.0 CG A:HIS95 3.3 20.9 1.0 CE1 A:HIS95 3.3 23.0 1.0 CA A:HIS95 3.5 21.8 1.0 CB A:HIS95 3.5 20.6 1.0 N A:ASN96 4.2 24.4 1.0 O A:LYS94 4.3 25.3 1.0 C A:HIS95 4.3 22.6 1.0 NE2 A:HIS95 4.4 23.7 1.0 CD2 A:HIS95 4.4 19.0 1.0 CG1 A:ILE20 4.4 16.1 1.0 N A:HIS95 4.5 21.5 1.0 C A:LYS94 4.8 23.7 1.0 CD1 A:ILE20 4.9 16.6 1.0 CB A:PRO19 5.0 19.2 1.0

Zinc binding site 8 out of 8 in the Crystal Structure of Versatile Peroxidase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of Versatile Peroxidase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1360 b:26.6 occ:1.00 O A:HOH2384 1.9 42.3 1.0 O A:HOH2383 2.1 34.0 1.0 O A:HOH2177 2.3 28.0 1.0 O A:HOH2382 2.8 41.2 1.0 OD1 A:ASP128 4.0 20.1 1.0 OD2 A:ASP128 4.1 27.6 1.0 O A:HOH2151 4.4 51.0 1.0 CG A:ASP128 4.5 20.4 1.0 O A:HOH2149 4.6 49.1 1.0 O A:ILE97 4.6 18.4 1.0 OD1 A:ASN96 4.7 39.8 1.0 C A:ILE97 4.9 16.3 1.0 CA A:SER98 5.0 14.0 1.0 O A:HOH2182 5.0 21.6 1.0

M.Perez-Boada, F.J.Ruiz-Duenas, R.Pogni, R.Basosi, T.Choinowski, M.J.Martinez, K.Piontek, A.T.Martinez. Versatile Peroxidase Oxidation of High Redox Potential Aromatic Compounds: Site-Directed Mutagenesis, Spectroscopic and Crystallographic Investigation of Three Long-Range Electron Transfer Pathways. J.Mol.Biol. V. 354 385 2005.
ISSN: ISSN 0022-2836
PubMed: 16246366
DOI: 10.1016/J.JMB.2005.09.047