Zinc in PDB 4ndi: Human Aprataxin (Aptx) AOA1 Variant K197Q Bound to Rna-Dna, Amp, and Zn - Product Complex

The structure of Human Aprataxin (Aptx) AOA1 Variant K197Q Bound to Rna-Dna, Amp, and Zn - Product Complex, PDB code: 4ndi 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)	38.22 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	40.468, 115.491, 116.173, 90.00, 90.00, 90.00
R / Rfree (%)	15.4 / 18.2

The structure of Human Aprataxin (Aptx) AOA1 Variant K197Q Bound to Rna-Dna, Amp, and Zn - Product Complex also contains other interesting chemical elements:

Potassium	(K)	2 atoms
Sodium	(Na)	1 atom

The binding sites of Zinc atom in the Human Aprataxin (Aptx) AOA1 Variant K197Q Bound to Rna-Dna, Amp, and Zn - Product Complex (pdb code 4ndi). 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) AOA1 Variant K197Q Bound to Rna-Dna, Amp, and Zn - Product Complex, PDB code: 4ndi:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Human Aprataxin (Aptx) AOA1 Variant K197Q 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) AOA1 Variant K197Q Bound to Rna-Dna, Amp, and Zn - Product Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:18.6 occ:1.00 NE2 A:HIS339 2.0 21.3 1.0 NE2 A:HIS335 2.0 15.6 1.0 SG A:CYS322 2.3 21.4 1.0 SG A:CYS319 2.3 16.0 1.0 CE1 A:HIS339 3.0 21.7 1.0 CD2 A:HIS335 3.0 17.7 1.0 CD2 A:HIS339 3.0 19.5 1.0 CE1 A:HIS335 3.0 24.0 1.0 CB A:CYS319 3.1 15.2 1.0 CB A:CYS322 3.4 23.6 1.0 N A:CYS322 3.7 20.6 1.0 CA A:CYS322 4.1 24.9 1.0 ND1 A:HIS339 4.1 22.9 1.0 ND1 A:HIS335 4.1 18.5 1.0 CG A:HIS339 4.1 21.1 1.0 CG A:HIS335 4.1 17.3 1.0 CB A:GLU321 4.4 25.3 1.0 CA A:CYS319 4.5 13.7 1.0 C A:GLU321 4.6 21.2 1.0 C A:CYS322 4.7 23.6 1.0 N A:GLU321 4.7 17.2 1.0 CD A:LYS338 4.8 39.5 1.0 CA A:GLU321 4.8 20.7 1.0 CB A:GLN324 4.8 25.4 1.0 N A:GLN323 4.9 21.2 1.0 CG A:LYS338 4.9 32.1 1.0

Zinc binding site 2 out of 2 in the Human Aprataxin (Aptx) AOA1 Variant K197Q 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) AOA1 Variant K197Q Bound to Rna-Dna, Amp, and Zn - Product Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn402 b:27.0 occ:1.00 NE2 B:HIS339 2.0 26.3 1.0 NE2 B:HIS335 2.0 24.4 1.0 SG B:CYS322 2.3 30.6 1.0 SG B:CYS319 2.4 23.8 1.0 CE1 B:HIS339 3.0 33.9 1.0 CE1 B:HIS335 3.0 29.0 1.0 CD2 B:HIS339 3.0 24.8 1.0 CD2 B:HIS335 3.1 23.8 1.0 CB B:CYS319 3.2 23.1 1.0 CB B:CYS322 3.4 30.8 1.0 N B:CYS322 3.7 28.9 1.0 CA B:CYS322 4.1 29.3 1.0 ND1 B:HIS339 4.1 29.9 1.0 ND1 B:HIS335 4.1 28.1 1.0 CG B:HIS339 4.1 30.5 1.0 CG B:HIS335 4.2 27.9 1.0 O B:HOH637 4.4 40.5 1.0 CB B:GLU321 4.4 30.1 1.0 C B:GLU321 4.6 29.2 1.0 CA B:CYS319 4.6 21.5 1.0 C B:CYS322 4.7 30.7 1.0 CB B:GLN324 4.7 29.1 1.0 N B:GLU321 4.8 21.5 1.0 CA B:GLU321 4.8 25.5 1.0 N B:GLN323 4.9 26.7 1.0 CD B:LYS338 4.9 45.6 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