Zinc in PDB 8wq9: Crystal Structure of Dihydropyrimidinase Complexed with Gamma- Aminobutyric Acid

All present enzymatic activity of Crystal Structure of Dihydropyrimidinase Complexed with Gamma- Aminobutyric Acid:
3.5.2.2;

The structure of Crystal Structure of Dihydropyrimidinase Complexed with Gamma- Aminobutyric Acid, PDB code: 8wq9 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)	27.74 / 1.97
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	88.314, 111.036, 112.941, 90, 90, 90
R / Rfree (%)	17.1 / 21.3

The binding sites of Zinc atom in the Crystal Structure of Dihydropyrimidinase Complexed with Gamma- Aminobutyric Acid (pdb code 8wq9). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Dihydropyrimidinase Complexed with Gamma- Aminobutyric Acid, PDB code: 8wq9:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Dihydropyrimidinase Complexed with Gamma- Aminobutyric Acid


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 Complexed with Gamma- Aminobutyric Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn503 b:52.9 occ:1.00 OQ1 A:KCX150 1.9 30.3 1.0 ND1 A:HIS183 2.4 32.3 1.0 CE1 A:HIS239 2.5 21.6 1.0 ZN A:ZN504 2.7 30.1 1.0 CX A:KCX150 2.7 28.4 1.0 OQ2 A:KCX150 2.8 25.3 1.0 CE1 A:HIS183 3.1 27.8 1.0 ND1 A:HIS239 3.4 23.4 1.0 NE2 A:HIS239 3.4 24.8 1.0 CG A:HIS183 3.6 23.9 1.0 NE2 A:HIS59 3.9 19.6 1.0 CE1 A:HIS59 4.0 25.3 1.0 NZ A:KCX150 4.0 20.3 1.0 O A:ABU502 4.0 52.0 1.0 CB A:HIS183 4.1 22.9 1.0 CE1 A:PHE152 4.2 24.5 1.0 HG1 A:ABU502 4.2 53.8 1.0 HB2 A:ABU502 4.3 50.1 1.0 OD1 A:ASP316 4.3 21.4 1.0 NE2 A:HIS183 4.3 29.1 1.0 O A:SER289 4.3 23.6 1.0 CG2 A:VAL238 4.5 20.8 1.0 OD2 A:ASP316 4.5 30.9 1.0 CG A:HIS239 4.6 22.1 1.0 CD2 A:HIS239 4.6 16.6 1.0 CD2 A:HIS183 4.6 30.5 1.0 CE A:KCX150 4.6 19.0 1.0 CG A:ASP316 4.7 27.2 1.0 C A:ABU502 4.8 48.0 1.0 HA2 A:ABU502 4.8 57.2 1.0 CD1 A:PHE152 4.8 24.6 1.0 NE2 A:HIS61 4.8 20.9 1.0 CG A:ABU502 4.8 44.8 1.0 OH A:TYR155 5.0 35.8 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Dihydropyrimidinase Complexed with Gamma- Aminobutyric Acid


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 Complexed with Gamma- Aminobutyric Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn504 b:30.1 occ:1.00 OQ2 A:KCX150 2.1 25.3 1.0 NE2 A:HIS59 2.2 19.6 1.0 OD1 A:ASP316 2.3 21.4 1.0 NE2 A:HIS61 2.3 20.9 1.0 ZN A:ZN503 2.7 52.9 1.0 O A:ABU502 2.9 52.0 1.0 CX A:KCX150 3.0 28.4 1.0 CE1 A:HIS59 3.1 25.3 1.0 CD2 A:HIS61 3.2 22.0 1.0 CD2 A:HIS59 3.3 17.6 1.0 OQ1 A:KCX150 3.3 30.3 1.0 CG A:ASP316 3.3 27.2 1.0 CE1 A:HIS61 3.4 24.1 1.0 C A:ABU502 3.6 48.0 1.0 OD2 A:ASP316 3.7 30.9 1.0 HB2 A:ABU502 3.9 50.1 1.0 NZ A:KCX150 4.2 20.3 1.0 CE1 A:HIS239 4.3 21.6 1.0 OXT A:ABU502 4.3 44.5 1.0 ND1 A:HIS59 4.3 23.8 1.0 CG A:HIS59 4.4 20.6 1.0 HG1 A:ABU502 4.4 53.8 1.0 ND1 A:HIS239 4.4 23.4 1.0 CG A:HIS61 4.4 21.5 1.0 ND1 A:HIS61 4.5 21.7 1.0 CB A:ASP316 4.5 19.8 1.0 CG A:ABU502 4.5 44.8 1.0 CB A:ABU502 4.7 41.8 1.0 CA A:ASP316 4.9 21.5 1.0 CE1 A:PHE93 4.9 19.6 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Dihydropyrimidinase Complexed with Gamma- Aminobutyric Acid


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 Complexed with Gamma- Aminobutyric Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn503 b:45.4 occ:1.00 OQ2 B:KCX150 2.0 29.6 1.0 CE1 B:HIS239 2.2 19.7 1.0 ND1 B:HIS183 2.3 25.2 1.0 CX B:KCX150 3.0 31.2 1.0 OXT B:ABU502 3.0 48.4 1.0 CE1 B:HIS183 3.1 24.0 1.0 NE2 B:HIS239 3.1 25.0 1.0 ND1 B:HIS239 3.3 24.5 1.0 OQ1 B:KCX150 3.3 30.7 1.0 ZN B:ZN504 3.3 31.8 1.0 CG B:HIS183 3.3 24.4 1.0 CB B:HIS183 3.7 20.4 1.0 O B:SER289 4.0 24.3 1.0 NZ B:KCX150 4.2 20.3 1.0 C B:ABU502 4.2 44.1 1.0 CE1 B:HIS59 4.2 23.2 1.0 NE2 B:HIS183 4.2 25.0 1.0 CE1 B:PHE152 4.3 23.4 1.0 NE2 B:HIS59 4.3 22.1 1.0 CG2 B:VAL238 4.3 19.0 1.0 CD2 B:HIS239 4.3 18.2 1.0 CD2 B:HIS183 4.4 26.0 1.0 CG B:HIS239 4.4 23.1 1.0 OD2 B:ASP316 4.4 30.9 1.0 HB2 B:ABU502 4.6 53.2 1.0 CE B:KCX150 4.6 23.7 1.0 OD1 B:ASP316 4.7 22.9 1.0 CD1 B:PHE152 4.7 22.8 1.0 CA B:HIS183 4.8 20.7 1.0 O B:ABU502 4.8 45.0 1.0 CG B:ASP316 4.9 24.8 1.0 OH B:TYR155 5.0 38.7 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Dihydropyrimidinase Complexed with Gamma- Aminobutyric Acid


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 Complexed with Gamma- Aminobutyric Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn504 b:31.8 occ:1.00 OQ1 B:KCX150 2.0 30.7 1.0 OD1 B:ASP316 2.2 22.9 1.0 NE2 B:HIS59 2.2 22.1 1.0 NE2 B:HIS61 2.2 23.3 1.0 OXT B:ABU502 2.8 48.4 1.0 CX B:KCX150 3.0 31.2 1.0 CG B:ASP316 3.1 24.8 1.0 O B:ABU502 3.1 45.0 1.0 CD2 B:HIS61 3.1 23.1 1.0 CE1 B:HIS59 3.2 23.2 1.0 CD2 B:HIS59 3.2 20.9 1.0 C B:ABU502 3.2 44.1 1.0 OQ2 B:KCX150 3.2 29.6 1.0 CE1 B:HIS61 3.3 23.8 1.0 ZN B:ZN503 3.3 45.4 1.0 OD2 B:ASP316 3.5 30.9 1.0 NZ B:KCX150 4.1 20.3 1.0 CG B:HIS61 4.3 24.2 1.0 ND1 B:HIS59 4.3 20.3 1.0 CB B:ASP316 4.3 20.2 1.0 ND1 B:HIS61 4.3 26.5 1.0 CG B:HIS59 4.3 18.9 1.0 CE1 B:HIS239 4.4 19.7 1.0 ND1 B:HIS239 4.5 24.5 1.0 CG B:ABU502 4.7 45.2 1.0 HB1 B:ABU502 4.7 53.2 1.0 CA B:ASP316 4.7 18.1 1.0 CE1 B:PHE93 4.8 18.7 1.0 HG2 B:ABU502 5.0 54.1 1.0

Y.H.Huang, C.Y.Huang. The Complexed Crystal Structure of Dihydropyrimidinase Reveals A Potential Interactive Link with the Neurotransmitter Gamma-Aminobutyric Acid (Gaba). Biochem.Biophys.Res.Commun. V. 692 49351 2024.
ISSN: ESSN 1090-2104
PubMed: 38056157
DOI: 10.1016/J.BBRC.2023.149351