Atomistry » Sodium » PDB 6ah7-6awx » 6ak9
Atomistry »
  Sodium »
    PDB 6ah7-6awx »
      6ak9 »

Sodium in PDB 6ak9: Pre-Catalytic Ternary Complex of Human Dna Polymerase Mu with Templating Cytosine and Incoming Ca-8OXODGTP

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

All present enzymatic activity of Pre-Catalytic Ternary Complex of Human Dna Polymerase Mu with Templating Cytosine 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 Cytosine and Incoming Ca-8OXODGTP, PDB code: 6ak9 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 / 1.91
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 59.907, 68.742, 110.211, 90.00, 90.00, 90.00
R / Rfree (%) 16.5 / 20.4

Other elements in 6ak9:

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

Calcium (Ca) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Pre-Catalytic Ternary Complex of Human Dna Polymerase Mu with Templating Cytosine and Incoming Ca-8OXODGTP (pdb code 6ak9). 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 Cytosine and Incoming Ca-8OXODGTP, PDB code: 6ak9:

Sodium binding site 1 out of 1 in 6ak9

Go back to Sodium Binding Sites List in 6ak9
Sodium binding site 1 out of 1 in the Pre-Catalytic Ternary Complex of Human Dna Polymerase Mu with Templating Cytosine 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 Cytosine and Incoming Ca-8OXODGTP within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na504

b:14.8
occ:1.00
 O P:HOH115 2.3 18.3 1.0
O A:THR241 2.3 19.1 1.0
O A:HOH856 2.3 22.0 1.0
O A:VAL246 2.4 17.3 1.0
O A:ILE243 2.4 16.7 1.0
OP1 P:DT3 2.6 14.7 1.0
C A:THR241 3.4 20.0 1.0
C A:ILE243 3.5 18.1 1.0
C A:VAL246 3.5 17.5 1.0
P P:DT3 3.7 15.6 1.0
N A:VAL246 3.9 16.3 1.0
O P:HOH114 3.9 33.6 1.0
OP2 P:DT3 3.9 14.5 1.0
N A:ILE243 4.0 19.8 1.0
CA A:VAL246 4.1 17.4 1.0
C A:GLN242 4.1 21.1 1.0
CA A:THR241 4.2 19.5 1.0
N A:PHE244 4.2 17.3 1.0
CA A:PHE244 4.3 17.4 1.0
N A:GLY245 4.3 16.3 1.0
N A:GLN242 4.4 20.9 1.0
CA A:ILE243 4.4 19.1 1.0
O A:GLN242 4.5 20.4 1.0
CB A:VAL246 4.5 17.2 1.0
N A:GLY247 4.5 17.4 1.0
CA A:GLN242 4.5 22.9 1.0
O A:HOH865 4.5 41.8 1.0
C A:PHE244 4.7 17.2 1.0
O3' P:DG2 4.7 15.2 1.0
O A:PHE240 4.7 17.2 1.0
CA A:GLY247 4.8 18.4 1.0
CB A:THR241 4.9 19.0 1.0
C A:GLY245 4.9 16.6 1.0
O5' P:DT3 4.9 15.0 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 Dec 15 11:56:51 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy