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Zinc in PDB 9fs3: Mutant S1538L of the Dihydroorotase Domain of Human Cad Protein Bound to Carbamoyl Aspartate

Enzymatic activity of Mutant S1538L of the Dihydroorotase Domain of Human Cad Protein Bound to Carbamoyl Aspartate

All present enzymatic activity of Mutant S1538L of the Dihydroorotase Domain of Human Cad Protein Bound to Carbamoyl Aspartate:
2.1.3.2; 3.5.1.2; 3.5.2.3; 6.3.4.16; 6.3.5.5;

Protein crystallography data

The structure of Mutant S1538L of the Dihydroorotase Domain of Human Cad Protein Bound to Carbamoyl Aspartate, PDB code: 9fs3 was solved by F.Del Cano-Ochoa, S.Ramon-Maiques, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.75 / 1.18
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 82.099, 158.499, 61.842, 90, 90, 90
R / Rfree (%) 15.5 / 17.9

Other elements in 9fs3:

The structure of Mutant S1538L of the Dihydroorotase Domain of Human Cad Protein Bound to Carbamoyl Aspartate also contains other interesting chemical elements:

Sodium (Na) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Mutant S1538L of the Dihydroorotase Domain of Human Cad Protein Bound to Carbamoyl Aspartate (pdb code 9fs3). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Mutant S1538L of the Dihydroorotase Domain of Human Cad Protein Bound to Carbamoyl Aspartate, PDB code: 9fs3:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 9fs3

Go back to Zinc Binding Sites List in 9fs3
Zinc binding site 1 out of 4 in the Mutant S1538L of the Dihydroorotase Domain of Human Cad Protein Bound to Carbamoyl Aspartate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Mutant S1538L of the Dihydroorotase Domain of Human Cad Protein Bound to Carbamoyl Aspartate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1910

b:9.9
occ:1.00
 OQ1 A:KCX1556 1.9 10.2 1.0
O A:HOH2134 2.0 9.3 1.0
NE2 A:HIS1614 2.1 9.6 1.0
ND1 A:HIS1590 2.1 10.2 1.0
CX A:KCX1556 2.9 10.4 1.0
CE1 A:HIS1590 3.0 10.2 1.0
CE1 A:HIS1614 3.0 9.5 1.0
HB2 A:HIS1590 3.0 11.9 1.0
HE1 A:HIS1590 3.1 12.2 1.0
CD2 A:HIS1614 3.1 9.0 1.0
HE1 A:HIS1614 3.1 11.4 1.0
CG A:HIS1590 3.1 9.8 1.0
HE1 A:HIS1471 3.2 11.8 1.0
OQ2 A:KCX1556 3.2 11.3 1.0
ZN A:ZN1911 3.3 9.7 1.0
HD2 A:HIS1614 3.3 10.8 1.0
HE2 A:TYR1558 3.4 14.8 0.3
CB A:HIS1590 3.6 9.9 1.0
O A:HOH2008 3.6 23.0 1.0
CE1 A:HIS1471 3.8 9.8 1.0
CE2 A:TYR1558 3.9 12.3 0.3
NE2 A:HIS1471 4.0 9.0 1.0
OD2 A:ASP1686 4.0 10.4 1.0
HE1 A:TYR1558 4.0 14.9 0.7
NZ A:KCX1556 4.1 11.1 1.0
NE2 A:HIS1590 4.1 10.9 1.0
ND1 A:HIS1614 4.1 8.6 1.0
HA A:HIS1590 4.1 11.4 1.0
CD2 A:HIS1590 4.2 10.8 1.0
HD3 A:PRO1662 4.2 13.2 1.0
CG A:HIS1614 4.2 8.1 1.0
HB3 A:HIS1590 4.3 11.9 1.0
HE2 A:KCX1556 4.3 13.2 1.0
HB3 A:CYS1613 4.5 11.2 1.0
CA A:HIS1590 4.5 9.5 1.0
HD2 A:TYR1558 4.5 15.3 0.3
O A:ARG1661 4.5 13.2 1.0
H32 A:GOL1914 4.6 26.1 0.7
HB2 A:CYS1613 4.6 11.2 1.0
CE A:KCX1556 4.6 11.0 1.0
CG A:ASP1686 4.6 9.6 1.0
OD1 A:ASP1686 4.6 10.6 1.0
OH A:TYR1558 4.6 10.6 0.3
CD2 A:TYR1558 4.6 12.7 0.3
HE3 A:KCX1556 4.6 13.2 1.0
CZ A:TYR1558 4.6 11.7 0.3
CE1 A:TYR1558 4.7 12.4 0.7
HD1 A:TYR1558 4.7 15.2 0.7
HZ A:KCX1556 4.8 13.3 1.0
HE2 A:HIS1590 4.8 13.1 1.0
HD1 A:HIS1614 4.9 10.4 1.0
CB A:CYS1613 5.0 9.3 1.0
HO3 A:GOL1914 5.0 28.8 0.7

Zinc binding site 2 out of 4 in 9fs3

Go back to Zinc Binding Sites List in 9fs3
Zinc binding site 2 out of 4 in the Mutant S1538L of the Dihydroorotase Domain of Human Cad Protein Bound to Carbamoyl Aspartate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Mutant S1538L of the Dihydroorotase Domain of Human Cad Protein Bound to Carbamoyl Aspartate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1911

b:9.7
occ:1.00
 O A:HOH2134 2.0 9.3 1.0
NE2 A:HIS1471 2.1 9.0 1.0
NE2 A:HIS1473 2.1 9.1 1.0
OQ2 A:KCX1556 2.2 11.3 1.0
OD1 A:ASP1686 2.2 10.6 1.0
CE1 A:HIS1473 3.0 9.9 1.0
CD2 A:HIS1471 3.0 8.1 1.0
CX A:KCX1556 3.0 10.4 1.0
CE1 A:HIS1471 3.1 9.8 1.0
CG A:ASP1686 3.1 9.6 1.0
CD2 A:HIS1473 3.1 9.2 1.0
HD2 A:HIS1471 3.2 9.7 1.0
HE1 A:HIS1473 3.2 11.9 1.0
H32 A:GOL1914 3.2 26.1 0.7
HE1 A:HIS1471 3.3 11.8 1.0
HD2 A:HIS1473 3.3 11.0 1.0
ZN A:ZN1910 3.3 9.9 1.0
OQ1 A:KCX1556 3.4 10.2 1.0
OD2 A:ASP1686 3.4 10.4 1.0
HG3 A:MET1503 3.5 12.9 1.0
HD2 A:HIS1614 3.9 10.8 1.0
H31 A:GOL1914 4.1 26.1 0.7
C3 A:GOL1914 4.1 21.7 0.7
HA A:ASP1686 4.1 10.6 1.0
HH A:TYR1558 4.1 12.7 0.7
ND1 A:HIS1471 4.1 10.5 1.0
ND1 A:HIS1473 4.1 10.0 1.0
CG A:HIS1471 4.2 8.9 1.0
NZ A:KCX1556 4.2 11.1 1.0
O A:HOH2008 4.2 23.0 1.0
CG A:HIS1473 4.2 9.6 1.0
HZ A:KCX1556 4.3 13.3 1.0
CB A:ASP1686 4.3 9.1 1.0
HE1 A:TYR1558 4.3 14.9 0.7
NE2 A:HIS1614 4.4 9.6 1.0
CG A:MET1503 4.4 10.8 1.0
CD2 A:HIS1614 4.5 9.0 1.0
HB2 A:ASP1686 4.5 11.0 1.0
HE3 A:MET1503 4.6 13.7 1.0
CA A:ASP1686 4.7 8.8 1.0
HB2 A:ALA1688 4.7 13.1 1.0
HO3 A:GOL1914 4.8 28.8 0.7
HE2 A:TYR1558 4.8 14.8 0.3
OH A:TYR1558 4.8 10.6 0.7
HB2 A:MET1503 4.9 12.0 1.0
HG2 A:MET1503 4.9 12.9 1.0
HD1 A:HIS1473 4.9 12.0 1.0
C2 A:GOL1914 4.9 22.3 0.7
O2 A:GOL1914 4.9 22.3 0.7
H2 A:GOL1914 4.9 26.7 0.7

Zinc binding site 3 out of 4 in 9fs3

Go back to Zinc Binding Sites List in 9fs3
Zinc binding site 3 out of 4 in the Mutant S1538L of the Dihydroorotase Domain of Human Cad Protein Bound to Carbamoyl Aspartate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Mutant S1538L of the Dihydroorotase Domain of Human Cad Protein Bound to Carbamoyl Aspartate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1912

b:11.9
occ:0.57
 O A:HOH2181 2.0 11.3 1.0
ND1 A:HIS1471 2.1 10.5 1.0
OE2 A:GLU1637 2.1 10.8 1.0
SG A:CYS1613 2.3 10.3 1.0
HB3 A:CYS1613 2.8 11.2 1.0
HB2 A:HIS1471 2.8 10.5 1.0
CD A:GLU1637 2.9 10.2 1.0
CE1 A:HIS1471 2.9 9.8 1.0
CB A:CYS1613 3.0 9.3 1.0
OE1 A:GLU1637 3.0 10.7 1.0
CG A:HIS1471 3.1 8.9 1.0
HE1 A:HIS1471 3.1 11.8 1.0
HA A:CYS1613 3.1 10.5 1.0
HE3 A:MET1503 3.3 13.7 1.0
CB A:HIS1471 3.4 8.8 1.0
HE1 A:MET1503 3.6 13.7 1.0
CA A:CYS1613 3.6 8.8 1.0
CE A:MET1503 3.8 11.4 1.0
HB2 A:CYS1613 3.9 11.2 1.0
H A:HIS1614 4.0 10.4 1.0
HB3 A:HIS1471 4.0 10.5 1.0
NE2 A:HIS1471 4.0 9.0 1.0
HE2 A:MET1503 4.1 13.7 1.0
CD2 A:HIS1471 4.1 8.1 1.0
HD2 A:HIS1611 4.2 11.1 1.0
HB A:VAL1588 4.2 12.4 1.0
CG A:GLU1637 4.3 9.8 1.0
HG23 A:VAL1470 4.3 12.5 1.0
HG21 A:VAL1588 4.3 14.2 1.0
HE2 A:HIS1611 4.4 11.2 1.0
HG2 A:GLU1637 4.4 11.8 1.0
O A:VAL1470 4.4 9.8 1.0
HG23 A:VAL1588 4.5 14.2 1.0
HA A:HIS1471 4.5 11.1 1.0
CA A:HIS1471 4.6 9.3 1.0
HG3 A:GLU1637 4.6 11.8 1.0
N A:CYS1613 4.6 8.8 1.0
N A:HIS1614 4.6 8.7 1.0
O A:HOH2266 4.6 14.6 1.0
C A:CYS1613 4.7 8.7 1.0
CG2 A:VAL1588 4.8 11.8 1.0
HB3 A:ALA1684 4.8 11.9 1.0
H A:CYS1613 4.8 10.5 1.0
HG11 A:VAL1588 4.8 13.1 1.0
HE2 A:KCX1556 4.8 13.2 1.0
CD2 A:HIS1611 4.9 9.3 1.0
CB A:VAL1588 4.9 10.4 1.0
NE2 A:HIS1611 4.9 9.3 1.0
HD2 A:HIS1471 5.0 9.7 1.0

Zinc binding site 4 out of 4 in 9fs3

Go back to Zinc Binding Sites List in 9fs3
Zinc binding site 4 out of 4 in the Mutant S1538L of the Dihydroorotase Domain of Human Cad Protein Bound to Carbamoyl Aspartate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Mutant S1538L of the Dihydroorotase Domain of Human Cad Protein Bound to Carbamoyl Aspartate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1913

b:11.8
occ:0.72
 O1 A:FMT1906 2.0 18.1 1.0
NE2 A:HIS1734 2.1 12.2 1.0
O A:HOH2319 2.2 22.6 1.0
HO2 A:FMT1906 2.6 26.0 1.0
C A:FMT1906 2.9 20.8 1.0
CE1 A:HIS1734 2.9 11.8 1.0
HE1 A:HIS1734 3.0 14.2 1.0
O2 A:FMT1906 3.1 21.7 1.0
CD2 A:HIS1734 3.3 11.4 1.0
HD2 A:HIS1734 3.5 13.6 1.0
H A:FMT1906 3.9 24.9 1.0
HD2 A:HIS1733 4.1 13.0 1.0
ND1 A:HIS1734 4.1 10.5 1.0
CG A:HIS1734 4.3 10.3 1.0
O A:HOH2207 4.5 26.6 1.0
HG3 A:PRO1465 4.5 17.5 1.0
HB3 A:LEU1729 4.7 16.3 1.0
CD2 A:HIS1733 4.8 10.8 1.0
HD1 A:HIS1734 4.8 12.6 1.0
O A:HOH2251 4.9 18.9 1.0
HD13 A:LEU1729 4.9 19.0 1.0

Reference:

F.Del Cano-Ochoa, L.Ramadane-Morchadi, L.Eixeres, M.Moreno-Morcillo, R.Fernandez-Leiro, S.Ramon-Maiques. Disruption of Cad Oligomerization By Pathogenic Variants. J.Mol.Biol. V. 436 68832 2024.
ISSN: ESSN 1089-8638
PubMed: 39447673
DOI: 10.1016/J.JMB.2024.168832
Page generated: Fri Aug 22 17:35:58 2025

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