Potassium 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:

Zinc	(Zn)	2 atoms
Sodium	(Na)	1 atom

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

Potassium 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 Potassium with other atoms in the K 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 D:K101 b:23.2 occ:1.00 O2 E:DT4 2.6 16.9 1.0 O2 D:DT8 2.7 19.2 1.0 O D:HOH220 2.7 23.8 1.0 O D:HOH240 2.7 34.1 1.0 O E:HOH142 2.7 36.9 1.0 O4' E:DC5 3.3 24.1 1.0 O4' D:DT9 3.4 24.2 1.0 C2 E:DT4 3.8 18.6 1.0 C2 D:DT8 3.8 18.1 1.0 C4' D:DT9 4.0 22.3 1.0 C4' E:DC5 4.0 25.1 1.0 C1' E:DT4 4.2 17.1 1.0 C5' E:DC5 4.3 23.0 1.0 C1' E:DC5 4.3 24.1 1.0 C5' D:DT9 4.3 22.5 1.0 C1' D:DT8 4.3 23.9 1.0 C1' D:DT9 4.3 24.4 1.0 N1 E:DT4 4.5 17.2 1.0 C2 D:DA7 4.6 18.9 1.0 N1 D:DT8 4.6 22.0 1.0 O4' E:DT4 4.6 16.1 1.0 C2 E:DA3 4.6 18.7 1.0 N1 D:DT9 4.7 20.9 1.0 O D:HOH224 4.7 37.8 1.0 O D:HOH225 4.7 39.1 1.0 O2 D:DT9 4.7 20.5 1.0 N3 E:DT4 4.8 15.9 1.0 N1 E:DC5 4.8 20.7 1.0 O D:HOH202 4.8 24.8 1.0 C2 D:DT9 4.8 18.6 1.0 N3 D:DT8 4.8 17.4 1.0 O D:HOH241 5.0 40.5 1.0

Potassium 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 Potassium with other atoms in the K 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 G:K101 b:34.9 occ:1.00 O2 H:DT4 2.7 20.6 1.0 O2 G:DT8 2.7 22.7 1.0 O G:HOH218 2.9 29.5 1.0 O G:HOH213 3.0 29.8 1.0 O4' H:DC5 3.0 32.6 1.0 O4' G:DT9 3.1 24.4 1.0 C4' H:DC5 3.7 31.6 1.0 C4' G:DT9 3.7 24.4 1.0 C2 H:DT4 3.8 19.2 1.0 C2 G:DT8 3.9 23.0 1.0 C1' H:DC5 4.1 30.5 1.0 C1' G:DT9 4.2 26.2 1.0 C5' G:DT9 4.2 26.3 1.0 C5' H:DC5 4.2 33.5 1.0 C1' H:DT4 4.2 21.9 1.0 C1' G:DT8 4.4 32.9 1.0 C2 H:DA3 4.4 22.1 1.0 N1 H:DC5 4.4 22.9 1.0 C2 G:DA7 4.5 21.5 1.0 O H:HOH104 4.5 28.2 1.0 O G:HOH221 4.5 21.2 1.0 N1 H:DT4 4.5 19.8 1.0 N1 G:DT9 4.6 23.2 1.0 N1 G:DT8 4.7 26.4 1.0 O2 G:DT9 4.8 22.0 1.0 O4' H:DT4 4.8 21.5 1.0 C2 G:DT9 4.8 23.5 1.0 N3 H:DT4 4.8 16.1 1.0 C2 H:DC5 4.9 24.2 1.0 N3 G:DT8 4.9 23.2 1.0 C6 H:DC5 4.9 22.8 1.0 O2 H:DC5 4.9 27.2 1.0 O4' G:DT8 5.0 35.4 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