Sodium in PDB 4rzr: Bypass of A Bulky Adduct DG1,8 By DPO4

All present enzymatic activity of Bypass of A Bulky Adduct DG1,8 By DPO4:
2.7.7.7;

The structure of Bypass of A Bulky Adduct DG1,8 By DPO4, PDB code: 4rzr was solved by R.Vyas, Z.Suo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.23 / 2.20
Space group	P 31
Cell size a, b, c (Å), α, β, γ (°)	56.397, 56.397, 288.776, 90.00, 90.00, 120.00
R / Rfree (%)	19.9 / 25

The structure of Bypass of A Bulky Adduct DG1,8 By DPO4 also contains other interesting chemical elements:

Calcium

(Ca)

4 atoms

The binding sites of Sodium atom in the Bypass of A Bulky Adduct DG1,8 By DPO4 (pdb code 4rzr). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Bypass of A Bulky Adduct DG1,8 By DPO4, PDB code: 4rzr:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Bypass of A Bulky Adduct DG1,8 By DPO4


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Bypass of A Bulky Adduct DG1,8 By DPO4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na403 b:28.7 occ:1.00 O C:HOH101 2.3 35.5 1.0 O A:ALA181 2.3 29.5 1.0 O A:ILE186 2.3 28.0 1.0 O A:HOH508 2.3 31.4 1.0 O A:HOH522 2.6 44.2 1.0 C A:ALA181 3.5 29.9 1.0 C A:ILE186 3.5 26.9 1.0 CA A:GLY187 4.0 28.9 1.0 OP2 C:DT12 4.2 31.3 1.0 N A:GLY187 4.2 28.0 1.0 CA A:ALA181 4.2 30.4 1.0 N A:ASP182 4.5 30.4 1.0 C A:GLY187 4.5 31.1 1.0 CB A:ALA181 4.6 31.0 1.0 CA A:ILE186 4.6 25.8 1.0 CA A:ASP182 4.7 30.3 1.0 O A:VAL183 4.7 26.2 1.0 CB A:ILE186 4.8 25.6 1.0 OP1 C:DT12 4.8 30.7 1.0 O A:GLY187 4.9 30.2 1.0 N A:ASN188 5.0 32.8 1.0 CG2 A:ILE186 5.0 26.1 1.0 P C:DT12 5.0 31.2 1.0

Sodium binding site 2 out of 2 in the Bypass of A Bulky Adduct DG1,8 By DPO4


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Bypass of A Bulky Adduct DG1,8 By DPO4 within 5.0Å range: probe atom residue distance (Å) B Occ D:Na404 b:39.4 occ:1.00 O F:HOH101 2.0 36.7 1.0 O D:ALA181 2.2 31.4 1.0 O D:HOH506 2.5 36.1 1.0 O D:ILE186 2.8 39.2 1.0 C D:ALA181 3.3 32.9 1.0 C D:ILE186 4.0 37.2 1.0 CA D:ALA181 4.1 33.7 1.0 CB D:ALA181 4.2 33.4 1.0 CA D:GLY187 4.2 41.2 1.0 N D:ASP182 4.3 33.1 1.0 OP1 F:DC13 4.4 42.5 1.0 CA D:ASP182 4.5 32.5 1.0 C D:GLY187 4.5 42.5 1.0 OP2 F:DC13 4.6 42.0 1.0 N D:GLY187 4.6 39.9 1.0 O D:VAL183 4.8 27.6 1.0 N D:ASN188 4.9 43.9 1.0 O D:GLY187 5.0 45.2 1.0 OD1 D:ASP182 5.0 39.2 1.0

R.Vyas, G.Efthimiopoulos, E.J.Tokarsky, C.K.Malik, A.K.Basu, Z.Suo. Mechanistic Basis For the Bypass of A Bulky Dna Adduct Catalyzed By A Y-Family Dna Polymerase. J.Am.Chem.Soc. V. 137 12131 2015.
ISSN: ISSN 0002-7863
PubMed: 26327169
DOI: 10.1021/JACS.5B08027