Atomistry » Sodium » PDB 4qon-4r3n » 4qzi
Atomistry »
  Sodium »
    PDB 4qon-4r3n »
      4qzi »

Sodium in PDB 4qzi: Mouse Tdt, F401A Mutant, in Complex with A Dsb Substrate and ZN2+

Enzymatic activity of Mouse Tdt, F401A Mutant, in Complex with A Dsb Substrate and ZN2+

All present enzymatic activity of Mouse Tdt, F401A Mutant, in Complex with A Dsb Substrate and ZN2+:
2.7.7.31;

Protein crystallography data

The structure of Mouse Tdt, F401A Mutant, in Complex with A Dsb Substrate and ZN2+, PDB code: 4qzi 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) 22.42 / 2.65
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 57.700, 71.523, 113.035, 90.00, 94.17, 90.00
R / Rfree (%) 18.5 / 20.3

Other elements in 4qzi:

The structure of Mouse Tdt, F401A Mutant, in Complex with A Dsb Substrate and ZN2+ also contains other interesting chemical elements:

Magnesium (Mg) 1 atom
Zinc (Zn) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Mouse Tdt, F401A Mutant, in Complex with A Dsb Substrate and ZN2+ (pdb code 4qzi). 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, F401A Mutant, in Complex with A Dsb Substrate and ZN2+, PDB code: 4qzi:

Sodium binding site 1 out of 1 in 4qzi

Go back to Sodium Binding Sites List in 4qzi
Sodium binding site 1 out of 1 in the Mouse Tdt, F401A Mutant, in Complex with A Dsb Substrate and ZN2+


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Mouse Tdt, F401A Mutant, in Complex with A Dsb Substrate and ZN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na604

b:68.3
occ:1.00
 OP1 U:DA4 2.2 72.7 1.0
O A:VAL258 2.4 62.2 1.0
O A:THR253 2.6 59.4 1.0
O A:VAL255 2.8 57.2 1.0
P U:DA4 3.2 73.9 1.0
OP2 U:DA4 3.4 74.3 1.0
C A:VAL258 3.4 63.7 1.0
C A:THR253 3.6 60.4 1.0
N A:VAL258 3.8 57.4 1.0
C A:VAL255 3.8 57.3 1.0
CA A:THR253 4.0 56.4 1.0
CA A:VAL258 4.1 57.4 1.0
N A:GLY257 4.3 57.5 1.0
O3' U:DA3 4.3 77.2 1.0
CB A:THR253 4.4 60.7 1.0
CA A:PHE256 4.4 52.2 1.0
N A:GLY259 4.4 61.9 1.0
O5' U:DA4 4.5 72.7 1.0
N A:PHE256 4.5 52.9 1.0
N A:VAL255 4.6 53.9 1.0
CB A:VAL258 4.6 59.6 1.0
CA A:GLY259 4.7 61.5 1.0
C A:PHE256 4.7 59.7 1.0
N A:SER254 4.8 57.4 1.0
C A:GLY257 4.8 63.9 1.0
CA A:VAL255 4.9 54.2 1.0
C A:SER254 4.9 58.7 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 18:08:25 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy