Zinc in PDB 6hg2: Hybrid Dihydroorotase Domain of Human Cad with E. Coli Flexible Loop, Bound to Fluoroorotate
Enzymatic activity of Hybrid Dihydroorotase Domain of Human Cad with E. Coli Flexible Loop, Bound to Fluoroorotate
All present enzymatic activity of Hybrid Dihydroorotase Domain of Human Cad with E. Coli Flexible Loop, Bound to Fluoroorotate:
2.1.3.2;
3.5.2.3;
6.3.5.5;
Protein crystallography data
The structure of Hybrid Dihydroorotase Domain of Human Cad with E. Coli Flexible Loop, Bound to Fluoroorotate, PDB code: 6hg2
was solved by
S.Ramon-Maiques,
F.Del Cano-Ochoa,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
48.34 /
1.83
|
Space group
|
C 2 2 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
81.573,
159.288,
60.829,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
15 /
16
|
Other elements in 6hg2:
The structure of Hybrid Dihydroorotase Domain of Human Cad with E. Coli Flexible Loop, Bound to Fluoroorotate also contains other interesting chemical elements:
Zinc Binding Sites:
The binding sites of Zinc atom in the Hybrid Dihydroorotase Domain of Human Cad with E. Coli Flexible Loop, Bound to Fluoroorotate
(pdb code 6hg2). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the
Hybrid Dihydroorotase Domain of Human Cad with E. Coli Flexible Loop, Bound to Fluoroorotate, PDB code: 6hg2:
Jump to Zinc binding site number:
1;
2;
Zinc binding site 1 out
of 2 in 6hg2
Go back to
Zinc Binding Sites List in 6hg2
Zinc binding site 1 out
of 2 in the Hybrid Dihydroorotase Domain of Human Cad with E. Coli Flexible Loop, Bound to Fluoroorotate
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of Hybrid Dihydroorotase Domain of Human Cad with E. Coli Flexible Loop, Bound to Fluoroorotate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn1901
b:32.4
occ:0.70
|
OQ1
|
A:KCX1556
|
1.9
|
35.3
|
1.0
|
O
|
A:HOH2078
|
2.0
|
35.2
|
1.0
|
NE2
|
A:HIS1614
|
2.1
|
32.1
|
1.0
|
ND1
|
A:HIS1590
|
2.1
|
33.5
|
1.0
|
O6
|
A:FOT1903
|
2.6
|
44.5
|
1.0
|
CX
|
A:KCX1556
|
2.9
|
34.4
|
1.0
|
CE1
|
A:HIS1590
|
3.0
|
34.5
|
1.0
|
CE1
|
A:HIS1614
|
3.0
|
32.2
|
1.0
|
HB2
|
A:HIS1590
|
3.0
|
35.4
|
1.0
|
HE1
|
A:HIS1590
|
3.1
|
41.4
|
1.0
|
HE2
|
A:TYR1558
|
3.1
|
51.1
|
0.6
|
CD2
|
A:HIS1614
|
3.1
|
32.7
|
1.0
|
HE1
|
A:HIS1614
|
3.2
|
38.7
|
1.0
|
CG
|
A:HIS1590
|
3.2
|
31.9
|
1.0
|
HE1
|
A:HIS1471
|
3.2
|
34.1
|
1.0
|
OQ2
|
A:KCX1556
|
3.2
|
33.5
|
1.0
|
ZN
|
A:ZN1902
|
3.3
|
33.6
|
0.8
|
HD2
|
A:HIS1614
|
3.4
|
39.3
|
1.0
|
C6
|
A:FOT1903
|
3.4
|
44.1
|
1.0
|
CB
|
A:HIS1590
|
3.6
|
29.5
|
1.0
|
CE2
|
A:TYR1558
|
3.9
|
42.6
|
0.6
|
HE1
|
A:TYR1558
|
3.9
|
48.9
|
0.4
|
CE1
|
A:HIS1471
|
3.9
|
28.4
|
1.0
|
HH
|
A:TYR1558
|
4.0
|
53.7
|
0.6
|
HN1
|
A:FOT1903
|
4.0
|
52.2
|
1.0
|
NE2
|
A:HIS1590
|
4.1
|
34.0
|
1.0
|
N1
|
A:FOT1903
|
4.1
|
43.5
|
1.0
|
ND1
|
A:HIS1614
|
4.2
|
33.5
|
1.0
|
NE2
|
A:HIS1471
|
4.2
|
26.8
|
1.0
|
NZ
|
A:KCX1556
|
4.2
|
34.5
|
1.0
|
CD2
|
A:HIS1590
|
4.2
|
33.6
|
1.0
|
CG
|
A:HIS1614
|
4.2
|
32.7
|
1.0
|
HB3
|
A:HIS1590
|
4.2
|
35.4
|
1.0
|
HD3
|
A:PRO1662
|
4.3
|
43.0
|
1.0
|
C5
|
A:FOT1903
|
4.3
|
45.4
|
1.0
|
O
|
A:ARG1661
|
4.3
|
37.0
|
1.0
|
HE2
|
A:KCX1556
|
4.4
|
41.0
|
1.0
|
F5
|
A:FOT1903
|
4.4
|
49.1
|
1.0
|
HA
|
A:HIS1590
|
4.4
|
33.4
|
1.0
|
HD2
|
A:TYR1558
|
4.4
|
48.0
|
0.6
|
OD2
|
A:ASP1686
|
4.4
|
40.2
|
1.0
|
HB2
|
A:CYS1613
|
4.5
|
38.7
|
1.0
|
HD1
|
A:TYR1558
|
4.5
|
48.8
|
0.4
|
CD2
|
A:TYR1558
|
4.6
|
40.0
|
0.6
|
HE3
|
A:KCX1556
|
4.6
|
41.0
|
1.0
|
CE
|
A:KCX1556
|
4.6
|
34.1
|
1.0
|
OH
|
A:TYR1558
|
4.6
|
44.7
|
0.6
|
CE1
|
A:TYR1558
|
4.6
|
40.7
|
0.4
|
CZ
|
A:TYR1558
|
4.7
|
42.8
|
0.6
|
CA
|
A:HIS1590
|
4.7
|
27.9
|
1.0
|
HB3
|
A:CYS1613
|
4.7
|
38.7
|
1.0
|
OD1
|
A:ASP1686
|
4.7
|
34.7
|
1.0
|
HE2
|
A:HIS1590
|
4.9
|
40.8
|
1.0
|
CG
|
A:ASP1686
|
4.9
|
35.7
|
1.0
|
HZ
|
A:KCX1556
|
4.9
|
41.4
|
1.0
|
HD1
|
A:HIS1614
|
4.9
|
40.2
|
1.0
|
CD1
|
A:TYR1558
|
5.0
|
40.6
|
0.4
|
|
Zinc binding site 2 out
of 2 in 6hg2
Go back to
Zinc Binding Sites List in 6hg2
Zinc binding site 2 out
of 2 in the Hybrid Dihydroorotase Domain of Human Cad with E. Coli Flexible Loop, Bound to Fluoroorotate
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of Hybrid Dihydroorotase Domain of Human Cad with E. Coli Flexible Loop, Bound to Fluoroorotate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn1902
b:33.6
occ:0.85
|
O
|
A:HOH2078
|
1.9
|
35.2
|
1.0
|
NE2
|
A:HIS1473
|
2.0
|
29.1
|
1.0
|
NE2
|
A:HIS1471
|
2.0
|
26.8
|
1.0
|
OQ2
|
A:KCX1556
|
2.1
|
33.5
|
1.0
|
OD1
|
A:ASP1686
|
2.4
|
34.7
|
1.0
|
CE1
|
A:HIS1473
|
2.8
|
30.7
|
1.0
|
CE1
|
A:HIS1471
|
2.9
|
28.4
|
1.0
|
CX
|
A:KCX1556
|
2.9
|
34.4
|
1.0
|
HE1
|
A:HIS1473
|
2.9
|
36.8
|
1.0
|
CD2
|
A:HIS1471
|
3.0
|
26.8
|
1.0
|
HE1
|
A:HIS1471
|
3.1
|
34.1
|
1.0
|
CD2
|
A:HIS1473
|
3.1
|
28.2
|
1.0
|
OQ1
|
A:KCX1556
|
3.3
|
35.3
|
1.0
|
HD2
|
A:HIS1471
|
3.3
|
32.2
|
1.0
|
ZN
|
A:ZN1901
|
3.3
|
32.4
|
0.7
|
HG3
|
A:MET1503
|
3.4
|
38.7
|
1.0
|
HD2
|
A:HIS1473
|
3.4
|
33.9
|
1.0
|
CG
|
A:ASP1686
|
3.4
|
35.7
|
1.0
|
OD2
|
A:ASP1686
|
3.8
|
40.2
|
1.0
|
HD2
|
A:HIS1614
|
3.9
|
39.3
|
1.0
|
ND1
|
A:HIS1473
|
4.0
|
31.3
|
1.0
|
F5
|
A:FOT1903
|
4.0
|
49.1
|
1.0
|
ND1
|
A:HIS1471
|
4.0
|
29.1
|
1.0
|
HH
|
A:TYR1558
|
4.1
|
53.7
|
0.4
|
C5
|
A:FOT1903
|
4.1
|
45.4
|
1.0
|
CG
|
A:HIS1471
|
4.1
|
27.0
|
1.0
|
NZ
|
A:KCX1556
|
4.1
|
34.5
|
1.0
|
CG
|
A:HIS1473
|
4.2
|
28.9
|
1.0
|
O6
|
A:FOT1903
|
4.2
|
44.5
|
1.0
|
C6
|
A:FOT1903
|
4.2
|
44.1
|
1.0
|
HE1
|
A:TYR1558
|
4.2
|
48.9
|
0.4
|
HA
|
A:ASP1686
|
4.3
|
34.8
|
1.0
|
HZ
|
A:KCX1556
|
4.3
|
41.4
|
1.0
|
CG
|
A:MET1503
|
4.3
|
32.2
|
1.0
|
NE2
|
A:HIS1614
|
4.4
|
32.1
|
1.0
|
CD2
|
A:HIS1614
|
4.4
|
32.7
|
1.0
|
HE3
|
A:MET1503
|
4.5
|
40.7
|
1.0
|
CB
|
A:ASP1686
|
4.6
|
31.0
|
1.0
|
HE2
|
A:TYR1558
|
4.7
|
51.1
|
0.6
|
HD1
|
A:HIS1473
|
4.8
|
37.5
|
1.0
|
HG2
|
A:MET1503
|
4.8
|
38.7
|
1.0
|
HB2
|
A:ASP1686
|
4.8
|
37.2
|
1.0
|
HD1
|
A:HIS1471
|
4.8
|
35.0
|
1.0
|
HB2
|
A:ALA1688
|
4.8
|
33.7
|
1.0
|
C4
|
A:FOT1903
|
4.8
|
42.8
|
1.0
|
HB2
|
A:MET1503
|
4.9
|
38.4
|
1.0
|
OH
|
A:TYR1558
|
4.9
|
44.7
|
0.4
|
CA
|
A:ASP1686
|
4.9
|
29.0
|
1.0
|
N1
|
A:FOT1903
|
5.0
|
43.5
|
1.0
|
HB3
|
A:MET1503
|
5.0
|
38.4
|
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 23:02:46 2024
|