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Zinc in PDB 2boq: Crystal Structure of Versatile Peroxidase

Protein crystallography data

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

Other elements in 2boq:

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

Zinc Binding Sites:

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 2boq

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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 2boq

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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 2boq

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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 2boq

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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 2boq

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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 2boq

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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 2boq

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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 2boq

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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

Reference:

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
Page generated: Wed Dec 16 03:18:36 2020

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