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Zinc in PDB 2fvk: Crystal Structure of Dihydropyrimidinase From Saccharomyces Kluyveri in Complex with the Substrate Dihydrouracil

Enzymatic activity of Crystal Structure of Dihydropyrimidinase From Saccharomyces Kluyveri in Complex with the Substrate Dihydrouracil

All present enzymatic activity of Crystal Structure of Dihydropyrimidinase From Saccharomyces Kluyveri in Complex with the Substrate Dihydrouracil:
3.5.2.2;

Protein crystallography data

The structure of Crystal Structure of Dihydropyrimidinase From Saccharomyces Kluyveri in Complex with the Substrate Dihydrouracil, PDB code: 2fvk 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) 54.23 / 2.40
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 90.130, 71.600, 161.890, 90.00, 91.40, 90.00
R / Rfree (%) 17.8 / 23.4

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Dihydropyrimidinase From Saccharomyces Kluyveri in Complex with the Substrate Dihydrouracil (pdb code 2fvk). 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 Substrate Dihydrouracil, PDB code: 2fvk:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 2fvk

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Zinc binding site 1 out of 8 in the Crystal Structure of Dihydropyrimidinase From Saccharomyces Kluyveri in Complex with the Substrate Dihydrouracil


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 Substrate Dihydrouracil within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn601

b:46.5
occ:0.90
 OQ2 A:KCX167 2.0 46.9 1.0
OD1 A:ASP358 2.0 39.1 1.0
NE2 A:HIS64 2.1 40.5 1.0
NE2 A:HIS62 2.1 40.8 1.0
O4 A:DUC604 2.4 52.7 1.0
CD2 A:HIS62 2.9 38.2 1.0
CD2 A:HIS64 3.0 37.9 1.0
CX A:KCX167 3.0 45.7 1.0
C4 A:DUC604 3.0 55.2 1.0
CG A:ASP358 3.1 35.6 1.0
CE1 A:HIS64 3.1 38.4 1.0
CE1 A:HIS62 3.2 40.3 1.0
OQ1 A:KCX167 3.4 46.9 1.0
C5 A:DUC604 3.5 55.7 1.0
OD2 A:ASP358 3.6 37.1 1.0
C6 A:DUC604 3.8 55.9 1.0
N3 A:DUC604 3.9 55.9 1.0
ZN A:ZN602 3.9 49.6 0.6
CD2 A:HIS255 3.9 39.2 1.0
NE2 A:HIS255 4.0 42.0 1.0
NZ A:KCX167 4.1 43.2 1.0
CG A:HIS62 4.1 37.0 1.0
CG A:HIS64 4.1 36.4 1.0
ND1 A:HIS62 4.2 39.9 1.0
ND1 A:HIS64 4.2 37.4 1.0
CB A:ASP358 4.2 34.9 1.0
N1 A:DUC604 4.4 56.3 1.0
CA A:ASP358 4.5 34.7 1.0
C2 A:DUC604 4.5 56.2 1.0
CE1 A:PHE97 4.8 31.5 1.0

Zinc binding site 2 out of 8 in 2fvk

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Zinc binding site 2 out of 8 in the Crystal Structure of Dihydropyrimidinase From Saccharomyces Kluyveri in Complex with the Substrate Dihydrouracil


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 Substrate Dihydrouracil within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn602

b:49.6
occ:0.60
 O4 A:DUC604 2.0 52.7 1.0
OQ1 A:KCX167 2.0 46.9 1.0
NE2 A:HIS255 2.1 42.0 1.0
ND1 A:HIS199 2.1 40.2 1.0
CE1 A:HIS255 2.6 39.9 1.0
CE1 A:HIS199 2.8 38.5 1.0
C4 A:DUC604 2.9 55.2 1.0
CX A:KCX167 3.1 45.7 1.0
CG A:HIS199 3.2 35.9 1.0
CD2 A:HIS255 3.3 39.2 1.0
N3 A:DUC604 3.6 55.9 1.0
OQ2 A:KCX167 3.6 46.9 1.0
CB A:HIS199 3.8 34.8 1.0
O A:SER331 3.9 34.8 1.0
ND1 A:HIS255 3.9 39.9 1.0
ZN A:ZN601 3.9 46.5 0.9
CE2 A:PHE169 3.9 34.5 1.0
NE2 A:HIS199 4.0 36.8 1.0
C5 A:DUC604 4.0 55.7 1.0
CD2 A:HIS199 4.2 36.9 1.0
NZ A:KCX167 4.2 43.2 1.0
CG A:HIS255 4.2 37.4 1.0
CE A:KCX167 4.5 40.5 1.0
CD2 A:PHE169 4.5 34.5 1.0
CE1 A:TYR172 4.6 38.7 0.7
CG2 A:VAL254 4.6 34.4 1.0
NE2 A:HIS62 4.7 40.8 1.0
OD2 A:ASP358 4.7 37.1 1.0
CE1 A:HIS62 4.7 40.3 1.0
C A:SER331 4.9 34.4 1.0
CZ A:PHE169 4.9 33.7 1.0
C2 A:DUC604 4.9 56.2 1.0
OH A:TYR172 4.9 40.1 0.7
OD1 A:ASP358 5.0 39.1 1.0
CA A:HIS199 5.0 34.6 1.0

Zinc binding site 3 out of 8 in 2fvk

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Zinc binding site 3 out of 8 in the Crystal Structure of Dihydropyrimidinase From Saccharomyces Kluyveri in Complex with the Substrate Dihydrouracil


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 Substrate Dihydrouracil within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn601

b:45.6
occ:0.90
 OD1 B:ASP358 2.0 38.6 1.0
NE2 B:HIS64 2.1 39.8 1.0
NE2 B:HIS62 2.1 41.2 1.0
O4 B:DUC604 2.7 56.9 1.0
CD2 B:HIS62 2.8 39.3 1.0
CE1 B:HIS64 3.0 38.1 1.0
CD2 B:HIS64 3.0 37.4 1.0
CG B:ASP358 3.1 35.8 1.0
CE1 B:HIS62 3.2 40.7 1.0
C4 B:DUC604 3.4 58.9 1.0
OD2 B:ASP358 3.7 37.8 1.0
ZN B:ZN602 3.8 53.8 0.6
C5 B:DUC604 3.9 59.0 1.0
CG B:HIS62 4.0 37.7 1.0
CD2 B:HIS255 4.0 39.9 1.0
NZ B:KCX167 4.1 39.3 1.0
ND1 B:HIS64 4.1 36.6 1.0
CB B:ASP358 4.2 34.9 1.0
CG B:HIS64 4.2 35.9 1.0
ND1 B:HIS62 4.2 40.7 1.0
N3 B:DUC604 4.2 59.4 1.0
NE2 B:HIS255 4.3 42.4 1.0
C6 B:DUC604 4.4 59.0 1.0
N1 B:DUC604 4.4 59.0 1.0
CA B:ASP358 4.5 34.7 1.0
C2 B:DUC604 4.7 59.2 1.0
CE1 B:PHE97 4.8 31.7 1.0
CZ B:PHE97 4.9 31.8 1.0

Zinc binding site 4 out of 8 in 2fvk

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Zinc binding site 4 out of 8 in the Crystal Structure of Dihydropyrimidinase From Saccharomyces Kluyveri in Complex with the Substrate Dihydrouracil


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 Substrate Dihydrouracil within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn602

b:53.8
occ:0.60
 O4 B:DUC604 2.0 56.9 1.0
NE2 B:HIS255 2.1 42.4 1.0
ND1 B:HIS199 2.1 41.1 1.0
CE1 B:HIS199 2.9 38.7 1.0
CE1 B:HIS255 3.0 40.0 1.0
C4 B:DUC604 3.1 58.9 1.0
CD2 B:HIS255 3.1 39.9 1.0
CG B:HIS199 3.2 36.3 1.0
NZ B:KCX167 3.6 39.3 1.0
CE2 B:PHE169 3.6 33.9 1.0
CB B:HIS199 3.8 34.7 1.0
ZN B:ZN601 3.8 45.6 0.9
N3 B:DUC604 3.8 59.4 1.0
NE2 B:HIS199 4.0 38.0 1.0
C5 B:DUC604 4.1 59.0 1.0
ND1 B:HIS255 4.1 40.1 1.0
O B:SER331 4.2 34.8 1.0
CE B:KCX167 4.2 38.1 1.0
CD2 B:HIS199 4.2 37.1 1.0
CG B:HIS255 4.2 37.8 1.0
CG2 B:VAL254 4.3 34.1 1.0
CZ B:PHE169 4.3 33.5 1.0
CD2 B:PHE169 4.4 34.0 1.0
NE2 B:HIS62 4.5 41.2 1.0
CE1 B:HIS62 4.6 40.7 1.0
CA B:HIS199 4.9 34.6 1.0
OD1 B:ASP358 5.0 38.6 1.0
OD2 B:ASP358 5.0 37.8 1.0

Zinc binding site 5 out of 8 in 2fvk

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Zinc binding site 5 out of 8 in the Crystal Structure of Dihydropyrimidinase From Saccharomyces Kluyveri in Complex with the Substrate Dihydrouracil


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 Substrate Dihydrouracil within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn601

b:44.7
occ:0.80
 OD1 C:ASP358 2.0 40.4 1.0
NE2 C:HIS62 2.1 40.5 1.0
NE2 C:HIS64 2.1 39.5 1.0
O4 C:DUC604 2.4 55.8 1.0
CE1 C:HIS64 2.9 37.8 1.0
CE1 C:HIS62 2.9 39.8 1.0
C4 C:DUC604 3.0 58.8 1.0
CD2 C:HIS62 3.0 38.9 1.0
CG C:ASP358 3.1 37.0 1.0
CD2 C:HIS64 3.2 37.5 1.0
C5 C:DUC604 3.4 58.5 1.0
ZN C:ZN602 3.6 50.3 0.6
OD2 C:ASP358 3.6 37.9 1.0
C6 C:DUC604 3.7 59.4 1.0
NZ C:KCX167 3.8 38.0 1.0
N3 C:DUC604 3.8 59.9 1.0
CD2 C:HIS255 3.9 39.0 1.0
NE2 C:HIS255 3.9 42.0 1.0
ND1 C:HIS62 4.0 40.3 1.0
ND1 C:HIS64 4.0 36.4 1.0
CG C:HIS62 4.1 37.5 1.0
N1 C:DUC604 4.2 59.9 1.0
CG C:HIS64 4.3 36.3 1.0
CB C:ASP358 4.4 35.3 1.0
C2 C:DUC604 4.4 60.5 1.0
CA C:ASP358 4.8 34.8 1.0
CE1 C:PHE97 4.8 32.0 1.0

Zinc binding site 6 out of 8 in 2fvk

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Zinc binding site 6 out of 8 in the Crystal Structure of Dihydropyrimidinase From Saccharomyces Kluyveri in Complex with the Substrate Dihydrouracil


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 Substrate Dihydrouracil within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn602

b:50.3
occ:0.60
 O4 C:DUC604 2.0 55.8 1.0
NE2 C:HIS255 2.1 42.0 1.0
ND1 C:HIS199 2.1 41.0 1.0
CE1 C:HIS255 2.8 39.8 1.0
CE1 C:HIS199 2.9 39.2 1.0
C4 C:DUC604 3.0 58.8 1.0
CG C:HIS199 3.2 36.2 1.0
CD2 C:HIS255 3.3 39.0 1.0
ZN C:ZN601 3.6 44.7 0.8
N3 C:DUC604 3.6 59.9 1.0
CE2 C:PHE169 3.6 34.0 1.0
CB C:HIS199 3.7 34.6 1.0
NZ C:KCX167 3.8 38.0 1.0
CE C:KCX167 4.0 37.8 1.0
ND1 C:HIS255 4.0 39.8 1.0
NE2 C:HIS199 4.1 37.8 1.0
O C:SER331 4.2 34.8 1.0
CD2 C:HIS199 4.2 36.6 1.0
CG C:HIS255 4.3 37.5 1.0
C5 C:DUC604 4.3 58.5 1.0
CZ C:PHE169 4.3 33.3 1.0
CG2 C:VAL254 4.3 33.6 1.0
CD2 C:PHE169 4.4 34.3 1.0
CE1 C:HIS62 4.4 39.8 1.0
OH C:TYR172 4.6 44.0 1.0
CE1 C:TYR172 4.6 44.3 1.0
NE2 C:HIS62 4.6 40.5 1.0
CA C:HIS199 4.8 34.5 1.0
OD1 C:ASP358 4.8 40.4 1.0
C2 C:DUC604 4.9 60.5 1.0

Zinc binding site 7 out of 8 in 2fvk

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Zinc binding site 7 out of 8 in the Crystal Structure of Dihydropyrimidinase From Saccharomyces Kluyveri in Complex with the Substrate Dihydrouracil


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 Substrate Dihydrouracil within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn601

b:47.1
occ:0.90
 OQ2 D:KCX167 2.0 45.6 0.6
O4 D:DUC604 2.0 52.4 1.0
OD1 D:ASP358 2.0 40.0 1.0
NE2 D:HIS64 2.1 39.5 1.0
NE2 D:HIS62 2.1 41.0 1.0
C4 D:DUC604 2.7 55.9 1.0
CD2 D:HIS62 2.9 38.0 1.0
CX D:KCX167 2.9 44.6 0.6
CE1 D:HIS64 2.9 37.9 1.0
CG D:ASP358 3.0 36.5 1.0
CE1 D:HIS62 3.1 39.6 1.0
CD2 D:HIS64 3.1 37.6 1.0
OQ1 D:KCX167 3.2 46.1 0.6
C5 D:DUC604 3.2 55.5 1.0
OD2 D:ASP358 3.6 37.8 1.0
C6 D:DUC604 3.7 56.0 1.0
N3 D:DUC604 3.7 57.0 1.0
ZN D:ZN602 3.8 51.1 0.5
NE2 D:HIS255 3.9 40.3 1.0
CD2 D:HIS255 3.9 39.3 1.0
NZ D:KCX167 4.0 43.4 1.0
CG D:HIS62 4.1 36.9 1.0
ND1 D:HIS64 4.1 36.8 1.0
ND1 D:HIS62 4.2 39.7 1.0
CB D:ASP358 4.2 35.1 1.0
CG D:HIS64 4.2 36.3 1.0
C2 D:DUC604 4.4 57.4 1.0
N1 D:DUC604 4.4 56.9 1.0
CA D:ASP358 4.6 34.7 1.0
CE1 D:PHE97 4.7 31.1 1.0
CZ D:PHE97 4.9 30.8 1.0

Zinc binding site 8 out of 8 in 2fvk

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Zinc binding site 8 out of 8 in the Crystal Structure of Dihydropyrimidinase From Saccharomyces Kluyveri in Complex with the Substrate Dihydrouracil


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 Substrate Dihydrouracil within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn602

b:51.1
occ:0.50
 OQ1 D:KCX167 2.0 46.1 0.6
O4 D:DUC604 2.0 52.4 1.0
ND1 D:HIS199 2.1 40.5 1.0
NE2 D:HIS255 2.2 40.3 1.0
C4 D:DUC604 2.7 55.9 1.0
CE1 D:HIS199 2.7 38.0 1.0
CE1 D:HIS255 2.8 39.9 1.0
N3 D:DUC604 3.1 57.0 1.0
CX D:KCX167 3.1 44.6 0.6
CG D:HIS199 3.3 36.5 1.0
CD2 D:HIS255 3.5 39.3 1.0
OQ2 D:KCX167 3.6 45.6 0.6
CE2 D:PHE169 3.7 33.5 1.0
ZN D:ZN601 3.8 47.1 0.9
C5 D:DUC604 3.8 55.5 1.0
NE2 D:HIS199 3.8 37.3 1.0
O D:SER331 3.8 34.8 1.0
CB D:HIS199 3.9 34.7 1.0
OH D:TYR172 3.9 39.3 0.5
ND1 D:HIS255 4.1 40.0 1.0
CD2 D:HIS199 4.1 36.9 1.0
NZ D:KCX167 4.2 43.4 1.0
CE1 D:TYR172 4.2 38.8 0.5
CG D:HIS255 4.4 37.5 1.0
CD2 D:PHE169 4.5 33.6 1.0
C2 D:DUC604 4.5 57.4 1.0
CE D:KCX167 4.5 41.3 1.0
CZ D:PHE169 4.6 32.5 1.0
CZ D:TYR172 4.6 38.8 0.5
OD2 D:ASP358 4.7 37.8 1.0
CG2 D:VAL254 4.7 33.6 1.0
NE2 D:HIS62 4.8 41.0 1.0
CE1 D:HIS62 4.8 39.6 1.0
C D:SER331 4.9 34.5 1.0
OD1 D:ASP358 4.9 40.0 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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