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Sodium in PDB 5vz8: Post-Catalytic Complex of Human Polymerase Mu (G433A) Mutant with Incoming Utp

Enzymatic activity of Post-Catalytic Complex of Human Polymerase Mu (G433A) Mutant with Incoming Utp

All present enzymatic activity of Post-Catalytic Complex of Human Polymerase Mu (G433A) Mutant with Incoming Utp:
2.7.7.7;

Protein crystallography data

The structure of Post-Catalytic Complex of Human Polymerase Mu (G433A) Mutant with Incoming Utp, PDB code: 5vz8 was solved by A.F.Moon, J.M.Pryor, D.A.Ramsden, T.A.Kunkel, K.Bebenek, L.C.Pedersen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.91 / 1.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 59.934, 69.031, 109.825, 90.00, 90.00, 90.00
R / Rfree (%) 17.2 / 19.4

Other elements in 5vz8:

The structure of Post-Catalytic Complex of Human Polymerase Mu (G433A) Mutant with Incoming Utp 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 Polymerase Mu (G433A) Mutant with Incoming Utp (pdb code 5vz8). 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 Polymerase Mu (G433A) Mutant with Incoming Utp, PDB code: 5vz8:

Sodium binding site 1 out of 1 in 5vz8

Go back to Sodium Binding Sites List in 5vz8
Sodium binding site 1 out of 1 in the Post-Catalytic Complex of Human Polymerase Mu (G433A) Mutant with Incoming Utp


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 Polymerase Mu (G433A) Mutant with Incoming Utp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na503

b:4.7
occ:1.00
 OP1 P:U5 2.3 16.9 1.0
O A:VAL246 2.3 9.9 1.0
O A:THR241 2.3 10.5 1.0
O P:HOH107 2.4 11.7 1.0
OP1 P:DT3 2.4 10.3 1.0
O A:ILE243 2.4 11.2 1.0
C A:VAL246 3.4 12.0 1.0
C A:THR241 3.5 11.3 1.0
P P:DT3 3.5 16.1 1.0
C A:ILE243 3.5 13.6 1.0
P P:U5 3.7 17.7 1.0
N A:VAL246 3.8 14.2 1.0
OP2 P:DT3 3.9 11.8 1.0
CA A:THR241 4.1 11.6 1.0
CA A:VAL246 4.2 15.0 1.0
N A:ILE243 4.2 14.6 1.0
C A:GLN242 4.3 14.8 1.0
N A:GLY245 4.3 9.5 1.0
C5' P:U5 4.3 20.3 1.0
N A:PHE244 4.3 11.2 1.0
O5' P:U5 4.3 21.4 1.0
N A:GLY247 4.4 11.1 1.0
CA A:PHE244 4.4 11.7 1.0
CA A:ILE243 4.5 13.2 1.0
N A:GLN242 4.5 14.2 1.0
O A:GLN242 4.5 17.1 1.0
O A:HOH774 4.6 32.4 1.0
O3' P:DG2 4.6 14.9 1.0
CA A:GLY247 4.6 11.5 1.0
C3' P:DA4 4.6 13.4 1.0
OP2 P:DA4 4.6 12.1 1.0
O5' P:DT3 4.6 12.0 1.0
CB A:VAL246 4.6 13.2 1.0
OP2 P:U5 4.7 24.9 1.0
CA A:GLN242 4.7 14.2 1.0
O3' P:DA4 4.7 16.6 1.0
CB A:THR241 4.7 11.0 1.0
C A:PHE244 4.8 16.9 1.0
O A:PHE240 4.9 12.8 1.0
C A:GLY245 4.9 12.8 1.0

Reference:

A.F.Moon, J.M.Pryor, D.A.Ramsden, T.A.Kunkel, K.Bebenek, L.C.Pedersen. Structural Accommodation of Ribonucleotide Incorporation By the Dna Repair Enzyme Polymerase Mu. Nucleic Acids Res. V. 45 9138 2017.
ISSN: ESSN 1362-4962
PubMed: 28911097
DOI: 10.1093/NAR/GKX527
Page generated: Tue Oct 8 00:57:26 2024

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