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

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

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

Protein crystallography data

The structure of Post-Catalytic Complex of Human Dna Polymerase Mu with Templating Adenine and Mg-8OXODGMP, PDB code: 6ipe 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 / 1.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 59.889, 68.402, 110.512, 90.00, 90.00, 90.00
R / Rfree (%) 17.3 / 20.4

Other elements in 6ipe:

The structure of Post-Catalytic Complex of Human Dna Polymerase Mu with Templating Adenine 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 Adenine and Mg-8OXODGMP (pdb code 6ipe). 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 Adenine and Mg-8OXODGMP, PDB code: 6ipe:

Sodium binding site 1 out of 1 in 6ipe

Go back to Sodium Binding Sites List in 6ipe
Sodium binding site 1 out of 1 in the Post-Catalytic Complex of Human Dna Polymerase Mu with Templating Adenine 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 Adenine and Mg-8OXODGMP within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na503

b:10.3
occ:1.00
 O P:HOH216 2.3 15.5 1.0
O A:VAL246 2.4 11.8 1.0
O A:THR241 2.4 15.0 1.0
O A:HOH871 2.4 17.1 1.0
O A:ILE243 2.4 12.0 1.0
OP1 P:DT3 2.6 10.4 1.0
C A:ILE243 3.4 13.1 1.0
C A:VAL246 3.4 11.5 1.0
C A:THR241 3.4 14.9 1.0
O P:HOH215 3.6 33.1 1.0
P P:DT3 3.7 10.0 1.0
N A:VAL246 3.8 11.0 1.0
OP2 P:DT3 3.9 9.7 1.0
O A:HOH761 4.0 37.3 1.0
N A:ILE243 4.0 14.3 1.0
CA A:VAL246 4.1 11.5 1.0
C A:GLN242 4.2 16.3 1.0
N A:PHE244 4.2 12.3 1.0
CA A:THR241 4.2 14.2 1.0
CA A:PHE244 4.2 12.4 1.0
N A:GLY245 4.3 11.7 1.0
CA A:ILE243 4.4 13.5 1.0
N A:GLN242 4.4 16.3 1.0
CB A:VAL246 4.4 11.4 1.0
N A:GLY247 4.5 11.8 1.0
O A:GLN242 4.5 17.4 1.0
O A:HOH897 4.5 36.6 1.0
CA A:GLN242 4.6 17.5 1.0
C A:PHE244 4.6 12.1 1.0
O3' P:DG2 4.6 10.3 1.0
O A:PHE240 4.8 12.7 1.0
CA A:GLY247 4.8 12.5 1.0
C A:GLY245 4.8 11.3 1.0
O5' P:DT3 4.9 9.3 1.0
CB A:THR241 4.9 14.1 1.0
O A:HOH882 4.9 36.0 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: Mon Aug 18 05:31:19 2025

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