Zinc in PDB 6hfu: Human Dihydroorotase Mutant F1563Y Co-Crystallized with Carbamoyl Aspartate at pH 7.5

All present enzymatic activity of Human Dihydroorotase Mutant F1563Y Co-Crystallized with Carbamoyl Aspartate at pH 7.5:
2.1.3.2; 3.5.2.3; 6.3.5.5;

The structure of Human Dihydroorotase Mutant F1563Y Co-Crystallized with Carbamoyl Aspartate at pH 7.5, PDB code: 6hfu was solved by S.Ramon-Maiques, A.Grande Garcia, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.74 / 1.40
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	81.813, 159.112, 60.985, 90.00, 90.00, 90.00
R / Rfree (%)	12.7 / 15.1

The binding sites of Zinc atom in the Human Dihydroorotase Mutant F1563Y Co-Crystallized with Carbamoyl Aspartate at pH 7.5 (pdb code 6hfu). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Human Dihydroorotase Mutant F1563Y Co-Crystallized with Carbamoyl Aspartate at pH 7.5, PDB code: 6hfu:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Human Dihydroorotase Mutant F1563Y Co-Crystallized with Carbamoyl Aspartate at pH 7.5


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Human Dihydroorotase Mutant F1563Y Co-Crystallized with Carbamoyl Aspartate at pH 7.5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1901 b:15.8 occ:0.78 OQ1 A:KCX1556 1.9 17.5 1.0 ND1 A:HIS1590 2.0 17.9 1.0 NE2 A:HIS1614 2.0 18.3 1.0 O5 A:NCD1904 2.1 19.0 0.8 O4 A:NCD1904 2.4 16.5 0.8 C4 A:NCD1904 2.6 18.9 0.8 CE1 A:HIS1590 2.9 19.3 1.0 CX A:KCX1556 2.9 18.1 1.0 CE1 A:HIS1614 2.9 18.2 1.0 HB2 A:HIS1590 3.0 17.5 1.0 HE1 A:HIS1590 3.0 23.2 1.0 HE1 A:HIS1614 3.1 21.8 1.0 CG A:HIS1590 3.1 16.9 1.0 CD2 A:HIS1614 3.1 16.6 1.0 HD2 A:HIS1614 3.4 19.9 1.0 OQ2 A:KCX1556 3.4 18.5 1.0 CB A:HIS1590 3.6 14.6 1.0 HE1 A:HIS1471 3.6 19.5 1.0 HE1 A:TYR1558 3.7 21.4 1.0 ZN A:ZN1902 3.8 15.9 0.8 HG21 A:THR1562 3.8 26.3 0.7 HG1 A:THR1562 3.8 23.3 0.7 H31 A:NCD1904 3.8 27.4 0.8 NE2 A:HIS1590 4.0 19.8 1.0 C5 A:NCD1904 4.1 17.6 0.8 ND1 A:HIS1614 4.1 17.6 1.0 CD2 A:HIS1590 4.1 18.8 1.0 NZ A:KCX1556 4.2 17.4 1.0 CG A:HIS1614 4.2 16.5 1.0 HB3 A:HIS1590 4.2 17.5 1.0 CE1 A:HIS1471 4.3 16.3 1.0 HE2 A:KCX1556 4.3 19.4 1.0 HA A:HIS1590 4.3 16.6 1.0 N3 A:NCD1904 4.4 22.8 0.8 H52 A:NCD1904 4.4 21.1 0.8 H51 A:NCD1904 4.4 21.1 0.8 CE1 A:TYR1558 4.4 17.8 1.0 HD1 A:TYR1558 4.5 20.2 1.0 NE2 A:HIS1471 4.5 16.1 1.0 H32 A:NCD1904 4.5 27.4 0.8 HE3 A:KCX1556 4.5 19.4 1.0 HD3 A:PRO1662 4.5 24.0 1.0 OD2 A:ASP1686 4.6 19.3 1.0 CE A:KCX1556 4.6 16.1 1.0 CA A:HIS1590 4.6 13.8 1.0 OG1 A:THR1562 4.6 19.4 0.7 O A:ARG1661 4.6 23.2 1.0 HB2 A:CYS1613 4.6 20.4 1.0 CG2 A:THR1562 4.7 21.9 0.7 HE2 A:HIS1590 4.8 23.8 1.0 HB3 A:CYS1613 4.8 20.4 1.0 CD1 A:TYR1558 4.8 16.8 1.0 HD1 A:HIS1614 4.8 21.1 1.0 HZ A:KCX1556 4.9 20.9 1.0 HB A:THR1562 5.0 24.5 0.7

Zinc binding site 2 out of 3 in the Human Dihydroorotase Mutant F1563Y Co-Crystallized with Carbamoyl Aspartate at pH 7.5


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Human Dihydroorotase Mutant F1563Y Co-Crystallized with Carbamoyl Aspartate at pH 7.5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1902 b:15.9 occ:0.85 O4 A:NCD1904 1.9 16.5 0.8 NE2 A:HIS1471 2.0 16.1 1.0 NE2 A:HIS1473 2.0 16.2 1.0 OD1 A:ASP1686 2.2 18.3 1.0 OQ2 A:KCX1556 2.2 18.5 1.0 CD2 A:HIS1471 2.9 15.2 1.0 C4 A:NCD1904 3.0 18.9 0.8 CE1 A:HIS1473 3.0 17.0 1.0 CE1 A:HIS1471 3.0 16.3 1.0 CD2 A:HIS1473 3.0 17.6 1.0 HD2 A:HIS1471 3.1 18.3 1.0 CG A:ASP1686 3.1 18.3 1.0 CX A:KCX1556 3.1 18.1 1.0 HE1 A:HIS1473 3.1 20.4 1.0 HE1 A:HIS1471 3.2 19.5 1.0 HD2 A:HIS1473 3.3 21.2 1.0 H61 A:NCD1904 3.3 21.2 0.8 HG3 A:MET1503 3.4 20.7 1.0 H52 A:NCD1904 3.4 21.1 0.8 OD2 A:ASP1686 3.5 19.3 1.0 OQ1 A:KCX1556 3.6 17.5 1.0 C5 A:NCD1904 3.6 17.6 0.8 H31 A:NCD1904 3.6 27.4 0.8 ZN A:ZN1901 3.8 15.8 0.8 HD2 A:HIS1614 3.8 19.9 1.0 C6 A:NCD1904 3.9 17.6 0.8 O5 A:NCD1904 4.0 19.0 0.8 CG A:HIS1471 4.1 15.3 1.0 ND1 A:HIS1471 4.1 17.2 1.0 HH A:TYR1558 4.1 22.0 1.0 HA A:ASP1686 4.1 19.0 1.0 ND1 A:HIS1473 4.1 18.2 1.0 CG A:HIS1473 4.2 17.6 1.0 NZ A:KCX1556 4.2 17.4 1.0 CB A:ASP1686 4.3 17.1 1.0 CG A:MET1503 4.3 17.3 1.0 HZ A:KCX1556 4.4 20.9 1.0 CD2 A:HIS1614 4.4 16.6 1.0 HB2 A:ASP1686 4.5 20.5 1.0 H51 A:NCD1904 4.5 21.1 0.8 N3 A:NCD1904 4.5 22.8 0.8 NE2 A:HIS1614 4.5 18.3 1.0 HE1 A:TYR1558 4.6 21.4 1.0 O61 A:NCD1904 4.7 18.3 0.8 HB2 A:ALA1688 4.7 22.1 1.0 HG2 A:MET1503 4.7 20.7 1.0 HE3 A:MET1503 4.7 23.5 1.0 CA A:ASP1686 4.7 15.9 1.0 C61 A:NCD1904 4.8 17.1 0.8 HB2 A:MET1503 4.8 20.4 1.0 OH A:TYR1558 4.9 18.3 1.0 HD1 A:HIS1473 4.9 21.8 1.0 HB3 A:MET1503 5.0 20.4 1.0

Zinc binding site 3 out of 3 in the Human Dihydroorotase Mutant F1563Y Co-Crystallized with Carbamoyl Aspartate at pH 7.5


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Human Dihydroorotase Mutant F1563Y Co-Crystallized with Carbamoyl Aspartate at pH 7.5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1903 b:14.8 occ:0.52 ND1 A:HIS1471 2.1 17.2 1.0 O A:HOH2128 2.1 17.5 1.0 OE1 A:GLU1637 2.1 18.1 1.0 SG A:CYS1613 2.3 17.4 1.0 HB3 A:CYS1613 2.7 20.4 1.0 CD A:GLU1637 2.9 15.4 1.0 HB2 A:HIS1471 2.9 17.4 1.0 CB A:CYS1613 2.9 17.0 1.0 CE1 A:HIS1471 3.0 16.3 1.0 OE2 A:GLU1637 3.0 17.3 1.0 HE3 A:MET1503 3.1 23.5 1.0 CG A:HIS1471 3.1 15.3 1.0 HE1 A:HIS1471 3.1 19.5 1.0 HA A:CYS1613 3.2 18.4 1.0 CB A:HIS1471 3.5 14.5 1.0 HE1 A:MET1503 3.6 23.5 1.0 CA A:CYS1613 3.6 15.3 1.0 CE A:MET1503 3.7 19.6 1.0 HB2 A:CYS1613 3.8 20.4 1.0 HE2 A:MET1503 3.9 23.5 1.0 H A:HIS1614 4.0 19.3 1.0 HB3 A:HIS1471 4.0 17.4 1.0 NE2 A:HIS1471 4.1 16.1 1.0 CD2 A:HIS1471 4.2 15.2 1.0 HD2 A:HIS1611 4.2 16.3 1.0 HB A:VAL1588 4.2 19.9 1.0 CG A:GLU1637 4.2 14.8 1.0 HG21 A:VAL1588 4.2 23.1 1.0 HG2 A:GLU1637 4.3 17.7 1.0 HE2 A:HIS1611 4.4 17.5 1.0 HG23 A:VAL1470 4.4 19.6 1.0 HA A:HIS1471 4.4 17.1 1.0 O A:VAL1470 4.5 15.2 1.0 HG3 A:GLU1637 4.5 17.7 1.0 CA A:HIS1471 4.6 14.3 1.0 N A:HIS1614 4.6 16.1 1.0 N A:CYS1613 4.6 13.0 1.0 O A:HOH2245 4.6 24.6 1.0 C A:CYS1613 4.7 14.8 1.0 HE2 A:KCX1556 4.7 19.4 1.0 H A:CYS1613 4.8 15.6 1.0 CD2 A:HIS1611 4.8 13.6 1.0 HG23 A:VAL1588 4.8 23.1 1.0 HD2 A:KCX1556 4.9 19.2 1.0 CG2 A:VAL1588 4.9 19.3 1.0 HG11 A:VAL1588 4.9 19.9 1.0 NE2 A:HIS1611 4.9 14.6 1.0 HB3 A:ALA1684 4.9 20.6 1.0 CB A:VAL1588 4.9 16.6 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