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Sodium in PDB 6akh: Pre-Catalytic Ternary Complex of Human Dna Polymerase Mu with Templating Adenine and Incoming Mn-Dumpnpp

Enzymatic activity of Pre-Catalytic Ternary Complex of Human Dna Polymerase Mu with Templating Adenine and Incoming Mn-Dumpnpp

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

Protein crystallography data

The structure of Pre-Catalytic Ternary Complex of Human Dna Polymerase Mu with Templating Adenine and Incoming Mn-Dumpnpp, PDB code: 6akh 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) 30.00 / 1.75
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 59.838, 68.800, 109.680, 90.00, 90.00, 90.00
R / Rfree (%) 16.4 / 19

Other elements in 6akh:

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

Manganese (Mn) 2 atoms

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 Mn-Dumpnpp (pdb code 6akh). 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 Mn-Dumpnpp, PDB code: 6akh:

Sodium binding site 1 out of 1 in 6akh

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


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 Mn-Dumpnpp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na504

b:16.9
occ:1.00
 O A:VAL246 2.3 18.0 1.0
O P:HOH114 2.4 29.3 1.0
O A:HOH905 2.4 26.3 1.0
O A:ILE243 2.4 15.9 1.0
O A:THR241 2.4 21.3 1.0
OP1 P:DT3 2.6 16.0 1.0
C A:ILE243 3.4 17.1 1.0
C A:VAL246 3.4 18.4 1.0
C A:THR241 3.5 21.2 1.0
P P:DT3 3.7 16.4 1.0
N A:VAL246 3.8 17.4 1.0
OP2 P:DT3 3.8 15.2 1.0
O P:HOH116 3.9 37.2 1.0
O A:HOH735 4.0 39.8 1.0
N A:ILE243 4.0 19.1 1.0
CA A:VAL246 4.1 17.8 1.0
C A:GLN242 4.2 20.9 1.0
N A:PHE244 4.2 16.7 1.0
CA A:THR241 4.2 20.5 1.0
N A:GLY245 4.2 16.9 1.0
CA A:PHE244 4.3 17.3 1.0
O P:HOH111 4.3 35.9 1.0
CA A:ILE243 4.4 17.9 1.0
N A:GLN242 4.4 22.0 1.0
CB A:VAL246 4.4 17.7 1.0
N A:GLY247 4.5 17.9 1.0
O A:GLN242 4.5 22.6 1.0
CA A:GLN242 4.6 23.4 1.0
C A:PHE244 4.6 17.2 1.0
O3' P:DG2 4.7 16.1 1.0
O P:HOH108 4.7 47.0 1.0
O A:PHE240 4.8 17.9 1.0
CA A:GLY247 4.8 18.5 1.0
C A:GLY245 4.8 17.1 1.0
O5' P:DT3 4.9 14.8 1.0
CB A:THR241 4.9 20.1 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 01:50:41 2024

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