Zinc in PDB 6hfs: Human Dihydroorotase Mutant F1563Y Co-Crystallized with Carbamoyl Aspartate at pH 6.5

All present enzymatic activity of Human Dihydroorotase Mutant F1563Y Co-Crystallized with Carbamoyl Aspartate at pH 6.5:
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 6.5, PDB code: 6hfs 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)	40.85 / 1.35
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	81.697, 159.029, 60.919, 90.00, 90.00, 90.00
R / Rfree (%)	12.5 / 14.6

The binding sites of Zinc atom in the Human Dihydroorotase Mutant F1563Y Co-Crystallized with Carbamoyl Aspartate at pH 6.5 (pdb code 6hfs). 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 6.5, PDB code: 6hfs:
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 6.5


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 6.5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1901 b:18.5 occ:0.79 OQ1 A:KCX1556 1.9 19.1 1.0 O5 A:NCD1905 2.0 20.8 0.8 ND1 A:HIS1590 2.1 19.2 1.0 NE2 A:HIS1614 2.1 20.1 1.0 O4 A:NCD1905 2.4 19.6 0.8 C4 A:NCD1905 2.6 20.8 0.8 CE1 A:HIS1590 2.9 20.9 1.0 CX A:KCX1556 3.0 19.4 1.0 HB2 A:HIS1590 3.0 20.2 1.0 CE1 A:HIS1614 3.0 19.6 1.0 HE1 A:HIS1590 3.1 25.1 1.0 CD2 A:HIS1614 3.1 18.7 1.0 CG A:HIS1590 3.1 18.2 1.0 HE1 A:HIS1614 3.1 23.5 1.0 HD2 A:HIS1614 3.3 22.4 1.0 OQ2 A:KCX1556 3.4 21.2 1.0 CB A:HIS1590 3.5 16.8 1.0 HE1 A:HIS1471 3.6 23.3 1.0 HE1 A:TYR1558 3.7 22.9 1.0 HG1 A:THR1562 3.8 25.3 0.7 ZN A:ZN1902 3.8 17.8 0.8 HG21 A:THR1562 3.8 26.1 0.7 H31 A:NCD1905 3.8 29.1 0.8 NE2 A:HIS1590 4.1 20.9 1.0 C5 A:NCD1905 4.1 20.3 0.8 ND1 A:HIS1614 4.1 18.5 1.0 NZ A:KCX1556 4.2 19.5 1.0 HB3 A:HIS1590 4.2 20.2 1.0 CD2 A:HIS1590 4.2 20.5 1.0 CG A:HIS1614 4.2 18.1 1.0 CE1 A:HIS1471 4.3 19.4 1.0 HE2 A:KCX1556 4.3 21.5 1.0 N3 A:NCD1905 4.4 24.2 0.8 H51 A:NCD1905 4.4 24.4 0.8 HA A:HIS1590 4.4 18.1 1.0 H52 A:NCD1905 4.4 24.4 0.8 CE1 A:TYR1558 4.4 19.1 1.0 HD1 A:TYR1558 4.4 22.5 1.0 NE2 A:HIS1471 4.5 18.1 1.0 H32 A:NCD1905 4.5 29.1 0.8 HD3 A:PRO1662 4.5 27.5 1.0 HE3 A:KCX1556 4.6 21.5 1.0 OD2 A:ASP1686 4.6 22.4 1.0 OG1 A:THR1562 4.6 21.1 0.7 CA A:HIS1590 4.6 15.1 1.0 CE A:KCX1556 4.6 17.9 1.0 HB2 A:CYS1613 4.6 23.1 1.0 O A:ARG1661 4.6 27.4 1.0 CG2 A:THR1562 4.7 21.8 0.7 HB3 A:CYS1613 4.7 23.1 1.0 CD1 A:TYR1558 4.8 18.8 1.0 HZ A:KCX1556 4.9 23.4 1.0 HB A:THR1562 5.0 25.9 0.7

Zinc binding site 2 out of 4 in the Human Dihydroorotase Mutant F1563Y Co-Crystallized with Carbamoyl Aspartate at pH 6.5


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 6.5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1902 b:17.8 occ:0.82 O4 A:NCD1905 1.9 19.6 0.8 NE2 A:HIS1471 2.0 18.1 1.0 NE2 A:HIS1473 2.0 19.9 1.0 OD1 A:ASP1686 2.2 20.2 1.0 OQ2 A:KCX1556 2.3 21.2 1.0 CD2 A:HIS1471 2.9 17.0 1.0 C4 A:NCD1905 3.0 20.8 0.8 CE1 A:HIS1473 3.0 19.6 1.0 CE1 A:HIS1471 3.0 19.4 1.0 CD2 A:HIS1473 3.0 19.7 1.0 HD2 A:HIS1471 3.1 20.4 1.0 CG A:ASP1686 3.1 20.5 1.0 CX A:KCX1556 3.1 19.4 1.0 HE1 A:HIS1473 3.2 23.5 1.0 HD2 A:HIS1473 3.2 23.6 1.0 HE1 A:HIS1471 3.2 23.3 1.0 H61 A:NCD1905 3.3 23.6 0.8 HG3 A:MET1503 3.4 22.7 1.0 H52 A:NCD1905 3.5 24.4 0.8 OD2 A:ASP1686 3.5 22.4 1.0 OQ1 A:KCX1556 3.5 19.1 1.0 C5 A:NCD1905 3.6 20.3 0.8 H31 A:NCD1905 3.7 29.1 0.8 HD2 A:HIS1614 3.8 22.4 1.0 ZN A:ZN1901 3.8 18.5 0.8 C6 A:NCD1905 3.9 19.7 0.8 O5 A:NCD1905 4.0 20.8 0.8 CG A:HIS1471 4.1 17.5 1.0 HA A:ASP1686 4.1 21.7 1.0 ND1 A:HIS1471 4.1 19.9 1.0 HH A:TYR1558 4.1 24.9 1.0 ND1 A:HIS1473 4.1 19.8 1.0 CG A:HIS1473 4.2 20.2 1.0 NZ A:KCX1556 4.3 19.5 1.0 CB A:ASP1686 4.3 19.1 1.0 HZ A:KCX1556 4.4 23.4 1.0 CG A:MET1503 4.4 18.9 1.0 CD2 A:HIS1614 4.4 18.7 1.0 HB2 A:ASP1686 4.5 22.9 1.0 N3 A:NCD1905 4.5 24.2 0.8 H51 A:NCD1905 4.5 24.4 0.8 NE2 A:HIS1614 4.6 20.1 1.0 HE1 A:TYR1558 4.6 22.9 1.0 HE3 A:MET1503 4.6 24.5 1.0 O61 A:NCD1905 4.7 20.5 0.8 HB2 A:ALA1688 4.7 24.1 1.0 CA A:ASP1686 4.7 18.1 1.0 C61 A:NCD1905 4.8 19.7 0.8 HB2 A:MET1503 4.8 21.6 1.0 HG2 A:MET1503 4.8 22.7 1.0 OH A:TYR1558 4.9 20.7 1.0 HB3 A:MET1503 5.0 21.6 1.0

Zinc binding site 3 out of 4 in the Human Dihydroorotase Mutant F1563Y Co-Crystallized with Carbamoyl Aspartate at pH 6.5


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 6.5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1903 b:19.2 occ:0.43 HG A:CYS1613 1.5 24.1 1.0 O A:HOH2149 2.1 19.7 1.0 ND1 A:HIS1471 2.1 19.9 1.0 OE1 A:GLU1637 2.2 20.2 1.0 SG A:CYS1613 2.3 20.1 1.0 HB3 A:CYS1613 2.7 23.1 1.0 CD A:GLU1637 2.9 17.8 1.0 HB2 A:HIS1471 2.9 19.7 1.0 OE2 A:GLU1637 2.9 20.1 1.0 CB A:CYS1613 2.9 19.3 1.0 CE1 A:HIS1471 3.0 19.4 1.0 HE3 A:MET1503 3.0 24.5 1.0 CG A:HIS1471 3.1 17.5 1.0 HE1 A:HIS1471 3.1 23.3 1.0 HA A:CYS1613 3.2 20.4 1.0 HE1 A:MET1503 3.5 24.5 1.0 CB A:HIS1471 3.5 16.4 1.0 CE A:MET1503 3.6 20.4 1.0 CA A:CYS1613 3.6 17.0 1.0 HE2 A:MET1503 3.8 24.5 1.0 HB2 A:CYS1613 3.8 23.1 1.0 H A:HIS1614 4.0 21.8 1.0 HB3 A:HIS1471 4.0 19.7 1.0 NE2 A:HIS1471 4.1 18.1 1.0 HD2 A:HIS1611 4.1 18.8 1.0 CD2 A:HIS1471 4.2 17.0 1.0 HB A:VAL1588 4.2 21.5 1.0 CG A:GLU1637 4.2 18.0 1.0 HG21 A:VAL1588 4.3 25.4 1.0 HG2 A:GLU1637 4.3 21.6 1.0 HG23 A:VAL1470 4.4 21.1 1.0 HA A:HIS1471 4.5 18.7 1.0 O A:VAL1470 4.5 16.9 1.0 HG3 A:GLU1637 4.5 21.6 1.0 N A:CYS1613 4.6 14.7 1.0 N A:HIS1614 4.6 18.1 1.0 CA A:HIS1471 4.6 15.6 1.0 C A:CYS1613 4.7 17.7 1.0 O A:HOH2219 4.7 27.4 1.0 CD2 A:HIS1611 4.8 15.7 1.0 HE2 A:KCX1556 4.8 21.5 1.0 H A:CYS1613 4.8 17.6 1.0 HG11 A:VAL1588 4.8 22.4 1.0 HD2 A:KCX1556 4.8 21.8 1.0 NE2 A:HIS1611 4.8 16.1 1.0 CG2 A:VAL1588 4.9 21.1 1.0 HG23 A:VAL1588 4.9 25.4 1.0 CB A:VAL1588 4.9 17.9 1.0 HB3 A:ALA1684 5.0 22.8 1.0

Zinc binding site 4 out of 4 in the Human Dihydroorotase Mutant F1563Y Co-Crystallized with Carbamoyl Aspartate at pH 6.5


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 6.5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1904 b:49.0 occ:1.00 O A:HOH2299 2.0 50.2 1.0 NE2 A:HIS1734 2.2 18.9 1.0 O A:HOH2303 2.3 51.6 1.0 HE1 A:HIS1734 2.9 23.2 1.0 CE1 A:HIS1734 2.9 19.4 1.0 CD2 A:HIS1734 3.4 17.4 1.0 HD2 A:HIS1734 3.7 20.9 1.0 O A:HOH2196 4.1 41.6 1.0 ND1 A:HIS1734 4.1 17.2 1.0 HD2 A:HIS1733 4.3 20.8 1.0 CG A:HIS1734 4.4 16.0 1.0 HG3 A:PRO1465 4.5 27.0 1.0 O A:HOH2155 4.6 42.6 1.0 HD13 A:LEU1729 4.8 27.4 1.0 HB3 A:LEU1729 4.8 22.1 1.0 HE22 A:GLN1730 4.8 20.7 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