Zinc in PDB 6hg3: Hybrid Dihydroorotase Domain of Human Cad with E. Coli Flexible Loop, Bound to Dihydroorotate

All present enzymatic activity of Hybrid Dihydroorotase Domain of Human Cad with E. Coli Flexible Loop, Bound to Dihydroorotate:
2.1.3.2; 3.5.2.3; 6.3.5.5;

The structure of Hybrid Dihydroorotase Domain of Human Cad with E. Coli Flexible Loop, Bound to Dihydroorotate, PDB code: 6hg3 was solved by S.Ramon-Maiques, F.Del Cano-Ochoa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.88 / 1.97
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	81.909, 159.472, 61.878, 90.00, 90.00, 90.00
R / Rfree (%)	16.7 / 19

The binding sites of Zinc atom in the Hybrid Dihydroorotase Domain of Human Cad with E. Coli Flexible Loop, Bound to Dihydroorotate (pdb code 6hg3). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Hybrid Dihydroorotase Domain of Human Cad with E. Coli Flexible Loop, Bound to Dihydroorotate, PDB code: 6hg3:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Hybrid Dihydroorotase Domain of Human Cad with E. Coli Flexible Loop, Bound to Dihydroorotate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Hybrid Dihydroorotase Domain of Human Cad with E. Coli Flexible Loop, Bound to Dihydroorotate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1903 b:28.9 occ:0.65 OQ1 A:KCX1556 1.6 64.8 1.0 NE2 A:HIS1616 2.0 40.8 1.0 O A:HOH2140 2.1 32.7 1.0 CX A:KCX1556 2.1 62.4 1.0 ND1 A:HIS1592 2.1 37.7 1.0 HZ A:KCX1556 2.7 56.4 1.0 NZ A:KCX1556 2.8 47.0 1.0 CE1 A:HIS1616 2.8 40.6 1.0 HE1 A:HIS1616 2.8 48.7 1.0 OQ2 A:KCX1556 2.9 70.0 1.0 CE1 A:HIS1592 3.0 45.7 1.0 HB2 A:HIS1592 3.0 35.7 1.0 HE1 A:HIS1592 3.1 54.9 1.0 CD2 A:HIS1616 3.1 36.3 1.0 HE2 A:TYR1558 3.1 62.6 1.0 CG A:HIS1592 3.2 34.7 1.0 O4 A:DOR1906 3.2 38.0 0.9 ZN A:ZN1904 3.4 30.5 0.8 O A:HOH2005 3.4 37.1 1.0 HD2 A:HIS1616 3.5 43.6 1.0 CB A:HIS1592 3.6 29.7 1.0 HE1 A:HIS1471 3.7 47.0 1.0 C4 A:DOR1906 3.8 47.2 0.9 H51 A:DOR1906 3.8 60.4 0.9 CE2 A:TYR1558 3.9 52.1 1.0 ND1 A:HIS1616 3.9 34.4 1.0 NE2 A:HIS1471 4.0 37.1 1.0 NE2 A:HIS1592 4.1 41.1 1.0 CE A:KCX1556 4.1 41.1 1.0 HH A:TYR1558 4.1 64.2 1.0 CG A:HIS1616 4.1 41.4 1.0 CE1 A:HIS1471 4.2 39.1 1.0 CD2 A:HIS1592 4.2 42.9 1.0 HB3 A:HIS1592 4.2 35.7 1.0 HD3 A:PRO1664 4.3 45.1 1.0 HD2 A:TYR1558 4.3 52.2 1.0 HE3 A:KCX1556 4.4 49.4 1.0 HA A:HIS1592 4.4 32.9 1.0 C5 A:DOR1906 4.4 50.3 0.9 HE2 A:KCX1556 4.4 49.4 1.0 OD2 A:ASP1688 4.4 37.5 1.0 O A:ARG1663 4.5 33.7 1.0 CD2 A:TYR1558 4.5 43.5 1.0 HB2 A:CYS1615 4.5 34.1 1.0 HB3 A:CYS1615 4.6 34.1 1.0 N3 A:DOR1906 4.6 46.6 0.9 CA A:HIS1592 4.6 27.4 1.0 HN3 A:DOR1906 4.7 56.0 0.9 HD1 A:HIS1616 4.7 41.3 1.0 CZ A:TYR1558 4.7 51.1 1.0 OD1 A:ASP1688 4.7 32.7 1.0 OH A:TYR1558 4.8 53.5 1.0 HE2 A:HIS1592 4.8 49.4 1.0 CG A:ASP1688 4.9 34.0 1.0 H52 A:DOR1906 5.0 60.4 0.9 CB A:CYS1615 5.0 28.4 1.0

Zinc binding site 2 out of 2 in the Hybrid Dihydroorotase Domain of Human Cad with E. Coli Flexible Loop, Bound to Dihydroorotate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Hybrid Dihydroorotase Domain of Human Cad with E. Coli Flexible Loop, Bound to Dihydroorotate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1904 b:30.5 occ:0.84 O A:HOH2140 2.0 32.7 1.0 O A:HOH2005 2.0 37.1 1.0 OQ2 A:KCX1556 2.0 70.0 1.0 NE2 A:HIS1473 2.1 25.9 1.0 OD1 A:ASP1688 2.3 32.7 1.0 NE2 A:HIS1471 2.3 37.1 1.0 CX A:KCX1556 2.8 62.4 1.0 CE1 A:HIS1473 3.0 33.5 1.0 H51 A:DOR1906 3.0 60.4 0.9 HD2 A:HIS1471 3.0 39.2 1.0 CD2 A:HIS1471 3.0 32.6 1.0 HE1 A:HIS1473 3.1 40.3 1.0 CD2 A:HIS1473 3.1 32.6 1.0 CG A:ASP1688 3.3 34.0 1.0 ZN A:ZN1903 3.4 28.9 0.7 HD2 A:HIS1473 3.4 39.2 1.0 HG3 A:MET1503 3.4 42.5 1.0 OQ1 A:KCX1556 3.5 64.8 1.0 CE1 A:HIS1471 3.5 39.1 1.0 OD2 A:ASP1688 3.7 37.5 1.0 H6 A:DOR1906 3.7 54.0 0.9 NZ A:KCX1556 3.8 47.0 1.0 HE2 A:KCX1556 3.8 49.4 1.0 HE1 A:HIS1471 3.8 47.0 1.0 HD2 A:HIS1616 3.8 43.6 1.0 C5 A:DOR1906 3.9 50.3 0.9 ND1 A:HIS1473 4.1 36.6 1.0 NE2 A:HIS1616 4.2 40.8 1.0 CE A:KCX1556 4.2 41.1 1.0 CG A:HIS1473 4.2 29.7 1.0 HA A:ASP1688 4.3 33.3 1.0 CG A:HIS1471 4.3 30.2 1.0 CD2 A:HIS1616 4.3 36.3 1.0 C6 A:DOR1906 4.4 44.9 0.9 HE3 A:KCX1556 4.4 49.4 1.0 CG A:MET1503 4.4 35.4 1.0 C4 A:DOR1906 4.4 47.2 0.9 HZ A:KCX1556 4.4 56.4 1.0 ND1 A:HIS1471 4.4 33.2 1.0 HE3 A:MET1503 4.5 42.6 1.0 CB A:ASP1688 4.5 29.9 1.0 O4 A:DOR1906 4.6 38.0 0.9 H52 A:DOR1906 4.6 60.4 0.9 HE2 A:TYR1558 4.7 62.6 1.0 HB2 A:ASP1688 4.7 35.9 1.0 HG2 A:MET1503 4.8 42.5 1.0 CA A:ASP1688 4.9 27.7 1.0 HD1 A:HIS1473 4.9 44.0 1.0 HB2 A:ALA1690 4.9 34.6 1.0 HB2 A:MET1503 4.9 37.8 1.0 O A:HOH2252 4.9 39.3 1.0

F.Del Cano-Ochoa, A.Grande-Garcia, M.Reverte-Lopez, M.D'abramo, S.Ramon-Maiques. Characterization of the Catalytic Flexible Loop in the Dihydroorotase Domain of the Human Multi-Enzymatic Protein Cad. J. Biol. Chem. V. 293 18903 2018.
ISSN: ESSN 1083-351X
PubMed: 30315107
DOI: 10.1074/JBC.RA118.005494