Zinc in PDB 8pbi: Mutant R1617Q of the Dihydroorotase Domain of Human Cad Protein Bound to the Inhibitor Fluoroorotate

All present enzymatic activity of Mutant R1617Q of the Dihydroorotase Domain of Human Cad Protein Bound to the Inhibitor Fluoroorotate:
2.1.3.2; 3.5.2.3; 6.3.5.5;

The structure of Mutant R1617Q of the Dihydroorotase Domain of Human Cad Protein Bound to the Inhibitor Fluoroorotate, PDB code: 8pbi was solved by F.Del Cano-Ochoa, S.Ramon-Maiques, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.12 / 1.50
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	82.237, 159.575, 61.844, 90, 90, 90
R / Rfree (%)	13.3 / 15.7

The structure of Mutant R1617Q of the Dihydroorotase Domain of Human Cad Protein Bound to the Inhibitor Fluoroorotate also contains other interesting chemical elements:

Fluorine

(F)

1 atom

The binding sites of Zinc atom in the Mutant R1617Q of the Dihydroorotase Domain of Human Cad Protein Bound to the Inhibitor Fluoroorotate (pdb code 8pbi). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Mutant R1617Q of the Dihydroorotase Domain of Human Cad Protein Bound to the Inhibitor Fluoroorotate, PDB code: 8pbi:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Mutant R1617Q of the Dihydroorotase Domain of Human Cad Protein Bound to the Inhibitor Fluoroorotate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Mutant R1617Q of the Dihydroorotase Domain of Human Cad Protein Bound to the Inhibitor Fluoroorotate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1905 b:17.4 occ:0.92 O A:HOH2133 1.9 19.5 1.0 NE2 A:HIS1473 2.1 17.7 1.0 NE2 A:HIS1471 2.1 17.2 1.0 OQ1 A:KCX1556 2.2 19.8 1.0 OD1 A:ASP1686 2.3 20.5 1.0 CE1 A:HIS1473 3.0 18.3 1.0 CX A:KCX1556 3.1 19.4 1.0 CE1 A:HIS1471 3.1 17.5 1.0 CD2 A:HIS1471 3.1 16.3 1.0 CD2 A:HIS1473 3.2 18.0 1.0 CG A:ASP1686 3.2 19.6 1.0 HE1 A:HIS1473 3.2 21.9 1.0 HE1 A:HIS1471 3.3 21.0 1.0 HD2 A:HIS1471 3.3 19.6 1.0 HG3 A:MET1503 3.3 23.2 1.0 HD2 A:HIS1473 3.4 21.6 1.0 ZN A:ZN1906 3.4 17.9 0.8 OQ2 A:KCX1556 3.4 20.0 1.0 OD2 A:ASP1686 3.5 21.2 1.0 HD2 A:HIS1614 3.9 22.8 1.0 F5 A:FOT1901 4.1 22.0 1.0 C5 A:FOT1901 4.1 18.7 1.0 NZ A:KCX1556 4.2 18.6 1.0 ND1 A:HIS1473 4.2 17.9 1.0 ND1 A:HIS1471 4.2 17.8 1.0 HA A:ASP1686 4.2 20.8 1.0 C6 A:FOT1901 4.2 19.4 1.0 CG A:HIS1471 4.2 16.1 1.0 CG A:HIS1473 4.3 17.7 1.0 O6 A:FOT1901 4.3 20.6 1.0 HZ A:KCX1556 4.3 22.4 1.0 CG A:MET1503 4.3 19.3 1.0 CB A:ASP1686 4.4 18.6 1.0 HE3 A:MET1503 4.4 23.7 1.0 HE1 A:TYR1558 4.4 22.2 1.0 NE2 A:HIS1614 4.5 18.4 1.0 CD2 A:HIS1614 4.5 19.0 1.0 HB2 A:ASP1686 4.6 22.4 1.0 HG2 A:MET1503 4.6 23.2 1.0 C4 A:FOT1901 4.7 19.8 1.0 HB2 A:ALA1688 4.7 22.8 1.0 OH A:TYR1558 4.7 19.4 1.0 CA A:ASP1686 4.8 17.4 1.0 N1 A:FOT1901 4.8 19.6 1.0 HB2 A:MET1503 4.9 22.1 1.0 HD1 A:HIS1473 4.9 21.4 1.0 HD1 A:HIS1471 4.9 21.4 1.0 HB3 A:MET1503 4.9 22.1 1.0

Zinc binding site 2 out of 2 in the Mutant R1617Q of the Dihydroorotase Domain of Human Cad Protein Bound to the Inhibitor Fluoroorotate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Mutant R1617Q of the Dihydroorotase Domain of Human Cad Protein Bound to the Inhibitor Fluoroorotate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1906 b:17.9 occ:0.82 O A:HOH2133 1.9 19.5 1.0 OQ2 A:KCX1556 1.9 20.0 1.0 ND1 A:HIS1590 2.2 19.2 1.0 NE2 A:HIS1614 2.2 18.4 1.0 O6 A:FOT1901 2.5 20.6 1.0 CX A:KCX1556 2.9 19.4 1.0 CE1 A:HIS1590 2.9 20.5 1.0 HE1 A:HIS1590 3.0 24.6 1.0 CE1 A:HIS1614 3.1 19.4 1.0 HB2 A:HIS1590 3.2 19.4 1.0 CD2 A:HIS1614 3.2 19.0 1.0 OQ1 A:KCX1556 3.3 19.8 1.0 CG A:HIS1590 3.3 18.0 1.0 HE1 A:HIS1614 3.3 23.3 1.0 C6 A:FOT1901 3.3 19.4 1.0 HD2 A:HIS1614 3.4 22.8 1.0 ZN A:ZN1905 3.4 17.4 0.9 HE1 A:HIS1471 3.4 21.0 1.0 CB A:HIS1590 3.7 16.1 1.0 HE1 A:TYR1558 3.8 22.2 1.0 HN1 A:FOT1901 3.9 23.5 1.0 N1 A:FOT1901 4.0 19.6 1.0 NE2 A:HIS1590 4.1 20.4 1.0 CE1 A:HIS1471 4.1 17.5 1.0 NZ A:KCX1556 4.1 18.6 1.0 HD3 A:PRO1662 4.2 24.7 1.0 ND1 A:HIS1614 4.3 18.6 1.0 O A:ARG1661 4.3 21.5 1.0 NE2 A:HIS1471 4.3 17.2 1.0 C5 A:FOT1901 4.3 18.7 1.0 CD2 A:HIS1590 4.3 19.5 1.0 OD2 A:ASP1686 4.3 21.2 1.0 CG A:HIS1614 4.3 18.4 1.0 F5 A:FOT1901 4.4 22.0 1.0 HB3 A:HIS1590 4.4 19.4 1.0 HA A:HIS1590 4.4 18.9 1.0 HE2 A:KCX1556 4.4 22.3 1.0 CE1 A:TYR1558 4.5 18.5 1.0 HE3 A:KCX1556 4.6 22.3 1.0 HD1 A:TYR1558 4.6 21.8 1.0 CE A:KCX1556 4.7 18.6 1.0 HB2 A:CYS1613 4.7 23.0 1.0 CA A:HIS1590 4.7 15.8 1.0 O A:HOH2081 4.8 45.7 1.0 OD1 A:ASP1686 4.8 20.5 1.0 HZ A:KCX1556 4.8 22.4 1.0 CG A:ASP1686 4.8 19.6 1.0 HB3 A:CYS1613 4.8 23.0 1.0 HE2 A:HIS1590 4.8 24.5 1.0 CD1 A:TYR1558 4.9 18.1 1.0

F.Del Cano-Ochoa, B.G.Ng, A.Rubio-Del-Campo, S.Mahajan, M.P.Wilson, M.Vilar, D.Rymen, P.Sanchez-Pintos, J.Kenny, M.Ley Martos, T.Campos, S.B.Wortmann, H.H.Freeze, S.Ramon-Maiques. Beyond Genetics: Deciphering the Impact of Missense Variants in Cad Deficiency. J Inherit Metab Dis 2023.
ISSN: ISSN 1573-2665
PubMed: 37540500
DOI: 10.1002/JIMD.12667