Sodium 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
Zinc	(Zn)	2 atoms

The binding sites of Sodium 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 Sodium atom.
In total only one binding site of Sodium was determined in the Human Aprataxin (Aptx) AOA1 Variant K197Q Bound to Rna-Dna, Amp, and Zn - Product Complex, PDB code: 4ndi:

Sodium binding site 1 out of 1 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 Sodium with other atoms in the Na 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:Na403 b:19.1 occ:1.00 O D:HOH242 2.3 32.7 1.0 OG A:SER255 2.3 11.3 1.0 O D:HOH211 2.4 21.1 1.0 O A:HOH625 2.4 18.5 1.0 O A:HOH554 2.5 18.7 1.0 O D:HOH218 2.6 20.9 1.0 CB A:SER255 3.5 9.3 1.0 O A:HOH502 3.6 9.7 1.0 O A:HOH603 3.9 17.6 1.0 O A:HOH646 4.0 24.8 1.0 O A:HOH573 4.0 9.9 1.0 OP1 D:G1 4.1 15.3 1.0 CA A:SER255 4.1 11.4 1.0 N7 D:G1 4.2 9.8 1.0 C8 D:G1 4.3 10.2 1.0 OP2 D:G1 4.6 15.4 1.0 O5' D:G1 4.7 14.0 1.0 N A:SER255 4.7 11.2 1.0 P D:G1 4.7 16.6 1.0 O A:PRO254 4.8 9.9 1.0 O D:HOH203 5.0 21.4 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