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Sodium in PDB 5vzd: Pre-Catalytic Ternary Complex of Human Polymerase Mu (W434A) Mutant with Incoming Nonhydrolyzable Umpnpp

Enzymatic activity of Pre-Catalytic Ternary Complex of Human Polymerase Mu (W434A) Mutant with Incoming Nonhydrolyzable Umpnpp

All present enzymatic activity of Pre-Catalytic Ternary Complex of Human Polymerase Mu (W434A) Mutant with Incoming Nonhydrolyzable Umpnpp:
2.7.7.7;

Protein crystallography data

The structure of Pre-Catalytic Ternary Complex of Human Polymerase Mu (W434A) Mutant with Incoming Nonhydrolyzable Umpnpp, PDB code: 5vzd 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) 32.33 / 1.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 59.818, 68.841, 109.855, 90.00, 90.00, 90.00
R / Rfree (%) 16.6 / 18.3

Other elements in 5vzd:

The structure of Pre-Catalytic Ternary Complex of Human Polymerase Mu (W434A) Mutant with Incoming Nonhydrolyzable Umpnpp also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Pre-Catalytic Ternary Complex of Human Polymerase Mu (W434A) Mutant with Incoming Nonhydrolyzable Umpnpp (pdb code 5vzd). 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 Polymerase Mu (W434A) Mutant with Incoming Nonhydrolyzable Umpnpp, PDB code: 5vzd:

Sodium binding site 1 out of 1 in 5vzd

Go back to Sodium Binding Sites List in 5vzd
Sodium binding site 1 out of 1 in the Pre-Catalytic Ternary Complex of Human Polymerase Mu (W434A) Mutant with Incoming Nonhydrolyzable Umpnpp


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 Polymerase Mu (W434A) Mutant with Incoming Nonhydrolyzable Umpnpp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na704

b:14.6
occ:1.00
 O A:VAL246 2.3 13.3 1.0
O P:HOH112 2.4 24.1 1.0
O A:ILE243 2.4 14.2 1.0
O A:THR241 2.4 15.7 1.0
O P:HOH111 2.5 27.3 1.0
OP1 P:DT3 2.6 14.7 1.0
C A:VAL246 3.4 15.9 1.0
C A:ILE243 3.4 15.0 1.0
C A:THR241 3.5 11.9 1.0
P P:DT3 3.7 13.1 1.0
N A:VAL246 3.7 14.0 1.0
OP2 P:DT3 3.9 11.1 1.0
CA A:VAL246 4.0 14.5 1.0
N A:ILE243 4.0 14.1 1.0
N A:GLY245 4.2 12.9 1.0
C A:GLN242 4.2 17.2 1.0
N A:PHE244 4.2 12.0 1.0
CA A:THR241 4.2 12.8 1.0
O A:HOH1033 4.2 41.5 1.0
CA A:PHE244 4.3 12.6 1.0
CA A:ILE243 4.3 13.0 1.0
N A:GLY247 4.4 14.2 1.0
N A:GLN242 4.4 16.7 1.0
CB A:VAL246 4.4 14.9 1.0
O A:GLN242 4.5 19.9 1.0
CA A:GLN242 4.6 17.6 1.0
C A:PHE244 4.6 15.2 1.0
O3' P:DG2 4.6 13.7 1.0
O A:HOH1059 4.7 37.2 1.0
C A:GLY245 4.8 14.6 1.0
O A:PHE240 4.8 14.0 1.0
CA A:GLY247 4.8 14.5 1.0
CB A:THR241 4.9 16.0 1.0
O5' P:DT3 4.9 11.5 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 00:58:02 2024

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