Sodium in PDB 5d49: Structural Basis For A New Templated Activity By Terminal Deoxynucleotidyl Transferase: Implications For V(D)J Recombination

The structure of Structural Basis For A New Templated Activity By Terminal Deoxynucleotidyl Transferase: Implications For V(D)J Recombination, PDB code: 5d49 was solved by J.Loc'h, S.Rosario, M.Delarue, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.02 / 1.99
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	56.550, 74.250, 126.150, 90.00, 101.84, 90.00
R / Rfree (%)	19.7 / 24.5

The structure of Structural Basis For A New Templated Activity By Terminal Deoxynucleotidyl Transferase: Implications For V(D)J Recombination also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Sodium atom in the Structural Basis For A New Templated Activity By Terminal Deoxynucleotidyl Transferase: Implications For V(D)J Recombination (pdb code 5d49). 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 Structural Basis For A New Templated Activity By Terminal Deoxynucleotidyl Transferase: Implications For V(D)J Recombination, PDB code: 5d49:

Sodium binding site 1 out of 1 in the Structural Basis For A New Templated Activity By Terminal Deoxynucleotidyl Transferase: Implications For V(D)J Recombination


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structural Basis For A New Templated Activity By Terminal Deoxynucleotidyl Transferase: Implications For V(D)J Recombination within 5.0Å range: probe atom residue distance (Å) B Occ A:Na602 b:37.9 occ:1.00 O A:VAL258 2.3 35.8 1.0 O A:VAL255 2.4 31.7 1.0 OP1 C:DG6 2.4 34.8 1.0 O A:THR253 2.5 33.3 1.0 O C:HOH104 2.5 37.4 1.0 O A:HOH1003 2.6 43.9 1.0 C A:VAL258 3.4 35.2 1.0 C A:VAL255 3.4 32.7 1.0 C A:THR253 3.5 35.5 1.0 P C:DG6 3.6 35.6 1.0 N A:VAL258 3.6 30.9 1.0 OP2 C:DG6 3.8 36.2 1.0 N A:GLY257 3.9 28.8 1.0 CA A:THR253 3.9 32.6 1.0 CA A:VAL258 4.0 30.6 1.0 O C:HOH113 4.1 51.2 1.0 CA A:PHE256 4.1 28.9 1.0 N A:PHE256 4.1 29.9 1.0 N A:VAL255 4.3 32.5 1.0 C A:PHE256 4.3 34.0 1.0 N A:GLY259 4.5 33.0 1.0 O3' C:DT5 4.5 35.5 1.0 CB A:THR253 4.5 36.0 1.0 CB A:VAL258 4.5 34.2 1.0 CA A:VAL255 4.5 31.8 1.0 C A:GLY257 4.5 32.5 1.0 O A:HOH974 4.6 48.1 1.0 N A:SER254 4.6 33.4 1.0 C A:SER254 4.6 36.9 1.0 CA A:GLY257 4.7 29.6 1.0 O5' C:DG6 4.8 34.4 1.0 CA A:GLY259 4.8 32.1 1.0 CA A:SER254 4.9 33.8 1.0

J.Loc'h, S.Rosario, M.Delarue. Structural Basis For A New Templated Activity By Terminal Deoxynucleotidyl Transferase: Implications For V(D)J Recombination. Structure V. 24 1452 2016.
ISSN: ISSN 0969-2126
PubMed: 27499438
DOI: 10.1016/J.STR.2016.06.014