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Sodium in PDB 4ndf: Human Aprataxin (Aptx) Bound to Rna-Dna, Amp, and Zn - Product Complex

Protein crystallography data

The structure of Human Aprataxin (Aptx) Bound to Rna-Dna, Amp, and Zn - Product Complex, PDB code: 4ndf 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) 32.41 / 1.94
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 40.429, 116.211, 117.141, 90.00, 90.00, 90.00
R / Rfree (%) 17.1 / 20.5

Other elements in 4ndf:

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

Potassium (K) 1 atom
Zinc (Zn) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Human Aprataxin (Aptx) Bound to Rna-Dna, Amp, and Zn - Product Complex (pdb code 4ndf). 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) Bound to Rna-Dna, Amp, and Zn - Product Complex, PDB code: 4ndf:

Sodium binding site 1 out of 1 in 4ndf

Go back to Sodium Binding Sites List in 4ndf
Sodium binding site 1 out of 1 in the Human Aprataxin (Aptx) 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) Bound to Rna-Dna, Amp, and Zn - Product Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na403

b:24.6
occ:1.00
O A:HOH681 2.3 15.5 0.5
OG A:SER255 2.3 12.3 1.0
O D:HOH109 2.4 32.9 1.0
O A:HOH555 2.4 30.3 1.0
O D:HOH116 2.5 31.9 1.0
O A:HOH629 2.5 26.8 1.0
CB A:SER255 3.5 13.8 1.0
O A:HOH502 3.6 12.9 1.0
O A:HOH681 3.8 24.8 0.5
O A:HOH574 4.0 12.3 1.0
O A:HOH605 4.0 27.7 1.0
CA A:SER255 4.2 11.2 1.0
O A:HOH655 4.2 33.8 1.0
OP1 D:G1 4.2 20.2 1.0
N7 D:G1 4.3 11.4 1.0
C8 D:G1 4.5 11.6 1.0
O A:PRO254 4.7 11.4 1.0
N A:SER255 4.7 8.7 1.0
O5' D:G1 4.8 13.8 1.0
P D:G1 4.9 16.6 1.0
OP2 D:G1 4.9 14.7 1.0
C A:PRO254 5.0 10.5 1.0

Reference:

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
Page generated: Tue Dec 15 06:55:15 2020

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