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Zinc in PDB 5ykd: Crystal Structure of Dihydropyrimidinase From Pseudomonas Aeruginosa PAO1 at 2.17 Angstrom Resolution

Enzymatic activity of Crystal Structure of Dihydropyrimidinase From Pseudomonas Aeruginosa PAO1 at 2.17 Angstrom Resolution

All present enzymatic activity of Crystal Structure of Dihydropyrimidinase From Pseudomonas Aeruginosa PAO1 at 2.17 Angstrom Resolution:
3.5.2.2;

Protein crystallography data

The structure of Crystal Structure of Dihydropyrimidinase From Pseudomonas Aeruginosa PAO1 at 2.17 Angstrom Resolution, PDB code: 5ykd was solved by Y.H.Huang, C.Y.Huang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.17
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 108.912, 155.699, 235.572, 90.00, 90.00, 90.00
R / Rfree (%) 17.6 / 23.1

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Dihydropyrimidinase From Pseudomonas Aeruginosa PAO1 at 2.17 Angstrom Resolution (pdb code 5ykd). 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 Pseudomonas Aeruginosa PAO1 at 2.17 Angstrom Resolution, PDB code: 5ykd:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 5ykd

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Zinc binding site 1 out of 8 in the Crystal Structure of Dihydropyrimidinase From Pseudomonas Aeruginosa PAO1 at 2.17 Angstrom Resolution


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 Pseudomonas Aeruginosa PAO1 at 2.17 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:40.7
occ:1.00
 OQ1 A:KCX150 2.1 28.8 1.0
CE1 A:HIS239 2.2 31.0 1.0
ND1 A:HIS183 2.3 37.8 1.0
CE1 A:HIS183 3.0 34.8 1.0
CX A:KCX150 3.1 29.8 1.0
NE2 A:HIS239 3.1 31.4 1.0
ND1 A:HIS239 3.2 35.2 1.0
OQ2 A:KCX150 3.3 28.7 1.0
CG A:HIS183 3.4 34.1 1.0
ZN A:ZN502 3.4 33.7 1.0
CB A:HIS183 3.9 33.6 1.0
O A:SER289 4.1 40.9 1.0
NE2 A:HIS183 4.2 35.8 1.0
NZ A:KCX150 4.2 29.7 1.0
CE1 A:PHE152 4.3 34.3 1.0
CD2 A:HIS239 4.3 28.8 1.0
CG A:HIS239 4.4 29.3 1.0
CG2 A:VAL238 4.4 31.9 1.0
CD2 A:HIS183 4.4 37.4 1.0
CE1 A:HIS59 4.4 35.7 1.0
NE2 A:HIS59 4.5 31.1 1.0
OH A:TYR155 4.6 36.2 1.0
CE A:KCX150 4.7 28.9 1.0
CD1 A:PHE152 4.7 36.5 1.0
OD1 A:ASP316 4.7 34.1 1.0
OD2 A:ASP316 4.7 35.2 1.0
CA A:HIS183 4.9 32.5 1.0
CG A:ASP316 5.0 32.5 1.0

Zinc binding site 2 out of 8 in 5ykd

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Zinc binding site 2 out of 8 in the Crystal Structure of Dihydropyrimidinase From Pseudomonas Aeruginosa PAO1 at 2.17 Angstrom Resolution


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 Pseudomonas Aeruginosa PAO1 at 2.17 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn502

b:33.7
occ:1.00
 OQ2 A:KCX150 2.0 28.7 1.0
NE2 A:HIS61 2.1 27.5 1.0
NE2 A:HIS59 2.2 31.1 1.0
OD1 A:ASP316 2.2 34.1 1.0
CE1 A:HIS61 2.9 26.4 1.0
CX A:KCX150 3.0 29.8 1.0
CD2 A:HIS59 3.1 33.6 1.0
CE1 A:HIS59 3.2 35.7 1.0
CD2 A:HIS61 3.2 27.7 1.0
CG A:ASP316 3.3 32.5 1.0
OQ1 A:KCX150 3.4 28.8 1.0
ZN A:ZN501 3.4 40.7 1.0
OD2 A:ASP316 3.8 35.2 1.0
ND1 A:HIS61 4.1 26.4 1.0
NZ A:KCX150 4.1 29.7 1.0
CG A:HIS61 4.2 27.1 1.0
ND1 A:HIS59 4.3 33.7 1.0
CG A:HIS59 4.3 30.6 1.0
CB A:ASP316 4.4 31.7 1.0
CE1 A:HIS239 4.6 31.0 1.0
CE1 A:PHE93 4.6 35.4 1.0
ND1 A:HIS239 4.6 35.2 1.0
CA A:ASP316 4.7 32.1 1.0
CD1 A:PHE93 5.0 30.7 1.0

Zinc binding site 3 out of 8 in 5ykd

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Zinc binding site 3 out of 8 in the Crystal Structure of Dihydropyrimidinase From Pseudomonas Aeruginosa PAO1 at 2.17 Angstrom Resolution


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 Pseudomonas Aeruginosa PAO1 at 2.17 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn501

b:41.7
occ:1.00
 OQ2 B:KCX150 2.1 28.9 1.0
CE1 B:HIS239 2.2 36.7 1.0
ND1 B:HIS183 2.2 37.0 1.0
NE2 B:HIS239 3.0 35.6 1.0
CE1 B:HIS183 3.0 37.3 1.0
CX B:KCX150 3.2 30.6 1.0
ND1 B:HIS239 3.2 39.7 1.0
CG B:HIS183 3.3 35.4 1.0
ZN B:ZN502 3.4 35.3 1.0
OQ1 B:KCX150 3.4 31.9 1.0
CB B:HIS183 3.8 35.0 1.0
O B:SER289 4.0 36.0 1.0
NE2 B:HIS183 4.2 39.8 1.0
CD2 B:HIS239 4.2 31.6 1.0
CE2 B:PHE152 4.3 34.9 1.0
NZ B:KCX150 4.3 31.4 1.0
CE1 B:HIS59 4.4 29.2 1.0
CG B:HIS239 4.4 37.9 1.0
CD2 B:HIS183 4.4 40.3 1.0
NE2 B:HIS59 4.5 25.6 1.0
CG2 B:VAL238 4.5 27.9 1.0
CD2 B:PHE152 4.6 35.4 1.0
OH B:TYR155 4.7 48.5 1.0
OD1 B:ASP316 4.8 36.6 1.0
OD2 B:ASP316 4.8 40.4 1.0
CE B:KCX150 4.8 28.7 1.0
CA B:HIS183 4.8 32.6 1.0

Zinc binding site 4 out of 8 in 5ykd

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Zinc binding site 4 out of 8 in the Crystal Structure of Dihydropyrimidinase From Pseudomonas Aeruginosa PAO1 at 2.17 Angstrom Resolution


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 Pseudomonas Aeruginosa PAO1 at 2.17 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn502

b:35.3
occ:1.00
 OQ1 B:KCX150 2.0 31.9 1.0
NE2 B:HIS61 2.1 33.4 1.0
NE2 B:HIS59 2.2 25.6 1.0
OD1 B:ASP316 2.3 36.6 1.0
CX B:KCX150 3.0 30.6 1.0
CD2 B:HIS61 3.1 33.6 1.0
CE1 B:HIS59 3.1 29.2 1.0
CE1 B:HIS61 3.1 32.5 1.0
CD2 B:HIS59 3.2 27.9 1.0
CG B:ASP316 3.2 33.8 1.0
OQ2 B:KCX150 3.3 28.9 1.0
ZN B:ZN501 3.4 41.7 1.0
OD2 B:ASP316 3.8 40.4 1.0
NZ B:KCX150 4.2 31.4 1.0
ND1 B:HIS61 4.2 32.2 1.0
CG B:HIS61 4.2 31.6 1.0
ND1 B:HIS59 4.2 29.7 1.0
CG B:HIS59 4.3 28.1 1.0
CB B:ASP316 4.3 32.0 1.0
CE1 B:HIS239 4.4 36.7 1.0
ND1 B:HIS239 4.6 39.7 1.0
CE1 B:PHE93 4.6 31.1 1.0
CA B:ASP316 4.7 31.5 1.0
CZ B:PHE93 5.0 29.9 1.0

Zinc binding site 5 out of 8 in 5ykd

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Zinc binding site 5 out of 8 in the Crystal Structure of Dihydropyrimidinase From Pseudomonas Aeruginosa PAO1 at 2.17 Angstrom Resolution


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 Pseudomonas Aeruginosa PAO1 at 2.17 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn501

b:41.9
occ:1.00
 OQ1 C:KCX150 2.1 35.1 1.0
CD2 C:HIS183 2.2 37.4 1.0
NE2 C:HIS239 2.2 33.4 1.0
CX C:KCX150 3.1 29.7 1.0
NE2 C:HIS183 3.2 39.1 1.0
CD2 C:HIS239 3.2 35.7 1.0
CE1 C:HIS239 3.2 32.6 1.0
CG C:HIS183 3.3 40.2 1.0
OQ2 C:KCX150 3.3 29.2 1.0
ZN C:ZN502 3.4 34.4 1.0
CB C:HIS183 3.9 36.2 1.0
O C:SER289 4.0 39.9 1.0
NZ C:KCX150 4.3 36.8 1.0
CE1 C:HIS183 4.3 36.6 1.0
ND1 C:HIS239 4.4 32.4 1.0
CE1 C:PHE152 4.4 35.1 1.0
CG C:HIS239 4.4 32.6 1.0
ND1 C:HIS183 4.4 43.2 1.0
CE1 C:HIS59 4.4 38.8 1.0
NE2 C:HIS59 4.5 35.2 1.0
CG2 C:VAL238 4.5 34.5 1.0
OD2 C:ASP316 4.6 41.6 1.0
OH C:TYR155 4.7 46.3 1.0
CD1 C:PHE152 4.8 34.9 1.0
CE C:KCX150 4.8 37.4 1.0
CA C:HIS183 4.9 34.6 1.0
OD1 C:ASP316 4.9 31.0 1.0

Zinc binding site 6 out of 8 in 5ykd

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Zinc binding site 6 out of 8 in the Crystal Structure of Dihydropyrimidinase From Pseudomonas Aeruginosa PAO1 at 2.17 Angstrom Resolution


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 Pseudomonas Aeruginosa PAO1 at 2.17 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn502

b:34.4
occ:1.00
 OQ2 C:KCX150 2.0 29.2 1.0
NE2 C:HIS61 2.1 30.8 1.0
NE2 C:HIS59 2.1 35.2 1.0
OD1 C:ASP316 2.3 31.0 1.0
CE1 C:HIS61 3.0 29.9 1.0
CX C:KCX150 3.0 29.7 1.0
CD2 C:HIS61 3.1 28.2 1.0
CE1 C:HIS59 3.1 38.8 1.0
CD2 C:HIS59 3.1 37.6 1.0
CG C:ASP316 3.2 34.0 1.0
OQ1 C:KCX150 3.3 35.1 1.0
ZN C:ZN501 3.4 41.9 1.0
OD2 C:ASP316 3.7 41.6 1.0
ND1 C:HIS61 4.1 29.8 1.0
NZ C:KCX150 4.1 36.8 1.0
CG C:HIS61 4.2 30.1 1.0
ND1 C:HIS59 4.2 39.6 1.0
CG C:HIS59 4.3 32.3 1.0
CB C:ASP316 4.3 32.3 1.0
CD2 C:HIS239 4.5 35.7 1.0
CE1 C:PHE93 4.6 31.6 1.0
NE2 C:HIS239 4.6 33.4 1.0
CA C:ASP316 4.7 31.6 1.0
CZ C:PHE93 4.9 31.4 1.0
CD1 C:PHE93 5.0 32.6 1.0

Zinc binding site 7 out of 8 in 5ykd

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Zinc binding site 7 out of 8 in the Crystal Structure of Dihydropyrimidinase From Pseudomonas Aeruginosa PAO1 at 2.17 Angstrom Resolution


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 Pseudomonas Aeruginosa PAO1 at 2.17 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn501

b:38.3
occ:1.00
 OQ1 D:KCX150 1.9 30.8 1.0
NE2 D:HIS61 2.0 36.7 1.0
NE2 D:HIS59 2.1 37.0 1.0
OD1 D:ASP316 2.2 34.3 1.0
CX D:KCX150 2.9 31.2 1.0
CD2 D:HIS61 3.0 34.1 1.0
CE1 D:HIS61 3.0 35.9 1.0
CE1 D:HIS59 3.0 36.0 1.0
CG D:ASP316 3.2 40.7 1.0
CD2 D:HIS59 3.2 34.5 1.0
OQ2 D:KCX150 3.3 30.1 1.0
ZN D:ZN502 3.3 42.6 1.0
OD2 D:ASP316 3.7 43.9 1.0
O D:HOH650 3.9 48.8 1.0
NZ D:KCX150 4.1 31.6 1.0
ND1 D:HIS61 4.1 36.2 1.0
CG D:HIS61 4.1 36.6 1.0
ND1 D:HIS59 4.2 37.4 1.0
CB D:ASP316 4.2 39.8 1.0
CG D:HIS59 4.3 34.4 1.0
CE1 D:HIS239 4.5 33.4 1.0
ND1 D:HIS239 4.6 36.0 1.0
CE1 D:PHE93 4.7 37.9 1.0
CA D:ASP316 4.7 36.4 1.0

Zinc binding site 8 out of 8 in 5ykd

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Zinc binding site 8 out of 8 in the Crystal Structure of Dihydropyrimidinase From Pseudomonas Aeruginosa PAO1 at 2.17 Angstrom Resolution


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 Pseudomonas Aeruginosa PAO1 at 2.17 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn502

b:42.6
occ:1.00
 OQ2 D:KCX150 2.0 30.1 1.0
CE1 D:HIS239 2.2 33.4 1.0
O D:HOH650 2.3 48.8 1.0
ND1 D:HIS183 2.4 37.0 1.0
CX D:KCX150 3.1 31.2 1.0
NE2 D:HIS239 3.2 35.0 1.0
CE1 D:HIS183 3.2 39.2 1.0
ND1 D:HIS239 3.2 36.0 1.0
ZN D:ZN501 3.3 38.3 1.0
OQ1 D:KCX150 3.4 30.8 1.0
CG D:HIS183 3.5 35.8 1.0
CB D:HIS183 3.8 36.4 1.0
O D:SER289 4.1 37.2 1.0
NZ D:KCX150 4.3 31.6 1.0
CG2 D:VAL238 4.3 32.2 1.0
CE1 D:HIS59 4.4 36.0 1.0
CE1 D:PHE152 4.4 35.7 1.0
CD2 D:HIS239 4.4 30.4 1.0
NE2 D:HIS183 4.4 42.2 1.0
CG D:HIS239 4.4 33.8 1.0
NE2 D:HIS59 4.5 37.0 1.0
CD2 D:HIS183 4.5 40.1 1.0
OD2 D:ASP316 4.6 43.9 1.0
CE D:KCX150 4.7 27.7 1.0
OD1 D:ASP316 4.7 34.3 1.0
OH D:TYR155 4.7 46.0 1.0
CA D:HIS183 4.8 34.0 1.0
CD1 D:PHE152 4.9 38.5 1.0
CG D:ASP316 4.9 40.7 1.0

Reference:

J.H.Cheng, C.C.Huang, Y.H.Huang, C.Y.Huang. Structural Basis For pH-Dependent Oligomerization of Dihydropyrimidinase Frompseudomonas AERUGINOSAPAO1. Bioinorg Chem Appl V.2018 64391 2018.
ISSN: ISSN 1565-3633
PubMed: 29666631
DOI: 10.1155/2018/9564391
Page generated: Thu Aug 21 11:36:16 2025

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