Zinc in PDB 6hfn: Human Dihydroorotase Mutant F1563L Co-Crystallized with Carbamoyl Aspartate at pH 7.5

All present enzymatic activity of Human Dihydroorotase Mutant F1563L 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 F1563L Co-Crystallized with Carbamoyl Aspartate at pH 7.5, PDB code: 6hfn 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)	35.96 / 1.45
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	81.865, 159.200, 60.985, 90.00, 90.00, 90.00
R / Rfree (%)	11.8 / 14.5

The binding sites of Zinc atom in the Human Dihydroorotase Mutant F1563L Co-Crystallized with Carbamoyl Aspartate at pH 7.5 (pdb code 6hfn). 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 F1563L Co-Crystallized with Carbamoyl Aspartate at pH 7.5, PDB code: 6hfn:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Human Dihydroorotase Mutant F1563L 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 F1563L Co-Crystallized with Carbamoyl Aspartate at pH 7.5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1901 b:20.2 occ:0.79 OQ1 A:KCX1556 1.9 22.6 1.0 O A:HOH2183 2.0 24.0 1.0 NE2 A:HIS1614 2.0 22.3 1.0 ND1 A:HIS1590 2.1 21.6 1.0 CX A:KCX1556 2.9 24.1 1.0 CE1 A:HIS1590 2.9 23.4 1.0 HB2 A:HIS1590 3.0 21.7 1.0 CE1 A:HIS1614 3.0 24.3 1.0 CD2 A:HIS1614 3.0 22.1 1.0 HE1 A:HIS1590 3.1 28.1 1.0 O4 A:DOR1907 3.1 27.8 0.7 CG A:HIS1590 3.1 19.4 1.0 HE1 A:HIS1614 3.2 29.1 1.0 HD2 A:HIS1614 3.2 26.6 1.0 HE1 A:HIS1471 3.3 25.4 1.0 OQ2 A:KCX1556 3.3 25.2 1.0 ZN A:ZN1902 3.4 19.8 0.8 CB A:HIS1590 3.5 18.1 1.0 C4 A:DOR1907 3.7 26.3 0.7 HE1 A:TYR1558 3.9 29.0 1.0 H52 A:DOR1907 3.9 34.4 0.7 CE1 A:HIS1471 3.9 21.1 1.0 NE2 A:HIS1590 4.1 23.5 1.0 NE2 A:HIS1471 4.1 20.2 1.0 ND1 A:HIS1614 4.1 22.7 1.0 NZ A:KCX1556 4.1 22.6 1.0 CG A:HIS1614 4.1 20.9 1.0 OD2 A:ASP1686 4.2 26.5 1.0 CD2 A:HIS1590 4.2 21.9 1.0 HB3 A:HIS1590 4.2 21.7 1.0 HE2 A:KCX1556 4.3 23.9 1.0 HA A:HIS1590 4.3 19.9 1.0 HD3 A:PRO1662 4.3 26.6 1.0 C5 A:DOR1907 4.4 28.6 0.7 N3 A:DOR1907 4.4 27.8 0.7 HN3 A:DOR1907 4.4 33.3 0.7 HB2 A:CYS1613 4.5 26.3 1.0 HB3 A:CYS1613 4.5 26.3 1.0 O A:ARG1661 4.5 27.1 1.0 HE3 A:KCX1556 4.5 23.9 1.0 CA A:HIS1590 4.5 16.6 1.0 CE1 A:TYR1558 4.6 24.1 1.0 CE A:KCX1556 4.6 19.9 1.0 HZ A:KCX1556 4.6 27.2 1.0 HD1 A:TYR1558 4.6 27.1 1.0 OD1 A:ASP1686 4.7 24.7 1.0 CG A:ASP1686 4.8 24.2 1.0 H51 A:DOR1907 4.9 34.4 0.7 CB A:CYS1613 4.9 21.9 1.0 CD1 A:TYR1558 5.0 22.6 1.0

Zinc binding site 2 out of 3 in the Human Dihydroorotase Mutant F1563L 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 F1563L Co-Crystallized with Carbamoyl Aspartate at pH 7.5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1902 b:19.8 occ:0.82 O A:HOH2183 2.0 24.0 1.0 NE2 A:HIS1471 2.0 20.2 1.0 NE2 A:HIS1473 2.0 20.0 1.0 OQ2 A:KCX1556 2.1 25.2 1.0 OD1 A:ASP1686 2.2 24.7 1.0 CE1 A:HIS1471 3.0 21.1 1.0 CD2 A:HIS1471 3.0 20.6 1.0 CE1 A:HIS1473 3.0 21.9 1.0 CX A:KCX1556 3.0 24.1 1.0 H52 A:DOR1907 3.0 34.4 0.7 CD2 A:HIS1473 3.1 21.7 1.0 HE1 A:HIS1473 3.1 26.3 1.0 CG A:ASP1686 3.1 24.2 1.0 HD2 A:HIS1471 3.2 24.7 1.0 HE1 A:HIS1471 3.2 25.4 1.0 HD2 A:HIS1473 3.3 26.1 1.0 ZN A:ZN1901 3.4 20.2 0.8 HG3 A:MET1503 3.4 27.7 1.0 OQ1 A:KCX1556 3.4 22.6 1.0 OD2 A:ASP1686 3.5 26.5 1.0 H6 A:DOR1907 3.6 31.9 0.7 HD2 A:HIS1614 3.8 26.6 1.0 C5 A:DOR1907 3.9 28.6 0.7 HH A:TYR1558 4.0 28.9 1.0 ND1 A:HIS1471 4.1 21.6 1.0 CG A:HIS1471 4.1 19.0 1.0 ND1 A:HIS1473 4.1 22.3 1.0 HZ A:KCX1556 4.1 27.2 1.0 NZ A:KCX1556 4.2 22.6 1.0 HA A:ASP1686 4.2 24.1 1.0 CG A:HIS1473 4.2 21.5 1.0 C6 A:DOR1907 4.3 26.6 0.7 C4 A:DOR1907 4.3 26.3 0.7 HE1 A:TYR1558 4.3 29.0 1.0 CG A:MET1503 4.3 23.1 1.0 CB A:ASP1686 4.4 22.9 1.0 CD2 A:HIS1614 4.4 22.1 1.0 NE2 A:HIS1614 4.4 22.3 1.0 O4 A:DOR1907 4.5 27.8 0.7 HE3 A:MET1503 4.6 30.0 1.0 H51 A:DOR1907 4.6 34.4 0.7 HB2 A:ASP1686 4.6 27.6 1.0 HG2 A:MET1503 4.7 27.7 1.0 OH A:TYR1558 4.8 24.1 1.0 CA A:ASP1686 4.8 20.1 1.0 HB2 A:ALA1688 4.9 27.0 1.0 HB2 A:MET1503 4.9 24.4 1.0 HB3 A:MET1503 5.0 24.4 1.0 N3 A:DOR1907 5.0 27.8 0.7

Zinc binding site 3 out of 3 in the Human Dihydroorotase Mutant F1563L 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 F1563L Co-Crystallized with Carbamoyl Aspartate at pH 7.5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1903 b:22.1 occ:0.52 ND1 A:HIS1471 2.1 21.6 1.0 O A:HOH2114 2.1 23.2 1.0 OE1 A:GLU1637 2.1 24.5 1.0 SG A:CYS1613 2.3 23.8 1.0 HB3 A:CYS1613 2.7 26.3 1.0 CD A:GLU1637 2.8 24.0 1.0 HB2 A:HIS1471 2.9 21.9 1.0 OE2 A:GLU1637 2.9 25.0 1.0 CE1 A:HIS1471 3.0 21.1 1.0 CB A:CYS1613 3.0 21.9 1.0 HE1 A:HIS1471 3.1 25.4 1.0 CG A:HIS1471 3.1 19.0 1.0 HE3 A:MET1503 3.1 30.0 1.0 HA A:CYS1613 3.3 23.4 1.0 HG11 A:VAL1588 3.3 25.8 0.5 CB A:HIS1471 3.5 18.3 1.0 HE1 A:MET1503 3.6 30.0 1.0 CA A:CYS1613 3.7 19.4 1.0 CE A:MET1503 3.7 25.0 1.0 HB2 A:CYS1613 3.8 26.3 1.0 HG13 A:VAL1588 3.9 25.8 0.5 CG1 A:VAL1588 4.0 21.5 0.5 HE2 A:MET1503 4.0 30.0 1.0 H A:HIS1614 4.1 24.9 1.0 NE2 A:HIS1471 4.1 20.2 1.0 HB3 A:HIS1471 4.1 21.9 1.0 HD2 A:HIS1611 4.1 20.9 1.0 CG A:GLU1637 4.1 23.4 1.0 CD2 A:HIS1471 4.2 20.6 1.0 HG12 A:VAL1588 4.2 25.8 0.5 HG2 A:GLU1637 4.3 28.1 1.0 HB A:VAL1588 4.3 20.0 0.6 HG21 A:VAL1588 4.3 19.1 0.6 HG23 A:VAL1470 4.3 25.6 1.0 HG3 A:GLU1637 4.4 28.1 1.0 HA A:HIS1471 4.5 21.7 1.0 O A:VAL1470 4.5 20.0 1.0 CA A:HIS1471 4.6 18.1 1.0 O A:HOH2234 4.6 34.4 1.0 N A:CYS1613 4.7 16.5 1.0 N A:HIS1614 4.7 20.8 1.0 HZ A:KCX1556 4.7 27.2 1.0 HE2 A:KCX1556 4.7 23.9 1.0 C A:CYS1613 4.7 19.8 1.0 CD2 A:HIS1611 4.8 17.4 1.0 H A:CYS1613 4.9 19.8 1.0 NE2 A:HIS1611 4.9 19.7 1.0 HB3 A:ALA1684 4.9 26.9 1.0 HG23 A:VAL1588 4.9 19.1 0.6 HG11 A:VAL1588 4.9 24.0 0.6 CG2 A:VAL1588 4.9 15.9 0.6 HD2 A:HIS1614 5.0 26.6 1.0 HD2 A:KCX1556 5.0 26.5 1.0 HG21 A:VAL1588 5.0 25.9 0.5

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