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 Dec 14 22:37:55 2020

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