Zinc in PDB 4ndh: Human Aprataxin (Aptx) Bound to Dna, Amp, and Zn - Product Complex

The structure of Human Aprataxin (Aptx) Bound to Dna, Amp, and Zn - Product Complex, PDB code: 4ndh 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)	32.69 / 1.85
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	40.397, 117.082, 118.202, 90.00, 90.00, 90.00
R / Rfree (%)	16.3 / 19.6

The binding sites of Zinc atom in the Human Aprataxin (Aptx) Bound to Dna, Amp, and Zn - Product Complex (pdb code 4ndh). 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 Dna, Amp, and Zn - Product Complex, PDB code: 4ndh:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Human Aprataxin (Aptx) Bound to 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 Dna, Amp, and Zn - Product Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:28.2 occ:1.00 NE2 A:HIS339 2.0 31.4 1.0 NE2 A:HIS335 2.0 28.3 1.0 SG A:CYS322 2.3 33.1 1.0 SG A:CYS319 2.3 27.7 1.0 CD2 A:HIS339 2.9 32.2 1.0 CD2 A:HIS335 2.9 29.8 1.0 CE1 A:HIS335 3.1 32.1 1.0 CE1 A:HIS339 3.1 34.1 1.0 CB A:CYS319 3.1 26.7 1.0 CB A:CYS322 3.4 34.0 1.0 N A:CYS322 3.7 32.0 1.0 CG A:HIS339 4.0 33.7 1.0 CA A:CYS322 4.0 33.5 1.0 CG A:HIS335 4.1 29.4 1.0 ND1 A:HIS339 4.1 37.1 1.0 ND1 A:HIS335 4.1 32.2 1.0 CB A:GLU321 4.4 34.5 1.0 CA A:CYS319 4.6 25.5 1.0 C A:GLU321 4.6 35.5 1.0 C A:CYS322 4.7 33.2 1.0 N A:GLN323 4.8 31.4 1.0 CB A:GLN324 4.8 40.0 1.0 N A:GLU321 4.8 29.6 1.0 CA A:GLU321 4.8 33.6 1.0 N A:GLN324 5.0 30.5 1.0

Zinc binding site 2 out of 2 in the Human Aprataxin (Aptx) Bound to 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 Dna, Amp, and Zn - Product Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn402 b:39.3 occ:1.00 NE2 B:HIS339 2.0 38.9 1.0 NE2 B:HIS335 2.0 41.1 1.0 SG B:CYS322 2.3 42.6 1.0 SG B:CYS319 2.3 35.2 1.0 CE1 B:HIS339 2.8 47.1 1.0 CD2 B:HIS335 2.9 37.2 1.0 CD2 B:HIS339 3.0 43.3 1.0 CE1 B:HIS335 3.1 44.9 1.0 CB B:CYS319 3.1 36.3 1.0 CB B:CYS322 3.5 46.0 1.0 N B:CYS322 3.7 41.4 1.0 ND1 B:HIS339 4.0 48.9 1.0 CG B:HIS339 4.1 45.2 1.0 CA B:CYS322 4.1 45.7 1.0 CG B:HIS335 4.1 38.4 1.0 ND1 B:HIS335 4.1 43.8 1.0 CB B:GLU321 4.4 45.1 1.0 CA B:CYS319 4.6 34.0 1.0 C B:GLU321 4.6 44.1 1.0 C B:CYS322 4.7 45.8 1.0 CB B:GLN324 4.7 51.2 1.0 N B:GLN323 4.8 42.3 1.0 N B:GLU321 4.8 35.9 1.0 CA B:GLU321 4.8 42.6 1.0 N B:GLN324 4.9 44.7 1.0

P.Tumbale, J.S.Williams, M.J.Schellenberg, T.A.Kunkel, R.S.Williams. Aprataxin Resolves Adenylated Rna-Dna Junctions to Maintain Genome Integrity. Nature V. 506 111 2013.
ISSN: ISSN 0028-0836
PubMed: 24362567
DOI: 10.1038/NATURE12824