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Sodium in PDB 5d46: Structural Basis For A New Templated Activity By Terminal Deoxynucleotidyl Transferase: Implications For V(D)J Recombination

Protein crystallography data

The structure of Structural Basis For A New Templated Activity By Terminal Deoxynucleotidyl Transferase: Implications For V(D)J Recombination, PDB code: 5d46 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) 44.57 / 2.80
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 55.980, 75.000, 125.910, 90.00, 98.13, 90.00
R / Rfree (%) 19.8 / 24.6

Other elements in 5d46:

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

Sodium Binding Sites:

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 5d46). 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: 5d46:

Sodium binding site 1 out of 1 in 5d46

Go back to Sodium Binding Sites List in 5d46
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:96.2
occ:1.00
O A:VAL258 2.2 72.4 1.0
O A:VAL255 2.4 71.1 1.0
OP1 C:DT5 2.5 83.5 1.0
O A:THR253 2.6 69.7 1.0
C A:VAL258 3.3 70.8 1.0
P C:DT5 3.5 82.7 1.0
N A:VAL258 3.5 69.1 1.0
C A:VAL255 3.5 72.4 1.0
OP2 C:DT5 3.6 82.3 1.0
C A:THR253 3.7 69.4 1.0
CA A:VAL258 3.9 68.2 1.0
N A:GLY257 3.9 69.2 1.0
CA A:PHE256 4.1 70.8 1.0
N A:PHE256 4.3 71.4 1.0
CA A:THR253 4.3 63.4 1.0
N A:VAL255 4.3 67.2 1.0
C A:PHE256 4.3 75.8 1.0
N A:GLY259 4.3 64.5 1.0
C A:GLY257 4.4 73.1 1.0
CB A:VAL258 4.5 72.3 1.0
O3' C:DT4 4.5 82.2 1.0
CA A:VAL255 4.6 67.7 1.0
O5' C:DT5 4.6 83.0 1.0
CA A:GLY257 4.7 68.9 1.0
CA A:GLY259 4.7 62.9 1.0
CB A:THR253 4.8 62.5 1.0
N A:SER254 4.8 67.5 1.0
C A:SER254 4.9 72.4 1.0

Reference:

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
Page generated: Tue Dec 15 10:47:40 2020

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