Sodium in PDB 2y3c: Treponema Denticola Variable Protein 1

The structure of Treponema Denticola Variable Protein 1, PDB code: 2y3c was solved by J.Le Coq, P.Ghosh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.58 / 1.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	41.393, 77.629, 88.917, 90.00, 90.00, 90.00
R / Rfree (%)	14.619 / 17.24

The structure of Treponema Denticola Variable Protein 1 also contains other interesting chemical elements:

Calcium

(Ca)

2 atoms

The binding sites of Sodium atom in the Treponema Denticola Variable Protein 1 (pdb code 2y3c). 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 Treponema Denticola Variable Protein 1, PDB code: 2y3c:

Sodium binding site 1 out of 1 in the Treponema Denticola Variable Protein 1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Treponema Denticola Variable Protein 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1339 b:28.0 occ:1.00 O A:HOH2247 2.7 28.1 1.0 O A:HOH2037 2.7 13.8 1.0 O A:HOH2145 2.8 18.2 1.0 CG2 A:VAL306 3.7 14.6 1.0 CE2 A:TYR82 3.8 17.3 1.0 CB A:HIS79 3.9 15.2 1.0 CH3 A:ACT1332 3.9 24.1 1.0 N A:GLY307 4.1 11.9 1.0 OXT A:ACT1332 4.2 24.2 1.0 O A:GLY78 4.2 14.4 1.0 CA A:GLY307 4.2 11.9 1.0 CD2 A:HIS79 4.3 16.1 1.0 CG A:HIS79 4.4 16.0 1.0 NZ A:LYS210 4.4 18.4 1.0 C A:ACT1332 4.5 24.2 1.0 OH A:TYR82 4.6 19.5 1.0 CD2 A:TYR82 4.6 16.5 1.0 C A:GLY78 4.7 13.9 1.0 O A:ASP215 4.7 15.1 1.0 CZ A:TYR82 4.7 17.4 1.0 O A:LYS216 4.8 12.8 1.0 C A:VAL306 4.9 12.9 1.0 CA A:LYS216 4.9 13.6 1.0 O A:HOH2150 4.9 21.0 1.0 OE2 A:GLU206 4.9 12.7 1.0

J.Le Coq, P.Ghosh. Conservation of the C-Type Lectin Fold For Massive Sequence Variation in A Treponema Diversity-Generating Retroelement. Proc.Natl.Acad.Sci.Usa V. 108 14649 2011.
ISSN: ISSN 0027-8424
PubMed: 21873231
DOI: 10.1073/PNAS.1105613108