Atomistry » Sodium » PDB 6iff-6jbd » 6ipg
Atomistry »
  Sodium »
    PDB 6iff-6jbd »
      6ipg »

Sodium in PDB 6ipg: Post-Catalytic Complex of Human Dna Polymerase Mu with Templating Cytosine and Mg-8OXODGMP

Enzymatic activity of Post-Catalytic Complex of Human Dna Polymerase Mu with Templating Cytosine and Mg-8OXODGMP

All present enzymatic activity of Post-Catalytic Complex of Human Dna Polymerase Mu with Templating Cytosine and Mg-8OXODGMP:
2.7.7.7;

Protein crystallography data

The structure of Post-Catalytic Complex of Human Dna Polymerase Mu with Templating Cytosine and Mg-8OXODGMP, PDB code: 6ipg 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 / 1.62
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 59.884, 68.403, 110.481, 90.00, 90.00, 90.00
R / Rfree (%) 17.4 / 20.1

Other elements in 6ipg:

The structure of Post-Catalytic Complex of Human Dna Polymerase Mu with Templating Cytosine and Mg-8OXODGMP also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Post-Catalytic Complex of Human Dna Polymerase Mu with Templating Cytosine and Mg-8OXODGMP (pdb code 6ipg). 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 Post-Catalytic Complex of Human Dna Polymerase Mu with Templating Cytosine and Mg-8OXODGMP, PDB code: 6ipg:

Sodium binding site 1 out of 1 in 6ipg

Go back to Sodium Binding Sites List in 6ipg
Sodium binding site 1 out of 1 in the Post-Catalytic Complex of Human Dna Polymerase Mu with Templating Cytosine and Mg-8OXODGMP


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Post-Catalytic Complex of Human Dna Polymerase Mu with Templating Cytosine and Mg-8OXODGMP within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na503

b:20.8
occ:1.00
 O P:HOH116 2.3 25.8 1.0
O A:VAL246 2.4 22.5 1.0
O A:HOH852 2.4 31.0 1.0
O A:THR241 2.4 24.0 1.0
O A:ILE243 2.4 22.1 1.0
OP1 P:DT3 2.6 20.6 1.0
C A:VAL246 3.4 22.4 1.0
C A:ILE243 3.4 23.8 1.0
C A:THR241 3.5 24.4 1.0
P P:DT3 3.6 20.4 1.0
N A:VAL246 3.8 21.4 1.0
OP2 P:DT3 3.8 19.5 1.0
N A:ILE243 4.1 24.6 1.0
C A:GLN242 4.1 27.0 1.0
CA A:VAL246 4.1 22.6 1.0
CA A:THR241 4.2 23.9 1.0
N A:PHE244 4.2 22.1 1.0
N A:GLY245 4.2 20.9 1.0
CA A:PHE244 4.3 23.6 1.0
CA A:ILE243 4.4 23.8 1.0
O A:GLN242 4.4 29.7 1.0
N A:GLN242 4.4 25.9 1.0
N A:GLY247 4.5 21.9 1.0
CB A:VAL246 4.5 22.5 1.0
O A:HOH889 4.5 47.0 1.0
CA A:GLN242 4.6 28.1 1.0
O3' P:DG2 4.6 21.2 1.0
C A:PHE244 4.6 23.4 1.0
CA A:GLY247 4.7 22.8 1.0
O A:PHE240 4.8 21.7 1.0
O5' P:DT3 4.8 19.7 1.0
CB A:THR241 4.9 24.1 1.0
C A:GLY245 4.9 21.2 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 09:39:31 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy