Atomistry » Zinc » PDB 2fnn-2g0d » 2fvm
Atomistry »
  Zinc »
    PDB 2fnn-2g0d »
      2fvm »

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

Go back to Zinc Binding Sites List in 2fvm
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

Go back to Zinc Binding Sites List in 2fvm
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

Go back to Zinc Binding Sites List in 2fvm
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

Go back to Zinc Binding Sites List in 2fvm
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

Go back to Zinc Binding Sites List in 2fvm
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

Go back to Zinc Binding Sites List in 2fvm
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

Go back to Zinc Binding Sites List in 2fvm
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

Go back to Zinc Binding Sites List in 2fvm
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 Dec 16 03:28:42 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy