Sodium in PDB 5d4b: 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: 5d4b 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)	49.23 / 2.66
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	56.730, 71.450, 198.170, 90.00, 90.00, 90.00
R / Rfree (%)	20.7 / 24.7

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)

2 atoms

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 5d4b). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Structural Basis For A New Templated Activity By Terminal Deoxynucleotidyl Transferase: Implications For V(D)J Recombination, PDB code: 5d4b:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 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:66.0 occ:1.00 O A:THR253 2.3 56.6 1.0 O A:VAL258 2.4 57.3 1.0 O A:VAL255 2.6 55.8 1.0 OP1 C:DA4 2.7 79.6 1.0 C A:THR253 3.3 56.9 1.0 C A:VAL258 3.5 55.6 1.0 C A:VAL255 3.6 56.1 1.0 P C:DA4 3.8 80.2 1.0 CA A:THR253 3.8 53.2 1.0 N A:VAL258 3.9 48.2 1.0 OP2 C:DA4 4.0 79.6 1.0 N A:VAL255 4.2 52.6 1.0 CA A:VAL258 4.2 47.7 1.0 N A:GLY257 4.2 53.6 1.0 CB A:THR253 4.3 55.5 1.0 CA A:PHE256 4.4 52.8 1.0 N A:PHE256 4.4 52.9 1.0 N A:SER254 4.4 53.7 1.0 N A:GLY259 4.5 52.0 1.0 C A:SER254 4.6 58.3 1.0 CA A:VAL255 4.6 51.9 1.0 CB A:VAL258 4.7 49.6 1.0 C A:PHE256 4.8 57.6 1.0 CA A:SER254 4.8 53.3 1.0 O5' C:DA4 4.8 81.3 1.0 CA A:GLY259 4.8 52.0 1.0 O3' C:DA3 4.9 81.9 1.0 C A:GLY257 4.9 54.4 1.0 O A:PHE252 5.0 56.8 1.0

Sodium binding site 2 out of 2 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 2 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 B:Na602 b:67.1 occ:1.00 O B:THR253 2.4 58.3 1.0 OP1 D:DA4 2.6 64.8 1.0 O B:VAL258 2.6 53.6 1.0 O B:VAL255 3.3 59.3 1.0 OP2 D:DA4 3.5 64.4 1.0 P D:DA4 3.5 65.1 1.0 C B:THR253 3.5 58.7 1.0 C B:VAL258 3.7 53.7 1.0 CA B:THR253 4.0 57.6 1.0 CB B:THR253 4.2 68.3 1.0 C B:VAL255 4.3 58.7 1.0 N B:VAL258 4.3 47.9 1.0 O5' D:DA4 4.5 64.0 1.0 N B:GLY259 4.5 52.7 1.0 CA B:VAL258 4.6 47.6 1.0 N B:GLY257 4.6 53.1 1.0 CA B:GLY259 4.7 52.7 1.0 O3' D:DA3 4.7 67.3 1.0 N B:SER254 4.7 53.5 1.0 N B:VAL255 4.8 54.0 1.0 CA B:PHE256 4.9 52.4 1.0 CG2 B:THR253 5.0 67.7 1.0 N B:PHE256 5.0 53.9 1.0 C B:SER254 5.0 56.4 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