Zinc in PDB 8pbh: Mutant R1617Q of the Dihydroorotase Domain of Human Cad Protein Bound to the Substrate Carbamoyl Aspartate

All present enzymatic activity of Mutant R1617Q of the Dihydroorotase Domain of Human Cad Protein Bound to the Substrate Carbamoyl Aspartate:
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 Substrate Carbamoyl Aspartate, PDB code: 8pbh 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)	48.76 / 1.87
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	82.413, 159.722, 61.575, 90, 90, 90
R / Rfree (%)	15.3 / 19.2

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

Sodium

(Na)

1 atom

The binding sites of Zinc atom in the Mutant R1617Q of the Dihydroorotase Domain of Human Cad Protein Bound to the Substrate Carbamoyl Aspartate (pdb code 8pbh). 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 Substrate Carbamoyl Aspartate, PDB code: 8pbh:
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 Substrate Carbamoyl Aspartate


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 Substrate Carbamoyl Aspartate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1904 b:23.0 occ:0.97 O4 A:NCD1901 2.0 26.5 1.0 NE2 A:HIS1471 2.2 21.0 1.0 OQ2 A:KCX1556 2.2 23.7 1.0 NE2 A:HIS1473 2.2 21.6 1.0 OD1 A:ASP1686 2.2 22.5 1.0 CD2 A:HIS1471 3.1 20.7 1.0 CD2 A:HIS1473 3.1 23.1 1.0 C4 A:NCD1901 3.1 32.8 1.0 CX A:KCX1556 3.1 22.1 1.0 HD2 A:HIS1473 3.2 27.7 1.0 HD2 A:HIS1471 3.2 24.9 1.0 CG A:ASP1686 3.2 23.3 1.0 H61 A:NCD1901 3.2 36.4 1.0 CE1 A:HIS1471 3.2 21.8 1.0 CE1 A:HIS1473 3.3 22.3 1.0 OQ1 A:KCX1556 3.4 20.8 1.0 HE1 A:HIS1471 3.4 26.2 1.0 HG3 A:MET1503 3.4 26.0 1.0 HE1 A:HIS1473 3.5 26.8 1.0 OD2 A:ASP1686 3.6 25.6 1.0 H51 A:NCD1901 3.6 38.0 1.0 ZN A:ZN1905 3.6 21.5 0.8 C5 A:NCD1901 3.7 31.6 1.0 C6 A:NCD1901 3.9 30.3 1.0 HD2 A:HIS1614 4.0 26.9 1.0 HH A:TYR1558 4.1 27.7 1.0 O5 A:NCD1901 4.2 35.0 1.0 HA A:ASP1686 4.2 25.4 1.0 NZ A:KCX1556 4.2 21.8 1.0 CG A:HIS1471 4.2 20.9 1.0 ND1 A:HIS1471 4.3 21.7 1.0 CG A:HIS1473 4.3 22.6 1.0 ND1 A:HIS1473 4.4 23.6 1.0 HZ A:KCX1556 4.4 26.1 1.0 CG A:MET1503 4.4 21.6 1.0 CB A:ASP1686 4.4 21.5 1.0 O2 A:NCD1901 4.5 36.3 1.0 HE3 A:MET1503 4.5 28.9 1.0 CD2 A:HIS1614 4.5 22.4 1.0 NE2 A:HIS1614 4.5 21.5 1.0 HE1 A:TYR1558 4.6 26.9 1.0 HB2 A:ASP1686 4.6 25.8 1.0 H52 A:NCD1901 4.6 38.0 1.0 O61 A:NCD1901 4.7 31.1 1.0 HB2 A:ALA1688 4.7 26.3 1.0 CA A:ASP1686 4.8 21.2 1.0 HG2 A:MET1503 4.8 26.0 1.0 C61 A:NCD1901 4.9 30.2 1.0 HB2 A:MET1503 4.9 25.3 1.0 OH A:TYR1558 4.9 23.1 1.0 N1 A:NCD1901 5.0 29.4 1.0

Zinc binding site 2 out of 2 in the Mutant R1617Q of the Dihydroorotase Domain of Human Cad Protein Bound to the Substrate Carbamoyl Aspartate


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 Substrate Carbamoyl Aspartate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1905 b:21.5 occ:0.84 OQ1 A:KCX1556 1.9 20.8 1.0 ND1 A:HIS1590 2.2 25.0 1.0 NE2 A:HIS1614 2.2 21.5 1.0 O4 A:NCD1901 2.3 26.5 1.0 O5 A:NCD1901 2.3 35.0 1.0 C4 A:NCD1901 2.6 32.8 1.0 CX A:KCX1556 3.0 22.1 1.0 HB2 A:HIS1590 3.0 24.5 1.0 CE1 A:HIS1590 3.1 24.8 1.0 CE1 A:HIS1614 3.1 22.6 1.0 HE1 A:HIS1614 3.2 27.1 1.0 HE1 A:HIS1590 3.2 29.8 1.0 CG A:HIS1590 3.2 22.6 1.0 CD2 A:HIS1614 3.3 22.4 1.0 OQ2 A:KCX1556 3.4 23.7 1.0 HD2 A:HIS1614 3.5 26.9 1.0 CB A:HIS1590 3.6 20.4 1.0 HE1 A:HIS1471 3.6 26.2 1.0 HG21 A:THR1562 3.6 55.7 1.0 ZN A:ZN1904 3.6 23.0 1.0 HE1 A:TYR1558 3.8 26.9 1.0 HG1 A:THR1562 4.0 46.5 1.0 C5 A:NCD1901 4.1 31.6 1.0 NZ A:KCX1556 4.1 21.8 1.0 O2 A:NCD1901 4.2 36.3 1.0 NE2 A:HIS1590 4.2 25.1 1.0 HB3 A:HIS1590 4.2 24.5 1.0 ND1 A:HIS1614 4.3 21.5 1.0 CE1 A:HIS1471 4.3 21.8 1.0 CD2 A:HIS1590 4.3 24.2 1.0 HE2 A:KCX1556 4.3 23.7 1.0 HA A:HIS1590 4.4 22.5 1.0 H51 A:NCD1901 4.4 38.0 1.0 CG A:HIS1614 4.4 22.4 1.0 NE2 A:HIS1471 4.4 21.0 1.0 CE1 A:TYR1558 4.5 22.4 1.0 H52 A:NCD1901 4.5 38.0 1.0 HD1 A:TYR1558 4.5 26.1 1.0 HE3 A:KCX1556 4.5 23.7 1.0 CG2 A:THR1562 4.6 46.5 1.0 OD2 A:ASP1686 4.6 25.6 1.0 HD3 A:PRO1662 4.6 37.0 1.0 CE A:KCX1556 4.6 19.7 1.0 O A:ARG1661 4.6 30.3 1.0 CA A:HIS1590 4.6 18.8 1.0 HB2 A:CYS1613 4.7 24.2 1.0 HB3 A:CYS1613 4.7 24.2 1.0 OG1 A:THR1562 4.8 38.7 1.0 HB A:THR1562 4.8 52.3 1.0 HZ A:KCX1556 4.8 26.1 1.0 CD1 A:TYR1558 4.9 21.7 1.0 HE2 A:HIS1590 5.0 30.2 1.0 OD1 A:ASP1686 5.0 22.5 1.0 HG23 A:THR1562 5.0 55.7 1.0 H61 A:NCD1901 5.0 36.4 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