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Sodium in PDB 5txx: Dna Polymerase Mu Pre-Catalytic Ground State Ternary Complex, CA2+

Enzymatic activity of Dna Polymerase Mu Pre-Catalytic Ground State Ternary Complex, CA2+

All present enzymatic activity of Dna Polymerase Mu Pre-Catalytic Ground State Ternary Complex, CA2+:
2.7.7.7;

Protein crystallography data

The structure of Dna Polymerase Mu Pre-Catalytic Ground State Ternary Complex, CA2+, PDB code: 5txx 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) 29.77 / 1.95
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 59.538, 68.243, 110.200, 90.00, 90.00, 90.00
R / Rfree (%) 15.9 / 19.5

Other elements in 5txx:

The structure of Dna Polymerase Mu Pre-Catalytic Ground State Ternary Complex, CA2+ also contains other interesting chemical elements:

Calcium (Ca) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Dna Polymerase Mu Pre-Catalytic Ground State Ternary Complex, CA2+ (pdb code 5txx). 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 Pre-Catalytic Ground State Ternary Complex, CA2+, PDB code: 5txx:

Sodium binding site 1 out of 1 in 5txx

Go back to Sodium Binding Sites List in 5txx
Sodium binding site 1 out of 1 in the Dna Polymerase Mu Pre-Catalytic Ground State Ternary Complex, CA2+


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 Pre-Catalytic Ground State Ternary Complex, CA2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na506

b:15.3
occ:1.00
 O A:VAL246 2.3 15.5 1.0
O A:THR241 2.4 22.3 1.0
O P:HOH209 2.4 23.3 1.0
O A:HOH818 2.4 17.1 0.6
O A:ILE243 2.4 16.2 1.0
OP1 P:DT3 2.6 14.9 1.0
C A:VAL246 3.4 15.2 1.0
C A:THR241 3.4 22.5 1.0
C A:ILE243 3.4 16.7 1.0
P P:DT3 3.7 15.2 1.0
N A:VAL246 3.7 16.9 1.0
OP2 P:DT3 3.8 12.6 1.0
O A:HOH818 3.9 18.6 0.4
CA A:VAL246 4.1 18.2 1.0
N A:ILE243 4.1 17.7 1.0
CA A:THR241 4.1 19.1 1.0
C A:GLN242 4.1 22.4 0.6
N A:PHE244 4.2 16.8 1.0
N A:GLY245 4.2 15.6 1.0
CA A:PHE244 4.2 12.7 1.0
C A:GLN242 4.3 22.1 0.4
N A:GLN242 4.4 22.1 0.4
N A:GLN242 4.4 22.1 0.6
CA A:ILE243 4.4 17.7 1.0
N A:GLY247 4.4 15.2 1.0
O A:GLN242 4.4 19.8 0.6
CB A:VAL246 4.5 17.6 1.0
CA A:GLN242 4.5 20.3 0.4
CA A:GLN242 4.5 20.2 0.6
C A:PHE244 4.6 17.2 1.0
O3' P:DG2 4.7 15.6 1.0
O A:PHE240 4.7 17.8 1.0
CA A:GLY247 4.7 18.2 1.0
C A:GLY245 4.8 19.7 1.0
CB A:THR241 4.8 17.8 1.0
O5' P:DT3 4.8 15.1 1.0
O A:GLN242 4.9 22.1 0.4

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 00:18:10 2024

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