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Magnesium in PDB 4m9l: Dna Polymerase Beta E295K Soaked with Dctp

Enzymatic activity of Dna Polymerase Beta E295K Soaked with Dctp

All present enzymatic activity of Dna Polymerase Beta E295K Soaked with Dctp:
2.7.7.7;

Protein crystallography data

The structure of Dna Polymerase Beta E295K Soaked with Dctp, PDB code: 4m9l was solved by B.E.Eckenroth, S.Doublie, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 13.84 / 2.09
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.362, 80.198, 54.599, 90.00, 108.59, 90.00
R / Rfree (%) 18.9 / 23.1

Other elements in 4m9l:

The structure of Dna Polymerase Beta E295K Soaked with Dctp also contains other interesting chemical elements:

Sodium (Na) 3 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Dna Polymerase Beta E295K Soaked with Dctp (pdb code 4m9l). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Dna Polymerase Beta E295K Soaked with Dctp, PDB code: 4m9l:

Magnesium binding site 1 out of 1 in 4m9l

Go back to Magnesium Binding Sites List in 4m9l
Magnesium binding site 1 out of 1 in the Dna Polymerase Beta E295K Soaked with Dctp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Dna Polymerase Beta E295K Soaked with Dctp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg404

b:26.7
occ:1.00
O2A A:DCP405 1.9 24.6 1.0
O2B A:DCP405 2.0 20.6 1.0
OD1 A:ASP190 2.1 25.0 1.0
O2G A:DCP405 2.1 26.7 1.0
OD2 A:ASP192 2.1 30.3 1.0
O A:HOH586 2.1 25.0 1.0
PB A:DCP405 3.1 27.4 1.0
CG A:ASP190 3.2 28.1 1.0
CG A:ASP192 3.2 28.9 1.0
PA A:DCP405 3.2 28.0 1.0
NA A:NA403 3.3 31.6 1.0
PG A:DCP405 3.3 28.0 1.0
O3A A:DCP405 3.5 44.0 1.0
OD1 A:ASP192 3.5 28.9 1.0
O3B A:DCP405 3.6 34.1 1.0
OD2 A:ASP190 3.7 31.9 1.0
O A:ASP190 4.0 24.1 1.0
O3G A:DCP405 4.0 24.3 1.0
O5' A:DCP405 4.2 30.2 1.0
C A:ASP190 4.2 29.3 1.0
O1A A:DCP405 4.2 28.6 1.0
N A:ASP190 4.3 24.7 1.0
O A:HOH560 4.3 25.8 1.0
C5' A:DCP405 4.3 31.9 1.0
O A:HOH642 4.4 51.5 1.0
O1B A:DCP405 4.4 27.3 1.0
CB A:ASP190 4.4 24.6 1.0
OG A:SER180 4.4 35.6 1.0
O1G A:DCP405 4.4 28.3 1.0
CB A:ASP192 4.5 31.9 1.0
CA A:ASP190 4.5 22.5 1.0
N A:SER180 4.6 35.9 1.0
N A:ASP192 4.8 26.6 1.0
N A:MET191 4.8 24.0 1.0
CA A:GLY179 4.9 34.9 1.0

Reference:

B.E.Eckenroth, J.B.Towle-Weicksel, J.B.Sweasy, S.Doublie. The E295K Cancer Variant of Human Polymerase Beta Favors the Mismatch Conformational Pathway During Nucleotide Selection. J.Biol.Chem. V. 288 34850 2013.
ISSN: ISSN 0021-9258
PubMed: 24133209
DOI: 10.1074/JBC.M113.510891
Page generated: Mon Dec 14 19:11:58 2020

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