Zinc in PDB 4c6d: Crystal Structure of the Dihydroorotase Domain of Human Cad Bound to Substrate at pH 6.0

All present enzymatic activity of Crystal Structure of the Dihydroorotase Domain of Human Cad Bound to Substrate at pH 6.0:
3.4.2.3;

The structure of Crystal Structure of the Dihydroorotase Domain of Human Cad Bound to Substrate at pH 6.0, PDB code: 4c6d 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)	19.867 / 1.30
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	82.080, 158.770, 61.560, 90.00, 90.00, 90.00
R / Rfree (%)	12.07 / 13.35

The binding sites of Zinc atom in the Crystal Structure of the Dihydroorotase Domain of Human Cad Bound to Substrate at pH 6.0 (pdb code 4c6d). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of the Dihydroorotase Domain of Human Cad Bound to Substrate at pH 6.0, PDB code: 4c6d:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of the Dihydroorotase Domain of Human Cad Bound to Substrate at pH 6.0


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 Bound to Substrate at pH 6.0 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2824 b:14.5 occ:0.27 O A:HOH2070 2.1 17.5 1.0 ND1 A:HIS1471 2.1 13.9 1.0 OE2 A:GLU1637 2.1 16.7 1.0 SG A:CYS1613 2.4 14.5 1.0 OE1 A:GLU1637 2.7 17.1 1.0 HB3 A:CYS1613 2.7 15.4 1.0 CD A:GLU1637 2.7 16.3 1.0 HB2 A:HIS1471 2.8 14.4 1.0 CB A:CYS1613 3.0 12.8 1.0 CE1 A:HIS1471 3.0 13.0 1.0 CG A:HIS1471 3.0 12.1 1.0 HE1 A:MET1503 3.1 18.0 1.0 HA A:CYS1613 3.2 13.5 1.0 HE1 A:HIS1471 3.2 15.6 1.0 CB A:HIS1471 3.4 12.0 1.0 HE2 A:MET1503 3.6 18.0 1.0 CA A:CYS1613 3.6 11.2 1.0 CE A:MET1503 3.7 15.0 1.0 HE3 A:MET1503 3.8 18.0 1.0 HB2 A:CYS1613 3.9 15.4 1.0 HB3 A:HIS1471 3.9 14.4 1.0 H A:HIS1614 4.0 13.4 1.0 NE2 A:HIS1471 4.1 12.4 1.0 CD2 A:HIS1471 4.1 11.6 1.0 HD2 A:HIS1611 4.2 15.2 1.0 CG A:GLU1637 4.2 15.6 1.0 HE2 A:HIS1611 4.2 16.1 1.0 HG2 A:GLU1637 4.3 18.8 1.0 HB A:VAL1588 4.3 16.5 1.0 HG21 A:VAL1470 4.3 17.5 1.0 HG22 A:VAL1588 4.4 19.2 1.0 HA A:HIS1471 4.4 13.6 1.0 HG3 A:GLU1637 4.5 18.8 1.0 O A:VAL1470 4.5 13.5 1.0 CA A:HIS1471 4.6 11.3 1.0 N A:HIS1614 4.6 11.2 1.0 N A:CYS1613 4.6 10.5 1.0 C A:CYS1613 4.7 11.0 1.0 O A:HOH2186 4.7 22.9 1.0 HZ A:KCX1556 4.7 15.2 1.0 CD2 A:HIS1611 4.8 12.7 1.0 NE2 A:HIS1611 4.8 13.4 1.0 H A:CYS1613 4.8 12.6 1.0 HE3 A:KCX1556 4.8 15.6 1.0 HB1 A:ALA1684 4.9 18.9 1.0 HG12 A:VAL1588 4.9 17.3 1.0 HD2 A:HIS1471 5.0 13.9 1.0 HD3 A:KCX1556 5.0 15.1 1.0 HG21 A:VAL1588 5.0 19.2 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of the Dihydroorotase Domain of Human Cad Bound to Substrate at pH 6.0


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 Bound to Substrate at pH 6.0 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2825 b:12.8 occ:0.98 O5 A:NCD2823 1.9 9.2 0.6 NE2 A:HIS1471 2.0 12.4 1.0 NE2 A:HIS1473 2.0 11.4 1.0 O A:HOH2071 2.1 27.0 0.5 OD1 A:ASP1686 2.2 13.5 1.0 OQ2 A:KCX1556 2.2 12.6 1.0 H52 A:DOR2822 2.6 24.7 0.5 C4 A:NCD2823 2.9 10.8 0.6 CD2 A:HIS1471 3.0 11.6 1.0 CE1 A:HIS1473 3.0 11.9 1.0 CE1 A:HIS1471 3.0 13.0 1.0 CD2 A:HIS1473 3.0 11.4 1.0 CG A:ASP1686 3.1 13.7 1.0 CX A:KCX1556 3.1 12.6 1.0 HD2 A:HIS1471 3.1 13.9 1.0 HE1 A:HIS1473 3.2 14.3 1.0 HE1 A:HIS1471 3.2 15.6 1.0 HD2 A:HIS1473 3.2 13.7 1.0 HG3 A:MET1503 3.4 15.4 1.0 H61 A:NCD2823 3.4 13.3 0.6 H6 A:DOR2822 3.4 25.7 0.5 OD2 A:ASP1686 3.5 15.2 1.0 OQ1 A:KCX1556 3.5 12.5 1.0 C5 A:DOR2822 3.5 20.6 0.5 H51 A:NCD2823 3.6 15.7 0.6 H32 A:NCD2823 3.6 16.2 0.6 ZN A:ZN2826 3.6 12.5 0.9 C5 A:NCD2823 3.7 13.0 0.6 HD2 A:HIS1614 3.8 14.9 1.0 O4 A:NCD2823 3.8 12.3 0.6 C6 A:NCD2823 4.0 11.1 0.6 C6 A:DOR2822 4.0 21.4 0.5 ND1 A:HIS1471 4.1 13.9 1.0 HA A:ASP1686 4.1 14.0 1.0 CG A:HIS1471 4.1 12.1 1.0 ND1 A:HIS1473 4.1 12.1 1.0 HH A:TYR1558 4.1 17.4 1.0 C4 A:DOR2822 4.1 18.0 0.5 HZ A:KCX1556 4.1 15.2 1.0 H51 A:DOR2822 4.2 24.7 0.5 CG A:HIS1473 4.2 11.9 1.0 NZ A:KCX1556 4.2 12.7 1.0 CB A:ASP1686 4.3 13.0 1.0 CG A:MET1503 4.4 12.8 1.0 CD2 A:HIS1614 4.4 12.4 1.0 O4 A:DOR2822 4.4 15.9 0.5 HB2 A:ASP1686 4.4 15.6 1.0 NE2 A:HIS1614 4.5 12.9 1.0 HE1 A:TYR1558 4.5 16.1 1.0 N3 A:NCD2823 4.5 13.5 0.6 HE1 A:MET1503 4.6 18.0 1.0 H52 A:NCD2823 4.6 15.7 0.6 HB3 A:ALA1688 4.7 15.0 1.0 CA A:ASP1686 4.7 11.7 1.0 O61 A:NCD2823 4.7 12.1 0.6 HG2 A:MET1503 4.7 15.4 1.0 OH A:TYR1558 4.8 14.5 1.0 HB2 A:MET1503 4.9 14.4 1.0 C61 A:NCD2823 4.9 11.3 0.6 HD1 A:HIS1473 4.9 14.6 1.0 N3 A:DOR2822 4.9 18.0 0.5 N1 A:DOR2822 4.9 20.4 0.5 O72 A:DOR2822 5.0 23.8 0.5 HB3 A:MET1503 5.0 14.4 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of the Dihydroorotase Domain of Human Cad Bound to Substrate at pH 6.0


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 Bound to Substrate at pH 6.0 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2826 b:12.5 occ:0.93 OQ1 A:KCX1556 1.9 12.5 1.0 O4 A:NCD2823 2.0 12.3 0.6 NE2 A:HIS1614 2.0 12.9 1.0 ND1 A:HIS1590 2.1 12.7 1.0 O A:HOH2071 2.1 27.0 0.5 O5 A:NCD2823 2.3 9.2 0.6 C4 A:NCD2823 2.6 10.8 0.6 O4 A:DOR2822 2.7 15.9 0.5 CE1 A:HIS1590 2.9 13.2 1.0 CX A:KCX1556 2.9 12.6 1.0 CE1 A:HIS1614 3.0 11.9 1.0 HB2 A:HIS1590 3.0 13.9 1.0 HE1 A:HIS1590 3.0 15.8 1.0 HE1 A:HIS1614 3.1 14.3 1.0 CD2 A:HIS1614 3.1 12.4 1.0 CG A:HIS1590 3.1 12.0 1.0 HD2 A:HIS1614 3.3 14.9 1.0 OQ2 A:KCX1556 3.4 12.6 1.0 C4 A:DOR2822 3.4 18.0 0.5 HE1 A:HIS1471 3.5 15.6 1.0 CB A:HIS1590 3.6 11.6 1.0 ZN A:ZN2825 3.6 12.8 1.0 H52 A:DOR2822 3.7 24.7 0.5 HE1 A:TYR1558 3.7 16.1 1.0 H32 A:NCD2823 3.8 16.2 0.6 HG22 A:THR1562 3.9 17.5 0.6 NE2 A:HIS1590 4.0 13.9 1.0 C5 A:NCD2823 4.1 13.0 0.6 ND1 A:HIS1614 4.1 11.5 1.0 C5 A:DOR2822 4.1 20.6 0.5 CE1 A:HIS1471 4.1 13.0 1.0 HN3 A:DOR2822 4.2 21.6 0.5 CD2 A:HIS1590 4.2 13.7 1.0 N3 A:DOR2822 4.2 18.0 0.5 NZ A:KCX1556 4.2 12.7 1.0 CG A:HIS1614 4.2 11.7 1.0 HB3 A:HIS1590 4.2 13.9 1.0 HE3 A:KCX1556 4.3 15.6 1.0 HA A:HIS1590 4.3 13.0 1.0 H52 A:NCD2823 4.4 15.7 0.6 NE2 A:HIS1471 4.4 12.4 1.0 H51 A:NCD2823 4.4 15.7 0.6 N3 A:NCD2823 4.4 13.5 0.6 CE1 A:TYR1558 4.4 13.4 1.0 HD3 A:PRO1662 4.5 17.4 1.0 OD2 A:ASP1686 4.5 15.2 1.0 HD1 A:TYR1558 4.5 15.9 1.0 H31 A:NCD2823 4.6 16.2 0.6 O A:ARG1661 4.6 18.4 1.0 HE2 A:KCX1556 4.6 15.6 1.0 CA A:HIS1590 4.6 10.8 1.0 CE A:KCX1556 4.6 13.0 1.0 H51 A:DOR2822 4.6 24.7 0.5 HB2 A:CYS1613 4.7 15.4 1.0 HZ A:KCX1556 4.7 15.2 1.0 OG1 A:THR1562 4.7 13.8 0.6 HB3 A:CYS1613 4.7 15.4 1.0 CG2 A:THR1562 4.8 14.6 0.6 HE2 A:HIS1590 4.8 16.7 1.0 CD1 A:TYR1558 4.9 13.3 1.0 HD1 A:HIS1614 4.9 13.8 1.0 OD1 A:ASP1686 4.9 13.5 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of the Dihydroorotase Domain of Human Cad Bound to Substrate at pH 6.0


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of the Dihydroorotase Domain of Human Cad Bound to Substrate at pH 6.0 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2828 b:30.0 occ:0.14 O A:HOH2391 2.2 35.0 1.0 ND1 A:HIS1741 2.2 23.2 1.0 HB3 A:HIS1741 2.7 19.5 1.0 CG A:HIS1741 3.1 19.1 1.0 HA A:HIS1741 3.1 16.7 1.0 CB A:HIS1741 3.2 16.3 1.0 CE1 A:HIS1741 3.3 23.2 1.0 HE1 A:HIS1741 3.5 27.9 1.0 HD2 A:PRO1818 3.6 28.6 1.0 CA A:HIS1741 3.7 13.9 1.0 HB2 A:HIS1741 4.1 19.5 1.0 HD3 A:PRO1818 4.3 28.6 1.0 HG11 A:VAL1817 4.3 21.7 1.0 HG2 A:PRO1818 4.3 30.4 1.0 CD2 A:HIS1741 4.3 19.7 1.0 CD A:PRO1818 4.3 23.8 1.0 NE2 A:HIS1741 4.4 21.6 1.0 O A:HOH2313 4.4 32.6 1.0 H A:HIS1741 4.5 15.7 1.0 N A:HIS1741 4.6 13.1 1.0 O A:ARG1738 4.6 13.7 1.0 HA A:ARG1738 4.7 14.7 1.0 CG A:PRO1818 4.8 25.3 1.0 C A:HIS1741 4.8 13.7 1.0 HA A:VAL1817 4.9 22.4 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