Atomistry » Magnesium » PDB 4nbm-4nlz » 4nlk
Atomistry »
  Magnesium »
    PDB 4nbm-4nlz »
      4nlk »

Magnesium in PDB 4nlk: Structure of Human Dna Polymerase Beta Complexed with 8BRG in the Template Base-Paired with Incoming Non-Hydrolyzable Ctp

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

All present enzymatic activity of Structure of Human Dna Polymerase Beta Complexed with 8BRG 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 8BRG in the Template Base-Paired with Incoming Non-Hydrolyzable Ctp, PDB code: 4nlk was solved by M.-C.Koag, K.Min, A.F.Monzingo, S.Lee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 53.01 / 2.49
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.807, 79.706, 55.683, 90.00, 107.83, 90.00
R / Rfree (%) 19.4 / 27

Other elements in 4nlk:

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

Bromine (Br) 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 8BRG in the Template Base-Paired with Incoming Non-Hydrolyzable Ctp (pdb code 4nlk). 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 8BRG in the Template Base-Paired with Incoming Non-Hydrolyzable Ctp, PDB code: 4nlk:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 4nlk

Go back to Magnesium Binding Sites List in 4nlk
Magnesium binding site 1 out of 2 in the Structure of Human Dna Polymerase Beta Complexed with 8BRG 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 8BRG in the Template Base-Paired with Incoming Non-Hydrolyzable Ctp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:17.6
occ:1.00
 O2G A:0KX405 1.9 21.9 1.0
OD1 A:ASP190 1.9 18.2 1.0
O2A A:0KX405 2.0 22.0 1.0
O1B A:0KX405 2.0 21.9 1.0
OD2 A:ASP192 2.0 22.6 1.0
O A:HOH502 2.4 19.5 1.0
PB A:0KX405 3.0 23.4 1.0
CG A:ASP190 3.0 20.0 1.0
CG A:ASP192 3.0 21.7 1.0
PA A:0KX405 3.2 23.6 1.0
OD1 A:ASP192 3.3 23.8 1.0
MG A:MG402 3.4 31.6 1.0
PG A:0KX405 3.4 21.8 1.0
OD2 A:ASP190 3.4 20.6 1.0
N3A A:0KX405 3.5 23.2 1.0
O3B A:0KX405 3.7 21.1 1.0
C5' A:0KX405 4.0 20.9 1.0
O A:ASP190 4.1 23.1 1.0
O5' A:0KX405 4.1 23.5 1.0
O A:HOH549 4.2 26.9 1.0
O1G A:0KX405 4.2 21.1 1.0
CB A:ASP190 4.3 20.3 1.0
O3G A:0KX405 4.3 22.6 1.0
CA A:GLY179 4.4 19.7 1.0
O2B A:0KX405 4.4 22.9 1.0
CB A:ASP192 4.4 20.7 1.0
C A:ASP190 4.4 22.0 1.0
N A:SER180 4.4 20.7 1.0
OG A:SER180 4.5 22.7 1.0
O1A A:0KX405 4.5 23.0 1.0
N A:ASP190 4.6 21.1 1.0
CA A:ASP190 4.7 20.6 1.0
N A:ASP192 4.9 22.3 1.0
C A:GLY179 4.9 20.5 1.0
N A:MET191 5.0 22.0 1.0

Magnesium binding site 2 out of 2 in 4nlk

Go back to Magnesium Binding Sites List in 4nlk
Magnesium binding site 2 out of 2 in the Structure of Human Dna Polymerase Beta Complexed with 8BRG 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 8BRG in the Template Base-Paired with Incoming Non-Hydrolyzable Ctp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:31.6
occ:1.00
 OD2 A:ASP190 2.0 20.6 1.0
O2A A:0KX405 2.2 22.0 1.0
OD2 A:ASP256 2.3 24.9 1.0
OD1 A:ASP192 2.4 23.8 1.0
O3' P:DA10 2.6 29.5 1.0
CG A:ASP190 2.9 20.0 1.0
PA A:0KX405 3.1 23.6 1.0
OD1 A:ASP190 3.2 18.2 1.0
CG A:ASP192 3.4 21.7 1.0
MG A:MG401 3.4 17.6 1.0
O5' A:0KX405 3.5 23.5 1.0
CG A:ASP256 3.5 24.8 1.0
OD2 A:ASP192 3.6 22.6 1.0
C3' P:DA10 3.6 27.7 1.0
O1A A:0KX405 3.7 23.0 1.0
C5' A:0KX405 3.9 20.9 1.0
CB A:ASP190 4.3 20.3 1.0
OP1 P:DA10 4.3 29.1 1.0
CB A:ASP256 4.3 22.5 1.0
OD1 A:ASP256 4.5 25.2 1.0
C4' P:DA10 4.5 27.2 1.0
O2G A:0KX405 4.6 21.9 1.0
O5' P:DA10 4.7 24.8 1.0
N3A A:0KX405 4.7 23.2 1.0
C5' P:DA10 4.7 26.7 1.0
CB A:ASP192 4.7 20.7 1.0
O1B A:0KX405 4.8 21.9 1.0
C2' P:DA10 4.8 27.6 1.0
O A:MET191 4.8 25.1 1.0
O A:HOH552 4.9 32.9 1.0

Reference:

M.C.Koag, K.Min, S.Lee. Structural Basis For Promutagenicity of 8-Halogenated Guanine. J.Biol.Chem. V. 289 6289 2014.
ISSN: ISSN 0021-9258
PubMed: 24425881
DOI: 10.1074/JBC.M113.537803
Page generated: Mon Aug 19 23:39:27 2024

Last articles

Cl in 7PJM
Cl in 7PJC
Cl in 7PI0
Cl in 7PIH
Cl in 7PIG
Cl in 7PHZ
Cl in 7PIF
Cl in 7PFH
Cl in 7PFJ
Cl in 7PFK
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy