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Zinc in PDB 2v8v: Crystal Structure of Mutant R322A of Beta-Alanine Synthase From Saccharomyces Kluyveri

Enzymatic activity of Crystal Structure of Mutant R322A of Beta-Alanine Synthase From Saccharomyces Kluyveri

All present enzymatic activity of Crystal Structure of Mutant R322A of Beta-Alanine Synthase From Saccharomyces Kluyveri:
3.5.1.6;

Protein crystallography data

The structure of Crystal Structure of Mutant R322A of Beta-Alanine Synthase From Saccharomyces Kluyveri, PDB code: 2v8v 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) 45.00 / 2.90
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 77.478, 84.903, 104.848, 67.45, 67.81, 62.75
R / Rfree (%) 19.4 / 24.6

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Mutant R322A of Beta-Alanine Synthase From Saccharomyces Kluyveri (pdb code 2v8v). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of Mutant R322A of Beta-Alanine Synthase From Saccharomyces Kluyveri, PDB code: 2v8v:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 2v8v

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Zinc binding site 1 out of 8 in the Crystal Structure of Mutant R322A of Beta-Alanine Synthase From Saccharomyces Kluyveri


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Mutant R322A of Beta-Alanine Synthase From Saccharomyces Kluyveri within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1455

b:29.2
occ:1.00
 O A:HOH2001 2.0 32.4 1.0
OD1 A:ASP125 2.0 32.8 1.0
NE2 A:HIS114 2.1 31.7 1.0
NE2 A:HIS226 2.1 35.0 1.0
CE1 A:HIS226 2.7 36.1 1.0
CD2 A:HIS114 3.0 33.2 1.0
CE1 A:HIS114 3.1 32.3 1.0
CG A:ASP125 3.2 33.7 1.0
CD2 A:HIS226 3.3 35.5 1.0
OD2 A:ASP125 3.6 35.0 1.0
ZN A:ZN1456 3.7 35.4 1.0
N A:GLY126 3.8 34.2 1.0
ND1 A:HIS226 3.9 36.8 1.0
OE2 A:GLU160 3.9 36.8 1.0
OE1 A:GLU159 4.0 43.2 1.0
CA A:GLY126 4.1 34.1 1.0
CG A:HIS114 4.2 33.2 1.0
ND1 A:HIS397 4.2 37.5 1.0
ND1 A:HIS114 4.2 32.6 1.0
CD A:GLU159 4.2 41.4 1.0
CG A:HIS226 4.2 35.9 1.0
OE2 A:GLU159 4.2 42.1 1.0
C A:ASP125 4.4 34.1 1.0
CB A:ASP125 4.5 33.4 1.0
NE2 A:GLN229 4.6 39.1 1.0
CE1 A:HIS397 4.7 38.7 1.0
CA A:ASP125 4.8 33.9 1.0

Zinc binding site 2 out of 8 in 2v8v

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Zinc binding site 2 out of 8 in the Crystal Structure of Mutant R322A of Beta-Alanine Synthase From Saccharomyces Kluyveri


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Mutant R322A of Beta-Alanine Synthase From Saccharomyces Kluyveri within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1456

b:35.4
occ:1.00
 OE2 A:GLU160 2.0 36.8 1.0
OD2 A:ASP125 2.0 35.0 1.0
O A:HOH2001 2.0 32.4 1.0
NE2 A:HIS421 2.1 34.3 1.0
CD A:GLU160 2.7 36.7 1.0
OE1 A:GLU160 2.8 36.7 1.0
CD2 A:HIS421 3.0 35.8 1.0
CG A:ASP125 3.0 33.7 1.0
CE1 A:HIS421 3.1 35.6 1.0
OD1 A:ASP125 3.3 32.8 1.0
ZN A:ZN1455 3.7 29.2 1.0
NE2 A:GLN229 3.7 39.1 1.0
OE1 A:GLU159 4.1 43.2 1.0
CG A:HIS421 4.1 35.9 1.0
CG A:GLU160 4.1 36.2 1.0
ND1 A:HIS421 4.1 36.8 1.0
NE2 A:HIS114 4.2 31.7 1.0
CE1 A:HIS114 4.2 32.3 1.0
CB A:ASP125 4.3 33.4 1.0
CD A:GLN229 4.8 37.8 1.0
CG A:GLN118 4.8 34.6 1.0
OE2 A:GLU159 4.9 42.1 1.0
CD A:GLU159 4.9 41.4 1.0

Zinc binding site 3 out of 8 in 2v8v

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Zinc binding site 3 out of 8 in the Crystal Structure of Mutant R322A 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 R322A of Beta-Alanine Synthase From Saccharomyces Kluyveri within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1454

b:36.1
occ:1.00
 O B:HOH2001 2.0 36.9 1.0
OD1 B:ASP125 2.0 36.8 1.0
NE2 B:HIS226 2.1 34.6 1.0
NE2 B:HIS114 2.1 32.8 1.0
CE1 B:HIS226 3.0 34.0 1.0
CE1 B:HIS114 3.0 32.5 1.0
CD2 B:HIS226 3.1 34.8 1.0
CD2 B:HIS114 3.1 33.1 1.0
CG B:ASP125 3.2 35.3 1.0
ZN B:ZN1455 3.5 38.5 1.0
OD2 B:ASP125 3.7 36.7 1.0
N B:GLY126 3.8 34.3 1.0
OE2 B:GLU159 4.0 42.3 1.0
ND1 B:HIS397 4.0 37.7 1.0
OE2 B:GLU160 4.0 37.1 1.0
ND1 B:HIS226 4.1 33.5 1.0
ND1 B:HIS114 4.1 33.0 1.0
CA B:GLY126 4.2 34.3 1.0
CG B:HIS226 4.2 34.7 1.0
CD B:GLU159 4.2 41.0 1.0
CG B:HIS114 4.2 33.7 1.0
CE1 B:HIS397 4.3 38.8 1.0
OE1 B:GLU159 4.4 41.8 1.0
C B:ASP125 4.4 34.2 1.0
CB B:ASP125 4.5 34.0 1.0
CA B:ASP125 4.8 34.1 1.0
OE1 B:GLN229 4.8 37.9 1.0
NE2 B:GLN229 4.9 38.4 1.0
CD B:GLU160 4.9 36.2 1.0

Zinc binding site 4 out of 8 in 2v8v

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Zinc binding site 4 out of 8 in the Crystal Structure of Mutant R322A 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 R322A of Beta-Alanine Synthase From Saccharomyces Kluyveri within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1455

b:38.5
occ:1.00
 O B:HOH2001 2.0 36.9 1.0
OD2 B:ASP125 2.0 36.7 1.0
OE2 B:GLU160 2.0 37.1 1.0
NE2 B:HIS421 2.1 35.9 1.0
CG B:ASP125 2.7 35.3 1.0
CD2 B:HIS421 2.8 36.3 1.0
OD1 B:ASP125 2.9 36.8 1.0
CD B:GLU160 2.9 36.2 1.0
OE1 B:GLU160 3.1 36.0 1.0
CE1 B:HIS421 3.2 36.7 1.0
NE2 B:GLN229 3.4 38.4 1.0
ZN B:ZN1454 3.5 36.1 1.0
CB B:ASP125 4.0 34.0 1.0
CG B:HIS421 4.1 36.5 1.0
CE1 B:HIS114 4.2 32.5 1.0
ND1 B:HIS421 4.2 37.0 1.0
CG B:GLU160 4.3 36.4 1.0
NE2 B:HIS114 4.4 32.8 1.0
CD B:GLN229 4.4 37.7 1.0
OE1 B:GLU159 4.6 41.8 1.0
OE1 B:GLN229 4.7 37.9 1.0
NE2 B:HIS226 4.9 34.6 1.0
CG B:GLN118 4.9 35.2 1.0
CE1 B:HIS226 4.9 34.0 1.0

Zinc binding site 5 out of 8 in 2v8v

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Zinc binding site 5 out of 8 in the Crystal Structure of Mutant R322A 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 5 of Crystal Structure of Mutant R322A of Beta-Alanine Synthase From Saccharomyces Kluyveri within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1454

b:34.9
occ:1.00
 O C:HOH2001 2.0 35.5 1.0
OD1 C:ASP125 2.0 36.0 1.0
NE2 C:HIS114 2.1 32.7 1.0
NE2 C:HIS226 2.1 35.4 1.0
CE1 C:HIS114 3.0 32.7 1.0
CE1 C:HIS226 3.0 35.0 1.0
CD2 C:HIS114 3.1 33.1 1.0
CG C:ASP125 3.1 35.2 1.0
CD2 C:HIS226 3.2 35.3 1.0
ZN C:ZN1455 3.6 36.1 1.0
OD2 C:ASP125 3.6 35.6 1.0
OE1 C:GLU159 3.8 42.6 1.0
OE2 C:GLU160 3.8 35.8 1.0
N C:GLY126 3.9 34.3 1.0
CD2 C:HIS397 3.9 38.1 1.0
ND1 C:HIS114 4.1 33.0 1.0
ND1 C:HIS226 4.1 34.5 1.0
CA C:GLY126 4.2 34.3 1.0
CG C:HIS114 4.2 33.6 1.0
CG C:HIS226 4.2 34.8 1.0
CD C:GLU159 4.3 41.5 1.0
NE2 C:HIS397 4.4 39.9 1.0
C C:ASP125 4.5 34.1 1.0
CB C:ASP125 4.5 34.1 1.0
OE2 C:GLU159 4.6 42.4 1.0
OE1 C:GLN229 4.7 38.1 1.0
CA C:ASP125 4.8 34.0 1.0
NE2 C:GLN229 4.8 37.6 1.0
CD C:GLU160 4.9 36.7 1.0

Zinc binding site 6 out of 8 in 2v8v

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Zinc binding site 6 out of 8 in the Crystal Structure of Mutant R322A 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 6 of Crystal Structure of Mutant R322A of Beta-Alanine Synthase From Saccharomyces Kluyveri within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1455

b:36.1
occ:1.00
 OD2 C:ASP125 2.0 35.6 1.0
OE2 C:GLU160 2.0 35.8 1.0
O C:HOH2001 2.0 35.5 1.0
NE2 C:HIS421 2.1 35.1 1.0
CD C:GLU160 2.8 36.7 1.0
CG C:ASP125 2.8 35.2 1.0
CD2 C:HIS421 2.8 35.9 1.0
OE1 C:GLU160 3.0 36.2 1.0
CE1 C:HIS421 3.1 35.5 1.0
OD1 C:ASP125 3.2 36.0 1.0
NE2 C:GLN229 3.4 37.6 1.0
ZN C:ZN1454 3.6 34.9 1.0
CG C:HIS421 4.0 36.4 1.0
CB C:ASP125 4.1 34.1 1.0
ND1 C:HIS421 4.1 36.1 1.0
CG C:GLU160 4.2 36.7 1.0
CE1 C:HIS114 4.2 32.7 1.0
OE1 C:GLU159 4.3 42.6 1.0
CD C:GLN229 4.4 37.2 1.0
NE2 C:HIS114 4.5 32.7 1.0
OE1 C:GLN229 4.6 38.1 1.0
CG C:GLN118 4.9 35.5 1.0
NE2 C:GLN118 4.9 37.0 1.0

Zinc binding site 7 out of 8 in 2v8v

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Zinc binding site 7 out of 8 in the Crystal Structure of Mutant R322A 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 7 of Crystal Structure of Mutant R322A of Beta-Alanine Synthase From Saccharomyces Kluyveri within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1454

b:29.5
occ:1.00
 O D:HOH2001 2.0 31.5 1.0
OD1 D:ASP125 2.0 33.7 1.0
NE2 D:HIS114 2.1 31.4 1.0
NE2 D:HIS226 2.1 34.9 1.0
CE1 D:HIS226 2.9 36.3 1.0
CE1 D:HIS114 3.0 32.1 1.0
CD2 D:HIS114 3.1 32.4 1.0
CG D:ASP125 3.2 34.1 1.0
CD2 D:HIS226 3.2 35.1 1.0
ZN D:ZN1455 3.6 33.9 1.0
OD2 D:ASP125 3.6 34.8 1.0
N D:GLY126 3.7 34.3 1.0
ND1 D:HIS226 4.1 36.0 1.0
CA D:GLY126 4.1 34.2 1.0
ND1 D:HIS397 4.1 38.6 1.0
ND1 D:HIS114 4.1 32.8 1.0
CG D:HIS114 4.2 33.0 1.0
OE1 D:GLU159 4.2 42.0 1.0
OE2 D:GLU160 4.2 37.0 1.0
CG D:HIS226 4.3 35.5 1.0
CD D:GLU159 4.4 40.8 1.0
C D:ASP125 4.4 34.1 1.0
OE2 D:GLU159 4.4 41.9 1.0
CB D:ASP125 4.5 33.5 1.0
CE1 D:HIS397 4.6 39.8 1.0
CA D:ASP125 4.8 33.9 1.0
NE2 D:GLN229 4.9 38.7 1.0
OG D:SER113 5.0 35.0 1.0

Zinc binding site 8 out of 8 in 2v8v

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Zinc binding site 8 out of 8 in the Crystal Structure of Mutant R322A 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 8 of Crystal Structure of Mutant R322A of Beta-Alanine Synthase From Saccharomyces Kluyveri within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1455

b:33.9
occ:1.00
 OD2 D:ASP125 2.0 34.8 1.0
O D:HOH2001 2.0 31.5 1.0
OE2 D:GLU160 2.0 37.0 1.0
NE2 D:HIS421 2.1 34.6 1.0
CD D:GLU160 2.7 36.5 1.0
OE1 D:GLU160 2.7 35.9 1.0
CG D:ASP125 2.9 34.1 1.0
CD2 D:HIS421 2.9 36.0 1.0
OD1 D:ASP125 3.2 33.7 1.0
CE1 D:HIS421 3.2 35.4 1.0
ZN D:ZN1454 3.6 29.5 1.0
NE2 D:GLN229 3.6 38.7 1.0
CE1 D:HIS114 4.0 32.1 1.0
CG D:HIS421 4.1 36.2 1.0
CG D:GLU160 4.2 36.0 1.0
CB D:ASP125 4.2 33.5 1.0
OE1 D:GLU159 4.2 42.0 1.0
ND1 D:HIS421 4.2 36.9 1.0
NE2 D:HIS114 4.3 31.4 1.0
CD D:GLN229 4.7 37.9 1.0
OE1 D:GLN229 4.8 39.5 1.0
CG D:GLN118 5.0 35.0 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: Thu Oct 17 04:11:38 2024

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