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
Go back to
Zinc Binding Sites List in 8pbq
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
Go back to
Zinc Binding Sites List in 8pbq
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
Go back to
Zinc Binding Sites List in 8pbq
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
Go back to
Zinc Binding Sites List in 8pbq
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
Go back to
Zinc Binding Sites List in 8pbq
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 Dec 28 13:34:34 2023
|
