Zinc in PDB 6hfd: Human Dihydroorotase Mutant F1563L Apo Structure

All present enzymatic activity of Human Dihydroorotase Mutant F1563L Apo Structure:
2.1.3.2; 3.5.2.3; 6.3.5.5;

The structure of Human Dihydroorotase Mutant F1563L Apo Structure, PDB code: 6hfd 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)	39.69 / 1.87
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	81.560, 158.770, 60.890, 90.00, 90.00, 90.00
R / Rfree (%)	13.2 / 16.7

The binding sites of Zinc atom in the Human Dihydroorotase Mutant F1563L Apo Structure (pdb code 6hfd). 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 F1563L Apo Structure, PDB code: 6hfd:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Human Dihydroorotase Mutant F1563L Apo Structure


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 F1563L Apo Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1901 b:23.7 occ:0.75 OQ1 A:KCX1556 1.6 33.6 1.0 NE2 A:HIS1614 2.0 27.8 1.0 O A:HOH2117 2.0 28.5 1.0 ND1 A:HIS1590 2.0 24.9 1.0 CX A:KCX1556 2.6 35.0 1.0 CE1 A:HIS1614 2.9 29.2 1.0 CE1 A:HIS1590 2.9 26.9 1.0 HB2 A:HIS1590 2.9 24.4 1.0 CD2 A:HIS1614 3.0 29.2 1.0 HE1 A:HIS1590 3.1 32.3 1.0 HE1 A:HIS1614 3.1 35.0 1.0 CG A:HIS1590 3.1 23.0 1.0 HE1 A:HIS1471 3.1 30.3 1.0 OQ2 A:KCX1556 3.2 34.6 1.0 HD2 A:HIS1614 3.2 35.0 1.0 ZN A:ZN1902 3.3 27.1 0.9 CB A:HIS1590 3.5 20.3 1.0 NZ A:KCX1556 3.6 37.6 1.0 HZ A:KCX1556 3.6 45.1 1.0 CE1 A:HIS1471 3.8 25.3 1.0 HE1 A:TYR1558 3.8 35.2 0.4 NE2 A:HIS1471 4.0 22.7 1.0 ND1 A:HIS1614 4.0 28.4 1.0 NE2 A:HIS1590 4.0 26.1 1.0 CG A:HIS1614 4.1 28.1 1.0 HE1 A:TYR1558 4.1 25.0 0.6 CD2 A:HIS1590 4.1 25.3 1.0 CE1 A:TYR1558 4.1 29.4 0.4 HB3 A:HIS1590 4.2 24.4 1.0 OD2 A:ASP1686 4.2 30.9 1.0 HA A:HIS1590 4.2 21.6 1.0 HB3 A:CYS1613 4.3 32.4 1.0 HD3 A:PRO1662 4.3 36.9 1.0 HB2 A:CYS1613 4.3 32.4 1.0 CA A:HIS1590 4.5 18.0 1.0 CZ A:TYR1558 4.6 30.3 0.4 OH A:TYR1558 4.6 32.2 0.4 O A:ARG1661 4.6 36.0 1.0 CB A:CYS1613 4.7 27.0 1.0 HD1 A:TYR1558 4.7 27.0 0.6 OD1 A:ASP1686 4.7 25.5 1.0 HE3 A:KCX1556 4.7 39.7 1.0 CE A:KCX1556 4.7 33.1 1.0 CE1 A:TYR1558 4.8 20.8 0.6 CG A:ASP1686 4.8 27.0 1.0 CD1 A:TYR1558 4.8 27.8 0.4 HD1 A:HIS1614 4.8 34.1 1.0 HE2 A:HIS1590 4.8 31.4 1.0 HD1 A:TYR1558 4.9 33.4 0.4

Zinc binding site 2 out of 4 in the Human Dihydroorotase Mutant F1563L Apo Structure


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 F1563L Apo Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1902 b:27.1 occ:0.87 O A:HOH2117 2.0 28.5 1.0 NE2 A:HIS1471 2.0 22.7 1.0 NE2 A:HIS1473 2.1 27.8 1.0 OD1 A:ASP1686 2.4 25.5 1.0 OQ2 A:KCX1556 2.4 34.6 1.0 CE1 A:HIS1473 2.9 28.2 1.0 CE1 A:HIS1471 3.0 25.3 1.0 CD2 A:HIS1471 3.0 22.8 1.0 HE1 A:HIS1473 3.0 33.8 1.0 OQ1 A:KCX1556 3.1 33.6 1.0 CX A:KCX1556 3.1 35.0 1.0 HE1 A:HIS1471 3.2 30.3 1.0 HD2 A:HIS1471 3.2 27.4 1.0 CD2 A:HIS1473 3.2 27.1 1.0 CG A:ASP1686 3.3 27.0 1.0 ZN A:ZN1901 3.3 23.7 0.8 HG3 A:MET1503 3.4 28.3 1.0 HD2 A:HIS1473 3.4 32.5 1.0 OD2 A:ASP1686 3.6 30.9 1.0 HD2 A:HIS1614 3.9 35.0 1.0 ND1 A:HIS1471 4.1 25.6 1.0 CG A:HIS1471 4.1 22.7 1.0 ND1 A:HIS1473 4.1 27.9 1.0 HH A:TYR1558 4.1 22.1 0.6 HA A:ASP1686 4.2 26.2 1.0 CG A:HIS1473 4.3 26.2 1.0 HE1 A:TYR1558 4.3 25.0 0.6 CG A:MET1503 4.4 23.6 1.0 NE2 A:HIS1614 4.4 27.8 1.0 CD2 A:HIS1614 4.5 29.2 1.0 HE3 A:KCX1556 4.5 39.7 1.0 HE3 A:MET1503 4.5 36.5 1.0 NZ A:KCX1556 4.5 37.6 1.0 CB A:ASP1686 4.5 25.2 1.0 HE2 A:KCX1556 4.6 39.7 1.0 HB2 A:ASP1686 4.7 30.2 1.0 H A:FMT1907 4.7 80.9 1.0 CE A:KCX1556 4.8 33.1 1.0 O2 A:FMT1907 4.8 67.0 1.0 CA A:ASP1686 4.9 21.9 1.0 HG2 A:MET1503 4.9 28.3 1.0 HD1 A:HIS1473 4.9 33.5 1.0 HB2 A:ALA1688 4.9 30.6 1.0 OH A:TYR1558 4.9 18.4 0.6 HB2 A:MET1503 4.9 25.9 1.0 HE1 A:TYR1558 4.9 35.2 0.4 HB3 A:MET1503 5.0 25.9 1.0 HZ A:KCX1556 5.0 45.1 1.0

Zinc binding site 3 out of 4 in the Human Dihydroorotase Mutant F1563L Apo Structure


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 F1563L Apo Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1903 b:32.7 occ:0.28 ND1 A:HIS1471 2.1 25.6 1.0 OE1 A:GLU1637 2.2 30.2 1.0 O A:HOH2120 2.2 27.6 1.0 SG A:CYS1613 2.3 32.9 1.0 CD A:GLU1637 2.8 29.2 1.0 HB3 A:CYS1613 2.8 32.4 1.0 OE2 A:GLU1637 2.9 30.0 1.0 CE1 A:HIS1471 2.9 25.3 1.0 HB2 A:HIS1471 3.0 24.5 1.0 HE1 A:HIS1471 3.1 30.3 1.0 HE3 A:MET1503 3.1 36.5 1.0 CB A:CYS1613 3.1 27.0 1.0 CG A:HIS1471 3.1 22.7 1.0 HG11 A:VAL1588 3.2 24.0 0.5 HA A:CYS1613 3.2 27.9 1.0 HE1 A:MET1503 3.5 36.5 1.0 CB A:HIS1471 3.5 20.4 1.0 CE A:MET1503 3.6 30.4 1.0 CA A:CYS1613 3.7 23.2 1.0 HG13 A:VAL1588 3.7 24.0 0.5 HE2 A:MET1503 3.8 36.5 1.0 CG1 A:VAL1588 3.9 20.0 0.5 HB2 A:CYS1613 3.9 32.4 1.0 NE2 A:HIS1471 4.0 22.7 1.0 HG12 A:VAL1588 4.1 24.0 0.5 CD2 A:HIS1471 4.1 22.8 1.0 H A:HIS1614 4.1 30.6 1.0 HD2 A:HIS1611 4.1 22.8 1.0 CG A:GLU1637 4.1 25.1 1.0 HB3 A:HIS1471 4.1 24.5 1.0 HG2 A:GLU1637 4.2 30.1 1.0 HE3 A:KCX1556 4.2 39.7 1.0 HB A:VAL1588 4.2 24.7 0.5 HG23 A:VAL1470 4.3 28.0 1.0 HE2 A:HIS1611 4.3 23.3 1.0 HG3 A:GLU1637 4.5 30.1 1.0 HA A:HIS1471 4.5 22.6 1.0 O A:VAL1470 4.5 21.9 1.0 N A:CYS1613 4.6 18.2 1.0 CA A:HIS1471 4.6 18.8 1.0 HG21 A:VAL1588 4.7 26.1 0.5 N A:HIS1614 4.7 25.5 1.0 O A:HOH2154 4.7 52.6 1.0 C A:CYS1613 4.8 23.3 1.0 CD2 A:HIS1611 4.8 19.0 1.0 H A:CYS1613 4.8 21.9 1.0 HD2 A:HIS1614 4.8 35.0 1.0 HG11 A:VAL1588 4.9 25.8 0.5 NE2 A:HIS1611 4.9 19.4 1.0 HG21 A:VAL1588 4.9 22.5 0.5 OQ1 A:KCX1556 4.9 33.6 1.0 HB3 A:ALA1684 4.9 25.1 1.0 HD2 A:HIS1471 4.9 27.4 1.0 HZ A:KCX1556 5.0 45.1 1.0

Zinc binding site 4 out of 4 in the Human Dihydroorotase Mutant F1563L Apo Structure


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 F1563L Apo Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1908 b:56.0 occ:1.00 NE2 A:HIS1734 2.2 19.6 1.0 O A:HOH2227 2.6 53.3 1.0 CE1 A:HIS1734 2.9 21.0 1.0 HE1 A:HIS1734 3.0 25.2 1.0 CD2 A:HIS1734 3.3 18.6 1.0 HD2 A:HIS1734 3.6 22.3 1.0 O A:HOH2188 4.1 42.1 1.0 ND1 A:HIS1734 4.2 19.7 1.0 HD2 A:HIS1733 4.3 22.1 1.0 CG A:HIS1734 4.4 18.2 1.0 HG3 A:PRO1465 4.5 32.1 1.0 HD13 A:LEU1729 4.7 36.9 1.0 HB3 A:LEU1729 4.7 27.8 1.0 O A:HOH2083 4.8 49.0 1.0 HE22 A:GLN1730 4.8 25.4 1.0 HD1 A:HIS1734 4.9 23.6 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