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Sodium in PDB 6cvp: Human Aprataxin (Aptx) R199H Bound to Rna-Dna, Amp and Zn Product Complex

Enzymatic activity of Human Aprataxin (Aptx) R199H Bound to Rna-Dna, Amp and Zn Product Complex

All present enzymatic activity of Human Aprataxin (Aptx) R199H Bound to Rna-Dna, Amp and Zn Product Complex:
3.1.11.7; 3.1.12.2;

Protein crystallography data

The structure of Human Aprataxin (Aptx) R199H Bound to Rna-Dna, Amp and Zn Product Complex, PDB code: 6cvp was solved by M.J.Schellenberg, R.S.Williams, P.S.Tumbale, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 27.62 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 39.507, 121.105, 122.314, 90.00, 90.00, 90.00
R / Rfree (%) 16.4 / 21.4

Other elements in 6cvp:

The structure of Human Aprataxin (Aptx) R199H Bound to Rna-Dna, Amp and Zn Product Complex also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Human Aprataxin (Aptx) R199H Bound to Rna-Dna, Amp and Zn Product Complex (pdb code 6cvp). 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) R199H Bound to Rna-Dna, Amp and Zn Product Complex, PDB code: 6cvp:

Sodium binding site 1 out of 1 in 6cvp

Go back to Sodium Binding Sites List in 6cvp
Sodium binding site 1 out of 1 in the Human Aprataxin (Aptx) R199H 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) R199H Bound to Rna-Dna, Amp and Zn Product Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na403

b:33.4
occ:1.00
 O B:HOH660 2.2 41.1 1.0
O G:HOH118 2.4 28.5 1.0
O B:HOH711 2.4 37.5 1.0
OG B:SER255 2.4 19.1 1.0
O B:HOH669 2.4 32.2 1.0
O G:HOH121 2.8 29.9 1.0
CB B:SER255 3.5 19.0 1.0
O B:HOH517 3.7 45.7 1.0
N7 G:G1 4.1 18.5 1.0
CA B:SER255 4.2 17.4 1.0
O B:HOH716 4.2 45.2 1.0
O G:HOH106 4.3 26.3 1.0
OP2 G:G1 4.3 22.7 1.0
C8 G:G1 4.4 17.1 1.0
O B:HOH539 4.5 27.1 1.0
O G:HOH120 4.5 34.2 1.0
N B:SER255 4.8 17.1 1.0
O B:PRO254 4.8 30.8 1.0
OP3 G:G1 4.9 31.4 1.0
O5' G:G1 5.0 21.4 1.0

Reference:

P.Tumbale, M.J.Schellenberg, G.A.Mueller, E.Fairweather, M.Watson, J.N.Little, J.Krahn, I.Waddell, R.E.London, R.S.Williams. Mechanism of Aptx Nicked Dna Sensing and Pleiotropic Inactivation in Neurodegenerative Disease. Embo J. V. 37 2018.
ISSN: ESSN 1460-2075
PubMed: 29934293
DOI: 10.15252/EMBJ.201798875
Page generated: Tue Dec 15 12:06:44 2020

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