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Zinc in PDB 6cvr: Human Aprataxin (Aptx) S242N Bound to Rna-Dna, Amp and Zn Product Complex

Enzymatic activity of Human Aprataxin (Aptx) S242N Bound to Rna-Dna, Amp and Zn Product Complex

All present enzymatic activity of Human Aprataxin (Aptx) S242N 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) S242N Bound to Rna-Dna, Amp and Zn Product Complex, PDB code: 6cvr 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) 38.39 / 1.88
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 40.616, 116.056, 117.563, 90.00, 90.00, 90.00
R / Rfree (%) 16.6 / 19

Zinc Binding Sites:

The binding sites of Zinc atom in the Human Aprataxin (Aptx) S242N Bound to Rna-Dna, Amp and Zn Product Complex (pdb code 6cvr). 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) S242N Bound to Rna-Dna, Amp and Zn Product Complex, PDB code: 6cvr:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 6cvr

Go back to Zinc Binding Sites List in 6cvr
Zinc binding site 1 out of 2 in the Human Aprataxin (Aptx) S242N 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) S242N Bound to Rna-Dna, Amp and Zn Product Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:34.9
occ:1.00
NE2 A:HIS335 2.1 38.8 1.0
NE2 A:HIS339 2.1 45.0 1.0
SG A:CYS322 2.3 45.5 1.0
SG A:CYS319 2.4 38.2 1.0
CD2 A:HIS335 2.9 36.3 1.0
HD2 A:HIS335 3.0 43.5 1.0
CE1 A:HIS339 3.0 46.7 1.0
CD2 A:HIS339 3.0 44.2 1.0
HB3 A:CYS322 3.0 57.1 1.0
CE1 A:HIS335 3.1 40.1 1.0
HB3 A:CYS319 3.1 44.4 1.0
CB A:CYS319 3.2 37.0 1.0
H A:CYS322 3.2 52.5 1.0
HE1 A:HIS339 3.2 56.0 1.0
HD2 A:HIS339 3.2 53.1 1.0
HB2 A:CYS319 3.3 44.4 1.0
CB A:CYS322 3.3 47.6 1.0
HE1 A:HIS335 3.4 48.2 1.0
HB2 A:GLU321 3.6 63.8 1.0
N A:CYS322 3.7 43.8 1.0
HD3 A:LYS338 4.0 74.5 1.0
CA A:CYS322 4.0 46.0 1.0
HB2 A:CYS322 4.1 57.1 1.0
CG A:HIS335 4.1 35.1 1.0
ND1 A:HIS339 4.1 47.0 1.0
CG A:HIS339 4.2 45.6 1.0
ND1 A:HIS335 4.2 38.4 1.0
H A:GLU321 4.2 47.3 1.0
HB3 A:GLN324 4.2 61.6 1.0
H A:GLN324 4.3 52.7 1.0
CB A:GLU321 4.4 53.2 1.0
HB3 A:GLU321 4.6 63.8 1.0
C A:GLU321 4.6 46.1 1.0
HG2 A:LYS338 4.6 69.8 1.0
H A:GLN323 4.6 57.1 1.0
C A:CYS322 4.7 45.0 1.0
CA A:CYS319 4.7 34.7 1.0
HD23 A:LEU336 4.8 32.8 1.0
HB2 A:GLN324 4.8 61.6 1.0
N A:GLU321 4.8 39.4 1.0
HA A:CYS322 4.8 55.2 1.0
CA A:GLU321 4.9 46.0 1.0
HD1 A:HIS339 4.9 56.4 1.0
N A:GLN323 4.9 47.6 1.0
CD A:LYS338 4.9 62.1 1.0
CB A:GLN324 5.0 51.4 1.0
HD1 A:HIS335 5.0 46.1 1.0
HA A:CYS319 5.0 41.6 1.0

Zinc binding site 2 out of 2 in 6cvr

Go back to Zinc Binding Sites List in 6cvr
Zinc binding site 2 out of 2 in the Human Aprataxin (Aptx) S242N 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) S242N Bound to Rna-Dna, Amp and Zn Product Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn402

b:59.6
occ:1.00
NE2 B:HIS335 2.1 57.8 1.0
NE2 B:HIS339 2.2 68.0 1.0
SG B:CYS319 2.4 45.5 1.0
SG B:CYS322 2.5 58.4 1.0
HB3 B:CYS322 2.9 72.5 1.0
CE1 B:HIS339 3.1 71.1 1.0
CE1 B:HIS335 3.1 60.2 1.0
CD2 B:HIS335 3.1 55.1 1.0
HB3 B:CYS319 3.1 54.1 1.0
H B:CYS322 3.2 76.3 1.0
CD2 B:HIS339 3.2 65.9 1.0
HE1 B:HIS339 3.2 85.3 1.0
CB B:CYS322 3.2 60.4 1.0
CB B:CYS319 3.2 45.0 1.0
HE1 B:HIS335 3.3 72.3 1.0
HD2 B:HIS335 3.3 66.2 1.0
HB2 B:CYS319 3.3 54.1 1.0
HD2 B:HIS339 3.4 79.0 1.0
N B:CYS322 3.7 63.6 1.0
HB2 B:GLU321 3.7 0.4 1.0
CA B:CYS322 4.0 61.5 1.0
HB2 B:CYS322 4.0 72.5 1.0
HB3 B:GLN324 4.1 71.2 1.0
H B:GLU321 4.2 92.3 1.0
ND1 B:HIS335 4.2 59.1 1.0
ND1 B:HIS339 4.2 70.9 1.0
H B:GLN324 4.2 66.5 1.0
HD3 B:LYS338 4.2 98.2 1.0
CG B:HIS335 4.3 55.5 1.0
CG B:HIS339 4.3 68.0 1.0
CB B:GLU321 4.6 88.6 1.0
C B:GLU321 4.6 88.8 1.0
H B:GLN323 4.6 77.2 1.0
C B:CYS322 4.6 61.0 1.0
CA B:CYS319 4.7 42.5 1.0
HG2 B:LYS338 4.8 92.5 1.0
HA B:CYS322 4.8 73.8 1.0
N B:GLU321 4.8 76.9 1.0
N B:GLN323 4.9 64.3 1.0
HB2 B:GLN324 4.9 71.2 1.0
CA B:GLU321 4.9 84.9 1.0
CB B:GLN324 4.9 59.3 1.0
HB3 B:GLU321 5.0 0.4 1.0
HD1 B:HIS339 5.0 85.0 1.0
HD1 B:HIS335 5.0 70.9 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 11:38:13 2020

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