Zinc in PDB 6hfp: Human Dihydroorotase Mutant F1563T Co-Crystallized with Carbamoyl Aspartate at pH 7.0
Enzymatic activity of Human Dihydroorotase Mutant F1563T Co-Crystallized with Carbamoyl Aspartate at pH 7.0
All present enzymatic activity of Human Dihydroorotase Mutant F1563T Co-Crystallized with Carbamoyl Aspartate at pH 7.0:
2.1.3.2;
3.5.2.3;
6.3.5.5;
Protein crystallography data
The structure of Human Dihydroorotase Mutant F1563T Co-Crystallized with Carbamoyl Aspartate at pH 7.0, PDB code: 6hfp
was solved by
S.Ramon-Maiques,
A.Grande Garcia,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
48.49 /
1.20
|
Space group
|
C 2 2 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
82.104,
158.948,
61.210,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
12.2 /
13.7
|
Zinc Binding Sites:
The binding sites of Zinc atom in the Human Dihydroorotase Mutant F1563T Co-Crystallized with Carbamoyl Aspartate at pH 7.0
(pdb code 6hfp). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the
Human Dihydroorotase Mutant F1563T Co-Crystallized with Carbamoyl Aspartate at pH 7.0, PDB code: 6hfp:
Jump to Zinc binding site number:
1;
2;
3;
4;
Zinc binding site 1 out
of 4 in 6hfp
Go back to
Zinc Binding Sites List in 6hfp
Zinc binding site 1 out
of 4 in the Human Dihydroorotase Mutant F1563T Co-Crystallized with Carbamoyl Aspartate 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 Human Dihydroorotase Mutant F1563T Co-Crystallized with Carbamoyl Aspartate at pH 7.0 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn1901
b:12.1
occ:0.84
|
OQ1
|
A:KCX1556
|
1.9
|
12.6
|
1.0
|
O
|
A:HOH2170
|
1.9
|
14.1
|
1.0
|
ND1
|
A:HIS1590
|
2.1
|
13.0
|
1.0
|
NE2
|
A:HIS1614
|
2.1
|
13.2
|
1.0
|
CX
|
A:KCX1556
|
2.9
|
12.8
|
1.0
|
CE1
|
A:HIS1590
|
2.9
|
12.5
|
1.0
|
O4
|
A:DOR1905
|
3.0
|
16.4
|
0.8
|
HB2
|
A:HIS1590
|
3.0
|
14.7
|
1.0
|
CE1
|
A:HIS1614
|
3.0
|
11.8
|
1.0
|
HE1
|
A:HIS1590
|
3.0
|
15.0
|
1.0
|
CD2
|
A:HIS1614
|
3.1
|
12.7
|
1.0
|
CG
|
A:HIS1590
|
3.1
|
12.3
|
1.0
|
HE1
|
A:HIS1614
|
3.2
|
14.1
|
1.0
|
HD2
|
A:HIS1614
|
3.3
|
15.3
|
1.0
|
OQ2
|
A:KCX1556
|
3.3
|
13.8
|
1.0
|
HE1
|
A:HIS1471
|
3.3
|
16.3
|
1.0
|
ZN
|
A:ZN1902
|
3.4
|
12.5
|
0.9
|
CB
|
A:HIS1590
|
3.6
|
12.3
|
1.0
|
C4
|
A:DOR1905
|
3.6
|
13.7
|
0.8
|
HE1
|
A:TYR1558
|
3.8
|
17.2
|
1.0
|
CE1
|
A:HIS1471
|
4.0
|
13.6
|
1.0
|
H52
|
A:DOR1905
|
4.0
|
17.9
|
0.8
|
NE2
|
A:HIS1590
|
4.1
|
13.4
|
1.0
|
NE2
|
A:HIS1471
|
4.1
|
11.7
|
1.0
|
NZ
|
A:KCX1556
|
4.1
|
13.5
|
1.0
|
OD2
|
A:ASP1686
|
4.1
|
14.6
|
1.0
|
ND1
|
A:HIS1614
|
4.2
|
12.1
|
1.0
|
CD2
|
A:HIS1590
|
4.2
|
13.0
|
1.0
|
CG
|
A:HIS1614
|
4.2
|
12.5
|
1.0
|
HD3
|
A:PRO1662
|
4.2
|
16.4
|
1.0
|
N3
|
A:DOR1905
|
4.2
|
15.4
|
0.8
|
HB3
|
A:HIS1590
|
4.3
|
14.7
|
1.0
|
HN3
|
A:DOR1905
|
4.3
|
18.5
|
0.8
|
HA
|
A:HIS1590
|
4.3
|
13.5
|
1.0
|
HE2
|
A:KCX1556
|
4.3
|
15.6
|
1.0
|
C5
|
A:DOR1905
|
4.4
|
14.9
|
0.8
|
O
|
A:ARG1661
|
4.5
|
15.7
|
1.0
|
O
|
A:HOH2096
|
4.5
|
25.9
|
1.0
|
CE1
|
A:TYR1558
|
4.5
|
14.4
|
1.0
|
CA
|
A:HIS1590
|
4.6
|
11.2
|
1.0
|
HB3
|
A:CYS1613
|
4.6
|
16.0
|
1.0
|
CE
|
A:KCX1556
|
4.6
|
13.0
|
1.0
|
HE3
|
A:KCX1556
|
4.6
|
15.6
|
1.0
|
HD1
|
A:TYR1558
|
4.7
|
17.4
|
1.0
|
HB2
|
A:CYS1613
|
4.7
|
16.0
|
1.0
|
OD1
|
A:ASP1686
|
4.7
|
13.9
|
1.0
|
CG
|
A:ASP1686
|
4.7
|
13.3
|
1.0
|
HE2
|
A:HIS1590
|
4.8
|
16.1
|
1.0
|
HZ
|
A:KCX1556
|
4.8
|
16.2
|
1.0
|
HD1
|
A:HIS1614
|
4.9
|
14.5
|
1.0
|
CD1
|
A:TYR1558
|
5.0
|
14.5
|
1.0
|
|
Zinc binding site 2 out
of 4 in 6hfp
Go back to
Zinc Binding Sites List in 6hfp
Zinc binding site 2 out
of 4 in the Human Dihydroorotase Mutant F1563T Co-Crystallized with Carbamoyl Aspartate 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 Human Dihydroorotase Mutant F1563T Co-Crystallized with Carbamoyl Aspartate at pH 7.0 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn1902
b:12.5
occ:0.93
|
O
|
A:HOH2170
|
1.9
|
14.1
|
1.0
|
NE2
|
A:HIS1471
|
2.0
|
11.7
|
1.0
|
NE2
|
A:HIS1473
|
2.0
|
12.6
|
1.0
|
OQ2
|
A:KCX1556
|
2.2
|
13.8
|
1.0
|
OD1
|
A:ASP1686
|
2.2
|
13.9
|
1.0
|
CE1
|
A:HIS1473
|
3.0
|
12.8
|
1.0
|
CD2
|
A:HIS1471
|
3.0
|
11.4
|
1.0
|
CE1
|
A:HIS1471
|
3.0
|
13.6
|
1.0
|
CX
|
A:KCX1556
|
3.0
|
12.8
|
1.0
|
CD2
|
A:HIS1473
|
3.1
|
12.9
|
1.0
|
CG
|
A:ASP1686
|
3.1
|
13.3
|
1.0
|
HE1
|
A:HIS1473
|
3.2
|
15.4
|
1.0
|
HD2
|
A:HIS1471
|
3.2
|
13.6
|
1.0
|
HE1
|
A:HIS1471
|
3.2
|
16.3
|
1.0
|
H52
|
A:DOR1905
|
3.2
|
17.9
|
0.8
|
HD2
|
A:HIS1473
|
3.3
|
15.5
|
1.0
|
ZN
|
A:ZN1901
|
3.4
|
12.1
|
0.8
|
OQ1
|
A:KCX1556
|
3.4
|
12.6
|
1.0
|
HG3
|
A:MET1503
|
3.4
|
17.1
|
1.0
|
OD2
|
A:ASP1686
|
3.4
|
14.6
|
1.0
|
H6
|
A:DOR1905
|
3.6
|
17.0
|
0.8
|
HD2
|
A:HIS1614
|
3.8
|
15.3
|
1.0
|
HH
|
A:TYR1558
|
3.9
|
17.3
|
1.0
|
C5
|
A:DOR1905
|
4.0
|
14.9
|
0.8
|
HA
|
A:ASP1686
|
4.1
|
14.4
|
1.0
|
ND1
|
A:HIS1473
|
4.1
|
13.5
|
1.0
|
ND1
|
A:HIS1471
|
4.1
|
14.6
|
1.0
|
CG
|
A:HIS1471
|
4.2
|
12.2
|
1.0
|
NZ
|
A:KCX1556
|
4.2
|
13.5
|
1.0
|
CG
|
A:HIS1473
|
4.2
|
12.8
|
1.0
|
HZ
|
A:KCX1556
|
4.3
|
16.2
|
1.0
|
C4
|
A:DOR1905
|
4.3
|
13.7
|
0.8
|
CB
|
A:ASP1686
|
4.3
|
13.2
|
1.0
|
C6
|
A:DOR1905
|
4.3
|
14.2
|
0.8
|
HE1
|
A:TYR1558
|
4.4
|
17.2
|
1.0
|
CG
|
A:MET1503
|
4.4
|
14.2
|
1.0
|
CD2
|
A:HIS1614
|
4.4
|
12.7
|
1.0
|
NE2
|
A:HIS1614
|
4.4
|
13.2
|
1.0
|
HB2
|
A:ASP1686
|
4.5
|
15.8
|
1.0
|
O4
|
A:DOR1905
|
4.5
|
16.4
|
0.8
|
HE3
|
A:MET1503
|
4.6
|
18.2
|
1.0
|
OH
|
A:TYR1558
|
4.7
|
14.4
|
1.0
|
CA
|
A:ASP1686
|
4.7
|
12.0
|
1.0
|
HB2
|
A:ALA1688
|
4.8
|
17.1
|
1.0
|
HG2
|
A:MET1503
|
4.8
|
17.1
|
1.0
|
HB2
|
A:MET1503
|
4.9
|
15.4
|
1.0
|
H51
|
A:DOR1905
|
4.9
|
17.9
|
0.8
|
HD1
|
A:HIS1473
|
4.9
|
16.2
|
1.0
|
N3
|
A:DOR1905
|
4.9
|
15.4
|
0.8
|
HB3
|
A:MET1503
|
5.0
|
15.4
|
1.0
|
|
Zinc binding site 3 out
of 4 in 6hfp
Go back to
Zinc Binding Sites List in 6hfp
Zinc binding site 3 out
of 4 in the Human Dihydroorotase Mutant F1563T Co-Crystallized with Carbamoyl Aspartate 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 Human Dihydroorotase Mutant F1563T Co-Crystallized with Carbamoyl Aspartate at pH 7.0 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn1903
b:12.9
occ:0.56
|
ND1
|
A:HIS1471
|
2.0
|
14.6
|
1.0
|
O
|
A:HOH2137
|
2.0
|
14.6
|
1.0
|
OE1
|
A:GLU1637
|
2.1
|
14.3
|
1.0
|
SG
|
A:CYS1613
|
2.3
|
13.4
|
1.0
|
HB3
|
A:CYS1613
|
2.7
|
16.0
|
1.0
|
HB2
|
A:HIS1471
|
2.8
|
14.1
|
1.0
|
CD
|
A:GLU1637
|
2.9
|
13.1
|
1.0
|
CE1
|
A:HIS1471
|
3.0
|
13.6
|
1.0
|
CB
|
A:CYS1613
|
3.0
|
13.3
|
1.0
|
OE2
|
A:GLU1637
|
3.0
|
13.7
|
1.0
|
CG
|
A:HIS1471
|
3.1
|
12.2
|
1.0
|
HE1
|
A:HIS1471
|
3.1
|
16.3
|
1.0
|
HE3
|
A:MET1503
|
3.1
|
18.2
|
1.0
|
HA
|
A:CYS1613
|
3.2
|
14.1
|
1.0
|
CB
|
A:HIS1471
|
3.4
|
11.8
|
1.0
|
HE1
|
A:MET1503
|
3.6
|
18.2
|
1.0
|
CA
|
A:CYS1613
|
3.6
|
11.7
|
1.0
|
CE
|
A:MET1503
|
3.7
|
15.2
|
1.0
|
HB2
|
A:CYS1613
|
3.9
|
16.0
|
1.0
|
HE2
|
A:MET1503
|
3.9
|
18.2
|
1.0
|
HB3
|
A:HIS1471
|
4.0
|
14.1
|
1.0
|
H
|
A:HIS1614
|
4.0
|
13.8
|
1.0
|
NE2
|
A:HIS1471
|
4.1
|
11.7
|
1.0
|
CD2
|
A:HIS1471
|
4.1
|
11.4
|
1.0
|
HD2
|
A:HIS1611
|
4.2
|
14.2
|
1.0
|
CG
|
A:GLU1637
|
4.2
|
13.4
|
1.0
|
HG21
|
A:VAL1588
|
4.2
|
17.9
|
1.0
|
HB
|
A:VAL1588
|
4.3
|
15.9
|
1.0
|
HG2
|
A:GLU1637
|
4.3
|
16.0
|
1.0
|
HG23
|
A:VAL1470
|
4.4
|
16.3
|
1.0
|
HE2
|
A:HIS1611
|
4.4
|
15.0
|
1.0
|
O
|
A:VAL1470
|
4.4
|
12.5
|
1.0
|
HA
|
A:HIS1471
|
4.4
|
13.7
|
1.0
|
HG3
|
A:GLU1637
|
4.5
|
16.0
|
1.0
|
CA
|
A:HIS1471
|
4.6
|
11.4
|
1.0
|
N
|
A:HIS1614
|
4.6
|
11.5
|
1.0
|
N
|
A:CYS1613
|
4.6
|
11.1
|
1.0
|
O
|
A:HOH2304
|
4.6
|
18.6
|
1.0
|
C
|
A:CYS1613
|
4.7
|
11.6
|
1.0
|
HE2
|
A:KCX1556
|
4.8
|
15.6
|
1.0
|
H
|
A:CYS1613
|
4.8
|
13.3
|
1.0
|
HG23
|
A:VAL1588
|
4.8
|
17.9
|
1.0
|
HB3
|
A:ALA1684
|
4.8
|
16.4
|
1.0
|
CD2
|
A:HIS1611
|
4.8
|
11.8
|
1.0
|
CG2
|
A:VAL1588
|
4.9
|
14.9
|
1.0
|
HG11
|
A:VAL1588
|
4.9
|
16.1
|
1.0
|
NE2
|
A:HIS1611
|
4.9
|
12.5
|
1.0
|
HD2
|
A:KCX1556
|
4.9
|
15.7
|
1.0
|
CB
|
A:VAL1588
|
5.0
|
13.2
|
1.0
|
HD2
|
A:HIS1471
|
5.0
|
13.6
|
1.0
|
|
Zinc binding site 4 out
of 4 in 6hfp
Go back to
Zinc Binding Sites List in 6hfp
Zinc binding site 4 out
of 4 in the Human Dihydroorotase Mutant F1563T Co-Crystallized with Carbamoyl Aspartate at pH 7.0
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of Human Dihydroorotase Mutant F1563T Co-Crystallized with Carbamoyl Aspartate at pH 7.0 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn1904
b:19.0
occ:1.00
|
HE2
|
A:HIS1734
|
1.2
|
17.3
|
1.0
|
O
|
A:HOH2336
|
1.9
|
19.9
|
1.0
|
NE2
|
A:HIS1734
|
2.1
|
14.4
|
1.0
|
CE1
|
A:HIS1734
|
2.8
|
14.6
|
1.0
|
HE1
|
A:HIS1734
|
2.9
|
17.5
|
1.0
|
CD2
|
A:HIS1734
|
3.2
|
13.4
|
1.0
|
HD2
|
A:HIS1734
|
3.5
|
16.0
|
1.0
|
ND1
|
A:HIS1734
|
4.0
|
12.9
|
1.0
|
HD2
|
A:HIS1733
|
4.1
|
16.9
|
1.0
|
CG
|
A:HIS1734
|
4.3
|
12.4
|
1.0
|
O
|
A:HOH2382
|
4.4
|
31.0
|
1.0
|
HG3
|
A:PRO1465
|
4.5
|
22.2
|
1.0
|
HB3
|
A:LEU1729
|
4.7
|
18.1
|
1.0
|
HD13
|
A:LEU1729
|
4.8
|
22.0
|
1.0
|
HD1
|
A:HIS1734
|
4.8
|
15.5
|
1.0
|
CD2
|
A:HIS1733
|
4.8
|
14.1
|
1.0
|
O
|
A:HOH2129
|
4.9
|
28.1
|
1.0
|
HE22
|
A:GLN1730
|
5.0
|
16.4
|
1.0
|
|
Reference:
F.Del Cano-Ochoa,
A.Grande-Garcia,
M.Reverte-Lopez,
M.D'abramo,
S.Ramon-Maiques.
Characterization of the Catalytic Flexible Loop in the Dihydroorotase Domain of the Human Multi-Enzymatic Protein Cad. J. Biol. Chem. V. 293 18903 2018.
ISSN: ESSN 1083-351X
PubMed: 30315107
DOI: 10.1074/JBC.RA118.005494
Page generated: Mon Oct 28 22:58:06 2024
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