Zinc in PDB 6cvs: Human Aprataxin (Aptx) L248M Bound to Dna, Amp and Zn Product

All present enzymatic activity of Human Aprataxin (Aptx) L248M Bound to Dna, Amp and Zn Product:
3.1.11.7; 3.1.12.2;

The structure of Human Aprataxin (Aptx) L248M Bound to Dna, Amp and Zn Product, PDB code: 6cvs 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)	28.89 / 2.11
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	40.384, 116.316, 117.559, 90.00, 90.00, 90.00
R / Rfree (%)	17.4 / 19.6

The binding sites of Zinc atom in the Human Aprataxin (Aptx) L248M Bound to Dna, Amp and Zn Product (pdb code 6cvs). 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) L248M Bound to Dna, Amp and Zn Product, PDB code: 6cvs:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Human Aprataxin (Aptx) L248M Bound to Dna, Amp and Zn Product


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) L248M Bound to Dna, Amp and Zn Product within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:36.3 occ:1.00 NE2 A:HIS339 2.0 53.9 1.0 NE2 A:HIS335 2.0 30.2 1.0 SG A:CYS322 2.3 37.2 1.0 SG A:CYS319 2.3 35.9 1.0 CD2 A:HIS339 2.9 50.0 1.0 CD2 A:HIS335 3.0 28.7 1.0 H A:CYS322 3.0 38.5 1.0 CE1 A:HIS339 3.0 52.9 1.0 CE1 A:HIS335 3.0 31.9 1.0 HD2 A:HIS339 3.1 50.0 1.0 HD2 A:HIS335 3.1 28.7 1.0 HB3 A:CYS319 3.1 36.4 1.0 CB A:CYS319 3.2 36.4 1.0 HE1 A:HIS339 3.2 52.9 1.0 HB2 A:CYS319 3.3 36.4 1.0 HE1 A:HIS335 3.3 31.9 1.0 HB3 A:CYS322 3.3 39.3 1.0 CB A:CYS322 3.4 39.3 1.0 HB2 A:GLU321 3.5 40.2 1.0 N A:CYS322 3.6 38.5 1.0 HB3 A:GLN324 4.0 46.6 1.0 CA A:CYS322 4.0 39.0 1.0 H A:GLN324 4.1 41.0 1.0 CG A:HIS339 4.1 50.0 1.0 ND1 A:HIS339 4.1 51.8 1.0 CG A:HIS335 4.1 31.8 1.0 ND1 A:HIS335 4.1 32.3 1.0 H A:GLU321 4.1 34.9 1.0 HB2 A:CYS322 4.2 39.3 1.0 CB A:GLU321 4.4 40.2 1.0 H A:GLN323 4.5 38.8 1.0 C A:CYS322 4.6 38.8 1.0 C A:GLU321 4.6 38.1 1.0 CA A:CYS319 4.6 34.3 1.0 HD23 A:LEU336 4.6 35.5 1.0 HB2 A:GLN324 4.7 46.6 1.0 CB A:GLN324 4.8 46.6 1.0 N A:GLN323 4.8 38.8 1.0 N A:GLU321 4.8 34.9 1.0 HB3 A:GLU321 4.8 40.2 1.0 CA A:GLU321 4.9 37.9 1.0 HD1 A:HIS339 4.9 51.8 1.0 N A:GLN324 4.9 41.0 1.0 HA A:CYS322 4.9 39.0 1.0 HD1 A:HIS335 4.9 32.3 1.0 HA A:CYS319 5.0 34.3 1.0

Zinc binding site 2 out of 2 in the Human Aprataxin (Aptx) L248M Bound to Dna, Amp and Zn Product


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) L248M Bound to Dna, Amp and Zn Product within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn402 b:60.1 occ:1.00 NE2 B:HIS335 2.0 55.9 1.0 NE2 B:HIS339 2.0 57.6 1.0 SG B:CYS319 2.3 48.4 1.0 SG B:CYS322 2.3 54.9 1.0 H B:CYS322 2.9 55.8 1.0 CE1 B:HIS335 2.9 58.9 1.0 CE1 B:HIS339 2.9 61.0 1.0 HB3 B:CYS319 2.9 48.7 1.0 HE1 B:HIS335 3.0 58.9 1.0 HE1 B:HIS339 3.0 61.0 1.0 CB B:CYS319 3.0 48.7 1.0 CD2 B:HIS335 3.1 53.3 1.0 CD2 B:HIS339 3.1 56.0 1.0 HB2 B:CYS319 3.2 48.7 1.0 HD2 B:HIS335 3.3 53.3 1.0 HD2 B:HIS339 3.3 56.0 1.0 HB3 B:CYS322 3.3 59.1 1.0 HB2 B:GLU321 3.3 55.1 1.0 CB B:CYS322 3.4 59.1 1.0 N B:CYS322 3.5 55.8 1.0 HB3 B:GLN324 3.9 66.6 1.0 H B:GLU321 4.0 49.0 1.0 CA B:CYS322 4.0 59.4 1.0 ND1 B:HIS339 4.0 61.6 1.0 H B:GLN324 4.0 61.1 1.0 ND1 B:HIS335 4.0 58.2 1.0 CG B:HIS339 4.1 59.4 1.0 CG B:HIS335 4.1 55.2 1.0 HB2 B:CYS322 4.2 59.1 1.0 CB B:GLU321 4.3 55.1 1.0 H B:GLN323 4.4 58.2 1.0 CA B:CYS319 4.5 47.0 1.0 C B:GLU321 4.5 55.9 1.0 HD23 B:LEU336 4.6 47.7 1.0 C B:CYS322 4.6 60.7 1.0 N B:GLU321 4.6 49.0 1.0 HB3 B:GLU321 4.7 55.1 1.0 N B:GLN323 4.7 58.2 1.0 HB2 B:GLN324 4.7 66.6 1.0 CB B:GLN324 4.7 66.6 1.0 CA B:GLU321 4.7 53.4 1.0 HD1 B:HIS339 4.8 61.6 1.0 HD1 B:HIS335 4.8 58.2 1.0 HA B:CYS322 4.8 59.4 1.0 N B:GLN324 4.9 61.1 1.0 HA B:CYS319 4.9 47.0 1.0 C B:CYS319 5.0 46.9 1.0

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