Sodium in PDB 5h8w: Xpd Mechanism

All present enzymatic activity of Xpd Mechanism:
3.6.4.12;

The structure of Xpd Mechanism, PDB code: 5h8w was solved by J.H.Naismith, D.Constantinescu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.22 / 2.20
Space group	P 65
Cell size a, b, c (Å), α, β, γ (°)	78.569, 78.569, 177.832, 90.00, 90.00, 120.00
R / Rfree (%)	20.8 / 24.3

The structure of Xpd Mechanism also contains other interesting chemical elements:

Iron

(Fe)

4 atoms

The binding sites of Sodium atom in the Xpd Mechanism (pdb code 5h8w). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Xpd Mechanism, PDB code: 5h8w:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Xpd Mechanism


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Xpd Mechanism within 5.0Å range: probe atom residue distance (Å) B Occ A:Na802 b:25.7 occ:1.00 O A:HOH914 2.0 27.4 1.0 O A:HOH908 2.2 25.4 1.0 OD1 A:ASN162 2.2 33.7 1.0 CG A:ASN162 3.3 31.8 1.0 O A:GLU159 3.6 33.0 1.0 ND2 A:ASN162 3.7 32.4 1.0 O A:ARG160 4.3 35.3 1.0 CB A:ASN162 4.6 31.2 1.0 C A:GLU159 4.7 32.9 1.0 N A:ASN162 4.8 30.4 1.0 C A:ARG160 4.9 34.4 1.0 CA A:ASN162 5.0 30.0 1.0

Sodium binding site 2 out of 2 in the Xpd Mechanism


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Xpd Mechanism within 5.0Å range: probe atom residue distance (Å) B Occ A:Na803 b:44.9 occ:1.00 O A:HOH941 2.0 37.5 1.0 O A:HOH917 2.2 30.7 1.0 O A:HOH921 2.2 36.2 1.0 OD2 A:ASP237 3.9 39.5 1.0 OD1 A:ASP237 4.0 37.3 1.0 CB A:SER255 4.3 37.3 1.0 NH2 A:ARG262 4.3 37.4 1.0 CG A:ASP237 4.4 37.2 1.0 O A:SER255 4.4 36.3 1.0 OE1 A:GLU259 4.6 41.8 1.0 CB A:GLU259 4.8 39.0 1.0 OG A:SER255 4.8 38.9 1.0 C A:SER255 4.9 36.3 1.0

D.Constantinescu-Aruxandei, B.Petrovic-Stojanovska, J.C.Penedo, M.F.White, J.H.Naismith. Mechanism of Dna Loading By the Dna Repair Helicase Xpd. Nucleic Acids Res. V. 44 2806 2016.
ISSN: ESSN 1362-4962
PubMed: 26896802
DOI: 10.1093/NAR/GKW102