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Zinc in PDB 2vl1: Crystal Structure of Beta-Alanine Synthase From Saccharomyces Kluyveri in Complex with A Gly-Gly Peptide

Enzymatic activity of Crystal Structure of Beta-Alanine Synthase From Saccharomyces Kluyveri in Complex with A Gly-Gly Peptide

All present enzymatic activity of Crystal Structure of Beta-Alanine Synthase From Saccharomyces Kluyveri in Complex with A Gly-Gly Peptide:
3.5.1.6;

Protein crystallography data

The structure of Crystal Structure of Beta-Alanine Synthase From Saccharomyces Kluyveri in Complex with A Gly-Gly Peptide, PDB code: 2vl1 was solved by B.Andersen, S.Lundgren, D.Dobritzsch, J.Piskur, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.15
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 49.835, 218.370, 81.499, 90.00, 91.85, 90.00
R / Rfree (%) 20.2 / 26.3

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Beta-Alanine Synthase From Saccharomyces Kluyveri in Complex with A Gly-Gly Peptide (pdb code 2vl1). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Crystal Structure of Beta-Alanine Synthase From Saccharomyces Kluyveri in Complex with A Gly-Gly Peptide, PDB code: 2vl1:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in 2vl1

Go back to Zinc Binding Sites List in 2vl1
Zinc binding site 1 out of 5 in the Crystal Structure of Beta-Alanine Synthase From Saccharomyces Kluyveri in Complex with A Gly-Gly Peptide


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 Beta-Alanine Synthase From Saccharomyces Kluyveri in Complex with A Gly-Gly Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn500

b:19.7
occ:1.00
N A:GLY601 1.9 20.4 1.0
NE2 A:HIS226 2.1 15.1 1.0
OD1 A:ASP125 2.2 21.6 1.0
NE2 A:HIS114 2.3 17.4 1.0
CA A:GLY601 3.0 20.5 1.0
CD2 A:HIS226 3.1 15.3 1.0
CD2 A:HIS114 3.1 16.9 1.0
CE1 A:HIS226 3.1 15.8 1.0
CE1 A:HIS114 3.3 18.0 1.0
CG A:ASP125 3.4 19.2 1.0
N A:GLY126 3.5 17.6 1.0
OE1 A:GLU159 3.8 25.7 1.0
CA A:GLY126 3.8 17.7 1.0
OE2 A:GLU160 3.9 22.9 1.0
OD2 A:ASP125 4.1 17.8 1.0
CD A:GLU159 4.1 23.0 1.0
OE2 A:GLU159 4.1 25.1 1.0
ND1 A:HIS397 4.1 17.2 1.0
C A:ASP125 4.2 17.7 1.0
CG A:HIS226 4.2 16.7 1.0
ND1 A:HIS226 4.2 14.9 1.0
C A:GLY601 4.3 20.5 1.0
CG A:HIS114 4.3 17.9 1.0
CE1 A:HIS397 4.3 17.7 1.0
ND1 A:HIS114 4.4 18.2 1.0
ZN A:ZN501 4.5 28.1 0.3
O A:HOH2145 4.5 20.4 1.0
OG A:SER113 4.6 18.0 1.0
CA A:ASP125 4.6 17.9 1.0
CB A:ASP125 4.6 17.9 1.0
O A:HOH2147 4.8 7.1 1.0
O A:GLY601 4.9 20.8 1.0
O A:ASP125 4.9 17.6 1.0
O A:HOH2146 4.9 10.2 1.0
OE1 A:GLU224 5.0 22.7 1.0

Zinc binding site 2 out of 5 in 2vl1

Go back to Zinc Binding Sites List in 2vl1
Zinc binding site 2 out of 5 in the Crystal Structure of Beta-Alanine Synthase From Saccharomyces Kluyveri in Complex with A Gly-Gly Peptide


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 Beta-Alanine Synthase From Saccharomyces Kluyveri in Complex with A Gly-Gly Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:28.1
occ:0.30
OD2 A:ASP125 2.1 17.8 1.0
OE1 A:GLU160 2.2 20.5 1.0
NE2 A:HIS421 2.3 16.8 1.0
OE2 A:GLU160 2.4 22.9 1.0
O A:GLY601 2.4 20.8 1.0
CD A:GLU160 2.6 21.2 1.0
N A:GLY601 2.9 20.4 1.0
CG A:ASP125 3.1 19.2 1.0
C A:GLY601 3.1 20.5 1.0
CD2 A:HIS421 3.1 17.7 1.0
CE1 A:HIS421 3.3 16.8 1.0
OD1 A:ASP125 3.5 21.6 1.0
CA A:GLY601 3.5 20.5 1.0
NE2 A:GLN229 3.7 20.8 1.0
O A:HOH2072 4.1 5.3 1.0
CG A:GLU160 4.1 18.6 1.0
N A:GLY602 4.2 20.5 1.0
NE2 B:HIS262 4.2 15.9 1.0
NE2 A:GLN118 4.2 16.9 1.0
CG A:HIS421 4.4 18.5 1.0
CB A:ASP125 4.4 17.9 1.0
CD2 B:HIS262 4.4 16.9 1.0
ND1 A:HIS421 4.4 18.1 1.0
ZN A:ZN500 4.5 19.7 1.0
OE1 A:GLU159 4.7 25.7 1.0
CG A:GLN118 4.7 17.1 1.0
CA A:GLY602 4.7 20.0 1.0
CD A:GLN229 4.8 18.8 1.0
CE1 A:HIS114 4.8 18.0 1.0
NE2 A:HIS114 5.0 17.4 1.0
CB A:GLU160 5.0 17.9 1.0
OE1 A:GLN229 5.0 19.2 1.0

Zinc binding site 3 out of 5 in 2vl1

Go back to Zinc Binding Sites List in 2vl1
Zinc binding site 3 out of 5 in the Crystal Structure of Beta-Alanine Synthase From Saccharomyces Kluyveri in Complex with A Gly-Gly Peptide


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 Beta-Alanine Synthase From Saccharomyces Kluyveri in Complex with A Gly-Gly Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn500

b:22.7
occ:1.00
N B:GLY601 1.8 23.5 1.0
NE2 B:HIS114 2.2 13.6 1.0
OD1 B:ASP125 2.2 20.3 1.0
NE2 B:HIS226 2.2 16.0 1.0
CD2 B:HIS114 3.0 14.3 1.0
CD2 B:HIS226 3.2 16.2 1.0
CA B:GLY601 3.2 23.7 1.0
CE1 B:HIS226 3.2 15.6 1.0
CE1 B:HIS114 3.3 14.3 1.0
CG B:ASP125 3.4 19.1 1.0
N B:GLY126 3.5 17.8 1.0
OE1 B:GLU159 3.6 24.1 1.0
CA B:GLY126 3.7 17.7 1.0
OE1 B:GLU160 3.9 23.1 1.0
OD2 B:ASP125 3.9 19.9 1.0
ND1 B:HIS397 4.1 15.8 1.0
CD B:GLU159 4.1 22.2 1.0
C B:ASP125 4.2 17.8 1.0
C B:GLY601 4.2 24.1 1.0
CG B:HIS114 4.2 15.8 1.0
ND1 B:HIS114 4.3 14.9 1.0
ND1 B:HIS226 4.3 14.4 1.0
CG B:HIS226 4.3 15.9 1.0
CE1 B:HIS397 4.3 15.6 1.0
OE2 B:GLU159 4.4 24.1 1.0
O B:HOH2097 4.4 19.4 1.0
OG B:SER113 4.5 18.0 1.0
O B:GLY601 4.5 24.6 1.0
CB B:ASP125 4.6 18.5 1.0
CA B:ASP125 4.6 17.9 1.0
OE1 B:GLU224 4.8 17.0 1.0
O B:ASP125 4.9 17.8 1.0

Zinc binding site 4 out of 5 in 2vl1

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Zinc binding site 4 out of 5 in the Crystal Structure of Beta-Alanine Synthase From Saccharomyces Kluyveri in Complex with A Gly-Gly Peptide


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 Beta-Alanine Synthase From Saccharomyces Kluyveri in Complex with A Gly-Gly Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn500

b:24.0
occ:1.00
N C:GLY601 1.8 19.8 1.0
NE2 C:HIS114 2.2 14.4 1.0
NE2 C:HIS226 2.2 19.7 1.0
OD1 C:ASP125 2.3 18.4 1.0
CD2 C:HIS114 3.1 15.7 1.0
CE1 C:HIS226 3.1 19.4 1.0
CA C:GLY601 3.2 20.5 1.0
CD2 C:HIS226 3.2 18.3 1.0
CE1 C:HIS114 3.2 16.4 1.0
CG C:ASP125 3.4 17.6 1.0
N C:GLY126 3.6 17.8 1.0
CA C:GLY126 3.8 17.7 1.0
OE1 C:GLU159 3.8 24.1 1.0
OD2 C:ASP125 4.0 16.9 1.0
O C:HOH2078 4.0 15.3 1.0
CD C:GLU159 4.1 22.9 1.0
ND1 C:HIS397 4.2 15.8 1.0
C C:GLY601 4.2 20.6 1.0
C C:ASP125 4.2 17.8 1.0
CG C:HIS114 4.2 16.6 1.0
ND1 C:HIS226 4.3 19.0 1.0
ND1 C:HIS114 4.3 15.4 1.0
CG C:HIS226 4.3 18.3 1.0
OE2 C:GLU159 4.3 25.2 1.0
CE1 C:HIS397 4.5 16.2 1.0
O C:GLY601 4.6 21.1 1.0
CB C:ASP125 4.6 18.1 1.0
CA C:ASP125 4.7 17.9 1.0
OG C:SER113 4.7 19.2 1.0
OE1 C:GLU224 4.9 20.6 1.0
O C:ASP125 5.0 17.8 1.0
NE2 C:GLN229 5.0 17.8 1.0
OE1 C:GLN229 5.0 18.3 1.0

Zinc binding site 5 out of 5 in 2vl1

Go back to Zinc Binding Sites List in 2vl1
Zinc binding site 5 out of 5 in the Crystal Structure of Beta-Alanine Synthase From Saccharomyces Kluyveri in Complex with A Gly-Gly Peptide


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 Beta-Alanine Synthase From Saccharomyces Kluyveri in Complex with A Gly-Gly Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn500

b:20.9
occ:1.00
N D:GLY601 1.9 23.4 1.0
NE2 D:HIS114 2.2 16.3 1.0
NE2 D:HIS226 2.3 16.3 1.0
OD1 D:ASP125 2.3 23.6 1.0
CD2 D:HIS114 3.0 16.5 1.0
CA D:GLY601 3.1 23.6 1.0
CE1 D:HIS226 3.2 17.0 1.0
CE1 D:HIS114 3.2 17.4 1.0
CD2 D:HIS226 3.3 16.2 1.0
CG D:ASP125 3.4 19.6 1.0
N D:GLY126 3.6 17.7 1.0
CA D:GLY126 3.8 17.7 1.0
OD2 D:ASP125 4.0 20.6 1.0
OE1 D:GLU160 4.0 20.7 1.0
ND1 D:HIS397 4.1 14.7 1.0
OE1 D:GLU159 4.1 24.9 1.0
O D:HOH2156 4.2 17.5 1.0
C D:ASP125 4.2 17.7 1.0
CG D:HIS114 4.2 16.7 1.0
OE2 D:GLU159 4.3 24.7 1.0
CD D:GLU159 4.3 21.2 1.0
C D:GLY601 4.3 23.7 1.0
ND1 D:HIS114 4.3 17.2 1.0
CE1 D:HIS397 4.3 15.3 1.0
ND1 D:HIS226 4.3 15.1 1.0
CG D:HIS226 4.4 16.5 1.0
OG D:SER113 4.6 19.1 1.0
CB D:ASP125 4.6 18.2 1.0
CA D:ASP125 4.6 18.0 1.0
O D:GLY601 4.8 23.9 1.0
O D:ASP125 4.8 17.5 1.0
NE2 D:GLN229 4.9 19.3 1.0
O D:HOH2082 4.9 12.5 1.0
CD D:GLU160 5.0 20.1 1.0

Reference:

B.Andersen, S.Lundgren, D.Dobritzsch, J.Piskur. A Recruited Protease Is Involved in Catabolism of Pyrimidines. J.Mol.Biol. V. 379 243 2008.
ISSN: ISSN 0022-2836
PubMed: 18448119
DOI: 10.1016/J.JMB.2008.03.073
Page generated: Sat Sep 26 04:06:29 2020
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