Zinc in PDB 4c6p: Crystal Structure of the Dihydroorotase Domain of Human Cad C1613S Mutant in Apo-Form at pH 7.0

All present enzymatic activity of Crystal Structure of the Dihydroorotase Domain of Human Cad C1613S Mutant in Apo-Form at pH 7.0:
3.5.2.3;

The structure of Crystal Structure of the Dihydroorotase Domain of Human Cad C1613S Mutant in Apo-Form at pH 7.0, PDB code: 4c6p was solved by S.Ramon-Maiques, N.Lallous, A.Grande-Garcia, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.879 / 1.52
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	82.060, 159.030, 61.440, 90.00, 90.00, 90.00
R / Rfree (%)	11.71 / 14.59

The binding sites of Zinc atom in the Crystal Structure of the Dihydroorotase Domain of Human Cad C1613S Mutant in Apo-Form at pH 7.0 (pdb code 4c6p). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure of the Dihydroorotase Domain of Human Cad C1613S Mutant in Apo-Form at pH 7.0, PDB code: 4c6p:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Crystal Structure of the Dihydroorotase Domain of Human Cad C1613S Mutant in Apo-Form 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 Crystal Structure of the Dihydroorotase Domain of Human Cad C1613S Mutant in Apo-Form at pH 7.0 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2822 b:19.9 occ:0.66 O A:HOH2084 2.0 18.6 1.0 NE2 A:HIS1471 2.0 16.2 1.0 NE2 A:HIS1473 2.0 16.5 1.0 OD1 A:ASP1686 2.2 18.5 1.0 OQ1 A:KCX1556 2.2 18.7 1.0 CE1 A:HIS1473 3.0 17.5 1.0 CD2 A:HIS1471 3.0 15.4 1.0 CE1 A:HIS1471 3.0 17.9 1.0 CX A:KCX1556 3.0 17.9 1.0 HE1 A:HIS1473 3.1 21.0 1.0 CG A:ASP1686 3.1 17.8 1.0 CD2 A:HIS1473 3.1 16.8 1.0 HD2 A:HIS1471 3.2 18.4 1.0 HE1 A:HIS1471 3.2 21.5 1.0 ZN A:ZN2823 3.3 19.8 0.6 HD2 A:HIS1473 3.3 20.1 1.0 OQ2 A:KCX1556 3.4 18.7 1.0 HG3 A:MET1503 3.5 21.1 1.0 OD2 A:ASP1686 3.5 18.5 1.0 O A:HOH2002 3.9 44.1 1.0 HD2 A:HIS1614 3.9 22.1 1.0 ND1 A:HIS1471 4.1 18.8 1.0 ND1 A:HIS1473 4.1 17.1 1.0 HA A:ASP1686 4.1 17.5 1.0 CG A:HIS1471 4.1 16.0 1.0 HH A:TYR1558 4.1 22.0 1.0 CG A:HIS1473 4.2 16.9 1.0 HZ A:KCX1556 4.2 20.0 1.0 NZ A:KCX1556 4.2 16.6 1.0 HE1 A:TYR1558 4.3 21.5 1.0 CB A:ASP1686 4.4 17.1 1.0 NE2 A:HIS1614 4.4 17.7 1.0 CG A:MET1503 4.4 17.6 1.0 CD2 A:HIS1614 4.5 18.4 1.0 HB2 A:ASP1686 4.6 20.5 1.0 HE1 A:MET1503 4.7 22.0 1.0 CA A:ASP1686 4.7 14.6 1.0 OH A:TYR1558 4.8 18.3 1.0 HG2 A:MET1503 4.8 21.1 1.0 HB3 A:ALA1688 4.8 21.5 1.0 HD1 A:HIS1473 4.9 20.6 1.0 HD1 A:HIS1471 4.9 22.6 1.0 HB2 A:MET1503 4.9 20.2 1.0 O2 A:FMT2825 5.0 35.9 1.0

Zinc binding site 2 out of 3 in the Crystal Structure of the Dihydroorotase Domain of Human Cad C1613S Mutant in Apo-Form 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 Crystal Structure of the Dihydroorotase Domain of Human Cad C1613S Mutant in Apo-Form at pH 7.0 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2823 b:19.8 occ:0.62 OQ2 A:KCX1556 1.9 18.7 1.0 O A:HOH2084 2.0 18.6 1.0 ND1 A:HIS1590 2.0 18.3 1.0 NE2 A:HIS1614 2.1 17.7 1.0 CE1 A:HIS1590 2.9 19.5 1.0 CX A:KCX1556 2.9 17.9 1.0 HB2 A:HIS1590 3.0 17.9 1.0 CE1 A:HIS1614 3.0 18.7 1.0 HE1 A:HIS1590 3.0 23.4 1.0 CG A:HIS1590 3.1 16.9 1.0 CD2 A:HIS1614 3.1 18.4 1.0 HE1 A:HIS1471 3.1 21.5 1.0 HE1 A:HIS1614 3.1 22.5 1.0 OQ1 A:KCX1556 3.3 18.7 1.0 HD2 A:HIS1614 3.3 22.1 1.0 ZN A:ZN2822 3.3 19.9 0.7 CB A:HIS1590 3.5 14.9 1.0 O A:HOH2002 3.7 44.1 1.0 CE1 A:HIS1471 3.8 17.9 1.0 HE1 A:TYR1558 3.9 21.5 1.0 NE2 A:HIS1590 4.0 20.3 1.0 NE2 A:HIS1471 4.0 16.2 1.0 CD2 A:HIS1590 4.1 19.8 1.0 ND1 A:HIS1614 4.1 18.8 1.0 OD2 A:ASP1686 4.2 18.5 1.0 HA A:HIS1590 4.2 17.5 1.0 NZ A:KCX1556 4.2 16.6 1.0 OG A:SER1613 4.2 19.0 0.0 CG A:HIS1614 4.2 16.4 1.0 HB3 A:HIS1590 4.2 17.9 1.0 HB2 A:SER1613 4.3 21.4 1.0 HB3 A:SER1613 4.4 21.8 0.0 HE3 A:KCX1556 4.4 18.4 1.0 HB3 A:SER1613 4.4 21.4 1.0 HD3 A:PRO1662 4.4 25.2 1.0 CA A:HIS1590 4.5 14.6 1.0 HE2 A:KCX1556 4.5 18.4 1.0 CE1 A:TYR1558 4.6 17.9 1.0 CE A:KCX1556 4.6 15.3 1.0 OD1 A:ASP1686 4.6 18.5 1.0 HZ A:KCX1556 4.7 20.0 1.0 CG A:ASP1686 4.7 17.8 1.0 HD1 A:TYR1558 4.7 21.1 1.0 HE2 A:HIS1590 4.7 24.4 1.0 HG A:SER1613 4.7 22.8 0.0 O A:ARG1661 4.8 24.2 1.0 CB A:SER1613 4.8 17.9 1.0 CB A:SER1613 4.8 18.2 0.0 HD1 A:HIS1614 4.9 22.5 1.0 HD2 A:HIS1590 5.0 23.8 1.0

Zinc binding site 3 out of 3 in the Crystal Structure of the Dihydroorotase Domain of Human Cad C1613S Mutant in Apo-Form 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 Crystal Structure of the Dihydroorotase Domain of Human Cad C1613S Mutant in Apo-Form at pH 7.0 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2824 b:34.0 occ:0.37 O A:HOH2314 2.0 40.2 1.0 NE2 A:HIS1734 2.1 22.2 1.0 O A:HOH2315 2.2 38.7 1.0 HE1 A:HIS1734 2.8 25.4 1.0 CE1 A:HIS1734 2.8 21.2 1.0 CD2 A:HIS1734 3.3 17.9 1.0 HD2 A:HIS1734 3.7 21.5 1.0 ND1 A:HIS1734 4.0 16.6 1.0 O A:HOH2304 4.1 33.2 1.0 HD2 A:HIS1733 4.3 20.1 1.0 CG A:HIS1734 4.3 15.6 1.0 HG3 A:PRO1465 4.6 25.4 1.0 HD1 A:HIS1734 4.8 19.9 1.0 HB3 A:LEU1729 4.8 21.5 1.0 HE22 A:GLN1730 4.8 20.7 1.0 HD11 A:LEU1729 4.9 28.0 1.0

A.Grande-Garcia, N.Lallous, C.Diaz-Tejada, S.Ramon-Maiques. Structure, Functional Characterization and Evolution of the Dihydroorotase Domain of Human Cad. Structure V. 22 185 2014.
ISSN: ISSN 0969-2126
PubMed: 24332717
DOI: 10.1016/J.STR.2013.10.016