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Zinc in PDB 8pbq: Mutant R1810Q of the Dihydroorotase Domain of Human Cad Protein Bound to the Substrates

Enzymatic activity of Mutant R1810Q of the Dihydroorotase Domain of Human Cad Protein Bound to the Substrates

All present enzymatic activity of Mutant R1810Q of the Dihydroorotase Domain of Human Cad Protein Bound to the Substrates:
2.1.3.2; 3.5.2.3; 6.3.5.5;

Protein crystallography data

The structure of Mutant R1810Q of the Dihydroorotase Domain of Human Cad Protein Bound to the Substrates, PDB code: 8pbq 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) 48.44 / 1.54
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 82.294, 158.81, 61.124, 90, 90, 90
R / Rfree (%) 14.7 / 17.6

Zinc Binding Sites:

The binding sites of Zinc atom in the Mutant R1810Q of the Dihydroorotase Domain of Human Cad Protein Bound to the Substrates (pdb code 8pbq). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Mutant R1810Q of the Dihydroorotase Domain of Human Cad Protein Bound to the Substrates, PDB code: 8pbq:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in 8pbq

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Zinc binding site 1 out of 5 in the Mutant R1810Q of the Dihydroorotase Domain of Human Cad Protein Bound to the Substrates


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Mutant R1810Q of the Dihydroorotase Domain of Human Cad Protein Bound to the Substrates within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1903

b:17.4
occ:1.00
 OQ2 A:KCX1556 1.9 16.3 1.0
ND1 A:HIS1590 2.1 17.4 1.0
NE2 A:HIS1614 2.1 16.2 1.0
O5 A:NCD1901 2.2 21.5 1.0
O4 A:NCD1901 2.3 19.9 1.0
C4 A:NCD1901 2.5 21.5 1.0
CX A:KCX1556 2.9 15.8 1.0
CE1 A:HIS1590 2.9 18.2 1.0
CE1 A:HIS1614 3.0 16.8 1.0
HB2 A:HIS1590 3.0 18.5 1.0
HE1 A:HIS1590 3.1 21.9 1.0
HE1 A:HIS1614 3.1 20.2 1.0
CG A:HIS1590 3.2 15.9 1.0
CD2 A:HIS1614 3.2 15.7 1.0
OQ1 A:KCX1556 3.3 15.6 1.0
HD2 A:HIS1614 3.5 18.8 1.0
HE1 A:HIS1471 3.5 20.3 1.0
CB A:HIS1590 3.6 15.4 1.0
HE1 A:TYR1558 3.7 20.0 1.0
ZN A:ZN1904 3.7 16.3 1.0
HG1 A:THR1562 3.8 29.2 1.0
H31 A:NCD1901 3.9 29.9 1.0
HG21 A:THR1562 4.0 31.2 1.0
C5 A:NCD1901 4.1 21.4 1.0
NE2 A:HIS1590 4.1 17.5 1.0
NZ A:KCX1556 4.1 14.5 1.0
ND1 A:HIS1614 4.2 16.1 1.0
CE1 A:HIS1471 4.2 16.9 1.0
CD2 A:HIS1590 4.2 17.4 1.0
HA A:HIS1590 4.3 17.4 1.0
HB3 A:HIS1590 4.3 18.5 1.0
CG A:HIS1614 4.3 16.0 1.0
HE2 A:KCX1556 4.4 19.0 1.0
H51 A:NCD1901 4.4 25.7 1.0
CE1 A:TYR1558 4.4 16.7 1.0
N3 A:NCD1901 4.4 24.9 1.0
H52 A:NCD1901 4.4 25.7 1.0
NE2 A:HIS1471 4.4 16.2 1.0
HD3 A:PRO1662 4.4 22.7 1.0
HD1 A:TYR1558 4.4 20.6 1.0
HE3 A:KCX1556 4.5 19.0 1.0
H32 A:NCD1901 4.5 29.9 1.0
OD2 A:ASP1686 4.5 17.7 1.0
CA A:HIS1590 4.6 14.5 1.0
CE A:KCX1556 4.6 15.8 1.0
O A:ARG1661 4.6 21.8 1.0
OG1 A:THR1562 4.7 24.4 1.0
HB2 A:CYS1613 4.7 18.1 1.0
HB3 A:CYS1613 4.8 18.1 1.0
HZ A:KCX1556 4.8 17.4 1.0
CD1 A:TYR1558 4.8 17.2 1.0
HE2 A:HIS1590 4.8 21.0 1.0
CG2 A:THR1562 4.8 26.0 1.0
OD1 A:ASP1686 4.9 16.2 1.0
HD1 A:HIS1614 4.9 19.3 1.0
HH A:TYR1558 5.0 22.7 1.0
H61 A:NCD1901 5.0 23.6 1.0

Zinc binding site 2 out of 5 in 8pbq

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Zinc binding site 2 out of 5 in the Mutant R1810Q of the Dihydroorotase Domain of Human Cad Protein Bound to the Substrates


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Mutant R1810Q of the Dihydroorotase Domain of Human Cad Protein Bound to the Substrates within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1904

b:16.3
occ:1.00
 O4 A:NCD1901 2.0 19.9 1.0
OD1 A:ASP1686 2.0 16.2 1.0
NE2 A:HIS1471 2.0 16.2 1.0
NE2 A:HIS1473 2.1 16.4 1.0
OQ1 A:KCX1556 2.2 15.6 1.0
CD2 A:HIS1471 3.0 15.7 1.0
C4 A:NCD1901 3.0 21.5 1.0
CE1 A:HIS1473 3.0 17.2 1.0
CG A:ASP1686 3.0 17.1 1.0
CE1 A:HIS1471 3.0 16.9 1.0
CD2 A:HIS1473 3.1 16.6 1.0
CX A:KCX1556 3.1 15.8 1.0
HD2 A:HIS1471 3.2 18.8 1.0
HE1 A:HIS1473 3.2 20.6 1.0
HE1 A:HIS1471 3.2 20.3 1.0
HD2 A:HIS1473 3.3 19.9 1.0
H61 A:NCD1901 3.3 23.6 1.0
HG3 A:MET1503 3.3 21.4 1.0
H51 A:NCD1901 3.5 25.7 1.0
OD2 A:ASP1686 3.5 17.7 1.0
OQ2 A:KCX1556 3.5 16.3 1.0
H31 A:NCD1901 3.6 29.9 1.0
C5 A:NCD1901 3.6 21.4 1.0
ZN A:ZN1903 3.7 17.4 1.0
HD2 A:HIS1614 3.8 18.8 1.0
HH A:TYR1558 4.0 22.7 1.0
C6 A:NCD1901 4.0 19.7 1.0
HA A:ASP1686 4.1 20.4 1.0
O5 A:NCD1901 4.1 21.5 1.0
ND1 A:HIS1471 4.1 16.7 1.0
CG A:HIS1471 4.1 15.7 1.0
ND1 A:HIS1473 4.1 17.1 1.0
NZ A:KCX1556 4.2 14.5 1.0
CG A:HIS1473 4.2 15.8 1.0
CB A:ASP1686 4.2 17.5 1.0
CG A:MET1503 4.3 17.8 1.0
HZ A:KCX1556 4.3 17.4 1.0
HB2 A:ASP1686 4.4 21.0 1.0
CD2 A:HIS1614 4.4 15.7 1.0
NE2 A:HIS1614 4.5 16.2 1.0
HG2 A:MET1503 4.5 21.4 1.0
N3 A:NCD1901 4.5 24.9 1.0
HE1 A:TYR1558 4.5 20.0 1.0
H52 A:NCD1901 4.6 25.7 1.0
HE3 A:MET1503 4.6 21.1 1.0
CA A:ASP1686 4.7 17.0 1.0
HB2 A:ALA1688 4.7 21.7 1.0
O61 A:NCD1901 4.7 20.0 1.0
OH A:TYR1558 4.8 18.9 1.0
HB2 A:MET1503 4.8 20.6 1.0
C61 A:NCD1901 4.9 19.4 1.0
HD1 A:HIS1473 4.9 20.5 1.0
HB3 A:MET1503 4.9 20.6 1.0
H32 A:NCD1901 5.0 29.9 1.0
CB A:MET1503 5.0 17.1 1.0

Zinc binding site 3 out of 5 in 8pbq

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Zinc binding site 3 out of 5 in the Mutant R1810Q of the Dihydroorotase Domain of Human Cad Protein Bound to the Substrates


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Mutant R1810Q of the Dihydroorotase Domain of Human Cad Protein Bound to the Substrates within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1905

b:18.3
occ:0.47
 O A:HOH2113 2.0 19.3 1.0
ND1 A:HIS1471 2.1 16.7 1.0
OE2 A:GLU1637 2.2 17.6 1.0
SG A:CYS1613 2.3 16.9 1.0
HB3 A:CYS1613 2.7 18.1 1.0
HB2 A:HIS1471 2.8 19.1 1.0
CD A:GLU1637 2.9 17.9 1.0
CB A:CYS1613 3.0 15.1 1.0
CE1 A:HIS1471 3.0 16.9 1.0
OE1 A:GLU1637 3.0 18.2 1.0
CG A:HIS1471 3.0 15.7 1.0
HE3 A:MET1503 3.0 21.1 1.0
HA A:CYS1613 3.2 16.6 1.0
HE1 A:HIS1471 3.2 20.3 1.0
CB A:HIS1471 3.4 15.9 1.0
HE1 A:MET1503 3.5 21.1 1.0
CE A:MET1503 3.6 17.6 1.0
CA A:CYS1613 3.6 13.8 1.0
HE2 A:MET1503 3.7 21.1 1.0
HB2 A:CYS1613 3.8 18.1 1.0
H A:HIS1614 4.0 18.1 1.0
HB3 A:HIS1471 4.0 19.1 1.0
NE2 A:HIS1471 4.0 16.2 1.0
CD2 A:HIS1471 4.1 15.7 1.0
HD2 A:HIS1611 4.2 18.8 1.0
HB A:VAL1588 4.2 21.7 1.0
CG A:GLU1637 4.3 16.5 1.0
HE2 A:HIS1611 4.4 19.6 1.0
HG23 A:VAL1470 4.4 20.7 1.0
O A:VAL1470 4.4 15.1 1.0
HG2 A:GLU1637 4.4 19.8 1.0
HA A:HIS1471 4.4 18.8 1.0
CA A:HIS1471 4.5 15.6 1.0
N A:CYS1613 4.6 15.7 1.0
HG3 A:GLU1637 4.6 19.8 1.0
N A:HIS1614 4.6 15.1 1.0
HG21 A:VAL1588 4.6 23.8 1.0
C A:CYS1613 4.7 14.0 1.0
HE2 A:KCX1556 4.7 19.0 1.0
O A:HOH2171 4.7 22.7 1.0
H A:CYS1613 4.8 18.9 1.0
HG23 A:VAL1588 4.8 23.8 1.0
CD2 A:HIS1611 4.8 15.7 1.0
HG11 A:VAL1588 4.9 21.8 1.0
HB3 A:ALA1684 4.9 20.5 1.0
NE2 A:HIS1611 4.9 16.3 1.0
HD2 A:HIS1471 4.9 18.8 1.0
HD2 A:KCX1556 5.0 19.7 1.0
CB A:VAL1588 5.0 18.1 1.0

Zinc binding site 4 out of 5 in 8pbq

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Zinc binding site 4 out of 5 in the Mutant R1810Q of the Dihydroorotase Domain of Human Cad Protein Bound to the Substrates


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Mutant R1810Q of the Dihydroorotase Domain of Human Cad Protein Bound to the Substrates within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1906

b:24.6
occ:0.30
 O A:GLY1806 2.3 22.8 1.0
O A:GLY1804 2.4 23.1 1.0
O A:HOH2182 2.4 34.4 1.0
O A:GLU1524 2.5 24.8 1.0
O A:HOH2205 2.5 32.0 1.0
O A:HOH2189 2.7 35.2 1.0
HA A:GLU1524 3.2 26.2 1.0
C A:GLY1804 3.3 22.4 1.0
O A:HOH2005 3.3 32.4 1.0
HA2 A:GLY1804 3.4 27.7 1.0
C A:GLU1524 3.4 23.4 1.0
C A:GLY1806 3.5 21.1 1.0
HB3 A:GLU1524 3.6 26.9 1.0
CA A:GLU1524 3.7 21.8 1.0
HA A:GLN1807 3.7 25.5 1.0
CA A:GLY1804 3.9 23.1 1.0
HG2 A:GLN1807 3.9 28.9 1.0
N A:GLY1806 4.1 21.8 1.0
C A:TYR1805 4.1 22.2 1.0
CB A:GLU1524 4.1 22.5 1.0
HG2 A:GLU1524 4.2 28.1 1.0
HA3 A:GLY1804 4.2 27.7 1.0
H A:GLY1806 4.3 26.1 1.0
O A:TYR1805 4.3 23.0 1.0
N A:TYR1805 4.3 22.3 1.0
CA A:GLY1806 4.4 21.5 1.0
N A:GLN1807 4.4 21.3 1.0
HG3 A:GLN1807 4.4 28.9 1.0
CA A:GLN1807 4.5 21.3 1.0
CG A:GLN1807 4.6 24.0 1.0
HA A:TYR1805 4.6 27.1 1.0
CA A:TYR1805 4.6 22.6 1.0
N A:ALA1525 4.7 23.1 1.0
HE2 A:PHE1531 4.7 23.4 1.0
HA A:ALA1525 4.7 27.5 1.0
CG A:GLU1524 4.7 23.4 1.0
HA3 A:GLY1806 4.9 25.8 1.0
O A:ALA1523 4.9 21.9 1.0
O A:HOH2210 4.9 45.4 1.0
O A:HOH2108 5.0 24.7 1.0
HB2 A:GLU1524 5.0 26.9 1.0

Zinc binding site 5 out of 5 in 8pbq

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Zinc binding site 5 out of 5 in the Mutant R1810Q of the Dihydroorotase Domain of Human Cad Protein Bound to the Substrates


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Mutant R1810Q of the Dihydroorotase Domain of Human Cad Protein Bound to the Substrates within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1907

b:22.6
occ:0.50
 O A:HOH2213 2.0 44.2 1.0
NE2 A:HIS1734 2.2 20.3 1.0
O A:HOH2207 2.3 33.9 1.0
HE1 A:HIS1734 2.8 24.8 1.0
CE1 A:HIS1734 2.8 20.7 1.0
CD2 A:HIS1734 3.4 19.3 1.0
HD2 A:HIS1734 3.7 23.1 1.0
ND1 A:HIS1734 4.1 18.8 1.0
HD2 A:HIS1733 4.1 22.6 1.0
CG A:HIS1734 4.3 17.6 1.0
HG3 A:PRO1465 4.4 29.7 1.0
HD13 A:LEU1729 4.4 37.9 1.0
HB3 A:LEU1729 4.5 30.6 1.0
HD1 A:HIS1734 4.8 22.5 1.0
CD2 A:HIS1733 4.9 18.8 1.0
HE22 A:GLN1730 4.9 24.6 1.0
HD12 A:LEU1729 5.0 37.9 1.0

Reference:

F.Del Cano-Ochoa, B.G.Ng, A.Rubio-Del-Campo, S.Mahajan, M.P.Wilson, M.Vilar, D.Rymen, P.Sanchez-Pintos, J.Kenny, M.Ley Martos, T.Campos, S.B.Wortmann, H.H.Freeze, S.Ramon-Maiques. Beyond Genetics: Deciphering the Impact of Missense Variants in Cad Deficiency. J Inherit Metab Dis 2023.
ISSN: ISSN 1573-2665
PubMed: 37540500
DOI: 10.1002/JIMD.12667
Page generated: Thu Oct 31 09:24:26 2024

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