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Zinc in PDB 2fvm: Crystal Structure of Dihydropyrimidinase From Saccharomyces Kluyveri in Complex with the Reaction Product N-Carbamyl-Beta-Alanine

Enzymatic activity of Crystal Structure of Dihydropyrimidinase From Saccharomyces Kluyveri in Complex with the Reaction Product N-Carbamyl-Beta-Alanine

All present enzymatic activity of Crystal Structure of Dihydropyrimidinase From Saccharomyces Kluyveri in Complex with the Reaction Product N-Carbamyl-Beta-Alanine:
3.5.2.2;

Protein crystallography data

The structure of Crystal Structure of Dihydropyrimidinase From Saccharomyces Kluyveri in Complex with the Reaction Product N-Carbamyl-Beta-Alanine, PDB code: 2fvm was solved by D.Dobritzsch, B.Lohkamp, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.37 / 2.45
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 91.141, 73.027, 164.105, 90.00, 91.98, 90.00
R / Rfree (%) 18.2 / 23.7

Zinc Binding Sites:

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

Zinc binding site 1 out of 8 in 2fvm

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Zinc binding site 1 out of 8 in the Crystal Structure of Dihydropyrimidinase From Saccharomyces Kluyveri in Complex with the Reaction Product 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 Dihydropyrimidinase From Saccharomyces Kluyveri in Complex with the Reaction Product N-Carbamyl-Beta-Alanine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn601

b:34.4
occ:1.00
 NE2 A:HIS62 2.1 25.2 1.0
NE2 A:HIS64 2.2 24.1 1.0
OQ2 A:KCX167 2.3 31.8 0.8
OD1 A:ASP358 2.4 25.0 1.0
O41 A:URP604 2.7 44.9 1.0
C4 A:URP604 2.7 46.0 1.0
CD2 A:HIS62 2.9 24.2 1.0
O42 A:URP604 3.0 46.3 1.0
CE1 A:HIS64 3.1 23.6 1.0
CE1 A:HIS62 3.1 25.4 1.0
CX A:KCX167 3.2 30.0 0.8
CD2 A:HIS64 3.3 23.5 1.0
C5 A:URP604 3.4 46.1 1.0
CG A:ASP358 3.5 23.5 1.0
OQ1 A:KCX167 3.5 30.9 0.8
ZN A:ZN602 3.7 48.1 1.0
OD2 A:ASP358 4.0 24.7 1.0
CG A:HIS62 4.1 23.8 1.0
ND1 A:HIS62 4.2 25.2 1.0
ND1 A:HIS64 4.2 23.5 1.0
CD2 A:HIS255 4.3 26.6 1.0
CG A:HIS64 4.4 23.4 1.0
NZ A:KCX167 4.4 27.9 1.0
NE2 A:HIS255 4.5 27.8 1.0
CB A:ASP358 4.6 23.1 1.0
CA A:ASP358 4.8 22.9 1.0
C6 A:URP604 4.8 47.2 1.0
CE1 A:PHE97 4.9 20.9 1.0
CZ A:PHE97 5.0 21.0 1.0

Zinc binding site 2 out of 8 in 2fvm

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Zinc binding site 2 out of 8 in the Crystal Structure of Dihydropyrimidinase From Saccharomyces Kluyveri in Complex with the Reaction Product 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 Dihydropyrimidinase From Saccharomyces Kluyveri in Complex with the Reaction Product N-Carbamyl-Beta-Alanine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn602

b:48.1
occ:1.00
 NE2 A:HIS255 2.3 27.8 1.0
OQ1 A:KCX167 2.3 30.9 0.8
O41 A:URP604 2.4 44.9 1.0
ND1 A:HIS199 2.4 23.9 1.0
CE1 A:HIS199 3.0 23.3 1.0
C4 A:URP604 3.2 46.0 1.0
CE1 A:HIS255 3.2 26.9 1.0
CX A:KCX167 3.3 30.0 0.8
CD2 A:HIS255 3.3 26.6 1.0
O42 A:URP604 3.4 46.3 1.0
OQ2 A:KCX167 3.5 31.8 0.8
CG A:HIS199 3.5 24.0 1.0
ZN A:ZN601 3.7 34.4 1.0
CE2 A:PHE169 3.8 22.7 1.0
CB A:HIS199 4.0 23.1 1.0
OH A:TYR172 4.1 27.7 0.8
O A:SER331 4.1 23.5 1.0
NE2 A:HIS199 4.2 23.2 1.0
N3 A:URP604 4.3 49.7 1.0
CE1 A:TYR172 4.3 26.9 0.8
ND1 A:HIS255 4.4 26.5 1.0
NZ A:KCX167 4.4 27.9 1.0
CG A:HIS255 4.4 25.4 1.0
CD2 A:PHE169 4.5 22.2 1.0
CD2 A:HIS199 4.5 23.8 1.0
C5 A:URP604 4.7 46.1 1.0
CG2 A:VAL254 4.7 22.0 1.0
CZ A:PHE169 4.7 22.4 1.0
CZ A:TYR172 4.7 27.3 0.8
NE2 A:HIS62 4.7 25.2 1.0
CE1 A:HIS62 4.8 25.4 1.0
CE A:KCX167 4.8 28.0 1.0
OD2 A:ASP358 4.9 24.7 1.0
OD1 A:ASP358 4.9 25.0 1.0

Zinc binding site 3 out of 8 in 2fvm

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Zinc binding site 3 out of 8 in the Crystal Structure of Dihydropyrimidinase From Saccharomyces Kluyveri in Complex with the Reaction Product 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 Dihydropyrimidinase From Saccharomyces Kluyveri in Complex with the Reaction Product N-Carbamyl-Beta-Alanine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn601

b:32.4
occ:1.00
 NE2 B:HIS64 2.1 24.1 1.0
NE2 B:HIS62 2.2 25.5 1.0
OQ2 B:KCX167 2.4 31.6 0.8
OD1 B:ASP358 2.5 23.2 1.0
O41 B:URP604 2.9 43.0 1.0
C4 B:URP604 2.9 44.6 1.0
CE1 B:HIS64 3.0 23.4 1.0
CD2 B:HIS62 3.0 24.6 1.0
CD2 B:HIS64 3.2 23.6 1.0
O42 B:URP604 3.2 44.5 1.0
CE1 B:HIS62 3.3 25.9 1.0
CX B:KCX167 3.3 29.7 0.8
C5 B:URP604 3.5 44.9 1.0
OQ1 B:KCX167 3.5 30.3 0.8
CG B:ASP358 3.6 23.0 1.0
ZN B:ZN602 3.8 50.5 1.0
OD2 B:ASP358 4.1 23.5 1.0
ND1 B:HIS64 4.2 23.9 1.0
CG B:HIS62 4.3 24.2 1.0
CG B:HIS64 4.3 23.4 1.0
CD2 B:HIS255 4.3 26.8 1.0
ND1 B:HIS62 4.4 25.3 1.0
NZ B:KCX167 4.5 28.8 1.0
NE2 B:HIS255 4.6 26.9 1.0
CB B:ASP358 4.7 22.8 1.0
CE1 B:PHE97 4.7 20.9 1.0
CZ B:PHE97 4.8 20.5 1.0
CA B:ASP358 4.9 22.9 1.0
C6 B:URP604 4.9 45.6 1.0

Zinc binding site 4 out of 8 in 2fvm

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Zinc binding site 4 out of 8 in the Crystal Structure of Dihydropyrimidinase From Saccharomyces Kluyveri in Complex with the Reaction Product 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 Dihydropyrimidinase From Saccharomyces Kluyveri in Complex with the Reaction Product N-Carbamyl-Beta-Alanine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn602

b:50.5
occ:1.00
 NE2 B:HIS255 2.2 26.9 1.0
OQ1 B:KCX167 2.4 30.3 0.8
ND1 B:HIS199 2.5 24.1 1.0
O41 B:URP604 2.6 43.0 1.0
CE1 B:HIS255 3.2 27.3 1.0
CD2 B:HIS255 3.2 26.8 1.0
CE1 B:HIS199 3.2 23.7 1.0
CX B:KCX167 3.4 29.7 0.8
C4 B:URP604 3.5 44.6 1.0
CG B:HIS199 3.5 23.7 1.0
O42 B:URP604 3.6 44.5 1.0
ZN B:ZN601 3.8 32.4 1.0
OQ2 B:KCX167 3.8 31.6 0.8
CE2 B:PHE169 3.9 22.5 1.0
O B:SER331 4.0 23.6 1.0
CB B:HIS199 4.0 22.7 1.0
ND1 B:HIS255 4.3 26.6 1.0
CG B:HIS255 4.3 24.9 1.0
NE2 B:HIS199 4.3 23.6 1.0
CE1 B:TYR172 4.5 26.5 0.8
CG2 B:VAL254 4.5 22.0 1.0
CD2 B:HIS199 4.5 23.4 1.0
OH B:TYR172 4.5 28.4 0.8
CD2 B:PHE169 4.5 22.3 1.0
N3 B:URP604 4.5 47.9 1.0
NZ B:KCX167 4.6 28.8 1.0
NE2 B:HIS62 4.8 25.5 1.0
CZ B:PHE169 4.8 22.8 1.0
CE B:KCX167 4.9 27.4 1.0
C5 B:URP604 4.9 44.9 1.0
CE1 B:HIS62 4.9 25.9 1.0
C B:SER331 5.0 23.1 1.0
OD2 B:ASP358 5.0 23.5 1.0

Zinc binding site 5 out of 8 in 2fvm

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Zinc binding site 5 out of 8 in the Crystal Structure of Dihydropyrimidinase From Saccharomyces Kluyveri in Complex with the Reaction Product 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 Dihydropyrimidinase From Saccharomyces Kluyveri in Complex with the Reaction Product N-Carbamyl-Beta-Alanine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn601

b:39.6
occ:1.00
 NE2 C:HIS64 2.1 23.9 1.0
OQ2 C:KCX167 2.2 31.1 0.8
NE2 C:HIS62 2.2 25.5 1.0
OD1 C:ASP358 2.4 25.9 1.0
O C:HOH1603 2.5 17.4 1.0
CE1 C:HIS64 2.9 23.6 1.0
CX C:KCX167 3.1 29.7 0.8
CE1 C:HIS62 3.2 25.3 1.0
CD2 C:HIS62 3.2 25.1 1.0
O C:HOH1802 3.2 18.1 1.0
CD2 C:HIS64 3.3 23.6 1.0
OQ1 C:KCX167 3.5 30.5 0.8
CG C:ASP358 3.5 23.9 1.0
ZN C:ZN602 3.6 45.2 1.0
OD2 C:ASP358 4.0 24.1 1.0
ND1 C:HIS64 4.1 24.1 1.0
CD2 C:HIS255 4.3 26.8 1.0
NZ C:KCX167 4.3 28.4 1.0
CG C:HIS64 4.3 23.5 1.0
ND1 C:HIS62 4.3 24.7 1.0
CG C:HIS62 4.4 24.0 1.0
NE2 C:HIS255 4.4 26.8 1.0
CB C:ASP358 4.7 23.1 1.0
CA C:ASP358 4.9 23.0 1.0
CE1 C:PHE97 4.9 21.6 1.0

Zinc binding site 6 out of 8 in 2fvm

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Zinc binding site 6 out of 8 in the Crystal Structure of Dihydropyrimidinase From Saccharomyces Kluyveri in Complex with the Reaction Product 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 Dihydropyrimidinase From Saccharomyces Kluyveri in Complex with the Reaction Product N-Carbamyl-Beta-Alanine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn602

b:45.2
occ:1.00
 OQ1 C:KCX167 2.2 30.5 0.8
NE2 C:HIS255 2.3 26.8 1.0
O C:HOH1603 2.4 17.4 1.0
ND1 C:HIS199 2.5 24.8 1.0
CE1 C:HIS199 3.1 23.9 1.0
CX C:KCX167 3.1 29.7 0.8
CE1 C:HIS255 3.2 26.9 1.0
CD2 C:HIS255 3.3 26.8 1.0
OQ2 C:KCX167 3.4 31.1 0.8
ZN C:ZN601 3.6 39.6 1.0
CG C:HIS199 3.7 24.0 1.0
CE2 C:PHE169 3.8 22.6 1.0
OH C:TYR172 3.9 28.0 1.0
O C:SER331 3.9 23.4 1.0
CB C:HIS199 4.2 23.2 1.0
CE1 C:TYR172 4.3 27.2 1.0
NZ C:KCX167 4.3 28.4 1.0
ND1 C:HIS255 4.3 26.9 1.0
NE2 C:HIS199 4.3 23.0 1.0
CG C:HIS255 4.4 25.3 1.0
O C:HOH1802 4.5 18.1 1.0
CD2 C:PHE169 4.6 22.4 1.0
CZ C:TYR172 4.6 27.2 1.0
CD2 C:HIS199 4.6 23.8 1.0
CG2 C:VAL254 4.7 22.5 1.0
CZ C:PHE169 4.7 23.1 1.0
CE1 C:HIS62 4.8 25.3 1.0
CE C:KCX167 4.8 27.7 1.0
NE2 C:HIS62 4.8 25.5 1.0
OD1 C:ASP358 4.8 25.9 1.0
OD2 C:ASP358 4.9 24.1 1.0
C C:SER331 5.0 23.1 1.0

Zinc binding site 7 out of 8 in 2fvm

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Zinc binding site 7 out of 8 in the Crystal Structure of Dihydropyrimidinase From Saccharomyces Kluyveri in Complex with the Reaction Product 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 Dihydropyrimidinase From Saccharomyces Kluyveri in Complex with the Reaction Product N-Carbamyl-Beta-Alanine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn601

b:36.4
occ:1.00
 NE2 D:HIS62 2.0 25.2 1.0
NE2 D:HIS64 2.0 23.9 1.0
OQ2 D:KCX167 2.2 30.6 0.8
OD1 D:ASP358 2.4 25.2 1.0
O D:HOH2603 2.5 19.6 1.0
CE1 D:HIS64 2.8 23.5 1.0
CD2 D:HIS62 2.9 24.9 1.0
CE1 D:HIS62 3.0 24.8 1.0
CD2 D:HIS64 3.2 23.5 1.0
CX D:KCX167 3.3 29.5 0.8
CG D:ASP358 3.4 23.9 1.0
O D:HOH2776 3.6 26.7 1.0
ZN D:ZN602 3.7 46.2 1.0
OQ1 D:KCX167 3.8 30.4 0.8
OD2 D:ASP358 3.9 24.9 1.0
ND1 D:HIS64 4.0 24.0 1.0
CG D:HIS62 4.1 24.1 1.0
ND1 D:HIS62 4.1 25.1 1.0
CG D:HIS64 4.2 23.6 1.0
NZ D:KCX167 4.3 27.8 1.0
CD2 D:HIS255 4.3 26.9 1.0
NE2 D:HIS255 4.5 27.6 1.0
CB D:ASP358 4.6 23.1 1.0
CE1 D:PHE97 4.7 21.8 1.0
CA D:ASP358 4.7 22.9 1.0
CZ D:PHE97 4.8 21.4 1.0

Zinc binding site 8 out of 8 in 2fvm

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Zinc binding site 8 out of 8 in the Crystal Structure of Dihydropyrimidinase From Saccharomyces Kluyveri in Complex with the Reaction Product 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 Dihydropyrimidinase From Saccharomyces Kluyveri in Complex with the Reaction Product N-Carbamyl-Beta-Alanine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn602

b:46.2
occ:1.00
 NE2 D:HIS255 2.1 27.6 1.0
OQ1 D:KCX167 2.2 30.4 0.8
O D:HOH2603 2.4 19.6 1.0
ND1 D:HIS199 2.6 24.2 1.0
CX D:KCX167 3.1 29.5 0.8
CE1 D:HIS255 3.1 27.5 1.0
CD2 D:HIS255 3.1 26.9 1.0
OQ2 D:KCX167 3.2 30.6 0.8
CE1 D:HIS199 3.2 24.1 1.0
ZN D:ZN601 3.7 36.4 1.0
CG D:HIS199 3.7 24.2 1.0
O D:SER331 3.9 23.4 1.0
OH D:TYR172 4.0 28.3 1.0
CE2 D:PHE169 4.0 21.8 1.0
CB D:HIS199 4.2 23.1 1.0
ND1 D:HIS255 4.2 27.6 1.0
CG D:HIS255 4.3 25.3 1.0
NZ D:KCX167 4.3 27.8 1.0
NE2 D:HIS199 4.4 24.0 1.0
CE1 D:TYR172 4.5 27.6 1.0
CG2 D:VAL254 4.5 22.1 1.0
OD2 D:ASP358 4.5 24.9 1.0
CE1 D:HIS62 4.5 24.8 1.0
NE2 D:HIS62 4.6 25.2 1.0
CD2 D:HIS199 4.7 24.1 1.0
CZ D:TYR172 4.7 27.6 1.0
CD2 D:PHE169 4.8 22.8 1.0
OD1 D:ASP358 4.8 25.2 1.0
O D:HOH2776 4.8 26.7 1.0
CZ D:PHE169 4.9 21.7 1.0
CE D:KCX167 4.9 28.0 1.0
C D:SER331 4.9 23.1 1.0

Reference:

B.Lohkamp, B.Andersen, J.Piskur, D.Dobritzsch. The Crystal Structures of Dihydropyrimidinases Reaffirm the Close Relationship Between Cyclic Amidohydrolases and Explain Their Substrate Specificity. J.Biol.Chem. V. 281 13762 2006.
ISSN: ISSN 0021-9258
PubMed: 16517602
DOI: 10.1074/JBC.M513266200
Page generated: Wed Oct 16 23:56:21 2024

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