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Magnesium in PDB 1mq3: Human Dna Polymerase Beta Complexed with Gapped Dna Containing An 8-Oxo-7,8-Dihydro-Guanine Template Paired with Dctp

Enzymatic activity of Human Dna Polymerase Beta Complexed with Gapped Dna Containing An 8-Oxo-7,8-Dihydro-Guanine Template Paired with Dctp

All present enzymatic activity of Human Dna Polymerase Beta Complexed with Gapped Dna Containing An 8-Oxo-7,8-Dihydro-Guanine Template Paired with Dctp:
2.7.7.7;

Protein crystallography data

The structure of Human Dna Polymerase Beta Complexed with Gapped Dna Containing An 8-Oxo-7,8-Dihydro-Guanine Template Paired with Dctp, PDB code: 1mq3 was solved by J.M.Krahn, W.A.Beard, H.Miller, A.P.Grollman, S.H.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.500, 79.900, 55.600, 90.00, 107.90, 90.00
R / Rfree (%) 23.5 / 29.5

Other elements in 1mq3:

The structure of Human Dna Polymerase Beta Complexed with Gapped Dna Containing An 8-Oxo-7,8-Dihydro-Guanine Template Paired with Dctp also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Human Dna Polymerase Beta Complexed with Gapped Dna Containing An 8-Oxo-7,8-Dihydro-Guanine Template Paired with Dctp (pdb code 1mq3). 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 Human Dna Polymerase Beta Complexed with Gapped Dna Containing An 8-Oxo-7,8-Dihydro-Guanine Template Paired with Dctp, PDB code: 1mq3:

Magnesium binding site 1 out of 1 in 1mq3

Go back to Magnesium Binding Sites List in 1mq3
Magnesium binding site 1 out of 1 in the Human Dna Polymerase Beta Complexed with Gapped Dna Containing An 8-Oxo-7,8-Dihydro-Guanine Template Paired with Dctp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Human Dna Polymerase Beta Complexed with Gapped Dna Containing An 8-Oxo-7,8-Dihydro-Guanine Template Paired with Dctp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg339

b:21.6
occ:1.00
 OD1 A:ASP190 1.8 23.3 1.0
O2B A:DCP338 1.9 24.7 1.0
O1A A:DCP338 2.0 25.7 1.0
O A:HOH346 2.0 24.0 1.0
O1G A:DCP338 2.1 25.6 1.0
OD2 A:ASP192 2.1 22.7 1.0
CG A:ASP190 3.0 21.5 1.0
PB A:DCP338 3.0 26.5 1.0
PA A:DCP338 3.0 28.1 1.0
O3A A:DCP338 3.1 28.1 1.0
CG A:ASP192 3.3 20.1 1.0
PG A:DCP338 3.3 28.2 1.0
O5' A:DCP338 3.5 25.9 1.0
OD2 A:ASP190 3.5 21.1 1.0
O3B A:DCP338 3.5 26.6 1.0
OD1 A:ASP192 3.8 23.5 1.0
N A:ASP190 3.9 20.1 1.0
O A:ASP190 4.0 19.0 1.0
C A:ASP190 4.2 19.1 1.0
CB A:ASP190 4.2 18.9 1.0
O A:HOH349 4.2 1.0 1.0
O2G A:DCP338 4.2 26.9 1.0
CA A:ASP190 4.3 19.1 1.0
O1B A:DCP338 4.3 26.3 1.0
O3G A:DCP338 4.4 28.6 1.0
O2A A:DCP338 4.4 25.0 1.0
N A:SER180 4.5 13.0 1.0
CB A:ASP192 4.5 17.1 1.0
CA A:GLY179 4.5 12.1 1.0
OG A:SER180 4.6 16.3 1.0
N A:ASP192 4.7 17.6 1.0
N A:MET191 4.8 18.4 1.0
C5' A:DCP338 4.8 24.0 1.0
N A:GLY189 4.9 20.2 1.0

Reference:

J.M.Krahn, W.A.Beard, H.Miller, A.P.Grollman, S.H.Wilson. Structure of Dna Polymerase Beta with the Mutagenic Dna Lesion 8-Oxodeoxyguanine Reveals Structural Insights Into Its Coding Potential Structure V. 11 121 2003.
ISSN: ISSN 0969-2126
PubMed: 12517346
DOI: 10.1016/S0969-2126(02)00930-9
Page generated: Mon Dec 14 06:29:30 2020

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