Zinc in PDB 6hfk: Human Dihydroorotase Mutant F1563L Co-Crystallized with Carbamoyl Aspartate at pH 6.5

All present enzymatic activity of Human Dihydroorotase Mutant F1563L 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 F1563L Co-Crystallized with Carbamoyl Aspartate at pH 6.5, PDB code: 6hfk 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)	44.47 / 1.46
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	81.731, 158.993, 60.954, 90.00, 90.00, 90.00
R / Rfree (%)	11.9 / 13.2

The binding sites of Zinc atom in the Human Dihydroorotase Mutant F1563L Co-Crystallized with Carbamoyl Aspartate at pH 6.5 (pdb code 6hfk). 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 Co-Crystallized with Carbamoyl Aspartate at pH 6.5, PDB code: 6hfk:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Human Dihydroorotase Mutant F1563L 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 F1563L Co-Crystallized with Carbamoyl Aspartate at pH 6.5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1901 b:18.1 occ:0.68 OQ1 A:KCX1556 1.9 23.8 1.0 O A:HOH2199 2.0 24.5 1.0 NE2 A:HIS1614 2.0 20.6 1.0 ND1 A:HIS1590 2.0 21.5 1.0 CX A:KCX1556 2.9 24.3 1.0 O4 A:DOR1907 2.9 27.1 0.8 CE1 A:HIS1590 2.9 22.8 1.0 CE1 A:HIS1614 3.0 23.2 1.0 HE1 A:HIS1590 3.0 27.3 1.0 CD2 A:HIS1614 3.0 21.1 1.0 HB2 A:HIS1590 3.0 19.6 1.0 CG A:HIS1590 3.1 18.9 1.0 HE1 A:HIS1614 3.2 27.8 1.0 HD2 A:HIS1614 3.2 25.3 1.0 HE1 A:HIS1471 3.2 24.2 1.0 OQ2 A:KCX1556 3.3 24.7 1.0 ZN A:ZN1902 3.4 17.4 0.7 C4 A:DOR1907 3.5 26.1 0.8 CB A:HIS1590 3.6 16.4 1.0 H52 A:DOR1907 3.8 31.3 0.8 HE1 A:TYR1558 3.8 25.8 1.0 CE1 A:HIS1471 3.9 20.2 1.0 NE2 A:HIS1590 4.0 21.4 1.0 ND1 A:HIS1614 4.1 22.4 1.0 NZ A:KCX1556 4.1 21.6 1.0 NE2 A:HIS1471 4.1 19.3 1.0 CG A:HIS1614 4.2 20.7 1.0 CD2 A:HIS1590 4.2 20.8 1.0 N3 A:DOR1907 4.2 25.4 0.8 HN3 A:DOR1907 4.2 30.5 0.8 OD2 A:ASP1686 4.2 25.1 1.0 HB3 A:HIS1590 4.3 19.6 1.0 C5 A:DOR1907 4.3 26.1 0.8 HD3 A:PRO1662 4.3 26.8 1.0 HA A:HIS1590 4.3 18.4 1.0 HE2 A:KCX1556 4.3 22.5 1.0 HB2 A:CYS1613 4.4 27.1 1.0 O A:ARG1661 4.5 25.7 1.0 CE1 A:TYR1558 4.5 21.5 1.0 HB3 A:CYS1613 4.6 27.1 1.0 O A:HOH2012 4.6 58.4 1.0 CA A:HIS1590 4.6 15.3 1.0 HE3 A:KCX1556 4.6 22.5 1.0 CE A:KCX1556 4.6 18.8 1.0 HD1 A:TYR1558 4.6 25.0 1.0 OD1 A:ASP1686 4.7 22.7 1.0 HE2 A:HIS1590 4.8 25.7 1.0 HZ A:KCX1556 4.8 25.9 1.0 CG A:ASP1686 4.8 22.7 1.0 H51 A:DOR1907 4.9 31.3 0.8 HD1 A:HIS1614 4.9 26.9 1.0 CD1 A:TYR1558 4.9 20.9 1.0 CB A:CYS1613 4.9 22.6 1.0

Zinc binding site 2 out of 4 in the Human Dihydroorotase Mutant F1563L 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 F1563L Co-Crystallized with Carbamoyl Aspartate at pH 6.5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1902 b:17.4 occ:0.71 O A:HOH2199 1.9 24.5 1.0 NE2 A:HIS1471 2.0 19.3 1.0 NE2 A:HIS1473 2.0 21.1 1.0 OQ2 A:KCX1556 2.2 24.7 1.0 OD1 A:ASP1686 2.3 22.7 1.0 CE1 A:HIS1473 3.0 21.4 1.0 CE1 A:HIS1471 3.0 20.2 1.0 CD2 A:HIS1471 3.0 18.4 1.0 CX A:KCX1556 3.0 24.3 1.0 H52 A:DOR1907 3.1 31.3 0.8 CD2 A:HIS1473 3.1 21.0 1.0 HE1 A:HIS1473 3.1 25.6 1.0 HE1 A:HIS1471 3.2 24.2 1.0 CG A:ASP1686 3.2 22.7 1.0 HD2 A:HIS1471 3.2 22.1 1.0 HD2 A:HIS1473 3.3 25.2 1.0 ZN A:ZN1901 3.4 18.1 0.7 HG3 A:MET1503 3.4 24.4 1.0 OQ1 A:KCX1556 3.4 23.8 1.0 OD2 A:ASP1686 3.5 25.1 1.0 H6 A:DOR1907 3.5 28.1 0.8 HD2 A:HIS1614 3.8 25.3 1.0 C5 A:DOR1907 3.9 26.1 0.8 HH A:TYR1558 4.0 27.1 1.0 ND1 A:HIS1471 4.1 20.2 1.0 ND1 A:HIS1473 4.1 22.1 1.0 CG A:HIS1471 4.1 18.1 1.0 NZ A:KCX1556 4.2 21.6 1.0 HA A:ASP1686 4.2 21.6 1.0 CG A:HIS1473 4.2 20.4 1.0 C4 A:DOR1907 4.3 26.1 0.8 C6 A:DOR1907 4.3 23.4 0.8 HZ A:KCX1556 4.3 25.9 1.0 CG A:MET1503 4.4 20.3 1.0 HE1 A:TYR1558 4.4 25.8 1.0 CD2 A:HIS1614 4.4 21.1 1.0 NE2 A:HIS1614 4.4 20.6 1.0 CB A:ASP1686 4.4 20.3 1.0 O4 A:DOR1907 4.5 27.1 0.8 HE3 A:MET1503 4.6 27.6 1.0 HB2 A:ASP1686 4.6 24.3 1.0 H51 A:DOR1907 4.7 31.3 0.8 OH A:TYR1558 4.8 22.6 1.0 HG2 A:MET1503 4.8 24.4 1.0 CA A:ASP1686 4.8 18.0 1.0 HD1 A:HIS1473 4.9 26.5 1.0 HB2 A:MET1503 4.9 23.8 1.0 HB2 A:ALA1688 4.9 25.0 1.0 N3 A:DOR1907 5.0 25.4 0.8 HB3 A:MET1503 5.0 23.8 1.0

Zinc binding site 3 out of 4 in the Human Dihydroorotase Mutant F1563L 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 F1563L Co-Crystallized with Carbamoyl Aspartate at pH 6.5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1903 b:68.0 occ:0.53 ND1 A:HIS1471 2.1 20.2 1.0 O A:HOH2172 2.2 23.4 1.0 OE1 A:GLU1637 2.2 22.0 1.0 SG A:CYS1613 2.4 23.8 1.0 HB3 A:CYS1613 2.6 27.1 1.0 CD A:GLU1637 2.8 19.9 1.0 OE2 A:GLU1637 2.8 21.1 1.0 HB2 A:HIS1471 2.9 20.3 1.0 CB A:CYS1613 2.9 22.6 1.0 CE1 A:HIS1471 3.0 20.2 1.0 HE3 A:MET1503 3.1 27.6 1.0 CG A:HIS1471 3.1 18.1 1.0 HE1 A:HIS1471 3.1 24.2 1.0 HA A:CYS1613 3.2 23.0 1.0 HG11 A:VAL1588 3.4 22.9 0.5 CB A:HIS1471 3.5 16.9 1.0 HE1 A:MET1503 3.6 27.6 1.0 CA A:CYS1613 3.6 19.2 1.0 CE A:MET1503 3.7 23.0 1.0 HB2 A:CYS1613 3.8 27.1 1.0 HE2 A:MET1503 3.9 27.6 1.0 HG13 A:VAL1588 3.9 22.9 0.5 CG1 A:VAL1588 4.0 19.1 0.5 H A:HIS1614 4.0 24.5 1.0 NE2 A:HIS1471 4.0 19.3 1.0 HB3 A:HIS1471 4.1 20.3 1.0 CD2 A:HIS1471 4.1 18.4 1.0 HD2 A:HIS1611 4.1 17.6 1.0 CG A:GLU1637 4.1 20.2 1.0 HG12 A:VAL1588 4.3 22.9 0.5 HE2 A:HIS1611 4.3 20.4 1.0 HG2 A:GLU1637 4.3 24.2 1.0 HG21 A:VAL1588 4.3 18.8 0.5 HG23 A:VAL1470 4.3 22.3 1.0 HB A:VAL1588 4.4 18.2 0.5 HA A:HIS1471 4.5 19.4 1.0 HG3 A:GLU1637 4.5 24.2 1.0 O A:VAL1470 4.6 18.0 1.0 CA A:HIS1471 4.6 16.2 1.0 N A:CYS1613 4.6 14.8 1.0 N A:HIS1614 4.6 20.4 1.0 C A:CYS1613 4.7 19.8 1.0 O A:HOH2185 4.7 30.8 1.0 CD2 A:HIS1611 4.8 14.6 1.0 HE2 A:KCX1556 4.8 22.5 1.0 H A:CYS1613 4.8 17.8 1.0 NE2 A:HIS1611 4.8 17.0 1.0 HG23 A:VAL1588 4.9 18.8 0.5 HB3 A:ALA1684 4.9 24.0 1.0 CG2 A:VAL1588 4.9 15.7 0.5 HD2 A:HIS1471 5.0 22.1 1.0 HD2 A:KCX1556 5.0 23.3 1.0 HG21 A:VAL1588 5.0 24.2 0.5

Zinc binding site 4 out of 4 in the Human Dihydroorotase Mutant F1563L 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 F1563L Co-Crystallized with Carbamoyl Aspartate at pH 6.5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1908 b:44.4 occ:1.00 NE2 A:HIS1734 2.1 18.9 1.0 HE1 A:HIS1734 2.8 23.4 1.0 CE1 A:HIS1734 2.8 19.5 1.0 CD2 A:HIS1734 3.4 16.2 1.0 HD2 A:HIS1734 3.7 19.5 1.0 ND1 A:HIS1734 4.1 17.2 1.0 O A:HOH2194 4.2 37.8 1.0 HD2 A:HIS1733 4.2 21.4 1.0 CG A:HIS1734 4.4 15.8 1.0 HG3 A:PRO1465 4.5 29.0 1.0 HD1 A:HIS1734 4.8 20.7 1.0 HB3 A:LEU1729 4.8 21.2 1.0 HD13 A:LEU1729 4.8 26.9 1.0 HE22 A:GLN1730 4.9 20.3 1.0 O A:HOH2125 4.9 39.9 1.0 CD2 A:HIS1733 5.0 17.9 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