Zinc in PDB 9fs2: Mutant S1538A of the Dihydroorotase Domain of Human Cad Protein Bound to Substrate

All present enzymatic activity of Mutant S1538A of the Dihydroorotase Domain of Human Cad Protein Bound to Substrate:
2.1.3.2; 3.5.1.2; 3.5.2.3; 6.3.4.16; 6.3.5.5;

The structure of Mutant S1538A of the Dihydroorotase Domain of Human Cad Protein Bound to Substrate, PDB code: 9fs2 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)	47.22 / 1.12
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	82.142, 158.579, 61.95, 90, 90, 90
R / Rfree (%)	14.7 / 16.9

The binding sites of Zinc atom in the Mutant S1538A of the Dihydroorotase Domain of Human Cad Protein Bound to Substrate (pdb code 9fs2). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Mutant S1538A of the Dihydroorotase Domain of Human Cad Protein Bound to Substrate, PDB code: 9fs2:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Mutant S1538A of the Dihydroorotase Domain of Human Cad Protein Bound to Substrate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Mutant S1538A of the Dihydroorotase Domain of Human Cad Protein Bound to Substrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1901 b:10.0 occ:1.00 O4 A:NCD1903 1.9 7.1 0.6 NE2 A:HIS1471 2.0 9.8 1.0 NE2 A:HIS1473 2.1 9.1 1.0 O A:HOH2212 2.1 26.6 0.9 OD1 A:ASP1686 2.1 10.2 1.0 OQ2 A:KCX1556 2.3 9.6 1.0 C4 A:NCD1903 2.9 9.4 0.6 CD2 A:HIS1471 3.0 9.4 1.0 CE1 A:HIS1473 3.0 9.2 1.0 CG A:ASP1686 3.1 9.6 1.0 CD2 A:HIS1473 3.1 10.1 1.0 CE1 A:HIS1471 3.1 9.8 1.0 CX A:KCX1556 3.1 9.5 1.0 H52 A:DOR1905 3.2 14.8 0.4 HD2 A:HIS1471 3.2 11.3 1.0 HE1 A:HIS1473 3.2 11.0 1.0 H51 A:NCD1903 3.2 14.1 0.6 HD2 A:HIS1473 3.2 12.1 1.0 HE1 A:HIS1471 3.3 11.7 1.0 H61 A:NCD1903 3.3 12.0 0.6 HG3 A:MET1503 3.4 11.6 1.0 C5 A:NCD1903 3.5 11.8 0.6 OD2 A:ASP1686 3.5 10.7 1.0 OQ1 A:KCX1556 3.5 9.3 1.0 H6 A:DOR1905 3.6 15.8 0.4 ZN A:ZN1902 3.6 9.7 1.0 H31 A:NCD1903 3.6 12.2 0.6 HD2 A:HIS1614 3.8 11.5 1.0 O5 A:NCD1903 3.9 10.1 0.6 HH A:TYR1558 3.9 13.2 1.0 C6 A:NCD1903 4.0 10.0 0.6 C5 A:DOR1905 4.0 12.3 0.4 HA A:ASP1686 4.1 9.6 1.0 ND1 A:HIS1471 4.1 9.8 1.0 ND1 A:HIS1473 4.2 8.9 1.0 CG A:HIS1471 4.2 9.2 1.0 NZ A:KCX1556 4.2 9.8 1.0 CG A:HIS1473 4.2 8.6 1.0 CB A:ASP1686 4.3 8.5 1.0 C6 A:DOR1905 4.3 13.2 0.4 HZ A:KCX1556 4.3 11.8 1.0 H52 A:NCD1903 4.4 14.1 0.6 CG A:MET1503 4.4 9.7 1.0 C4 A:DOR1905 4.4 9.2 0.4 HB2 A:ASP1686 4.4 10.2 1.0 CD2 A:HIS1614 4.4 9.6 1.0 HE1 A:TYR1558 4.5 12.1 1.0 NE2 A:HIS1614 4.5 10.2 1.0 N3 A:NCD1903 4.5 10.2 0.6 HE3 A:MET1503 4.5 12.3 1.0 O61 A:NCD1903 4.6 8.0 0.6 O4 A:DOR1905 4.7 10.1 0.4 HB2 A:ALA1688 4.7 11.5 1.0 CA A:ASP1686 4.7 8.0 1.0 OH A:TYR1558 4.7 11.0 1.0 HB2 A:MET1503 4.8 11.9 1.0 H51 A:DOR1905 4.8 14.8 0.4 HG2 A:MET1503 4.8 11.6 1.0 C61 A:NCD1903 4.9 8.1 0.6 HD1 A:HIS1473 4.9 10.7 1.0 N3 A:DOR1905 4.9 10.2 0.4 H32 A:NCD1903 5.0 12.2 0.6

Zinc binding site 2 out of 4 in the Mutant S1538A of the Dihydroorotase Domain of Human Cad Protein Bound to Substrate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Mutant S1538A of the Dihydroorotase Domain of Human Cad Protein Bound to Substrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1902 b:9.7 occ:0.96 OQ1 A:KCX1556 1.9 9.3 1.0 O A:HOH2212 2.0 26.6 0.9 NE2 A:HIS1614 2.1 10.2 1.0 ND1 A:HIS1590 2.1 9.9 1.0 O5 A:NCD1903 2.1 10.1 0.6 O4 A:NCD1903 2.3 7.1 0.6 C4 A:NCD1903 2.5 9.4 0.6 O4 A:DOR1905 2.9 10.1 0.4 CE1 A:HIS1590 2.9 10.6 1.0 CX A:KCX1556 3.0 9.5 1.0 HB2 A:HIS1590 3.0 10.9 1.0 CE1 A:HIS1614 3.0 9.9 1.0 HE1 A:HIS1590 3.1 12.7 1.0 CD2 A:HIS1614 3.1 9.6 1.0 CG A:HIS1590 3.2 9.5 1.0 HE1 A:HIS1614 3.2 11.8 1.0 HD2 A:HIS1614 3.3 11.5 1.0 OQ2 A:KCX1556 3.4 9.6 1.0 HE1 A:HIS1471 3.5 11.7 1.0 C4 A:DOR1905 3.5 9.2 0.4 CB A:HIS1590 3.6 9.1 1.0 ZN A:ZN1901 3.6 10.0 1.0 HE1 A:TYR1558 3.7 12.1 1.0 H52 A:DOR1905 3.8 14.8 0.4 H31 A:NCD1903 3.8 12.2 0.6 HG1 A:THR1562 3.9 36.0 0.6 HG21 A:THR1562 3.9 36.0 0.6 HN3 A:DOR1905 4.0 12.2 0.4 C5 A:NCD1903 4.1 11.8 0.6 NE2 A:HIS1590 4.1 11.0 1.0 N3 A:DOR1905 4.1 10.2 0.4 NZ A:KCX1556 4.1 9.8 1.0 ND1 A:HIS1614 4.1 8.2 1.0 CE1 A:HIS1471 4.2 9.8 1.0 CD2 A:HIS1590 4.2 10.1 1.0 CG A:HIS1614 4.2 8.7 1.0 HB3 A:HIS1590 4.2 10.9 1.0 C5 A:DOR1905 4.3 12.3 0.4 HA A:HIS1590 4.3 10.6 1.0 NE2 A:HIS1471 4.3 9.8 1.0 N3 A:NCD1903 4.4 10.2 0.6 HE2 A:KCX1556 4.4 11.5 1.0 H51 A:NCD1903 4.4 14.1 0.6 H52 A:NCD1903 4.4 14.1 0.6 OD2 A:ASP1686 4.4 10.7 1.0 HD3 A:PRO1662 4.4 15.2 1.0 CE1 A:TYR1558 4.4 10.0 1.0 H32 A:NCD1903 4.4 12.2 0.6 HE3 A:KCX1556 4.5 11.5 1.0 HD1 A:TYR1558 4.5 11.4 1.0 O A:ARG1661 4.5 14.2 1.0 CA A:HIS1590 4.6 8.9 1.0 CE A:KCX1556 4.6 9.6 1.0 OG1 A:THR1562 4.7 30.0 0.6 HB3 A:CYS1613 4.7 11.2 1.0 HB2 A:CYS1613 4.7 11.2 1.0 CG2 A:THR1562 4.8 30.0 0.6 HE2 A:HIS1590 4.8 13.2 1.0 H51 A:DOR1905 4.8 14.8 0.4 HZ A:KCX1556 4.8 11.8 1.0 CD1 A:TYR1558 4.9 9.5 1.0 OD1 A:ASP1686 4.9 10.2 1.0 H61 A:NCD1903 4.9 12.0 0.6 HD1 A:HIS1614 4.9 9.8 1.0 CG A:ASP1686 4.9 9.6 1.0 HH A:TYR1558 4.9 13.2 1.0 HB A:THR1562 5.0 35.8 0.6

Zinc binding site 3 out of 4 in the Mutant S1538A of the Dihydroorotase Domain of Human Cad Protein Bound to Substrate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Mutant S1538A of the Dihydroorotase Domain of Human Cad Protein Bound to Substrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1904 b:9.5 occ:0.25 O A:HOH2191 2.1 10.4 1.0 ND1 A:HIS1471 2.1 9.8 1.0 OE2 A:GLU1637 2.2 10.6 1.0 SG A:CYS1613 2.4 10.1 1.0 HB3 A:CYS1613 2.7 11.2 1.0 HB2 A:HIS1471 2.8 9.7 1.0 CD A:GLU1637 2.9 9.2 1.0 OE1 A:GLU1637 2.9 9.7 1.0 CE1 A:HIS1471 3.0 9.8 1.0 CB A:CYS1613 3.0 9.4 1.0 CG A:HIS1471 3.0 9.2 1.0 HE3 A:MET1503 3.1 12.3 1.0 HA A:CYS1613 3.1 9.4 1.0 HE1 A:HIS1471 3.1 11.7 1.0 CB A:HIS1471 3.4 8.1 1.0 HE1 A:MET1503 3.5 12.3 1.0 CA A:CYS1613 3.6 7.8 1.0 CE A:MET1503 3.6 10.3 1.0 HE2 A:MET1503 3.8 12.3 1.0 HB2 A:CYS1613 3.9 11.2 1.0 HB3 A:HIS1471 3.9 9.7 1.0 H A:HIS1614 4.0 10.0 1.0 NE2 A:HIS1471 4.0 9.8 1.0 CD2 A:HIS1471 4.1 9.4 1.0 HD2 A:HIS1611 4.2 9.5 1.0 CG A:GLU1637 4.3 8.9 1.0 HB A:VAL1588 4.3 12.4 1.0 HG23 A:VAL1470 4.3 12.3 1.0 HE2 A:HIS1611 4.4 11.3 1.0 HG2 A:GLU1637 4.4 10.6 1.0 O A:VAL1470 4.4 8.9 1.0 HA A:HIS1471 4.5 9.7 1.0 HG21 A:VAL1588 4.5 14.0 1.0 CA A:HIS1471 4.5 8.1 1.0 N A:HIS1614 4.6 8.3 1.0 N A:CYS1613 4.6 7.8 1.0 HG3 A:GLU1637 4.6 10.6 1.0 HG23 A:VAL1588 4.6 14.0 1.0 C A:CYS1613 4.6 8.0 1.0 O A:HOH2261 4.7 13.3 1.0 HE2 A:KCX1556 4.8 11.5 1.0 H A:CYS1613 4.8 9.4 1.0 CD2 A:HIS1611 4.8 7.9 1.0 HB3 A:ALA1684 4.8 11.7 1.0 HG11 A:VAL1588 4.9 12.4 1.0 CG2 A:VAL1588 4.9 11.6 1.0 NE2 A:HIS1611 4.9 9.4 1.0 HD2 A:HIS1471 4.9 11.3 1.0 HD2 A:KCX1556 5.0 11.6 1.0 CB A:VAL1588 5.0 10.4 1.0

Zinc binding site 4 out of 4 in the Mutant S1538A of the Dihydroorotase Domain of Human Cad Protein Bound to Substrate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Mutant S1538A of the Dihydroorotase Domain of Human Cad Protein Bound to Substrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1913 b:12.2 occ:0.59 O A:HOH2357 2.0 20.3 1.0 ND1 A:HIS1741 2.1 12.9 0.6 O A:HOH2366 2.2 11.8 1.0 HA A:HIS1741 3.0 13.4 0.4 HA A:HIS1741 3.0 12.5 0.6 CE1 A:HIS1741 3.0 12.4 0.6 HB3 A:HIS1741 3.1 14.4 0.4 HE1 A:HIS1741 3.2 14.9 0.6 CG A:HIS1741 3.2 10.4 0.6 HB3 A:HIS1741 3.3 13.7 0.6 O A:HOH2333 3.3 34.0 1.0 CB A:HIS1741 3.6 11.4 0.6 CA A:HIS1741 3.8 10.4 0.6 CB A:HIS1741 3.8 12.0 0.4 CA A:HIS1741 3.8 11.2 0.4 ND1 A:HIS1741 3.9 13.0 0.4 NE2 A:HIS1741 4.2 13.5 0.6 CG A:HIS1741 4.3 11.8 0.4 CD2 A:HIS1741 4.3 11.8 0.6 HA A:ARG1738 4.3 10.9 1.0 HD3 A:PRO1818 4.4 23.7 1.0 HD2 A:PRO1818 4.4 23.7 1.0 HG2 A:PRO1818 4.5 26.2 1.0 HB2 A:HIS1741 4.5 13.7 0.6 C A:HIS1741 4.6 10.2 0.6 HB2 A:HIS1741 4.6 14.4 0.4 C A:HIS1741 4.6 10.9 0.4 H A:HIS1741 4.7 13.0 0.4 H A:HIS1741 4.7 12.3 0.6 O A:ARG1737 4.8 10.5 1.0 CD A:PRO1818 4.8 19.8 1.0 N A:HIS1741 4.8 10.8 0.4 N A:HIS1741 4.8 10.2 0.6

F.Del Cano-Ochoa, L.Ramadane-Morchadi, L.Eixeres, M.Moreno-Morcillo, R.Fernandez-Leiro, S.Ramon-Maiques. Disruption of Cad Oligomerization By Pathogenic Variants. J.Mol.Biol. V. 436 68832 2024.
ISSN: ESSN 1089-8638
PubMed: 39447673
DOI: 10.1016/J.JMB.2024.168832