Atomistry » Zinc » PDB 2vh5-2vqw » 2vl1
Atomistry »
  Zinc »
    PDB 2vh5-2vqw »
      2vl1 »

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

Go back to Zinc Binding Sites List in 2vl1
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: Thu Oct 17 04:20:57 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy