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Zinc in PDB 2v8g: Crystal Structure of Beta-Alanine Synthase From Saccharomyces Kluyveri in Complex with the Product Beta- Alanine

Enzymatic activity of Crystal Structure of Beta-Alanine Synthase From Saccharomyces Kluyveri in Complex with the Product Beta- Alanine

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

Protein crystallography data

The structure of Crystal Structure of Beta-Alanine Synthase From Saccharomyces Kluyveri in Complex with the Product Beta- Alanine, PDB code: 2v8g 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) 19.84 / 2.5
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.100, 217.300, 81.600, 90.00, 91.90, 90.00
R / Rfree (%) 18.9 / 23.1

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Beta-Alanine Synthase From Saccharomyces Kluyveri in Complex with the Product Beta- Alanine (pdb code 2v8g). 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 Beta-Alanine Synthase From Saccharomyces Kluyveri in Complex with the Product Beta- Alanine, PDB code: 2v8g:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 2v8g

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Zinc binding site 1 out of 8 in the Crystal Structure of Beta-Alanine Synthase From Saccharomyces Kluyveri in Complex with the Product Beta- Alanine


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 the Product Beta- Alanine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn500

b:38.2
occ:1.00
 OD1 A:ASP125 2.2 28.9 1.0
NE2 A:HIS226 2.2 23.9 1.0
O A:HOH2077 2.3 12.8 1.0
NE2 A:HIS114 2.4 20.9 1.0
O A:HOH3001 2.4 34.6 1.0
CE1 A:HIS226 3.1 24.4 1.0
CE1 A:HIS114 3.3 21.9 1.0
CD2 A:HIS226 3.3 23.5 1.0
CG A:ASP125 3.3 28.1 1.0
CD2 A:HIS114 3.4 21.8 1.0
ZN A:ZN501 3.5 54.5 1.0
OE2 A:GLU159 3.8 37.0 1.0
N A:GLY126 3.8 25.1 1.0
OD2 A:ASP125 3.9 30.9 1.0
OE1 A:GLU159 4.0 35.4 1.0
ND1 A:HIS397 4.1 25.3 1.0
CD A:GLU159 4.1 33.4 1.0
CA A:GLY126 4.2 24.9 1.0
ND1 A:HIS226 4.2 24.0 1.0
OE2 A:GLU160 4.3 32.4 1.0
C A:ASP125 4.3 25.2 1.0
OE1 A:GLN229 4.3 29.4 1.0
CG A:HIS226 4.3 24.5 1.0
CE1 A:HIS397 4.4 24.9 1.0
ND1 A:HIS114 4.4 23.2 1.0
CG A:HIS114 4.5 23.3 1.0
CB A:ASP125 4.6 25.8 1.0
O A:HOH2030 4.6 15.9 1.0
CA A:ASP125 4.7 25.6 1.0
NE2 A:GLN229 4.7 27.8 1.0
CD A:GLN229 4.8 27.1 1.0
N A:BAL600 4.8 41.4 1.0
O A:ASP125 5.0 25.2 1.0
CD A:GLU160 5.0 30.6 1.0

Zinc binding site 2 out of 8 in 2v8g

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Zinc binding site 2 out of 8 in the Crystal Structure of Beta-Alanine Synthase From Saccharomyces Kluyveri in Complex with the Product Beta- Alanine


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 the Product Beta- Alanine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:54.5
occ:1.00
 OD2 A:ASP125 2.0 30.9 1.0
OE2 A:GLU160 2.4 32.4 1.0
NE2 A:HIS421 2.5 23.9 1.0
OE1 A:GLU160 2.7 32.4 1.0
O A:HOH3001 2.8 34.6 1.0
CG A:ASP125 2.8 28.1 1.0
CD A:GLU160 2.9 30.6 1.0
OD1 A:ASP125 3.0 28.9 1.0
CD2 A:HIS421 3.3 24.0 1.0
ZN A:ZN500 3.5 38.2 1.0
CE1 A:HIS421 3.6 23.6 1.0
NE2 A:GLN229 3.7 27.8 1.0
N A:BAL600 3.8 41.4 1.0
O A:HOH2020 4.0 5.6 1.0
CB A:ASP125 4.2 25.8 1.0
CE1 A:HIS114 4.4 21.9 1.0
CG A:GLU160 4.4 28.7 1.0
CG A:HIS421 4.5 24.4 1.0
NE2 B:HIS262 4.5 28.1 1.0
OE1 A:GLN229 4.5 29.4 1.0
CD A:GLN229 4.5 27.1 1.0
CD2 B:HIS262 4.5 28.1 1.0
NE2 A:GLN118 4.5 20.5 1.0
NE2 A:HIS114 4.6 20.9 1.0
OE1 A:GLU159 4.6 35.4 1.0
ND1 A:HIS421 4.6 23.6 1.0
CB A:BAL600 4.9 41.3 1.0
CG A:GLN118 5.0 24.1 1.0

Zinc binding site 3 out of 8 in 2v8g

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Zinc binding site 3 out of 8 in the Crystal Structure of Beta-Alanine Synthase From Saccharomyces Kluyveri in Complex with the Product Beta- Alanine


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 the Product Beta- Alanine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn500

b:38.8
occ:1.00
 NE2 B:HIS114 2.2 22.0 1.0
OD1 B:ASP125 2.2 29.0 1.0
NE2 B:HIS226 2.3 23.3 1.0
O B:HOH3001 2.4 22.4 1.0
CE1 B:HIS226 2.9 23.8 1.0
CD2 B:HIS114 3.2 21.9 1.0
CE1 B:HIS114 3.2 21.2 1.0
CG B:ASP125 3.4 27.1 1.0
CD2 B:HIS226 3.5 22.8 1.0
OE1 B:GLU159 3.5 32.0 1.0
ZN B:ZN501 3.7 58.9 1.0
N B:GLY126 3.8 25.1 1.0
OD2 B:ASP125 3.9 29.3 1.0
CD B:GLU159 4.0 31.6 1.0
OE2 B:GLU160 4.0 30.6 1.0
CA B:GLY126 4.1 24.9 1.0
ND1 B:HIS226 4.1 24.2 1.0
OE2 B:GLU159 4.2 34.2 1.0
ND1 B:HIS397 4.2 24.3 1.0
ND1 B:HIS114 4.3 21.2 1.0
C B:ASP125 4.3 25.4 1.0
CG B:HIS114 4.3 22.5 1.0
CG B:HIS226 4.4 23.9 1.0
O B:HOH2013 4.6 21.4 1.0
CE1 B:HIS397 4.6 24.3 1.0
CB B:ASP125 4.6 25.8 1.0
NE2 B:GLN229 4.7 25.0 1.0
CA B:ASP125 4.7 25.5 1.0
OE1 B:GLN229 4.8 25.7 1.0
OG B:SER113 5.0 27.7 1.0

Zinc binding site 4 out of 8 in 2v8g

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Zinc binding site 4 out of 8 in the Crystal Structure of Beta-Alanine Synthase From Saccharomyces Kluyveri in Complex with the Product Beta- Alanine


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 the Product Beta- Alanine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn501

b:58.9
occ:1.00
 OD2 B:ASP125 2.0 29.3 1.0
NE2 B:HIS421 2.2 24.6 1.0
OE2 B:GLU160 2.6 30.6 1.0
O B:HOH3001 2.6 22.4 1.0
OE1 B:GLU160 2.8 31.4 1.0
CG B:ASP125 2.9 27.1 1.0
CD B:GLU160 3.1 29.9 1.0
CD2 B:HIS421 3.1 23.1 1.0
OD1 B:ASP125 3.2 29.0 1.0
CE1 B:HIS421 3.2 24.1 1.0
NE2 B:GLN229 3.6 25.0 1.0
ZN B:ZN500 3.7 38.8 1.0
NE2 A:HIS262 4.2 29.2 1.0
CG B:HIS421 4.3 24.2 1.0
CB B:ASP125 4.3 25.8 1.0
ND1 B:HIS421 4.3 23.9 1.0
CD2 A:HIS262 4.4 27.5 1.0
OE1 B:GLU159 4.5 32.0 1.0
CG B:GLU160 4.6 28.6 1.0
CE1 B:HIS114 4.6 21.2 1.0
CD B:GLN229 4.6 25.6 1.0
NE2 B:HIS114 4.6 22.0 1.0
NE2 B:GLN118 4.7 23.1 1.0
CG B:GLN118 4.7 23.9 1.0
OE1 B:GLN229 4.8 25.7 1.0

Zinc binding site 5 out of 8 in 2v8g

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Zinc binding site 5 out of 8 in the Crystal Structure of Beta-Alanine Synthase From Saccharomyces Kluyveri in Complex with the Product Beta- Alanine


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 the Product Beta- Alanine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn500

b:36.7
occ:1.00
 O C:HOH2021 1.8 34.9 1.0
NE2 C:HIS114 2.2 20.9 1.0
NE2 C:HIS226 2.2 24.8 1.0
OD1 C:ASP125 2.2 28.6 1.0
CE1 C:HIS226 2.9 23.9 1.0
CE1 C:HIS114 3.0 21.6 1.0
CD2 C:HIS114 3.3 21.2 1.0
CD2 C:HIS226 3.3 24.3 1.0
CG C:ASP125 3.3 27.4 1.0
N C:GLY126 3.7 25.1 1.0
ZN C:ZN501 3.8 53.7 1.0
OD2 C:ASP125 3.8 29.1 1.0
OE1 C:GLU159 3.9 34.2 1.0
CA C:GLY126 4.0 24.8 1.0
ND1 C:HIS226 4.1 24.4 1.0
ND1 C:HIS397 4.1 25.1 1.0
ND1 C:HIS114 4.2 22.9 1.0
CD C:GLU159 4.2 33.2 1.0
C C:ASP125 4.3 25.4 1.0
OE2 C:GLU159 4.3 34.9 1.0
CG C:HIS226 4.3 24.7 1.0
O C:HOH2004 4.3 23.8 1.0
CG C:HIS114 4.3 22.8 1.0
CE1 C:HIS397 4.5 24.2 1.0
CB C:ASP125 4.6 26.1 1.0
CA C:ASP125 4.7 25.7 1.0
OE1 C:GLN229 4.7 27.4 1.0
OG C:SER113 4.8 26.9 1.0
NE2 C:GLN229 4.8 26.7 1.0
OE2 C:GLU160 4.8 31.8 1.0
O C:ASP125 4.9 25.4 1.0

Zinc binding site 6 out of 8 in 2v8g

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Zinc binding site 6 out of 8 in the Crystal Structure of Beta-Alanine Synthase From Saccharomyces Kluyveri in Complex with the Product Beta- Alanine


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

b:53.7
occ:1.00
 OD2 C:ASP125 1.8 29.1 1.0
NE2 C:HIS421 2.3 24.9 1.0
O C:HOH2021 2.5 34.9 1.0
OE2 C:GLU160 2.5 31.8 1.0
OE1 C:GLU160 2.7 30.8 1.0
CG C:ASP125 2.8 27.4 1.0
CD C:GLU160 2.9 30.8 1.0
CD2 C:HIS421 3.1 24.2 1.0
OD1 C:ASP125 3.1 28.6 1.0
CE1 C:HIS421 3.4 23.8 1.0
NE2 C:GLN229 3.6 26.7 1.0
ZN C:ZN500 3.8 36.7 1.0
CB C:ASP125 4.1 26.1 1.0
CG C:HIS421 4.3 23.8 1.0
CE1 C:HIS114 4.4 21.6 1.0
NE2 D:HIS262 4.4 29.1 1.0
CG C:GLU160 4.4 27.9 1.0
CD2 D:HIS262 4.4 27.9 1.0
ND1 C:HIS421 4.4 24.2 1.0
OE1 C:GLU159 4.6 34.2 1.0
CD C:GLN229 4.6 26.4 1.0
NE2 C:GLN118 4.6 22.1 1.0
NE2 C:HIS114 4.7 20.9 1.0
CG C:GLN118 4.7 24.0 1.0
OE1 C:GLN229 4.8 27.4 1.0

Zinc binding site 7 out of 8 in 2v8g

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Zinc binding site 7 out of 8 in the Crystal Structure of Beta-Alanine Synthase From Saccharomyces Kluyveri in Complex with the Product Beta- Alanine


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

b:42.1
occ:1.00
 OD1 D:ASP125 2.1 29.5 1.0
NE2 D:HIS114 2.2 21.0 1.0
NE2 D:HIS226 2.4 24.0 1.0
O D:HOH3001 2.8 29.8 1.0
CE1 D:HIS114 3.1 20.1 1.0
CE1 D:HIS226 3.2 23.7 1.0
CD2 D:HIS114 3.2 20.8 1.0
CG D:ASP125 3.3 28.4 1.0
CD2 D:HIS226 3.5 22.8 1.0
ZN D:ZN501 3.6 62.9 1.0
OE1 D:GLU159 3.7 34.9 1.0
OD2 D:ASP125 3.8 32.2 1.0
N D:GLY126 3.8 25.2 1.0
CD D:GLU159 4.0 33.3 1.0
OE2 D:GLU159 4.1 35.4 1.0
CA D:GLY126 4.2 24.7 1.0
ND1 D:HIS397 4.3 24.3 1.0
ND1 D:HIS114 4.3 22.2 1.0
C D:ASP125 4.3 25.5 1.0
ND1 D:HIS226 4.3 22.5 1.0
CG D:HIS114 4.4 22.5 1.0
N D:BAL600 4.5 38.7 1.0
CG D:HIS226 4.5 23.5 1.0
O D:HOH2035 4.5 15.6 1.0
CB D:ASP125 4.5 26.3 1.0
CE1 D:HIS397 4.6 24.5 1.0
NE2 D:GLN229 4.6 24.9 1.0
OE2 D:GLU160 4.6 31.9 1.0
OE1 D:GLN229 4.6 27.6 1.0
CA D:ASP125 4.7 25.6 1.0
CD D:GLN229 4.9 25.9 1.0
OE1 D:GLU160 4.9 31.1 1.0
O D:ASP125 4.9 25.3 1.0
CD D:GLU160 5.0 30.9 1.0

Zinc binding site 8 out of 8 in 2v8g

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Zinc binding site 8 out of 8 in the Crystal Structure of Beta-Alanine Synthase From Saccharomyces Kluyveri in Complex with the Product Beta- Alanine


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

b:62.9
occ:1.00
 OD2 D:ASP125 2.1 32.2 1.0
NE2 D:HIS421 2.2 24.8 1.0
OE1 D:GLU160 2.7 31.1 1.0
O D:HOH3001 2.8 29.8 1.0
OE2 D:GLU160 2.8 31.9 1.0
CG D:ASP125 2.9 28.4 1.0
CD2 D:HIS421 3.1 23.9 1.0
CD D:GLU160 3.1 30.9 1.0
OD1 D:ASP125 3.2 29.5 1.0
CE1 D:HIS421 3.2 23.6 1.0
N D:BAL600 3.5 38.7 1.0
NE2 D:GLN229 3.6 24.9 1.0
ZN D:ZN500 3.6 42.1 1.0
O D:HOH2018 3.9 11.1 1.0
CB D:ASP125 4.2 26.3 1.0
CG D:HIS421 4.3 24.8 1.0
ND1 D:HIS421 4.3 24.1 1.0
OE1 D:GLU159 4.5 34.9 1.0
NE2 C:HIS262 4.5 28.1 1.0
CE1 D:HIS114 4.5 20.1 1.0
CD2 C:HIS262 4.5 28.0 1.0
NE2 D:HIS114 4.6 21.0 1.0
CD D:GLN229 4.6 25.9 1.0
CG D:GLU160 4.6 29.1 1.0
CG D:GLN118 4.7 24.4 1.0
NE2 D:GLN118 4.7 22.7 1.0
OE1 D:GLN229 4.7 27.6 1.0
CB D:BAL600 4.7 38.4 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 04:10:04 2024

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