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

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

All present enzymatic activity of Structure of Human Dna Polymerase Beta Complexed with 8-Clg in the Template Base Paired with Incoming Non-Hydrolyzable Gtp:
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 Gtp, PDB code: 6crh 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) 19.91 / 2.33
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.985, 79.622, 55.179, 90.00, 107.88, 90.00
R / Rfree (%) 19.7 / 24.4

Other elements in 6crh:

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

Magnesium binding site 1 out of 2 in 6crh

Go back to Magnesium Binding Sites List in 6crh
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 Gtp


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 Gtp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:39.8
occ:1.00
 O1A A:XG4405 1.9 40.7 1.0
O A:HOH528 1.9 44.4 1.0
O A:HOH535 2.1 35.0 1.0
O1B A:XG4405 2.1 39.9 1.0
O2G A:XG4405 2.2 44.0 1.0
OD1 A:ASP190 2.2 32.7 1.0
PA A:XG4405 3.1 45.3 1.0
PB A:XG4405 3.1 33.5 1.0
PG A:XG4405 3.2 39.3 1.0
CG A:ASP190 3.3 31.9 1.0
OD1 A:ASP192 3.3 35.9 1.0
O3B A:XG4405 3.6 40.5 1.0
MG A:MG402 3.6 41.6 1.0
N3A A:XG4405 3.7 42.2 1.0
OD2 A:ASP190 3.8 37.2 1.0
O1G A:XG4405 3.8 38.5 1.0
OG A:SER180 4.0 35.8 1.0
O A:ASP190 4.1 30.3 1.0
O5' A:XG4405 4.1 40.2 1.0
N A:SER180 4.1 35.8 1.0
O A:HOH522 4.1 26.6 1.0
CA A:GLY179 4.2 38.1 1.0
C A:ASP190 4.3 29.2 1.0
O2A A:XG4405 4.3 41.9 1.0
CG A:ASP192 4.4 46.0 1.0
C5' A:XG4405 4.4 45.0 1.0
N A:ASP190 4.4 30.0 1.0
CB A:ASP190 4.6 28.3 1.0
O2B A:XG4405 4.6 42.2 1.0
O3G A:XG4405 4.6 45.7 1.0
CA A:ASP190 4.7 28.4 1.0
O A:HOH547 4.7 40.2 1.0
N A:ASP192 4.7 31.1 1.0
CB A:ASP192 4.7 33.5 1.0
C A:GLY179 4.7 35.2 1.0
N A:MET191 4.8 26.9 1.0
CB A:SER180 4.9 35.3 1.0
C A:MET191 5.0 27.4 1.0

Magnesium binding site 2 out of 2 in 6crh

Go back to Magnesium Binding Sites List in 6crh
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 Gtp


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 Gtp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:41.6
occ:1.00
 O A:HOH509 2.1 44.1 1.0
OD1 A:ASP192 2.2 35.9 1.0
OD2 A:ASP190 2.3 37.2 1.0
O1A A:XG4405 2.5 40.7 1.0
O A:HOH548 2.6 36.3 1.0
CG A:ASP190 2.8 31.9 1.0
OD1 A:ASP190 2.8 32.7 1.0
CG A:ASP192 3.2 46.0 1.0
PA A:XG4405 3.3 45.3 1.0
O2A A:XG4405 3.4 41.9 1.0
OD2 A:ASP192 3.6 42.2 1.0
MG A:MG401 3.6 39.8 1.0
O3' P:DA10 3.7 48.6 1.0
O5' A:XG4405 3.7 40.2 1.0
CB A:ASP190 4.1 28.3 1.0
O A:HOH528 4.1 44.4 1.0
O A:HOH547 4.1 40.2 1.0
OD2 A:ASP256 4.3 31.6 1.0
O2G A:XG4405 4.4 44.0 1.0
CG A:ASP256 4.5 30.9 1.0
CB A:ASP192 4.5 33.5 1.0
C3' P:DA10 4.6 43.8 1.0
C5' A:XG4405 4.7 45.0 1.0
O A:MET191 4.7 30.3 1.0
OD1 A:ASP256 4.8 34.3 1.0
C5' P:DA10 4.9 46.7 1.0
N3A A:XG4405 4.9 42.2 1.0
C A:MET191 4.9 27.4 1.0
CB A:ASP256 4.9 26.6 1.0
N A:ASP192 5.0 31.1 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 22:42:15 2024

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