Sodium in PDB 4c2u: Crystal Structure of Deinococcus Radiodurans Uvrd in Complex with Dna, Form 1

All present enzymatic activity of Crystal Structure of Deinococcus Radiodurans Uvrd in Complex with Dna, Form 1:
3.6.4.12;

The structure of Crystal Structure of Deinococcus Radiodurans Uvrd in Complex with Dna, Form 1, PDB code: 4c2u was solved by M.Stelter, S.Acajjaoui, S.Mcsweeney, J.Timmins, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.74 / 2.55
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	67.572, 67.448, 386.040, 90.00, 90.00, 90.00
R / Rfree (%)	21.143 / 26.651

The structure of Crystal Structure of Deinococcus Radiodurans Uvrd in Complex with Dna, Form 1 also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Sodium atom in the Crystal Structure of Deinococcus Radiodurans Uvrd in Complex with Dna, Form 1 (pdb code 4c2u). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Deinococcus Radiodurans Uvrd in Complex with Dna, Form 1, PDB code: 4c2u:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Deinococcus Radiodurans Uvrd in Complex with Dna, Form 1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Deinococcus Radiodurans Uvrd in Complex with Dna, Form 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1670 b:50.2 occ:1.00 O A:ILE60 2.7 34.3 1.0 O A:LYS220 2.8 43.0 1.0 O A:GLY58 3.1 42.8 1.0 C A:GLY58 3.2 43.1 1.0 CB A:TRP88 3.3 33.0 1.0 N A:ILE60 3.4 38.0 1.0 C A:ILE60 3.5 34.5 1.0 N A:GLU59 3.6 44.8 1.0 C A:LYS220 3.7 44.5 1.0 CA A:GLY58 3.8 42.5 1.0 C A:GLU59 3.8 40.7 1.0 O A:PRO57 3.8 44.7 1.0 N A:TRP88 3.9 35.5 1.0 CA A:GLU59 4.0 43.9 1.0 CE A:LYS220 4.0 57.9 1.0 CA A:ILE60 4.1 36.4 1.0 CB A:LYS220 4.1 48.1 1.0 CA A:LYS220 4.1 45.9 1.0 CA A:TRP88 4.2 34.3 1.0 CE3 A:TRP88 4.2 33.4 1.0 NZ A:LYS220 4.3 55.3 1.0 CG A:TRP88 4.4 33.5 1.0 N A:LEU61 4.5 32.8 1.0 O A:ASP86 4.5 42.6 1.0 O A:GLU59 4.6 39.5 1.0 C A:PRO57 4.6 44.7 1.0 N A:GLY58 4.7 44.1 1.0 CD2 A:TRP88 4.7 33.2 1.0 C A:LEU87 4.7 37.5 1.0 N A:ALA221 4.9 42.8 1.0 CD A:LYS220 4.9 54.9 1.0 CA A:LEU61 4.9 31.2 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Deinococcus Radiodurans Uvrd in Complex with Dna, Form 1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Deinococcus Radiodurans Uvrd in Complex with Dna, Form 1 within 5.0Å range: probe atom residue distance (Å) B Occ D:Na1670 b:45.4 occ:1.00 O D:ILE60 2.8 34.3 1.0 O D:LYS220 2.9 43.5 1.0 O D:GLY58 3.1 43.2 1.0 C D:GLY58 3.1 42.5 1.0 CB D:TRP88 3.3 31.4 1.0 N D:ILE60 3.4 38.0 1.0 N D:GLU59 3.6 43.8 1.0 CA D:GLY58 3.6 41.9 1.0 C D:ILE60 3.6 34.5 1.0 O D:PRO57 3.6 44.0 1.0 N D:TRP88 3.7 34.5 1.0 C D:GLU59 3.9 40.3 1.0 C D:LYS220 3.9 44.8 1.0 CA D:GLU59 4.0 43.2 1.0 CE D:LYS220 4.1 57.8 1.0 NZ D:LYS220 4.1 55.6 1.0 CA D:ILE60 4.1 36.4 1.0 CA D:TRP88 4.2 33.0 1.0 CA D:LYS220 4.2 46.1 1.0 CB D:LYS220 4.2 48.1 1.0 O D:ASP86 4.3 41.1 1.0 CE3 D:TRP88 4.4 30.9 1.0 CG D:TRP88 4.4 31.5 1.0 C D:PRO57 4.5 43.8 1.0 N D:GLY58 4.5 43.5 1.0 C D:LEU87 4.6 37.1 1.0 N D:LEU61 4.6 32.7 1.0 O D:GLU59 4.7 39.1 1.0 CD2 D:TRP88 4.7 30.9 1.0 CA D:LEU87 4.8 38.7 1.0 CD D:LYS220 5.0 54.3 1.0

M.Stelter, S.Acajjaoui, S.Mcsweeney, J.Timmins. Structural and Mechanistic Insight Into Dna Unwinding By Deinococcus Radiodurans Uvrd. Plos One V. 8 77364 2013.
ISSN: ISSN 1932-6203
PubMed: 24143224
DOI: 10.1371/JOURNAL.PONE.0077364