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Sodium in PDB 6p1r: Pre-Catalytic Ternary Complex of Human Dna Polymerase Mu with 1-Nt Gapped Substrate Containing Template 8OG and Bound Incoming Ampnpp

Enzymatic activity of Pre-Catalytic Ternary Complex of Human Dna Polymerase Mu with 1-Nt Gapped Substrate Containing Template 8OG and Bound Incoming Ampnpp

All present enzymatic activity of Pre-Catalytic Ternary Complex of Human Dna Polymerase Mu with 1-Nt Gapped Substrate Containing Template 8OG and Bound Incoming Ampnpp:
2.7.7.7;

Protein crystallography data

The structure of Pre-Catalytic Ternary Complex of Human Dna Polymerase Mu with 1-Nt Gapped Substrate Containing Template 8OG and Bound Incoming Ampnpp, PDB code: 6p1r was solved by A.M.Kaminski, L.C.Pedersen, K.Bebenek, K.K.Chiruvella, D.A.Ramsden, T.A.Kunkel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 31.37 / 1.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 59.889, 68.770, 110.489, 90.00, 90.00, 90.00
R / Rfree (%) 17.4 / 19.4

Other elements in 6p1r:

The structure of Pre-Catalytic Ternary Complex of Human Dna Polymerase Mu with 1-Nt Gapped Substrate Containing Template 8OG and Bound Incoming Ampnpp also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Chlorine (Cl) 3 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Pre-Catalytic Ternary Complex of Human Dna Polymerase Mu with 1-Nt Gapped Substrate Containing Template 8OG and Bound Incoming Ampnpp (pdb code 6p1r). 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 Pre-Catalytic Ternary Complex of Human Dna Polymerase Mu with 1-Nt Gapped Substrate Containing Template 8OG and Bound Incoming Ampnpp, PDB code: 6p1r:

Sodium binding site 1 out of 1 in 6p1r

Go back to Sodium Binding Sites List in 6p1r
Sodium binding site 1 out of 1 in the Pre-Catalytic Ternary Complex of Human Dna Polymerase Mu with 1-Nt Gapped Substrate Containing Template 8OG and Bound Incoming Ampnpp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Pre-Catalytic Ternary Complex of Human Dna Polymerase Mu with 1-Nt Gapped Substrate Containing Template 8OG and Bound Incoming Ampnpp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na504

b:24.1
occ:1.00
 O A:VAL246 2.3 24.1 1.0
O A:ILE243 2.3 23.0 1.0
OP1 P:DT3 2.4 22.1 0.4
O P:HOH113 2.4 29.0 1.0
O A:THR241 2.4 24.6 1.0
O P:HOH102 2.6 37.2 1.0
OP1 P:DT3 2.6 22.6 0.6
C A:VAL246 3.4 23.9 1.0
C A:ILE243 3.4 25.0 1.0
C A:THR241 3.5 23.7 1.0
P P:DT3 3.6 22.2 0.4
P P:DT3 3.6 22.3 0.6
N A:VAL246 3.7 22.8 1.0
OP2 P:DT3 3.7 19.2 0.6
OP2 P:DT3 3.9 20.7 0.4
CA A:VAL246 4.0 23.2 1.0
N A:ILE243 4.1 25.4 1.0
N A:PHE244 4.2 21.7 1.0
C A:GLN242 4.2 26.7 1.0
N A:GLY245 4.2 22.3 1.0
CA A:PHE244 4.2 23.5 1.0
CA A:THR241 4.2 23.5 1.0
CA A:ILE243 4.4 24.8 1.0
N A:GLY247 4.4 24.9 1.0
CB A:VAL246 4.4 21.7 1.0
N A:GLN242 4.4 26.0 1.0
O A:GLN242 4.5 27.6 1.0
OP2 P:DA4 4.6 19.5 0.4
C A:PHE244 4.6 25.1 1.0
CA A:GLN242 4.6 28.6 1.0
O3' P:DG2 4.6 22.3 1.0
O5' P:DT3 4.7 20.2 0.4
C A:GLY245 4.7 23.7 1.0
CA A:GLY247 4.7 24.5 1.0
O A:PHE240 4.8 23.4 1.0
C3' P:DA4 4.8 36.1 0.4
O3' P:DA4 4.8 33.1 0.4
O5' P:DT3 4.9 20.4 0.6
CB A:THR241 4.9 24.8 1.0

Reference:

A.M.Kaminski, K.K.Chiruvella, D.A.Ramsden, T.A.Kunkel, K.Bebenek, L.C.Pedersen. Unexpected Behavior of Dna Polymerase Mu Opposite Template 8-Oxo-7,8-Dihydro-2'-Guanosine. Nucleic Acids Res. V. 47 9410 2019.
ISSN: ESSN 1362-4962
PubMed: 31435651
DOI: 10.1093/NAR/GKZ680
Page generated: Tue Oct 8 12:39:53 2024

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