Atomistry » Magnesium » PDB 6dw5-6e80 » 6e3x
Atomistry »
  Magnesium »
    PDB 6dw5-6e80 »
      6e3x »

Magnesium in PDB 6e3x: Structure of Human Dna Polymerase Beta Complexed with 8OA in the Template Base Paired with Incoming Non-Hydrolyzable Atp

Enzymatic activity of Structure of Human Dna Polymerase Beta Complexed with 8OA in the Template Base Paired with Incoming Non-Hydrolyzable Atp

All present enzymatic activity of Structure of Human Dna Polymerase Beta Complexed with 8OA in the Template Base Paired with Incoming Non-Hydrolyzable Atp:
2.7.7.7;

Protein crystallography data

The structure of Structure of Human Dna Polymerase Beta Complexed with 8OA in the Template Base Paired with Incoming Non-Hydrolyzable Atp, PDB code: 6e3x 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) 19.74 / 2.65
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.964, 78.948, 54.823, 90.00, 106.53, 90.00
R / Rfree (%) 19.2 / 26.6

Other elements in 6e3x:

The structure of Structure of Human Dna Polymerase Beta Complexed with 8OA in the Template Base Paired with Incoming Non-Hydrolyzable Atp 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 8OA in the Template Base Paired with Incoming Non-Hydrolyzable Atp (pdb code 6e3x). 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 8OA in the Template Base Paired with Incoming Non-Hydrolyzable Atp, PDB code: 6e3x:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 6e3x

Go back to Magnesium Binding Sites List in 6e3x
Magnesium binding site 1 out of 2 in the Structure of Human Dna Polymerase Beta Complexed with 8OA in the Template Base Paired with Incoming Non-Hydrolyzable Atp


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 8OA in the Template Base Paired with Incoming Non-Hydrolyzable Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:8.1
occ:1.00
 O A:HOH507 1.9 22.4 1.0
OD1 A:ASP190 2.0 19.4 1.0
O2B A:DZ4405 2.0 27.2 1.0
O2A A:DZ4405 2.0 32.1 1.0
O1G A:DZ4405 2.0 28.3 1.0
OD2 A:ASP192 2.1 24.1 1.0
CG A:ASP190 3.1 20.1 1.0
CG A:ASP192 3.2 26.3 1.0
PB A:DZ4405 3.2 28.2 1.0
PG A:DZ4405 3.2 29.7 1.0
PA A:DZ4405 3.3 33.2 1.0
OD2 A:ASP190 3.6 23.5 1.0
OD1 A:ASP192 3.6 29.0 1.0
O3B A:DZ4405 3.7 27.9 1.0
MG A:MG404 3.8 28.3 1.0
N3A A:DZ4405 3.8 28.6 1.0
O A:ASP190 3.9 22.4 1.0
O2G A:DZ4405 4.0 31.1 1.0
C5' A:DZ4405 4.2 31.4 1.0
O5' A:DZ4405 4.2 31.5 1.0
N A:ASP190 4.3 22.1 1.0
CA A:GLY179 4.3 22.9 1.0
C A:ASP190 4.3 22.8 1.0
O A:HOH508 4.4 22.8 1.0
N A:SER180 4.4 24.8 1.0
CB A:ASP190 4.4 19.1 1.0
CB A:ASP192 4.5 19.7 1.0
O1A A:DZ4405 4.5 32.6 1.0
CA A:ASP190 4.5 20.0 1.0
O3G A:DZ4405 4.6 29.5 1.0
OG A:SER180 4.6 27.5 1.0
O1B A:DZ4405 4.6 25.5 1.0
N A:ASP192 4.9 20.1 1.0
C A:GLY179 4.9 23.8 1.0

Magnesium binding site 2 out of 2 in 6e3x

Go back to Magnesium Binding Sites List in 6e3x
Magnesium binding site 2 out of 2 in the Structure of Human Dna Polymerase Beta Complexed with 8OA in the Template Base Paired with Incoming Non-Hydrolyzable Atp


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 8OA in the Template Base Paired with Incoming Non-Hydrolyzable Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg404

b:28.3
occ:1.00
 OD1 A:ASP192 2.1 29.0 1.0
O3' P:DA10 2.4 28.5 1.0
OD2 A:ASP190 2.4 23.5 1.0
O2A A:DZ4405 2.6 32.1 1.0
CG A:ASP192 3.1 26.3 1.0
CG A:ASP190 3.4 20.1 1.0
PA A:DZ4405 3.4 33.2 1.0
O A:HOH511 3.5 30.6 1.0
OD2 A:ASP192 3.5 24.1 1.0
O1A A:DZ4405 3.6 32.6 1.0
OD1 A:ASP190 3.6 19.4 1.0
O5' A:DZ4405 3.6 31.5 1.0
C3' P:DA10 3.7 33.8 1.0
MG A:MG403 3.8 8.1 1.0
C4' P:DA10 4.2 28.1 1.0
C5' A:DZ4405 4.2 31.4 1.0
OD2 A:ASP256 4.3 31.6 1.0
CB A:ASP192 4.4 19.7 1.0
C5' P:DA10 4.7 25.7 1.0
CB A:ASP190 4.7 19.1 1.0
C2' P:DA10 4.8 29.0 1.0
CG A:ASP256 4.9 25.4 1.0
O1G A:DZ4405 4.9 28.3 1.0
O2B A:DZ4405 4.9 27.2 1.0

Reference:

M.-C.Koag, S.Lee. Structure of Human Dna Polymerase Beta Complexed with 8OA in the Template Base Paired with Incoming Non-Hydrolyzable Atp To Be Published.
Page generated: Mon Sep 30 23:48:40 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy