Zinc in PDB 8gvz: Crystal Structure of the Human Dihydroorotase Domain in Complex with the Anticancer Drug 5-Fluorouracil

All present enzymatic activity of Crystal Structure of the Human Dihydroorotase Domain in Complex with the Anticancer Drug 5-Fluorouracil:
3.5.2.3;

The structure of Crystal Structure of the Human Dihydroorotase Domain in Complex with the Anticancer Drug 5-Fluorouracil, PDB code: 8gvz was solved by H.W.Liu, P.C.Yang, H.Y.Huang, C.Y.Huang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.78 / 1.97
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	81.775, 157.788, 61.828, 90, 90, 90
R / Rfree (%)	17.7 / 21.5

The structure of Crystal Structure of the Human Dihydroorotase Domain in Complex with the Anticancer Drug 5-Fluorouracil also contains other interesting chemical elements:

Fluorine

(F)

1 atom

The binding sites of Zinc atom in the Crystal Structure of the Human Dihydroorotase Domain in Complex with the Anticancer Drug 5-Fluorouracil (pdb code 8gvz). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of the Human Dihydroorotase Domain in Complex with the Anticancer Drug 5-Fluorouracil, PDB code: 8gvz:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of the Human Dihydroorotase Domain in Complex with the Anticancer Drug 5-Fluorouracil


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 the Human Dihydroorotase Domain in Complex with the Anticancer Drug 5-Fluorouracil within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1902 b:23.3 occ:1.00 OD1 A:ASP1686 2.2 16.9 1.0 NE2 A:HIS1471 2.2 19.4 1.0 OQ1 A:KCX1556 2.2 18.6 1.0 NE2 A:HIS1473 2.2 20.4 1.0 HN3 A:URF1901 2.7 20.0 1.0 CD2 A:HIS1471 3.1 16.8 1.0 CG A:ASP1686 3.1 20.7 1.0 CD2 A:HIS1473 3.1 19.7 1.0 CX A:KCX1556 3.1 20.4 1.0 O2 A:URF1901 3.2 20.0 1.0 CE1 A:HIS1471 3.2 19.9 1.0 CE1 A:HIS1473 3.3 22.8 1.0 N3 A:URF1901 3.3 20.0 1.0 OQ2 A:KCX1556 3.5 20.4 1.0 ZN A:ZN1903 3.5 24.9 1.0 OD2 A:ASP1686 3.6 18.7 1.0 C2 A:URF1901 3.6 20.0 1.0 CG A:HIS1471 4.2 17.8 1.0 CB A:ASP1686 4.3 16.9 1.0 NZ A:KCX1556 4.3 19.9 1.0 ND1 A:HIS1471 4.3 14.7 1.0 CG A:HIS1473 4.3 21.6 1.0 ND1 A:HIS1473 4.3 20.3 1.0 CG A:MET1503 4.4 19.1 1.0 C4 A:URF1901 4.4 20.0 1.0 CD2 A:HIS1614 4.6 30.0 1.0 NE2 A:HIS1614 4.6 30.0 1.0 CA A:ASP1686 4.7 17.6 1.0 O4 A:URF1901 4.7 20.0 1.0 OH A:TYR1558 4.8 18.6 1.0 N1 A:URF1901 4.8 20.0 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of the Human Dihydroorotase Domain in Complex with the Anticancer Drug 5-Fluorouracil


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 the Human Dihydroorotase Domain in Complex with the Anticancer Drug 5-Fluorouracil within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1903 b:24.9 occ:1.00 OQ2 A:KCX1556 2.0 20.4 1.0 NE2 A:HIS1614 2.3 30.0 1.0 ND1 A:HIS1590 2.3 21.7 1.0 O2 A:URF1901 2.7 20.0 1.0 CX A:KCX1556 3.0 20.4 1.0 CE1 A:HIS1590 3.1 22.0 1.0 CG A:HIS1590 3.2 20.8 1.0 CE1 A:HIS1614 3.2 30.0 1.0 CD2 A:HIS1614 3.2 30.0 1.0 OQ1 A:KCX1556 3.3 18.6 1.0 ZN A:ZN1902 3.5 23.3 1.0 CB A:HIS1590 3.5 17.6 1.0 C2 A:URF1901 3.9 20.0 1.0 CE1 A:HIS1471 4.1 19.9 1.0 NE2 A:HIS1590 4.2 22.4 1.0 NZ A:KCX1556 4.2 19.9 1.0 CD2 A:HIS1590 4.2 22.1 1.0 NE2 A:HIS1471 4.2 19.4 1.0 ND1 A:HIS1614 4.3 30.0 1.0 HN3 A:URF1901 4.3 20.0 1.0 CG A:HIS1614 4.4 30.0 1.0 OD2 A:ASP1686 4.4 18.7 1.0 CA A:HIS1590 4.5 18.4 1.0 CE2 A:TYR1558 4.5 20.8 1.0 O A:ARG1661 4.5 22.8 1.0 N3 A:URF1901 4.6 20.0 1.0 CE A:KCX1556 4.7 18.4 1.0 OD1 A:ASP1686 4.7 16.9 1.0 CG A:ASP1686 4.8 20.7 1.0 HN1 A:URF1901 4.8 20.0 1.0 CG2 A:THR1562 4.8 27.5 1.0 N1 A:URF1901 4.9 20.0 1.0 CD2 A:TYR1558 4.9 18.7 1.0

E.S.Lin, Y.H.Huang, P.C.Yang, W.F.Peng, C.Y.Huang. Complexed Crystal Structure of the Dihydroorotase Domain of Human Cad Protein with the Anticancer Drug 5-Fluorouracil. Biomolecules V. 13 2023.
ISSN: ESSN 2218-273X
PubMed: 36671534
DOI: 10.3390/BIOM13010149