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Sodium in PDB 4qzd: Mouse Tdt, F405A Mutant, in Complex with A Dsb Substrate, C-C Base Pair

Enzymatic activity of Mouse Tdt, F405A Mutant, in Complex with A Dsb Substrate, C-C Base Pair

All present enzymatic activity of Mouse Tdt, F405A Mutant, in Complex with A Dsb Substrate, C-C Base Pair:
2.7.7.31;

Protein crystallography data

The structure of Mouse Tdt, F405A Mutant, in Complex with A Dsb Substrate, C-C Base Pair, PDB code: 4qzd was solved by J.Gouge, M.Delarue, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.56 / 2.70
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 55.933, 74.920, 125.633, 90.00, 98.43, 90.00
R / Rfree (%) 20 / 24.5

Other elements in 4qzd:

The structure of Mouse Tdt, F405A Mutant, in Complex with A Dsb Substrate, C-C Base Pair also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Mouse Tdt, F405A Mutant, in Complex with A Dsb Substrate, C-C Base Pair (pdb code 4qzd). 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 Mouse Tdt, F405A Mutant, in Complex with A Dsb Substrate, C-C Base Pair, PDB code: 4qzd:

Sodium binding site 1 out of 1 in 4qzd

Go back to Sodium Binding Sites List in 4qzd
Sodium binding site 1 out of 1 in the Mouse Tdt, F405A Mutant, in Complex with A Dsb Substrate, C-C Base Pair


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Mouse Tdt, F405A Mutant, in Complex with A Dsb Substrate, C-C Base Pair within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na603

b:75.2
occ:1.00
 O A:VAL255 2.3 73.5 1.0
OP1 U:DA4 2.4 0.9 1.0
O A:HOH723 2.5 55.2 1.0
O A:VAL258 2.6 62.4 1.0
O A:THR253 2.8 68.6 1.0
C A:VAL255 3.4 72.4 1.0
N A:VAL258 3.4 60.1 1.0
C A:VAL258 3.4 62.5 1.0
P U:DA4 3.5 0.5 1.0
N A:GLY257 3.7 63.1 1.0
OP2 U:DA4 3.7 0.5 1.0
C A:THR253 3.8 68.7 1.0
CA A:PHE256 3.8 66.2 1.0
CA A:VAL258 3.9 59.3 1.0
N A:PHE256 4.0 67.5 1.0
C A:PHE256 4.1 69.0 1.0
CA A:THR253 4.3 64.2 1.0
N A:VAL255 4.4 68.1 1.0
C A:GLY257 4.4 65.3 1.0
CB A:VAL258 4.4 62.7 1.0
O3' U:DA3 4.5 0.0 1.0
N A:GLY259 4.5 59.0 1.0
CA A:VAL255 4.5 68.4 1.0
CA A:GLY257 4.6 61.4 1.0
O5' U:DA4 4.7 1.0 1.0
CB A:THR253 4.7 66.2 1.0
C A:SER254 4.8 70.8 1.0
N A:SER254 4.9 64.7 1.0
CA A:GLY259 5.0 57.4 1.0

Reference:

J.Gouge, S.Rosario, F.Romain, F.Poitevin, P.Beguin, M.Delarue. Structural Basis For A Novel Mechanism of Dna Bridging and Alignment in Eukaryotic Dsb Dna Repair. Embo J. V. 34 1126 2015.
ISSN: ISSN 0261-4189
PubMed: 25762590
DOI: 10.15252/EMBJ.201489643
Page generated: Mon Oct 7 18:07:59 2024

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