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Zinc in PDB 2v8h: Crystal Structure of Mutant E159A of Beta-Alanine Synthase From Saccharomyces Kluyveri in Complex with Its Substrate N-Carbamyl-Beta-Alanine

Enzymatic activity of Crystal Structure of Mutant E159A of Beta-Alanine Synthase From Saccharomyces Kluyveri in Complex with Its Substrate N-Carbamyl-Beta-Alanine

All present enzymatic activity of Crystal Structure of Mutant E159A of Beta-Alanine Synthase From Saccharomyces Kluyveri in Complex with Its Substrate N-Carbamyl-Beta-Alanine:
3.5.1.6;

Protein crystallography data

The structure of Crystal Structure of Mutant E159A of Beta-Alanine Synthase From Saccharomyces Kluyveri in Complex with Its Substrate N-Carbamyl-Beta-Alanine, PDB code: 2v8h 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) 19.76 / 2.0
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 49.780, 218.300, 81.580, 90.00, 92.19, 90.00
R / Rfree (%) 17.8 / 20.8

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Mutant E159A of Beta-Alanine Synthase From Saccharomyces Kluyveri in Complex with Its Substrate N-Carbamyl-Beta-Alanine (pdb code 2v8h). 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 E159A of Beta-Alanine Synthase From Saccharomyces Kluyveri in Complex with Its Substrate N-Carbamyl-Beta-Alanine, PDB code: 2v8h:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 2v8h

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Zinc binding site 1 out of 8 in the Crystal Structure of Mutant E159A of Beta-Alanine Synthase From Saccharomyces Kluyveri in Complex with Its Substrate N-Carbamyl-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 Mutant E159A of Beta-Alanine Synthase From Saccharomyces Kluyveri in Complex with Its Substrate N-Carbamyl-Beta-Alanine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn500

b:46.2
occ:1.00
 OD1 A:ASP125 2.2 27.4 1.0
O A:HOH3001 2.2 18.0 1.0
NE2 A:HIS114 2.3 25.4 1.0
NE2 A:HIS226 2.4 23.9 1.0
N3 A:URP600 2.8 35.7 1.0
CE1 A:HIS114 3.2 27.1 1.0
CE1 A:HIS226 3.3 24.8 1.0
C2 A:URP600 3.3 36.1 1.0
CG A:ASP125 3.4 27.5 1.0
CD2 A:HIS114 3.4 25.6 1.0
CD2 A:HIS226 3.4 24.0 1.0
N A:GLY126 3.7 26.3 1.0
O2 A:URP600 3.7 37.0 1.0
OD2 A:ASP125 3.9 28.5 1.0
ZN A:ZN501 4.0 32.4 0.3
N1 A:URP600 4.0 36.2 1.0
CA A:GLY126 4.1 25.7 1.0
ND1 A:HIS397 4.1 25.7 1.0
C A:ASP125 4.3 25.8 1.0
ND1 A:HIS114 4.3 25.2 1.0
ND1 A:HIS226 4.4 24.1 1.0
CE1 A:HIS397 4.4 26.9 1.0
CG A:HIS114 4.5 26.8 1.0
CG A:HIS226 4.5 24.1 1.0
OE1 A:GLU160 4.5 36.4 1.0
CB A:ASP125 4.6 25.4 1.0
O A:HOH2146 4.6 25.9 1.0
CA A:ASP125 4.7 26.0 1.0
OE2 A:GLU160 4.7 39.2 1.0
CD A:GLU160 4.7 35.5 1.0
OE1 A:GLN229 4.8 26.2 1.0
NE2 A:GLN229 4.8 25.9 1.0
O A:GLY396 4.9 26.3 1.0

Zinc binding site 2 out of 8 in 2v8h

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Zinc binding site 2 out of 8 in the Crystal Structure of Mutant E159A of Beta-Alanine Synthase From Saccharomyces Kluyveri in Complex with Its Substrate N-Carbamyl-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 Mutant E159A of Beta-Alanine Synthase From Saccharomyces Kluyveri in Complex with Its Substrate N-Carbamyl-Beta-Alanine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:32.4
occ:0.30
 OD2 A:ASP125 1.8 28.5 1.0
O2 A:URP600 2.0 37.0 1.0
OE1 A:GLU160 2.1 36.4 1.0
NE2 A:HIS421 2.2 26.2 1.0
OE2 A:GLU160 2.7 39.2 1.0
CD A:GLU160 2.8 35.5 1.0
CG A:ASP125 2.8 27.5 1.0
CD2 A:HIS421 3.1 24.7 1.0
C2 A:URP600 3.1 36.1 1.0
OD1 A:ASP125 3.2 27.4 1.0
CE1 A:HIS421 3.3 25.7 1.0
NE2 A:GLN229 3.5 25.9 1.0
N3 A:URP600 3.8 35.7 1.0
N1 A:URP600 3.9 36.2 1.0
ZN A:ZN500 4.0 46.2 1.0
O A:HOH2095 4.0 17.8 1.0
C6 A:URP600 4.1 35.4 1.0
CB A:ASP125 4.1 25.4 1.0
CG A:HIS421 4.3 25.2 1.0
CG A:GLU160 4.3 30.4 1.0
NE2 B:HIS262 4.3 30.4 1.0
ND1 A:HIS421 4.4 24.6 1.0
CD2 B:HIS262 4.4 28.4 1.0
NE2 A:GLN118 4.4 25.0 1.0
CG A:GLN118 4.5 25.7 1.0
CD A:GLN229 4.6 25.5 1.0
CE1 A:HIS114 4.8 27.1 1.0
OE1 A:GLN229 4.9 26.2 1.0
NE2 A:HIS114 5.0 25.4 1.0

Zinc binding site 3 out of 8 in 2v8h

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Zinc binding site 3 out of 8 in the Crystal Structure of Mutant E159A of Beta-Alanine Synthase From Saccharomyces Kluyveri in Complex with Its Substrate N-Carbamyl-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 Mutant E159A of Beta-Alanine Synthase From Saccharomyces Kluyveri in Complex with Its Substrate N-Carbamyl-Beta-Alanine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn500

b:49.6
occ:1.00
 OD1 B:ASP125 2.2 27.0 1.0
NE2 B:HIS226 2.2 23.9 1.0
O B:HOH3001 2.3 20.4 1.0
NE2 B:HIS114 2.4 24.6 1.0
N3 B:URP600 2.8 36.2 1.0
CE1 B:HIS226 3.0 24.2 1.0
CD2 B:HIS226 3.3 24.3 1.0
CG B:ASP125 3.4 27.1 1.0
CD2 B:HIS114 3.4 25.1 1.0
C2 B:URP600 3.4 36.7 1.0
CE1 B:HIS114 3.4 25.9 1.0
N B:GLY126 3.7 25.9 1.0
O2 B:URP600 3.8 37.2 1.0
OD2 B:ASP125 3.9 28.8 1.0
ZN B:ZN501 4.0 39.1 0.3
ND1 B:HIS397 4.1 25.1 1.0
CA B:GLY126 4.1 25.7 1.0
N1 B:URP600 4.2 36.5 1.0
ND1 B:HIS226 4.2 24.2 1.0
C B:ASP125 4.3 25.9 1.0
CE1 B:HIS397 4.3 24.9 1.0
CG B:HIS226 4.3 24.4 1.0
ND1 B:HIS114 4.5 24.1 1.0
CG B:HIS114 4.6 25.6 1.0
NE2 B:GLN229 4.6 27.2 1.0
CB B:ASP125 4.6 26.5 1.0
CA B:ASP125 4.6 26.0 1.0
OE1 B:GLN229 4.7 27.2 1.0
O B:HOH2071 4.7 26.0 1.0
OE2 B:GLU160 4.8 35.8 1.0
OE1 B:GLU160 4.9 34.1 1.0
CD B:GLN229 4.9 26.7 1.0
O B:GLY396 4.9 26.1 1.0
CD B:GLU160 5.0 33.1 1.0

Zinc binding site 4 out of 8 in 2v8h

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Zinc binding site 4 out of 8 in the Crystal Structure of Mutant E159A of Beta-Alanine Synthase From Saccharomyces Kluyveri in Complex with Its Substrate N-Carbamyl-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 Mutant E159A of Beta-Alanine Synthase From Saccharomyces Kluyveri in Complex with Its Substrate N-Carbamyl-Beta-Alanine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn501

b:39.1
occ:0.30
 OD2 B:ASP125 1.9 28.8 1.0
O2 B:URP600 2.2 37.2 1.0
NE2 B:HIS421 2.2 24.8 1.0
OE1 B:GLU160 2.3 34.1 1.0
OE2 B:GLU160 2.6 35.8 1.0
CD B:GLU160 2.8 33.1 1.0
CG B:ASP125 2.9 27.1 1.0
CD2 B:HIS421 3.0 23.9 1.0
C2 B:URP600 3.2 36.7 1.0
OD1 B:ASP125 3.2 27.0 1.0
CE1 B:HIS421 3.3 24.0 1.0
NE2 B:GLN229 3.5 27.2 1.0
N3 B:URP600 3.9 36.2 1.0
O B:HOH2052 3.9 19.6 1.0
ZN B:ZN500 4.0 49.6 1.0
N1 B:URP600 4.0 36.5 1.0
NE2 A:HIS262 4.2 29.8 1.0
CB B:ASP125 4.2 26.5 1.0
C6 B:URP600 4.2 35.1 1.0
CG B:HIS421 4.2 24.3 1.0
CG B:GLU160 4.3 30.1 1.0
ND1 B:HIS421 4.3 23.4 1.0
CD2 A:HIS262 4.4 27.8 1.0
NE2 B:GLN118 4.4 24.8 1.0
CG B:GLN118 4.5 25.5 1.0
CD B:GLN229 4.7 26.7 1.0
CE1 B:HIS114 4.8 25.9 1.0
NE2 B:HIS114 4.9 24.6 1.0
OE1 B:GLN229 5.0 27.2 1.0

Zinc binding site 5 out of 8 in 2v8h

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Zinc binding site 5 out of 8 in the Crystal Structure of Mutant E159A of Beta-Alanine Synthase From Saccharomyces Kluyveri in Complex with Its Substrate N-Carbamyl-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 Mutant E159A of Beta-Alanine Synthase From Saccharomyces Kluyveri in Complex with Its Substrate N-Carbamyl-Beta-Alanine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn500

b:46.1
occ:1.00
 OD1 C:ASP125 2.2 26.4 1.0
O C:HOH3001 2.2 22.3 1.0
NE2 C:HIS114 2.2 24.1 1.0
NE2 C:HIS226 2.4 25.5 1.0
N3 C:URP600 2.9 35.5 1.0
CD2 C:HIS114 3.2 24.1 1.0
CE1 C:HIS114 3.2 23.8 1.0
CG C:ASP125 3.3 26.9 1.0
CE1 C:HIS226 3.4 24.9 1.0
CD2 C:HIS226 3.4 25.8 1.0
C2 C:URP600 3.4 35.9 1.0
N C:GLY126 3.8 26.0 1.0
OD2 C:ASP125 3.8 28.3 1.0
O2 C:URP600 4.0 36.8 1.0
N1 C:URP600 4.0 35.9 1.0
ZN C:ZN501 4.1 35.6 0.3
CA C:GLY126 4.1 25.6 1.0
O C:HOH2048 4.2 42.3 1.0
ND1 C:HIS397 4.2 24.4 1.0
C C:ASP125 4.3 25.8 1.0
ND1 C:HIS114 4.3 24.0 1.0
O C:HOH2066 4.3 25.6 1.0
CG C:HIS114 4.3 24.7 1.0
CE1 C:HIS397 4.5 24.5 1.0
ND1 C:HIS226 4.5 24.6 1.0
CG C:HIS226 4.6 24.4 1.0
OE2 C:GLU160 4.6 34.6 1.0
CB C:ASP125 4.6 26.2 1.0
OE1 C:GLU160 4.7 33.6 1.0
CA C:ASP125 4.7 26.0 1.0
CD C:GLU160 4.7 33.0 1.0
NE2 C:GLN229 4.8 26.9 1.0
OE1 C:GLN229 4.8 28.1 1.0
O C:GLY396 5.0 26.3 1.0

Zinc binding site 6 out of 8 in 2v8h

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Zinc binding site 6 out of 8 in the Crystal Structure of Mutant E159A of Beta-Alanine Synthase From Saccharomyces Kluyveri in Complex with Its Substrate N-Carbamyl-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 Mutant E159A of Beta-Alanine Synthase From Saccharomyces Kluyveri in Complex with Its Substrate N-Carbamyl-Beta-Alanine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn501

b:35.6
occ:0.30
 OD2 C:ASP125 1.9 28.3 1.0
OE1 C:GLU160 2.0 33.6 1.0
NE2 C:HIS421 2.2 23.4 1.0
O2 C:URP600 2.3 36.8 1.0
OE2 C:GLU160 2.4 34.6 1.0
CD C:GLU160 2.6 33.0 1.0
CG C:ASP125 3.0 26.9 1.0
CD2 C:HIS421 3.1 23.8 1.0
C2 C:URP600 3.2 35.9 1.0
CE1 C:HIS421 3.3 24.7 1.0
OD1 C:ASP125 3.4 26.4 1.0
NE2 C:GLN229 3.7 26.9 1.0
N1 C:URP600 3.9 35.9 1.0
N3 C:URP600 3.9 35.5 1.0
C6 C:URP600 4.0 34.5 1.0
ZN C:ZN500 4.1 46.1 1.0
CG C:GLU160 4.1 29.4 1.0
O C:HOH2049 4.1 21.9 1.0
NE2 C:GLN118 4.2 24.2 1.0
CB C:ASP125 4.3 26.2 1.0
CG C:HIS421 4.3 24.1 1.0
ND1 C:HIS421 4.4 23.7 1.0
NE2 D:HIS262 4.4 29.3 1.0
CG C:GLN118 4.4 25.7 1.0
CD2 D:HIS262 4.5 28.9 1.0
CE1 C:HIS114 4.8 23.8 1.0
CB C:GLU160 4.8 28.3 1.0
CD C:GLN229 4.9 27.1 1.0
CD C:GLN118 4.9 25.5 1.0
NE2 C:HIS114 4.9 24.1 1.0

Zinc binding site 7 out of 8 in 2v8h

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Zinc binding site 7 out of 8 in the Crystal Structure of Mutant E159A of Beta-Alanine Synthase From Saccharomyces Kluyveri in Complex with Its Substrate N-Carbamyl-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 Mutant E159A of Beta-Alanine Synthase From Saccharomyces Kluyveri in Complex with Its Substrate N-Carbamyl-Beta-Alanine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn500

b:47.4
occ:1.00
 O D:HOH3001 2.2 15.8 1.0
NE2 D:HIS114 2.2 23.9 1.0
OD1 D:ASP125 2.2 24.1 1.0
NE2 D:HIS226 2.4 29.0 1.0
N3 D:URP600 2.8 34.7 1.0
CE1 D:HIS114 3.1 24.7 1.0
CE1 D:HIS226 3.2 29.2 1.0
CD2 D:HIS114 3.2 25.2 1.0
CG D:ASP125 3.4 26.9 1.0
CD2 D:HIS226 3.4 28.2 1.0
C2 D:URP600 3.5 36.0 1.0
N D:GLY126 3.8 25.9 1.0
OD2 D:ASP125 3.9 28.1 1.0
O2 D:URP600 4.0 36.4 1.0
CA D:GLY126 4.1 25.7 1.0
ZN D:ZN501 4.1 30.8 0.3
N1 D:URP600 4.1 34.6 1.0
ND1 D:HIS397 4.2 26.1 1.0
ND1 D:HIS114 4.3 25.5 1.0
C D:ASP125 4.3 25.9 1.0
CG D:HIS114 4.3 25.0 1.0
ND1 D:HIS226 4.4 28.7 1.0
CE1 D:HIS397 4.5 26.9 1.0
O D:HOH2125 4.5 20.2 1.0
CG D:HIS226 4.5 27.5 1.0
CB D:ASP125 4.6 25.3 1.0
OE1 D:GLN229 4.7 28.1 1.0
CA D:ASP125 4.7 25.9 1.0
OE2 D:GLU160 4.8 38.2 1.0
NE2 D:GLN229 4.9 27.4 1.0
O D:GLY396 4.9 26.4 1.0
CD D:GLU160 5.0 33.9 1.0
OE1 D:GLU160 5.0 35.7 1.0

Zinc binding site 8 out of 8 in 2v8h

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Zinc binding site 8 out of 8 in the Crystal Structure of Mutant E159A of Beta-Alanine Synthase From Saccharomyces Kluyveri in Complex with Its Substrate N-Carbamyl-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 Mutant E159A of Beta-Alanine Synthase From Saccharomyces Kluyveri in Complex with Its Substrate N-Carbamyl-Beta-Alanine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn501

b:30.8
occ:0.30
 OD2 D:ASP125 1.9 28.1 1.0
NE2 D:HIS421 2.1 22.9 1.0
O2 D:URP600 2.1 36.4 1.0
OE1 D:GLU160 2.3 35.7 1.0
OE2 D:GLU160 2.5 38.2 1.0
CD D:GLU160 2.7 33.9 1.0
CG D:ASP125 2.9 26.9 1.0
CD2 D:HIS421 3.0 21.9 1.0
C2 D:URP600 3.1 36.0 1.0
CE1 D:HIS421 3.2 22.6 1.0
OD1 D:ASP125 3.3 24.1 1.0
NE2 D:GLN229 3.6 27.4 1.0
N3 D:URP600 3.8 34.7 1.0
N1 D:URP600 3.9 34.6 1.0
O D:HOH2078 4.0 14.8 1.0
ZN D:ZN500 4.1 47.4 1.0
C6 D:URP600 4.1 33.8 1.0
CG D:HIS421 4.2 22.5 1.0
NE2 C:HIS262 4.2 28.3 1.0
ND1 D:HIS421 4.2 22.9 1.0
CG D:GLU160 4.2 30.9 1.0
CB D:ASP125 4.2 25.3 1.0
CD2 C:HIS262 4.3 27.5 1.0
NE2 D:GLN118 4.4 26.1 1.0
CG D:GLN118 4.5 25.0 1.0
CD D:GLN229 4.7 26.6 1.0
CE1 D:HIS114 4.7 24.7 1.0
OE1 D:GLN229 4.9 28.1 1.0
NE2 D:HIS114 5.0 23.9 1.0
CD D:GLN118 5.0 26.3 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 04:10:56 2024

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