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:

Sodium (Na) 1 atom

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: Wed Dec 16 11:38:11 2020

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