Atomistry » Magnesium » PDB 4p9d-4pjj » 4pgq
Atomistry »
  Magnesium »
    PDB 4p9d-4pjj »
      4pgq »

Magnesium in PDB 4pgq: Structure of Human Dna Polymerase Beta Complexed with G in the Template Base Paired with Incoming Non-Hydrolyzable Ttp

Enzymatic activity of Structure of Human Dna Polymerase Beta Complexed with G in the Template Base Paired with Incoming Non-Hydrolyzable Ttp

All present enzymatic activity of Structure of Human Dna Polymerase Beta Complexed with G in the Template Base Paired with Incoming Non-Hydrolyzable Ttp:
2.7.7.7;

Protein crystallography data

The structure of Structure of Human Dna Polymerase Beta Complexed with G in the Template Base Paired with Incoming Non-Hydrolyzable Ttp, PDB code: 4pgq was solved by M.C.Koag, S.Lee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.27 / 2.30
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.898, 80.087, 55.077, 90.00, 106.15, 90.00
R / Rfree (%) 20.3 / 26

Other elements in 4pgq:

The structure of Structure of Human Dna Polymerase Beta Complexed with G in the Template Base Paired with Incoming Non-Hydrolyzable Ttp also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of Human Dna Polymerase Beta Complexed with G in the Template Base Paired with Incoming Non-Hydrolyzable Ttp (pdb code 4pgq). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Structure of Human Dna Polymerase Beta Complexed with G in the Template Base Paired with Incoming Non-Hydrolyzable Ttp, PDB code: 4pgq:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 4pgq

Go back to Magnesium Binding Sites List in 4pgq
Magnesium binding site 1 out of 2 in the Structure of Human Dna Polymerase Beta Complexed with G in the Template Base Paired with Incoming Non-Hydrolyzable Ttp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Human Dna Polymerase Beta Complexed with G in the Template Base Paired with Incoming Non-Hydrolyzable Ttp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg400

b:19.3
occ:1.00
 O A:HOH557 1.9 35.9 1.0
O1G A:1FZ404 1.9 40.9 1.0
O1A A:1FZ404 1.9 39.9 1.0
O2B A:1FZ404 2.0 37.9 1.0
OD1 A:ASP190 2.1 33.3 1.0
OD1 A:ASP192 2.2 32.5 1.0
PB A:1FZ404 3.1 44.5 1.0
CG A:ASP190 3.1 31.3 1.0
CG A:ASP192 3.1 35.7 1.0
PA A:1FZ404 3.2 42.7 1.0
PG A:1FZ404 3.3 44.7 1.0
MG A:MG401 3.3 37.1 1.0
OD2 A:ASP190 3.4 35.0 1.0
OD2 A:ASP192 3.4 31.2 1.0
N3A A:1FZ404 3.6 41.4 1.0
O3B A:1FZ404 3.6 39.4 1.0
O A:HOH559 4.0 42.2 1.0
O3G A:1FZ404 4.1 43.5 1.0
O5' A:1FZ404 4.2 42.8 1.0
C5' A:1FZ404 4.2 48.4 1.0
O A:ASP190 4.3 30.1 1.0
O2G A:1FZ404 4.4 44.8 1.0
O1B A:1FZ404 4.4 43.7 1.0
CB A:ASP190 4.5 30.4 1.0
O2A A:1FZ404 4.5 45.7 1.0
O A:HOH530 4.5 32.0 1.0
CB A:ASP192 4.5 28.1 1.0
N A:ASP190 4.5 31.6 1.0
C A:ASP190 4.6 34.3 1.0
CA A:GLY179 4.6 36.5 1.0
N A:SER180 4.7 38.1 1.0
CA A:ASP190 4.8 30.1 1.0
N A:ASP192 5.0 26.8 1.0

Magnesium binding site 2 out of 2 in 4pgq

Go back to Magnesium Binding Sites List in 4pgq
Magnesium binding site 2 out of 2 in the Structure of Human Dna Polymerase Beta Complexed with G in the Template Base Paired with Incoming Non-Hydrolyzable Ttp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Human Dna Polymerase Beta Complexed with G in the Template Base Paired with Incoming Non-Hydrolyzable Ttp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:37.1
occ:1.00
 O1A A:1FZ404 2.3 39.9 1.0
OD2 A:ASP190 2.4 35.0 1.0
O A:HOH536 2.4 29.3 1.0
OD2 A:ASP192 2.5 31.2 1.0
O3' P:DA10 2.5 32.2 1.0
CG A:ASP190 3.3 31.3 1.0
PA A:1FZ404 3.3 42.7 1.0
C3' P:DA10 3.3 33.3 1.0
MG A:MG400 3.3 19.3 1.0
CG A:ASP192 3.4 35.7 1.0
OD1 A:ASP190 3.5 33.3 1.0
O2A A:1FZ404 3.5 45.7 1.0
OD1 A:ASP192 3.6 32.5 1.0
O A:HOH558 3.8 28.7 1.0
O5' A:1FZ404 4.0 42.8 1.0
C4' P:DA10 4.1 31.2 1.0
O A:HOH559 4.1 42.2 1.0
O1G A:1FZ404 4.4 40.9 1.0
CB A:ASP190 4.6 30.4 1.0
O A:HOH579 4.6 42.2 1.0
C5' A:1FZ404 4.7 48.4 1.0
OD2 A:ASP256 4.7 29.8 1.0
C2' P:DA10 4.7 34.0 1.0
N3A A:1FZ404 4.7 41.4 1.0
O2B A:1FZ404 4.7 37.9 1.0
CB A:ASP192 4.7 28.1 1.0
C5' P:DA10 4.8 27.9 1.0

Reference:

M.C.Koag, K.Nam, S.Lee. The Spontaneous Replication Error and the Mismatch Discrimination Mechanisms of Human Dna Polymerase Beta. Nucleic Acids Res. V. 42 11233 2015.
ISSN: ESSN 1362-4962
PubMed: 25200079
DOI: 10.1093/NAR/GKU789
Page generated: Mon Aug 11 21:53:57 2025

Last articles

Mg in 5IT9
Mg in 5IVG
Mg in 5IUL
Mg in 5IUM
Mg in 5IRP
Mg in 5IUK
Mg in 5IUJ
Mg in 5IUC
Mg in 5IU0
Mg in 5IT5
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy