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Sodium in PDB 6ak8: Pre-Catalytic Ternary Complex of Human Dna Polymerase Mu with Templating Adenine and Incoming Ca-8OXODGTP

Enzymatic activity of Pre-Catalytic Ternary Complex of Human Dna Polymerase Mu with Templating Adenine and Incoming Ca-8OXODGTP

All present enzymatic activity of Pre-Catalytic Ternary Complex of Human Dna Polymerase Mu with Templating Adenine and Incoming Ca-8OXODGTP:
2.7.7.7;

Protein crystallography data

The structure of Pre-Catalytic Ternary Complex of Human Dna Polymerase Mu with Templating Adenine and Incoming Ca-8OXODGTP, PDB code: 6ak8 was solved by Y.K.Chang, W.J.Wu, M.D.Tsai, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.74
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 59.750, 68.548, 110.165, 90.00, 90.00, 90.00
R / Rfree (%) 17.4 / 20.1

Other elements in 6ak8:

The structure of Pre-Catalytic Ternary Complex of Human Dna Polymerase Mu with Templating Adenine and Incoming Ca-8OXODGTP also contains other interesting chemical elements:

Calcium (Ca) 2 atoms
Chlorine (Cl) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Pre-Catalytic Ternary Complex of Human Dna Polymerase Mu with Templating Adenine and Incoming Ca-8OXODGTP (pdb code 6ak8). 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 Templating Adenine and Incoming Ca-8OXODGTP, PDB code: 6ak8:

Sodium binding site 1 out of 1 in 6ak8

Go back to Sodium Binding Sites List in 6ak8
Sodium binding site 1 out of 1 in the Pre-Catalytic Ternary Complex of Human Dna Polymerase Mu with Templating Adenine and Incoming Ca-8OXODGTP


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 Templating Adenine and Incoming Ca-8OXODGTP within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na503

b:20.7
occ:1.00
 O A:VAL246 2.3 23.3 1.0
O A:HOH855 2.3 29.3 1.0
O A:THR241 2.3 25.0 1.0
O P:HOH109 2.4 25.2 1.0
O A:ILE243 2.4 22.4 1.0
OP1 P:DT3 2.8 22.1 1.0
C A:VAL246 3.4 23.4 1.0
C A:ILE243 3.4 24.4 1.0
C A:THR241 3.4 25.5 1.0
P P:DT3 3.8 23.3 1.0
N A:VAL246 3.8 22.2 1.0
OP2 P:DT3 3.8 22.7 1.0
O P:HOH114 3.9 32.9 1.0
N A:ILE243 4.0 25.4 1.0
CA A:VAL246 4.1 23.0 1.0
C A:GLN242 4.1 27.7 1.0
CA A:THR241 4.2 24.9 1.0
N A:PHE244 4.2 22.6 1.0
O A:HOH827 4.2 42.6 1.0
CA A:PHE244 4.3 23.2 1.0
N A:GLY245 4.3 22.2 1.0
CA A:ILE243 4.4 24.5 1.0
N A:GLN242 4.4 26.1 1.0
CB A:VAL246 4.4 22.5 1.0
N A:GLY247 4.5 23.6 1.0
O A:HOH870 4.5 37.8 1.0
O A:GLN242 4.5 26.7 1.0
CA A:GLN242 4.5 28.0 1.0
C A:PHE244 4.7 23.2 1.0
O3' P:DG2 4.7 23.1 1.0
O A:PHE240 4.7 24.5 1.0
CA A:GLY247 4.8 23.6 1.0
C A:GLY245 4.9 22.0 1.0
CB A:THR241 4.9 23.9 1.0
O5' P:DT3 5.0 21.9 1.0

Reference:

Y.K.Chang, Y.P.Huang, X.X.Liu, T.P.Ko, Y.Bessho, Y.Kawano, M.Maestre-Reyna, W.J.Wu, M.D.Tsai. Human Dna Polymerase Mu Can Use A Noncanonical Mechanism For Multiple MN2+-Mediated Functions. J.Am.Chem.Soc. V. 141 8489 2019.
ISSN: ESSN 1520-5126
PubMed: 31067051
DOI: 10.1021/JACS.9B01741
Page generated: Tue Oct 8 01:50:37 2024

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