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Zinc in PDB 4bll: Crystal Structure of Fungal Versatile Peroxidase I From Pleurotus Ostreatus - Crystal Form II

Enzymatic activity of Crystal Structure of Fungal Versatile Peroxidase I From Pleurotus Ostreatus - Crystal Form II

All present enzymatic activity of Crystal Structure of Fungal Versatile Peroxidase I From Pleurotus Ostreatus - Crystal Form II:
1.11.1.16;

Protein crystallography data

The structure of Crystal Structure of Fungal Versatile Peroxidase I From Pleurotus Ostreatus - Crystal Form II, PDB code: 4bll was solved by F.J.Medrano, A.Romero, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.477 / 1.10
Space group P 43
Cell size a, b, c (Å), α, β, γ (°) 62.900, 62.900, 99.170, 90.00, 90.00, 90.00
R / Rfree (%) 12.32 / 13.56

Other elements in 4bll:

The structure of Crystal Structure of Fungal Versatile Peroxidase I From Pleurotus Ostreatus - Crystal Form II also contains other interesting chemical elements:

Iron (Fe) 1 atom
Calcium (Ca) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Fungal Versatile Peroxidase I From Pleurotus Ostreatus - Crystal Form II (pdb code 4bll). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure of Fungal Versatile Peroxidase I From Pleurotus Ostreatus - Crystal Form II, PDB code: 4bll:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 4bll

Go back to Zinc Binding Sites List in 4bll
Zinc binding site 1 out of 3 in the Crystal Structure of Fungal Versatile Peroxidase I From Pleurotus Ostreatus - Crystal Form II


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 Fungal Versatile Peroxidase I From Pleurotus Ostreatus - Crystal Form II within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1320

b:16.4
occ:1.00
 O A:HOH2320 1.9 25.5 1.0
OD2 A:ASP238 1.9 13.7 1.0
O A:HOH2226 2.4 27.7 1.0
CG A:ASP238 2.7 12.1 1.0
OD1 A:ASP238 2.8 12.2 1.0
HE21 A:GLN240 3.3 29.1 1.0
HD2 A:PRO239 3.7 16.8 1.0
HG3 A:GLN240 3.7 22.8 1.0
HB A:VAL146 4.0 9.3 1.0
NE2 A:GLN240 4.1 24.3 1.0
OD1 A:ASP147 4.1 15.4 1.0
O A:HOH2221 4.2 9.4 1.0
O A:HOH2321 4.2 9.3 1.0
CB A:ASP238 4.2 11.6 1.0
HG12 A:VAL146 4.2 11.4 1.0
O A:HOH2225 4.4 23.9 1.0
HB2 A:ASP238 4.4 13.9 1.0
H A:GLN240 4.4 14.3 1.0
HB2 A:GLN240 4.6 18.0 1.0
HE22 A:GLN240 4.6 29.1 1.0
CG A:GLN240 4.6 19.0 1.0
HG13 A:VAL146 4.6 11.4 1.0
CD A:PRO239 4.6 14.0 1.0
HB3 A:ASP238 4.7 13.9 1.0
CG1 A:VAL146 4.7 9.5 1.0
CB A:VAL146 4.8 7.8 1.0
HA A:ASP238 4.8 11.0 1.0
CD A:GLN240 4.9 23.5 1.0
CG A:ASP147 4.9 13.2 1.0
HG22 A:VAL146 4.9 10.8 1.0

Zinc binding site 2 out of 3 in 4bll

Go back to Zinc Binding Sites List in 4bll
Zinc binding site 2 out of 3 in the Crystal Structure of Fungal Versatile Peroxidase I From Pleurotus Ostreatus - Crystal Form II


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 Fungal Versatile Peroxidase I From Pleurotus Ostreatus - Crystal Form II within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1321

b:9.6
occ:1.00
 OE2 A:GLU38 1.9 10.1 1.0
OD2 A:ASP31 2.0 9.4 1.0
O A:HOH2047 2.1 11.0 1.0
OD1 A:ASP31 2.6 11.3 1.0
CG A:ASP31 2.6 9.6 1.0
CD A:GLU38 2.7 8.3 1.0
OE1 A:GLU38 2.8 8.8 1.0
O A:HOH2069 3.8 16.4 1.0
OE1 A:GLU37 3.9 15.1 1.0
HB3 A:GLU37 4.0 12.7 1.0
CB A:ASP31 4.1 9.3 1.0
O A:HOH2063 4.1 16.3 1.0
O A:HOH2046 4.1 16.8 1.0
CG A:GLU38 4.2 8.5 1.0
HB2 A:ASP31 4.4 11.2 1.0
O A:HOH2048 4.4 26.9 1.0
HG2 A:GLU38 4.4 10.2 1.0
HG3 A:GLU38 4.5 10.2 1.0
O A:HOH2067 4.5 16.6 1.0
HB3 A:ASP31 4.5 11.2 1.0
H A:GLU38 4.6 8.0 1.0
O A:LEU29 4.9 9.1 1.0
CB A:GLU37 5.0 10.6 1.0
CD A:GLU37 5.0 13.8 1.0

Zinc binding site 3 out of 3 in 4bll

Go back to Zinc Binding Sites List in 4bll
Zinc binding site 3 out of 3 in the Crystal Structure of Fungal Versatile Peroxidase I From Pleurotus Ostreatus - Crystal Form II


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 Fungal Versatile Peroxidase I From Pleurotus Ostreatus - Crystal Form II within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1322

b:16.3
occ:1.00
 OE2 A:GLU41 1.9 15.2 1.0
O A:HOH2065 1.9 27.1 1.0
OE2 A:GLU37 1.9 16.4 1.0
OE1 A:GLU84 2.1 21.1 1.0
OE2 A:GLU84 2.6 17.2 1.0
O A:HOH2064 2.6 21.2 1.0
CD A:GLU84 2.6 16.1 1.0
CD A:GLU41 2.8 14.1 1.0
CD A:GLU37 3.0 13.8 1.0
OE1 A:GLU41 3.0 17.9 1.0
HG3 A:GLU37 3.1 15.2 1.0
HG2 A:GLU37 3.3 15.2 1.0
CG A:GLU37 3.4 12.7 1.0
O A:HOH2066 3.4 27.2 1.0
OE1 A:GLU37 4.1 15.1 1.0
CG A:GLU84 4.1 12.1 1.0
O A:HOH2072 4.1 19.0 1.0
CG A:GLU41 4.2 9.6 1.0
O A:HOH2139 4.3 34.7 1.0
HG2 A:GLU41 4.3 11.6 1.0
HG2 A:GLU84 4.4 14.5 1.0
HB3 A:GLU84 4.4 12.8 1.0
HG3 A:GLU41 4.4 11.6 1.0
OD2 A:ASP176 4.5 21.7 1.0
HG3 A:GLU84 4.7 14.5 1.0
O A:HOH2140 4.7 15.1 1.0
CB A:GLU84 4.8 10.6 1.0
CB A:GLU37 4.9 10.6 1.0

Reference:

E.Fernandez-Fueyo, F.J.Ruiz-Duenas, M.J.Martinez, A.Romero, K.E.Hammel, F.J.Medrano, A.T.Martinez. Ligninolytic Peroxidase Genes in the Oyster Mushroom Genome: Heterologous Expression, Molecular Structure, Catalytic and Stability Properties, and Lignin-Degrading Ability. Biotechnol.Biofuels V. 7 2 2014.
ISSN: ISSN 1754-6834
PubMed: 24387130
DOI: 10.1186/1754-6834-7-2
Page generated: Sat Oct 26 19:50:36 2024

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