Zinc in PDB 6cvq: Human Aprataxin (Aptx) H201Q Bound to Rna-Dna, Amp and Zn Product Complex
Enzymatic activity of Human Aprataxin (Aptx) H201Q Bound to Rna-Dna, Amp and Zn Product Complex
All present enzymatic activity of Human Aprataxin (Aptx) H201Q Bound to Rna-Dna, Amp and Zn Product Complex:
3.1.11.7;
3.1.12.2;
Protein crystallography data
The structure of Human Aprataxin (Aptx) H201Q Bound to Rna-Dna, Amp and Zn Product Complex, PDB code: 6cvq
was solved by
M.J.Schellenberg,
P.S.Tumbale,
R.S.Williams,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
32.41 /
1.65
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
40.571,
116.049,
117.215,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
11.8 /
16.8
|
Other elements in 6cvq:
The structure of Human Aprataxin (Aptx) H201Q Bound to Rna-Dna, Amp and Zn Product Complex also contains other interesting chemical elements:
Zinc Binding Sites:
The binding sites of Zinc atom in the Human Aprataxin (Aptx) H201Q Bound to Rna-Dna, Amp and Zn Product Complex
(pdb code 6cvq). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the
Human Aprataxin (Aptx) H201Q Bound to Rna-Dna, Amp and Zn Product Complex, PDB code: 6cvq:
Jump to Zinc binding site number:
1;
2;
Zinc binding site 1 out
of 2 in 6cvq
Go back to
Zinc Binding Sites List in 6cvq
Zinc binding site 1 out
of 2 in the Human Aprataxin (Aptx) H201Q Bound to Rna-Dna, Amp and Zn Product Complex
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of Human Aprataxin (Aptx) H201Q Bound to Rna-Dna, Amp and Zn Product Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn402
b:23.0
occ:1.00
|
NE2
|
A:HIS335
|
2.0
|
22.2
|
1.0
|
NE2
|
A:HIS339
|
2.1
|
23.4
|
1.0
|
SG
|
A:CYS322
|
2.2
|
23.8
|
1.0
|
SG
|
A:CYS319
|
2.3
|
20.9
|
1.0
|
CD2
|
A:HIS339
|
3.0
|
25.7
|
1.0
|
CE1
|
A:HIS335
|
3.0
|
22.9
|
1.0
|
CD2
|
A:HIS335
|
3.0
|
21.1
|
1.0
|
CE1
|
A:HIS339
|
3.1
|
25.3
|
1.0
|
HD2
|
A:HIS339
|
3.1
|
30.9
|
1.0
|
HB3
|
A:CYS319
|
3.1
|
24.2
|
1.0
|
H
|
A:CYS322
|
3.2
|
30.3
|
1.0
|
CB
|
A:CYS319
|
3.2
|
20.2
|
1.0
|
HE1
|
A:HIS335
|
3.2
|
27.5
|
1.0
|
HD2
|
A:HIS335
|
3.2
|
25.3
|
1.0
|
HB2
|
A:CYS319
|
3.3
|
24.2
|
1.0
|
HB3
|
A:CYS322
|
3.3
|
30.7
|
1.0
|
HB2
|
A:GLU321
|
3.3
|
34.9
|
1.0
|
HE1
|
A:HIS339
|
3.3
|
30.4
|
1.0
|
CB
|
A:CYS322
|
3.4
|
25.6
|
1.0
|
N
|
A:CYS322
|
3.7
|
25.2
|
1.0
|
HD2
|
A:LYS338
|
3.9
|
47.5
|
1.0
|
CA
|
A:CYS322
|
4.1
|
24.1
|
1.0
|
ND1
|
A:HIS335
|
4.1
|
21.8
|
1.0
|
H
|
A:GLU321
|
4.1
|
29.2
|
1.0
|
CG
|
A:HIS339
|
4.1
|
27.3
|
1.0
|
CG
|
A:HIS335
|
4.1
|
20.7
|
1.0
|
ND1
|
A:HIS339
|
4.2
|
25.8
|
1.0
|
HB2
|
A:CYS322
|
4.2
|
30.7
|
1.0
|
HB3
|
A:GLN324
|
4.2
|
34.4
|
1.0
|
H
|
A:GLN324
|
4.3
|
30.3
|
1.0
|
CB
|
A:GLU321
|
4.3
|
29.1
|
1.0
|
HG2
|
A:LYS338
|
4.5
|
43.6
|
1.0
|
H
|
A:GLN323
|
4.6
|
31.8
|
1.0
|
C
|
A:GLU321
|
4.6
|
26.2
|
1.0
|
CA
|
A:CYS319
|
4.6
|
18.6
|
1.0
|
HB3
|
A:GLU321
|
4.6
|
34.9
|
1.0
|
HD23
|
A:LEU336
|
4.7
|
28.3
|
1.0
|
C
|
A:CYS322
|
4.7
|
25.7
|
1.0
|
HG3
|
A:LYS338
|
4.7
|
43.6
|
1.0
|
HB2
|
A:GLN324
|
4.7
|
34.4
|
1.0
|
CD
|
A:LYS338
|
4.7
|
39.6
|
1.0
|
N
|
A:GLU321
|
4.8
|
24.4
|
1.0
|
CA
|
A:GLU321
|
4.8
|
26.3
|
1.0
|
HD1
|
A:HIS335
|
4.9
|
26.1
|
1.0
|
N
|
A:GLN323
|
4.9
|
26.5
|
1.0
|
CG
|
A:LYS338
|
4.9
|
36.4
|
1.0
|
HA
|
A:CYS322
|
4.9
|
28.9
|
1.0
|
CB
|
A:GLN324
|
4.9
|
28.6
|
1.0
|
HD1
|
A:HIS339
|
4.9
|
31.0
|
1.0
|
HA
|
A:CYS319
|
5.0
|
22.4
|
1.0
|
HA
|
A:LEU336
|
5.0
|
26.4
|
1.0
|
|
Zinc binding site 2 out
of 2 in 6cvq
Go back to
Zinc Binding Sites List in 6cvq
Zinc binding site 2 out
of 2 in the Human Aprataxin (Aptx) H201Q Bound to Rna-Dna, Amp and Zn Product Complex
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of Human Aprataxin (Aptx) H201Q Bound to Rna-Dna, Amp and Zn Product Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn402
b:26.7
occ:1.00
|
NE2
|
B:HIS339
|
2.1
|
28.0
|
1.0
|
NE2
|
B:HIS335
|
2.1
|
26.0
|
1.0
|
SG
|
B:CYS322
|
2.3
|
27.9
|
1.0
|
SG
|
B:CYS319
|
2.3
|
23.4
|
1.0
|
CE1
|
B:HIS339
|
3.0
|
29.8
|
1.0
|
CD2
|
B:HIS335
|
3.0
|
26.0
|
1.0
|
HB3
|
B:CYS319
|
3.1
|
26.8
|
1.0
|
CE1
|
B:HIS335
|
3.1
|
26.6
|
1.0
|
CD2
|
B:HIS339
|
3.1
|
28.3
|
1.0
|
HB3
|
B:CYS322
|
3.1
|
32.0
|
1.0
|
HE1
|
B:HIS339
|
3.1
|
35.7
|
1.0
|
CB
|
B:CYS319
|
3.1
|
22.3
|
1.0
|
H
|
B:CYS322
|
3.1
|
33.5
|
1.0
|
HD2
|
B:HIS335
|
3.2
|
31.2
|
1.0
|
HB2
|
B:CYS319
|
3.2
|
26.8
|
1.0
|
CB
|
B:CYS322
|
3.3
|
26.7
|
1.0
|
HE1
|
B:HIS335
|
3.3
|
31.9
|
1.0
|
HD2
|
B:HIS339
|
3.3
|
34.0
|
1.0
|
HB2
|
B:GLU321
|
3.5
|
34.3
|
1.0
|
N
|
B:CYS322
|
3.7
|
28.0
|
1.0
|
CA
|
B:CYS322
|
4.0
|
26.6
|
1.0
|
HB3
|
B:GLN324
|
4.0
|
39.4
|
1.0
|
HD3
|
B:LYS338
|
4.0
|
52.3
|
1.0
|
HB2
|
B:CYS322
|
4.1
|
32.0
|
1.0
|
ND1
|
B:HIS339
|
4.1
|
29.1
|
1.0
|
O
|
B:HOH560
|
4.1
|
53.6
|
1.0
|
H
|
B:GLN324
|
4.1
|
34.3
|
1.0
|
ND1
|
B:HIS335
|
4.2
|
25.1
|
1.0
|
CG
|
B:HIS335
|
4.2
|
26.2
|
1.0
|
CG
|
B:HIS339
|
4.2
|
29.7
|
1.0
|
H
|
B:GLU321
|
4.2
|
30.6
|
1.0
|
CB
|
B:GLU321
|
4.5
|
28.6
|
1.0
|
CA
|
B:CYS319
|
4.6
|
21.5
|
1.0
|
HB2
|
B:GLN324
|
4.6
|
39.4
|
1.0
|
C
|
B:CYS322
|
4.6
|
26.9
|
1.0
|
H
|
B:GLN323
|
4.6
|
32.9
|
1.0
|
C
|
B:GLU321
|
4.6
|
28.0
|
1.0
|
HD23
|
B:LEU336
|
4.7
|
31.6
|
1.0
|
HG2
|
B:LYS338
|
4.7
|
52.0
|
1.0
|
CB
|
B:GLN324
|
4.8
|
32.9
|
1.0
|
HA
|
B:CYS322
|
4.8
|
31.9
|
1.0
|
N
|
B:GLN323
|
4.9
|
27.4
|
1.0
|
N
|
B:GLU321
|
4.9
|
25.5
|
1.0
|
HB3
|
B:GLU321
|
4.9
|
34.3
|
1.0
|
HD1
|
B:HIS339
|
4.9
|
35.0
|
1.0
|
CA
|
B:GLU321
|
4.9
|
27.0
|
1.0
|
HA
|
B:CYS319
|
4.9
|
25.8
|
1.0
|
CD
|
B:LYS338
|
4.9
|
43.6
|
1.0
|
HD1
|
B:HIS335
|
5.0
|
30.2
|
1.0
|
N
|
B:GLN324
|
5.0
|
28.6
|
1.0
|
|
Reference:
P.Tumbale,
M.J.Schellenberg,
G.A.Mueller,
E.Fairweather,
M.Watson,
J.N.Little,
J.Krahn,
I.Waddell,
R.E.London,
R.S.Williams.
Mechanism of Aptx Nicked Dna Sensing and Pleiotropic Inactivation in Neurodegenerative Disease. Embo J. V. 37 2018.
ISSN: ESSN 1460-2075
PubMed: 29934293
DOI: 10.15252/EMBJ.201798875
Page generated: Mon Oct 28 19:10:55 2024
|