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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

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