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Magnesium in PDB 6cpq: Structure of Human Dna Polymerase Beta Complexed with 8-Clg in the Template Base Paired with Incoming Non-Hydrolyzable Ctp

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

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

Protein crystallography data

The structure of Structure of Human Dna Polymerase Beta Complexed with 8-Clg in the Template Base Paired with Incoming Non-Hydrolyzable Ctp, PDB code: 6cpq 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) 19.85 / 1.93
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.829, 80.243, 55.836, 90.00, 107.80, 90.00
R / Rfree (%) 19.1 / 23.9

Other elements in 6cpq:

The structure of Structure of Human Dna Polymerase Beta Complexed with 8-Clg in the Template Base Paired with Incoming Non-Hydrolyzable Ctp also contains other interesting chemical elements:

Chlorine (Cl) 1 atom
Sodium (Na) 2 atoms

Magnesium Binding Sites:

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

Magnesium binding site 1 out of 2 in 6cpq

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


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 8-Clg in the Template Base Paired with Incoming Non-Hydrolyzable Ctp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:11.5
occ:1.00
 OD2 A:ASP192 2.0 14.2 1.0
O1B A:0KX405 2.0 10.6 1.0
OD1 A:ASP190 2.0 14.1 1.0
O1G A:0KX405 2.0 13.0 1.0
O A:HOH569 2.0 11.8 1.0
O2A A:0KX405 2.0 13.7 1.0
CG A:ASP192 3.0 14.8 1.0
PB A:0KX405 3.1 14.8 1.0
CG A:ASP190 3.1 15.9 1.0
PA A:0KX405 3.3 15.2 1.0
PG A:0KX405 3.4 15.4 1.0
OD1 A:ASP192 3.4 13.6 1.0
MG A:MG402 3.5 14.3 1.0
OD2 A:ASP190 3.6 24.1 1.0
O3B A:0KX405 3.6 13.4 1.0
N3A A:0KX405 3.6 12.2 1.0
O A:ASP190 4.0 13.8 1.0
O2G A:0KX405 4.0 13.6 1.0
O A:HOH681 4.1 26.2 1.0
O5' A:0KX405 4.3 15.7 1.0
C5' A:0KX405 4.3 15.3 1.0
C A:ASP190 4.3 13.4 1.0
O A:HOH595 4.3 13.8 1.0
OG A:SER180 4.3 13.7 1.0
CB A:ASP192 4.4 14.1 1.0
N A:ASP190 4.4 13.2 1.0
CB A:ASP190 4.4 14.7 1.0
N A:SER180 4.4 13.6 1.0
O1A A:0KX405 4.4 17.8 1.0
CA A:GLY179 4.5 13.3 1.0
O2B A:0KX405 4.5 13.6 1.0
O3G A:0KX405 4.5 19.0 1.0
CA A:ASP190 4.6 13.5 1.0
O A:HOH582 4.8 21.8 1.0
N A:ASP192 4.8 13.4 1.0
N A:MET191 4.9 12.6 1.0
C A:MET191 5.0 13.5 1.0

Magnesium binding site 2 out of 2 in 6cpq

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


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 8-Clg in the Template Base Paired with Incoming Non-Hydrolyzable Ctp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:14.3
occ:1.00
 OD1 A:ASP192 2.1 13.6 1.0
OD2 A:ASP190 2.2 24.1 1.0
O A:HOH582 2.3 21.8 1.0
OD2 A:ASP256 2.4 19.0 1.0
O2A A:0KX405 2.4 13.7 1.0
CG A:ASP190 3.0 15.9 1.0
OD1 A:ASP190 3.1 14.1 1.0
CG A:ASP192 3.1 14.8 1.0
O3' P:DA10 3.3 24.7 1.0
PA A:0KX405 3.4 15.2 1.0
OD2 A:ASP192 3.5 14.2 1.0
MG A:MG401 3.5 11.5 1.0
CG A:ASP256 3.5 19.1 1.0
C3' P:DA10 3.5 19.0 1.0
O5' A:0KX405 3.9 15.7 1.0
O1A A:0KX405 3.9 17.8 1.0
C5' A:0KX405 4.1 15.3 1.0
CB A:ASP256 4.1 17.7 1.0
O A:HOH681 4.2 26.2 1.0
CB A:ASP190 4.3 14.7 1.0
CB A:ASP192 4.5 14.1 1.0
OD1 A:ASP256 4.5 19.1 1.0
O A:HOH696 4.5 25.3 1.0
O1G A:0KX405 4.6 13.0 1.0
C4' P:DA10 4.6 19.9 1.0
C2' P:DA10 4.6 17.9 1.0
OP1 P:DA10 4.6 17.8 1.0
O A:MET191 4.6 13.1 1.0
C5' P:DA10 4.8 21.0 1.0
O5' P:DA10 4.8 16.5 1.0
NH2 A:ARG254 4.8 18.2 1.0
O1B A:0KX405 4.9 10.6 1.0
CA A:ASP192 5.0 11.7 1.0
C A:MET191 5.0 13.5 1.0

Reference:

M.-C.Koag, S.Lee. Structure of Human Dna Polymerase Beta Complexed with 8-Clg in the Template Base Paired with Incoming Non-Hydrolyzable Ctp To Be Published.
Page generated: Mon Sep 30 22:28:28 2024

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