Zinc in PDB 6hfr: Human Dihydroorotase Mutant F1563Y Co-Crystallized with Carbamoyl Aspartate at pH 7.0

All present enzymatic activity of Human Dihydroorotase Mutant F1563Y Co-Crystallized with Carbamoyl Aspartate at pH 7.0:
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 7.0, PDB code: 6hfr 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)	46.75 / 1.30
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	81.863, 159.088, 60.989, 90.00, 90.00, 90.00
R / Rfree (%)	12.6 / 14.4

The binding sites of Zinc atom in the Human Dihydroorotase Mutant F1563Y Co-Crystallized with Carbamoyl Aspartate at pH 7.0 (pdb code 6hfr). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Human Dihydroorotase Mutant F1563Y Co-Crystallized with Carbamoyl Aspartate at pH 7.0, PDB code: 6hfr:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Human Dihydroorotase Mutant F1563Y Co-Crystallized with Carbamoyl Aspartate at pH 7.0


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 7.0 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1901 b:15.0 occ:0.75 OQ1 A:KCX1556 1.9 16.9 1.0 NE2 A:HIS1614 2.0 17.6 1.0 ND1 A:HIS1590 2.0 17.1 1.0 O5 A:NCD1904 2.1 18.2 0.8 O4 A:NCD1904 2.4 16.8 0.8 C4 A:NCD1904 2.6 17.3 0.8 CE1 A:HIS1590 2.9 18.5 1.0 CX A:KCX1556 2.9 16.9 1.0 CE1 A:HIS1614 3.0 16.7 1.0 HB2 A:HIS1590 3.0 17.6 1.0 HE1 A:HIS1590 3.0 22.2 1.0 CD2 A:HIS1614 3.1 16.3 1.0 HE1 A:HIS1614 3.1 20.1 1.0 CG A:HIS1590 3.1 16.2 1.0 HD2 A:HIS1614 3.3 19.6 1.0 OQ2 A:KCX1556 3.4 18.3 1.0 CB A:HIS1590 3.6 14.7 1.0 HE1 A:HIS1471 3.6 19.6 1.0 HE1 A:TYR1558 3.7 21.0 1.0 HG1 A:THR1562 3.8 24.3 0.8 ZN A:ZN1902 3.8 15.3 0.8 HG21 A:THR1562 3.8 25.6 0.8 H31 A:NCD1904 3.9 24.6 0.8 NE2 A:HIS1590 4.0 18.6 1.0 C5 A:NCD1904 4.1 16.8 0.8 ND1 A:HIS1614 4.1 16.1 1.0 CD2 A:HIS1590 4.2 18.4 1.0 NZ A:KCX1556 4.2 17.5 1.0 CG A:HIS1614 4.2 15.9 1.0 HB3 A:HIS1590 4.2 17.6 1.0 CE1 A:HIS1471 4.3 16.3 1.0 HE2 A:KCX1556 4.3 19.3 1.0 HA A:HIS1590 4.4 16.4 1.0 H52 A:NCD1904 4.4 20.2 0.8 H51 A:NCD1904 4.4 20.2 0.8 N3 A:NCD1904 4.4 20.5 0.8 CE1 A:TYR1558 4.4 17.5 1.0 HD1 A:TYR1558 4.5 20.3 1.0 NE2 A:HIS1471 4.5 15.5 1.0 HE3 A:KCX1556 4.5 19.3 1.0 HD3 A:PRO1662 4.5 22.7 1.0 H32 A:NCD1904 4.5 24.6 0.8 CE A:KCX1556 4.6 16.1 1.0 OD2 A:ASP1686 4.6 19.0 1.0 CA A:HIS1590 4.6 13.7 1.0 OG1 A:THR1562 4.6 20.3 0.8 O A:ARG1661 4.6 21.4 1.0 HB2 A:CYS1613 4.7 20.2 1.0 CG2 A:THR1562 4.7 21.3 0.8 HB3 A:CYS1613 4.8 20.2 1.0 HE2 A:HIS1590 4.8 22.3 1.0 CD1 A:TYR1558 4.8 16.9 1.0 HD1 A:HIS1614 4.9 19.3 1.0 HZ A:KCX1556 4.9 21.0 1.0 HB A:THR1562 5.0 25.5 0.8

Zinc binding site 2 out of 4 in the Human Dihydroorotase Mutant F1563Y Co-Crystallized with Carbamoyl Aspartate at pH 7.0


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 7.0 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1902 b:15.3 occ:0.83 O4 A:NCD1904 2.0 16.8 0.8 NE2 A:HIS1471 2.0 15.5 1.0 NE2 A:HIS1473 2.0 16.9 1.0 OD1 A:ASP1686 2.1 17.2 1.0 OQ2 A:KCX1556 2.3 18.3 1.0 CD2 A:HIS1471 2.9 14.5 1.0 CE1 A:HIS1473 3.0 16.6 1.0 C4 A:NCD1904 3.0 17.3 0.8 CE1 A:HIS1471 3.0 16.3 1.0 CD2 A:HIS1473 3.0 17.1 1.0 HD2 A:HIS1471 3.1 17.4 1.0 CG A:ASP1686 3.1 16.9 1.0 CX A:KCX1556 3.1 16.9 1.0 HE1 A:HIS1473 3.1 19.9 1.0 HE1 A:HIS1471 3.2 19.6 1.0 HD2 A:HIS1473 3.2 20.6 1.0 H61 A:NCD1904 3.3 20.1 0.8 HG3 A:MET1503 3.4 21.3 1.0 H52 A:NCD1904 3.5 20.2 0.8 OD2 A:ASP1686 3.5 19.0 1.0 OQ1 A:KCX1556 3.5 16.9 1.0 C5 A:NCD1904 3.6 16.8 0.8 H31 A:NCD1904 3.7 24.6 0.8 HD2 A:HIS1614 3.8 19.6 1.0 ZN A:ZN1901 3.8 15.0 0.8 C6 A:NCD1904 3.9 16.7 0.8 O5 A:NCD1904 4.0 18.2 0.8 HA A:ASP1686 4.1 18.9 1.0 CG A:HIS1471 4.1 15.1 1.0 ND1 A:HIS1471 4.1 17.4 1.0 HH A:TYR1558 4.1 22.3 1.0 ND1 A:HIS1473 4.1 17.0 1.0 CG A:HIS1473 4.2 17.5 1.0 NZ A:KCX1556 4.3 17.5 1.0 CB A:ASP1686 4.3 16.4 1.0 CG A:MET1503 4.4 17.7 1.0 CD2 A:HIS1614 4.4 16.3 1.0 HZ A:KCX1556 4.4 21.0 1.0 HB2 A:ASP1686 4.5 19.7 1.0 N3 A:NCD1904 4.5 20.5 0.8 H51 A:NCD1904 4.5 20.2 0.8 NE2 A:HIS1614 4.6 17.6 1.0 HE1 A:TYR1558 4.6 21.0 1.0 HE3 A:MET1503 4.6 22.6 1.0 HB2 A:ALA1688 4.6 22.4 1.0 O61 A:NCD1904 4.6 17.8 0.8 CA A:ASP1686 4.7 15.8 1.0 HG2 A:MET1503 4.8 21.3 1.0 C61 A:NCD1904 4.8 17.5 0.8 HB2 A:MET1503 4.8 19.9 1.0 OH A:TYR1558 4.9 18.6 1.0 HD1 A:HIS1473 4.9 20.4 1.0 HB3 A:MET1503 5.0 19.9 1.0

Zinc binding site 3 out of 4 in the Human Dihydroorotase Mutant F1563Y Co-Crystallized with Carbamoyl Aspartate at pH 7.0


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 7.0 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1903 b:14.9 occ:0.49 ND1 A:HIS1471 2.1 17.4 1.0 O A:HOH2108 2.1 17.4 1.0 OE1 A:GLU1637 2.1 18.4 1.0 SG A:CYS1613 2.3 17.0 1.0 HB3 A:CYS1613 2.7 20.2 1.0 CD A:GLU1637 2.8 16.1 1.0 HB2 A:HIS1471 2.9 17.8 1.0 CB A:CYS1613 3.0 16.8 1.0 OE2 A:GLU1637 3.0 16.9 1.0 CE1 A:HIS1471 3.0 16.3 1.0 HE3 A:MET1503 3.1 22.6 1.0 CG A:HIS1471 3.1 15.1 1.0 HE1 A:HIS1471 3.1 19.6 1.0 HA A:CYS1613 3.2 17.6 1.0 CB A:HIS1471 3.5 14.8 1.0 HE1 A:MET1503 3.6 22.6 1.0 CA A:CYS1613 3.6 14.7 1.0 CE A:MET1503 3.7 18.8 1.0 HB2 A:CYS1613 3.8 20.2 1.0 HE2 A:MET1503 3.8 22.6 1.0 H A:HIS1614 4.0 17.9 1.0 HB3 A:HIS1471 4.0 17.8 1.0 NE2 A:HIS1471 4.1 15.5 1.0 CD2 A:HIS1471 4.2 14.5 1.0 HD2 A:HIS1611 4.2 16.5 1.0 CG A:GLU1637 4.2 16.0 1.0 HB A:VAL1588 4.2 19.2 1.0 HG21 A:VAL1588 4.3 23.0 1.0 HG2 A:GLU1637 4.3 19.2 1.0 HE2 A:HIS1611 4.4 17.3 1.0 HG23 A:VAL1470 4.4 19.2 1.0 O A:VAL1470 4.5 15.2 1.0 HA A:HIS1471 4.5 16.6 1.0 HG3 A:GLU1637 4.5 19.2 1.0 N A:HIS1614 4.6 14.9 1.0 CA A:HIS1471 4.6 13.8 1.0 N A:CYS1613 4.6 13.0 1.0 O A:HOH2253 4.6 23.5 1.0 C A:CYS1613 4.7 14.8 1.0 HE2 A:KCX1556 4.7 19.3 1.0 CD2 A:HIS1611 4.8 13.8 1.0 H A:CYS1613 4.8 15.6 1.0 HG11 A:VAL1588 4.8 20.5 1.0 HD2 A:KCX1556 4.9 19.7 1.0 NE2 A:HIS1611 4.9 14.4 1.0 HG23 A:VAL1588 4.9 23.0 1.0 HB3 A:ALA1684 4.9 20.3 1.0 CG2 A:VAL1588 4.9 19.1 1.0 CB A:VAL1588 5.0 16.0 1.0

Zinc binding site 4 out of 4 in the Human Dihydroorotase Mutant F1563Y Co-Crystallized with Carbamoyl Aspartate at pH 7.0


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Human Dihydroorotase Mutant F1563Y Co-Crystallized with Carbamoyl Aspartate at pH 7.0 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1908 b:28.3 occ:1.00 O A:HOH2285 1.8 43.1 1.0 NE2 A:HIS1734 2.1 17.9 1.0 O A:HOH2312 2.2 46.0 1.0 HE1 A:HIS1734 2.8 21.3 1.0 CE1 A:HIS1734 2.8 17.8 1.0 CD2 A:HIS1734 3.3 16.3 1.0 HD2 A:HIS1734 3.7 19.6 1.0 ND1 A:HIS1734 4.0 16.1 1.0 HD2 A:HIS1733 4.2 18.8 1.0 CG A:HIS1734 4.3 14.9 1.0 O A:HOH2194 4.4 35.5 1.0 HG3 A:PRO1465 4.5 25.8 1.0 O A:HOH2128 4.7 38.8 1.0 HD1 A:HIS1734 4.8 19.3 1.0 HB3 A:LEU1729 4.9 20.9 1.0 HE22 A:GLN1730 4.9 19.2 1.0 CD2 A:HIS1733 4.9 15.7 1.0 HD13 A:LEU1729 4.9 24.9 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