Atomistry » Sodium » PDB 5txu-5u63 » 5tyb
Atomistry »
  Sodium »
    PDB 5txu-5u63 »
      5tyb »

Sodium in PDB 5tyb: Dna Polymerase Mu Reactant Complex, 10MM MG2+ (7.5 Min)

Enzymatic activity of Dna Polymerase Mu Reactant Complex, 10MM MG2+ (7.5 Min)

All present enzymatic activity of Dna Polymerase Mu Reactant Complex, 10MM MG2+ (7.5 Min):
2.7.7.7;

Protein crystallography data

The structure of Dna Polymerase Mu Reactant Complex, 10MM MG2+ (7.5 Min), PDB code: 5tyb was solved by J.A.Jamsen, S.H.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 31.39 / 1.85
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 60.047, 68.488, 110.450, 90.00, 90.00, 90.00
R / Rfree (%) 16.7 / 19.9

Other elements in 5tyb:

The structure of Dna Polymerase Mu Reactant Complex, 10MM MG2+ (7.5 Min) also contains other interesting chemical elements:

Magnesium (Mg) 1 atom
Calcium (Ca) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Dna Polymerase Mu Reactant Complex, 10MM MG2+ (7.5 Min) (pdb code 5tyb). 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 Dna Polymerase Mu Reactant Complex, 10MM MG2+ (7.5 Min), PDB code: 5tyb:

Sodium binding site 1 out of 1 in 5tyb

Go back to Sodium Binding Sites List in 5tyb
Sodium binding site 1 out of 1 in the Dna Polymerase Mu Reactant Complex, 10MM MG2+ (7.5 Min)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Dna Polymerase Mu Reactant Complex, 10MM MG2+ (7.5 Min) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na503

b:18.0
occ:1.00
O A:VAL246 2.3 21.3 1.0
O A:ILE243 2.3 16.4 1.0
O P:HOH215 2.4 27.2 1.0
O A:THR241 2.4 22.3 1.0
O A:HOH841 2.5 25.9 1.0
OP1 P:DT3 2.6 16.1 1.0
C A:VAL246 3.3 19.2 1.0
C A:ILE243 3.4 19.8 1.0
C A:THR241 3.5 24.9 1.0
P P:DT3 3.6 17.3 1.0
N A:VAL246 3.6 20.0 1.0
OP2 P:DT3 3.8 16.5 1.0
CA A:VAL246 4.0 20.3 1.0
O A:HOH721 4.1 35.9 1.0
N A:ILE243 4.1 20.7 1.0
N A:GLY245 4.1 17.6 1.0
N A:PHE244 4.2 17.3 1.0
CA A:THR241 4.2 22.4 1.0
C A:GLN242 4.2 24.2 0.4
CA A:PHE244 4.2 17.2 1.0
C A:GLN242 4.3 24.2 0.6
N A:GLY247 4.4 17.8 1.0
CA A:ILE243 4.4 18.4 1.0
CB A:VAL246 4.4 19.4 1.0
N A:GLN242 4.5 22.8 0.6
O A:GLN242 4.5 23.2 0.4
N A:GLN242 4.5 22.8 0.4
C A:PHE244 4.5 20.5 1.0
CA A:GLN242 4.6 22.5 0.6
O3' P:DG2 4.6 17.2 1.0
O A:HOH862 4.6 38.2 1.0
CA A:GLN242 4.6 22.5 0.4
C A:GLY245 4.7 20.8 1.0
CA A:GLY247 4.7 20.8 1.0
O A:GLN242 4.8 23.1 0.6
O A:PHE240 4.8 16.9 1.0
O5' P:DT3 4.8 14.8 1.0
CB A:THR241 4.9 21.2 1.0
CA A:GLY245 5.0 18.4 1.0

Reference:

J.A.Jamsen, W.A.Beard, L.C.Pedersen, D.D.Shock, A.F.Moon, J.M.Krahn, K.Bebenek, T.A.Kunkel, S.H.Wilson. Time-Lapse Crystallography Snapshots of A Double-Strand Break Repair Polymerase in Action. Nat Commun V. 8 253 2017.
ISSN: ESSN 2041-1723
PubMed: 28811466
DOI: 10.1038/S41467-017-00271-7
Page generated: Tue Oct 8 00:18:11 2024

Last articles

Cl in 5FST
Cl in 5FUP
Cl in 5FUL
Cl in 5FU0
Cl in 5FU8
Cl in 5FUD
Cl in 5FUB
Cl in 5FS0
Cl in 5FTS
Cl in 5FTV
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy