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Zinc in PDB 3fkg: Crystal Structure Analysis of Fungal Versatile Peroxidase From Pleurotus Eryngii

Enzymatic activity of Crystal Structure Analysis of Fungal Versatile Peroxidase From Pleurotus Eryngii

All present enzymatic activity of Crystal Structure Analysis of Fungal Versatile Peroxidase From Pleurotus Eryngii:
1.11.1.16;

Protein crystallography data

The structure of Crystal Structure Analysis of Fungal Versatile Peroxidase From Pleurotus Eryngii, PDB code: 3fkg was solved by K.Piontek, A.T.Martinez, T.Choinowski, D.A.Plattner, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.90 / 1.81
Space group P 43
Cell size a, b, c (Å), α, β, γ (°) 62.683, 62.683, 98.217, 90.00, 90.00, 90.00
R / Rfree (%) 15.2 / 20.1

Zinc Binding Sites:

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

Zinc binding site 1 out of 7 in 3fkg

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Zinc binding site 1 out of 7 in the Crystal Structure Analysis of Fungal Versatile Peroxidase From Pleurotus Eryngii


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure Analysis of Fungal Versatile Peroxidase From Pleurotus Eryngii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn332

b:17.2
occ:0.80
O A:HOH404 1.9 19.2 1.0
OE2 A:GLU37 2.0 23.7 1.0
OD2 A:ASP30 2.0 20.2 1.0
CD A:GLU37 2.6 18.2 1.0
OE1 A:GLU37 2.6 19.0 1.0
CG A:ASP30 2.7 21.7 1.0
OD1 A:ASP30 2.7 21.8 1.0
O A:HOH610 3.8 34.5 1.0
OE2 A:GLU36 4.0 35.2 1.0
CG A:GLU37 4.1 20.6 1.0
O A:HOH563 4.2 33.1 1.0
CB A:ASP30 4.2 20.3 1.0
O A:HOH624 4.2 33.5 1.0
CD A:GLU36 4.9 36.7 1.0
O A:LEU28 4.9 20.7 1.0

Zinc binding site 2 out of 7 in 3fkg

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Zinc binding site 2 out of 7 in the Crystal Structure Analysis of Fungal Versatile Peroxidase From Pleurotus Eryngii


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure Analysis of Fungal Versatile Peroxidase From Pleurotus Eryngii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn333

b:18.2
occ:0.70
O A:HOH406 1.9 27.1 1.0
OD2 A:ASP237 2.0 19.8 1.0
O A:HOH405 2.2 25.8 0.7
CG A:ASP237 2.8 20.3 1.0
OD1 A:ASP237 2.9 22.3 1.0
NE2 A:GLN239 4.1 27.5 1.0
CB A:ASP237 4.2 21.0 1.0
OD1 A:ASP146 4.2 25.0 1.0
O A:HOH401 4.3 20.1 0.5
O A:HOH475 4.4 22.2 1.0
CG1 A:VAL145 4.6 17.6 1.0
CG A:GLN239 4.7 29.2 1.0
O A:HOH488 4.7 8.7 0.5
O A:HOH509 4.7 32.8 1.0
CB A:VAL145 4.7 19.9 1.0
CD A:PRO238 4.7 21.8 1.0
CD A:GLN239 4.9 30.2 1.0
O A:HOH407 5.0 42.2 1.0
O A:HOH609 5.0 12.4 0.5

Zinc binding site 3 out of 7 in 3fkg

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Zinc binding site 3 out of 7 in the Crystal Structure Analysis of Fungal Versatile Peroxidase From Pleurotus Eryngii


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure Analysis of Fungal Versatile Peroxidase From Pleurotus Eryngii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn334

b:15.3
occ:0.45
OE1 A:GLU140 1.9 28.4 1.0
O1 A:CAC342 2.0 19.6 0.5
O2 A:CAC343 2.0 24.3 0.4
OD1 A:ASP143 2.0 24.3 1.0
CG A:ASP143 2.7 21.3 1.0
OD2 A:ASP143 2.8 21.4 1.0
CD A:GLU140 3.1 24.1 1.0
AS A:CAC343 3.2 27.6 0.4
AS A:CAC342 3.2 17.5 0.5
O2 A:CAC342 3.5 21.2 0.5
O A:HOH418 3.5 37.9 1.0
O1 A:CAC343 3.6 33.4 0.4
C2 A:CAC343 3.7 23.5 0.4
CG A:GLU140 3.8 23.1 1.0
O A:HOH484 3.9 32.8 0.5
CB A:GLU140 3.9 21.3 1.0
CE1 A:PHE142 4.0 22.0 1.0
ZN A:ZN338 4.0 27.3 0.6
OE2 A:GLU140 4.1 23.4 1.0
CB A:ASP143 4.2 20.1 1.0
C1 A:CAC342 4.2 19.5 0.5
O A:HOH413 4.5 48.0 0.6
CD1 A:PHE142 4.6 21.1 1.0
O A:HOH374 4.7 37.2 0.5
CZ A:PHE142 4.7 22.5 1.0
N A:GLU140 4.7 16.1 1.0
CA A:ASP143 4.8 22.7 1.0
C2 A:CAC342 4.8 19.6 0.5
C1 A:CAC343 4.9 30.1 0.4
CA A:GLU140 4.9 19.0 1.0

Zinc binding site 4 out of 7 in 3fkg

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Zinc binding site 4 out of 7 in the Crystal Structure Analysis of Fungal Versatile Peroxidase From Pleurotus Eryngii


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure Analysis of Fungal Versatile Peroxidase From Pleurotus Eryngii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn336

b:28.6
occ:0.50
ND1 A:HIS95 2.1 29.6 1.0
O A:HOH411 2.1 24.6 1.0
O A:HOH412 2.1 25.2 0.5
O A:HOH410 2.3 29.5 0.5
CE1 A:HIS95 3.0 30.9 1.0
CG A:HIS95 3.1 31.5 1.0
CB A:HIS95 3.4 28.8 1.0
CA A:HIS95 3.5 25.8 1.0
NE2 A:HIS95 4.2 32.3 1.0
CD2 A:HIS95 4.2 32.5 1.0
N A:ASN96 4.2 30.9 1.0
C A:HIS95 4.4 28.0 1.0
O A:LYS94 4.4 29.6 1.0
CG1 A:ILE20 4.4 21.1 1.0
N A:HIS95 4.5 24.9 1.0
CD1 A:ILE20 4.7 20.3 1.0
C A:LYS94 4.9 30.3 1.0

Zinc binding site 5 out of 7 in 3fkg

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Zinc binding site 5 out of 7 in the Crystal Structure Analysis of Fungal Versatile Peroxidase From Pleurotus Eryngii


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure Analysis of Fungal Versatile Peroxidase From Pleurotus Eryngii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn337

b:17.9
occ:0.33
O1D A:HEM350 2.0 25.0 1.0
OD2 A:ASP175 2.6 37.3 1.0
CGD A:HEM350 3.0 19.1 1.0
CG A:ASP175 3.3 33.6 1.0
O2D A:HEM350 3.3 15.8 1.0
OD1 A:ASP175 3.3 31.3 1.0
FE A:FE340 3.7 32.8 0.3
CG A:GLU40 3.8 23.9 1.0
O A:HOH458 3.9 24.4 0.7
OE2 A:GLU40 4.0 35.5 1.0
O A:HOH414 4.1 25.7 0.3
CD A:GLU40 4.2 30.2 1.0
ZN A:ZN339 4.3 24.1 0.3
CBD A:HEM350 4.5 16.6 1.0
O A:HOH569 4.5 8.5 0.3
CB A:ASP175 4.6 26.4 1.0
O A:ALA173 4.6 17.2 1.0
CG A:GLU36 4.8 30.2 1.0
OE1 A:GLU83 4.9 36.0 1.0

Zinc binding site 6 out of 7 in 3fkg

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Zinc binding site 6 out of 7 in the Crystal Structure Analysis of Fungal Versatile Peroxidase From Pleurotus Eryngii


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure Analysis of Fungal Versatile Peroxidase From Pleurotus Eryngii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn338

b:27.3
occ:0.60
O2 A:CAC342 2.0 21.2 0.5
O1 A:CAC343 2.0 33.4 0.4
ND1 A:HIS136 2.1 30.8 1.0
O A:HOH413 2.2 48.0 0.6
CE1 A:HIS136 3.0 35.5 1.0
CG A:HIS136 3.1 29.0 1.0
AS A:CAC343 3.2 27.6 0.4
AS A:CAC342 3.3 17.5 0.5
C2 A:CAC343 3.4 23.5 0.4
CB A:HIS136 3.5 26.7 1.0
OE1 A:GLU140 3.6 28.4 1.0
O1 A:CAC342 3.7 19.6 0.5
CA A:HIS136 3.8 22.9 1.0
O A:HOH461 3.9 29.6 1.0
C2 A:CAC342 4.0 19.6 0.5
ZN A:ZN334 4.0 15.3 0.5
NE2 A:HIS136 4.1 33.9 1.0
O2 A:CAC343 4.2 24.3 0.4
CD2 A:HIS136 4.2 30.8 1.0
CD A:GLU140 4.3 24.1 1.0
OE2 A:GLU140 4.4 23.4 1.0
N A:HIS136 4.7 20.9 1.0
C A:HIS136 4.7 22.5 1.0
O A:HOH554 4.8 25.8 1.0
C1 A:CAC343 4.8 30.1 0.4
O A:HIS136 4.8 23.3 1.0
C1 A:CAC342 4.9 19.5 0.5

Zinc binding site 7 out of 7 in 3fkg

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Zinc binding site 7 out of 7 in the Crystal Structure Analysis of Fungal Versatile Peroxidase From Pleurotus Eryngii


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure Analysis of Fungal Versatile Peroxidase From Pleurotus Eryngii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn339

b:24.1
occ:0.33
OE1 A:GLU36 2.0 40.6 1.0
OE2 A:GLU83 2.0 37.5 1.0
OE1 A:GLU83 2.0 36.0 1.0
OE2 A:GLU40 2.0 35.5 1.0
CD A:GLU83 2.3 35.8 1.0
CD A:GLU40 2.7 30.2 1.0
CD A:GLU36 3.0 36.7 1.0
OE1 A:GLU40 3.0 35.8 1.0
FE A:FE340 3.3 32.8 0.3
CG A:GLU36 3.3 30.2 1.0
O A:HOH625 3.6 46.2 1.0
CG A:GLU83 3.8 33.5 1.0
CG A:GLU40 4.0 23.9 1.0
OE2 A:GLU36 4.1 35.2 1.0
ZN A:ZN337 4.3 17.9 0.3
OD2 A:ASP175 4.5 37.3 1.0
CB A:GLU83 4.7 27.3 1.0
CB A:GLU36 4.8 22.1 1.0
O A:HOH542 4.9 21.0 1.0

Reference:

K.Piontek, T.Choinowski, M.Perez-Boada, F.J.Ruiz-Duenas, M.J.Martinez, D.A.Plattner, A.T.Martinez. Structural and Site-Directed Mutagenesis Study of Versatile Peroxidase Oxidizing Both Mn(II) and Aromatic Substrates To Be Published.
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