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

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

The structure of Human Aprataxin (Aptx) Bound to Nicked Rna-Dna, Amp and Zn Product Complex, PDB code: 6cvo was solved by M.J.Schellenberg, P.P.Tumbale, R.S.Williams, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.67 / 2.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	58.913, 72.547, 147.164, 90.00, 90.00, 90.00
R / Rfree (%)	18.4 / 22.2

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

Zinc binding site 1 out of 2 in the Human Aprataxin (Aptx) Bound to Nicked 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) Bound to Nicked Rna-Dna, Amp and Zn Product Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:29.0 occ:1.00 NE2 A:HIS335 2.0 29.3 1.0 NE2 A:HIS339 2.1 35.5 1.0 SG A:CYS322 2.2 31.1 1.0 SG A:CYS319 2.4 28.7 1.0 CE1 A:HIS335 2.9 32.0 1.0 H A:CYS322 3.0 41.9 1.0 CD2 A:HIS335 3.0 27.0 1.0 CD2 A:HIS339 3.0 34.5 1.0 HB3 A:CYS322 3.1 40.3 1.0 CE1 A:HIS339 3.1 37.9 1.0 HE1 A:HIS335 3.1 38.5 1.0 HB3 A:CYS319 3.1 33.8 1.0 HD2 A:HIS339 3.2 41.3 1.0 CB A:CYS322 3.2 33.6 1.0 HD2 A:HIS335 3.2 32.4 1.0 CB A:CYS319 3.2 28.2 1.0 HE1 A:HIS339 3.3 45.5 1.0 HB2 A:CYS319 3.4 33.8 1.0 HB2 A:GLU321 3.5 44.1 1.0 N A:CYS322 3.6 34.9 1.0 CA A:CYS322 4.0 34.2 1.0 HB2 A:CYS322 4.0 40.3 1.0 ND1 A:HIS335 4.1 31.5 1.0 HB3 A:GLN324 4.1 43.8 1.0 H A:GLN324 4.1 42.0 1.0 CG A:HIS335 4.1 28.3 1.0 ND1 A:HIS339 4.2 39.2 1.0 CG A:HIS339 4.2 37.8 1.0 H A:GLU321 4.2 37.4 1.0 CB A:GLU321 4.4 36.8 1.0 H A:GLN323 4.5 43.4 1.0 C A:GLU321 4.6 35.7 1.0 C A:CYS322 4.6 34.1 1.0 HB2 A:GLN324 4.7 43.8 1.0 CA A:CYS319 4.7 26.2 1.0 HB3 A:GLU321 4.7 44.1 1.0 HA A:CYS322 4.8 41.1 1.0 N A:GLN323 4.8 36.2 1.0 HD1 A:HIS335 4.8 37.8 1.0 CB A:GLN324 4.8 36.5 1.0 HE3 A:LYS338 4.9 73.8 1.0 CA A:GLU321 4.9 35.0 1.0 N A:GLU321 4.9 31.1 1.0 HD23 A:LEU336 4.9 26.7 1.0 HD1 A:HIS339 4.9 47.1 1.0 N A:GLN324 5.0 35.0 1.0 HD21 A:LEU326 5.0 31.4 1.0

Zinc binding site 2 out of 2 in the Human Aprataxin (Aptx) Bound to Nicked 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) Bound to Nicked Rna-Dna, Amp and Zn Product Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn402 b:24.0 occ:1.00 NE2 B:HIS339 2.0 35.4 1.0 NE2 B:HIS335 2.0 24.8 1.0 SG B:CYS322 2.2 28.2 1.0 SG B:CYS319 2.3 26.3 1.0 CE1 B:HIS339 2.7 27.3 1.0 HE1 B:HIS339 2.7 32.8 1.0 H B:CYS322 2.9 34.1 1.0 CD2 B:HIS335 3.0 23.3 1.0 CE1 B:HIS335 3.0 26.7 1.0 HB3 B:CYS319 3.1 28.9 1.0 HB3 B:CYS322 3.1 35.8 1.0 HD2 B:HIS335 3.2 28.0 1.0 CB B:CYS319 3.2 24.1 1.0 CD2 B:HIS339 3.2 31.7 1.0 HE1 B:HIS335 3.2 32.0 1.0 CB B:CYS322 3.3 29.8 1.0 HB2 B:CYS319 3.3 28.9 1.0 HB2 B:GLU321 3.4 40.4 1.0 N B:CYS322 3.6 28.5 1.0 HD2 B:HIS339 3.6 38.0 1.0 ND1 B:HIS339 3.9 27.9 1.0 CA B:CYS322 4.0 28.8 1.0 HB2 B:CYS322 4.1 35.8 1.0 ND1 B:HIS335 4.1 26.5 1.0 HB3 B:GLN324 4.1 35.8 1.0 CG B:HIS335 4.1 24.3 1.0 CG B:HIS339 4.1 29.6 1.0 H B:GLN324 4.1 33.3 1.0 H B:GLU321 4.2 36.7 1.0 CB B:GLU321 4.3 33.7 1.0 H B:GLN323 4.5 30.7 1.0 C B:GLU321 4.6 33.1 1.0 HD1 B:HIS339 4.6 33.5 1.0 CA B:CYS319 4.6 28.0 1.0 HB3 B:GLU321 4.6 40.4 1.0 C B:CYS322 4.7 27.2 1.0 HD23 B:LEU336 4.7 28.2 1.0 HB2 B:GLN324 4.7 35.8 1.0 HA B:CYS322 4.8 34.6 1.0 N B:GLN323 4.8 25.6 1.0 CA B:GLU321 4.8 32.0 1.0 N B:GLU321 4.8 30.6 1.0 CB B:GLN324 4.8 29.8 1.0 HD1 B:HIS335 4.9 31.8 1.0 HA B:CYS319 5.0 33.6 1.0 N B:GLN324 5.0 27.8 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