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Zinc in PDB 2v8d: Crystal Structure of Mutant E159A of Beta-Alanine Synthase From Saccharomyces Kluyveri

Enzymatic activity of Crystal Structure of Mutant E159A of Beta-Alanine Synthase From Saccharomyces Kluyveri

All present enzymatic activity of Crystal Structure of Mutant E159A of Beta-Alanine Synthase From Saccharomyces Kluyveri:
3.5.1.6;

Protein crystallography data

The structure of Crystal Structure of Mutant E159A of Beta-Alanine Synthase From Saccharomyces Kluyveri, PDB code: 2v8d was solved by S.Lundgren, B.Andersen, J.Piskur, D.Dobritzsch, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.22 / 2.30
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 61.117, 77.143, 108.228, 90.00, 97.12, 90.00
R / Rfree (%) 23 / 27.6

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Mutant E159A of Beta-Alanine Synthase From Saccharomyces Kluyveri (pdb code 2v8d). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Mutant E159A of Beta-Alanine Synthase From Saccharomyces Kluyveri, PDB code: 2v8d:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 2v8d

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Zinc binding site 1 out of 4 in the Crystal Structure of Mutant E159A of Beta-Alanine Synthase From Saccharomyces Kluyveri


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 Mutant E159A of Beta-Alanine Synthase From Saccharomyces Kluyveri within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn500

b:27.5
occ:1.00
OD1 A:ASP125 2.0 29.1 1.0
O A:HOH3001 2.1 13.2 1.0
NE2 A:HIS114 2.1 27.8 1.0
NE2 A:HIS226 2.1 21.2 1.0
O A:HOH2041 2.4 15.5 1.0
CE1 A:HIS226 2.8 19.3 1.0
CE1 A:HIS114 2.9 26.7 1.0
CG A:ASP125 3.2 25.9 1.0
CD2 A:HIS114 3.3 26.1 1.0
CD2 A:HIS226 3.3 19.6 1.0
N A:GLY126 3.4 24.6 1.0
ZN A:ZN501 3.6 12.6 0.3
CA A:GLY126 3.8 23.9 1.0
OD2 A:ASP125 3.8 27.9 1.0
ND1 A:HIS226 4.0 18.2 1.0
ND1 A:HIS114 4.1 25.2 1.0
C A:ASP125 4.1 24.6 1.0
OE2 A:GLU160 4.2 29.6 1.0
CG A:HIS114 4.3 25.5 1.0
CG A:HIS226 4.3 20.1 1.0
O A:HOH2038 4.5 13.6 1.0
ND1 A:HIS397 4.5 23.8 1.0
CB A:ASP125 4.5 25.6 1.0
CA A:ASP125 4.6 25.1 1.0
NE2 A:GLN229 4.7 27.4 1.0
O A:ASP125 4.9 24.7 1.0
OE1 A:GLN229 4.9 24.7 1.0
O A:HOH2011 4.9 4.2 1.0
CD A:GLU160 4.9 30.6 1.0
CE1 A:HIS397 4.9 20.9 1.0

Zinc binding site 2 out of 4 in 2v8d

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Zinc binding site 2 out of 4 in the Crystal Structure of Mutant E159A of Beta-Alanine Synthase From Saccharomyces Kluyveri


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 Mutant E159A of Beta-Alanine Synthase From Saccharomyces Kluyveri within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:12.6
occ:0.30
O A:HOH3001 1.9 13.2 1.0
OE2 A:GLU160 2.1 29.6 1.0
NE2 A:HIS421 2.1 33.5 1.0
OD2 A:ASP125 2.1 27.9 1.0
CD A:GLU160 2.9 30.6 1.0
CG A:ASP125 2.9 25.9 1.0
OE1 A:GLU160 3.0 31.5 1.0
CD2 A:HIS421 3.0 32.9 1.0
CE1 A:HIS421 3.1 33.2 1.0
OD1 A:ASP125 3.1 29.1 1.0
NE2 A:GLN229 3.5 27.4 1.0
ZN A:ZN500 3.6 27.5 1.0
O A:HOH2013 3.9 12.7 1.0
ND1 A:HIS421 4.2 32.4 1.0
CG A:HIS421 4.2 32.6 1.0
CG A:GLU160 4.3 29.8 1.0
CB A:ASP125 4.3 25.6 1.0
CE1 A:HIS114 4.3 26.7 1.0
NE2 A:HIS114 4.5 27.8 1.0
CD A:GLN229 4.6 24.1 1.0
NE2 A:GLN118 4.7 29.9 1.0
OE1 A:GLN229 4.8 24.7 1.0
CG A:GLN118 4.8 27.8 1.0

Zinc binding site 3 out of 4 in 2v8d

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Zinc binding site 3 out of 4 in the Crystal Structure of Mutant E159A of Beta-Alanine Synthase From Saccharomyces Kluyveri


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 Mutant E159A of Beta-Alanine Synthase From Saccharomyces Kluyveri within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn500

b:48.2
occ:1.00
OD1 B:ASP125 2.0 41.2 1.0
NE2 B:HIS226 2.1 37.2 1.0
NE2 B:HIS114 2.1 40.4 1.0
O B:HOH3001 2.4 31.4 1.0
CE1 B:HIS114 2.8 38.4 1.0
CE1 B:HIS226 2.9 34.0 1.0
CD2 B:HIS226 3.2 33.5 1.0
CG B:ASP125 3.2 37.6 1.0
CD2 B:HIS114 3.3 37.5 1.0
N B:GLY126 3.6 35.4 1.0
OD2 B:ASP125 3.7 37.5 1.0
ZN B:ZN501 3.8 33.8 0.3
CA B:GLY126 3.9 34.9 1.0
ND1 B:HIS114 4.0 37.2 1.0
C B:ASP125 4.1 35.8 1.0
ND1 B:HIS226 4.1 32.9 1.0
OE1 B:GLU160 4.1 33.4 1.0
CG B:HIS226 4.3 30.9 1.0
CG B:HIS114 4.3 36.8 1.0
CB B:ASP125 4.4 36.4 1.0
ND1 B:HIS397 4.4 30.4 1.0
O B:HOH2015 4.5 14.7 0.5
CE1 B:HIS397 4.5 30.1 1.0
CA B:ASP125 4.6 36.1 1.0
O B:ASP125 4.6 35.8 1.0
NE2 B:GLN229 4.8 27.5 1.0
OG B:SER113 4.8 34.2 1.0
OE1 B:GLN229 4.8 26.7 1.0
CD B:GLU160 4.8 33.1 1.0

Zinc binding site 4 out of 4 in 2v8d

Go back to Zinc Binding Sites List in 2v8d
Zinc binding site 4 out of 4 in the Crystal Structure of Mutant E159A of Beta-Alanine Synthase From Saccharomyces Kluyveri


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 Mutant E159A of Beta-Alanine Synthase From Saccharomyces Kluyveri within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn501

b:33.8
occ:0.30
OD2 B:ASP125 1.9 37.5 1.0
OE2 B:GLU160 1.9 33.4 1.0
CD B:GLU160 2.7 33.1 1.0
CG B:ASP125 2.8 37.6 1.0
NE2 B:HIS421 2.9 36.3 1.0
OE1 B:GLU160 2.9 33.4 1.0
O B:HOH3001 3.0 31.4 1.0
OD1 B:ASP125 3.1 41.2 1.0
CD2 B:HIS421 3.5 36.4 1.0
ZN B:ZN500 3.8 48.2 1.0
CE1 B:HIS421 3.8 36.8 1.0
NE2 B:GLN229 3.9 27.5 1.0
CB B:ASP125 4.0 36.4 1.0
CG B:GLU160 4.0 33.2 1.0
CE1 B:HIS114 4.1 38.4 1.0
NE2 B:GLN118 4.2 35.6 1.0
CG B:GLN118 4.4 35.2 1.0
CG B:HIS421 4.5 36.1 1.0
NE2 B:HIS114 4.6 40.4 1.0
ND1 B:HIS421 4.7 36.8 1.0
CD B:GLN118 4.9 35.7 1.0
O B:HOH2015 5.0 14.7 0.5
OG B:SER420 5.0 34.0 1.0
CD B:GLN229 5.0 27.2 1.0

Reference:

S.Lundgren, B.Andersen, J.Piskur, D.Dobritzsch. Crystal Structures of Yeast -Alanine Synthase Complexes Reveal the Mode of Substrate Binding and Large Scale Domain Closure Movements. J.Biol.Chem. V. 282 36037 2007.
ISSN: ISSN 0021-9258
PubMed: 17916556
DOI: 10.1074/JBC.M705517200
Page generated: Wed Dec 16 03:54:37 2020

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