Atomistry » Magnesium » PDB 4nlz-4nxm » 4nm1
Atomistry »
  Magnesium »
    PDB 4nlz-4nxm »
      4nm1 »

Magnesium in PDB 4nm1: Structure of Human Dna Polymerase Beta Complexed with A Nicked Dna Containing A 8BRG-C at N-1 Position and G-C at N Position

Enzymatic activity of Structure of Human Dna Polymerase Beta Complexed with A Nicked Dna Containing A 8BRG-C at N-1 Position and G-C at N Position

All present enzymatic activity of Structure of Human Dna Polymerase Beta Complexed with A Nicked Dna Containing A 8BRG-C at N-1 Position and G-C at N Position:
2.7.7.7;

Protein crystallography data

The structure of Structure of Human Dna Polymerase Beta Complexed with A Nicked Dna Containing A 8BRG-C at N-1 Position and G-C at N Position, PDB code: 4nm1 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) 52.71 / 2.42
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.749, 80.114, 55.272, 90.00, 107.52, 90.00
R / Rfree (%) 19.8 / 25.6

Other elements in 4nm1:

The structure of Structure of Human Dna Polymerase Beta Complexed with A Nicked Dna Containing A 8BRG-C at N-1 Position and G-C at N Position 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 A Nicked Dna Containing A 8BRG-C at N-1 Position and G-C at N Position (pdb code 4nm1). 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 A Nicked Dna Containing A 8BRG-C at N-1 Position and G-C at N Position, PDB code: 4nm1:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 4nm1

Go back to Magnesium Binding Sites List in 4nm1
Magnesium binding site 1 out of 2 in the Structure of Human Dna Polymerase Beta Complexed with A Nicked Dna Containing A 8BRG-C at N-1 Position and G-C at N Position


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 A Nicked Dna Containing A 8BRG-C at N-1 Position and G-C at N Position within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:48.5
occ:1.00
 OD1 A:ASP190 1.9 29.6 1.0
O2 P:PO4101 2.0 43.8 1.0
OD2 A:ASP192 2.4 21.5 1.0
O A:HOH569 2.5 31.5 1.0
OP1 P:DC11 2.6 27.9 1.0
P P:PO4101 3.1 44.9 1.0
CG A:ASP190 3.1 28.7 1.0
O A:ASP190 3.3 22.8 1.0
O4 P:PO4101 3.3 47.1 1.0
CG A:ASP192 3.5 21.2 1.0
O3 P:PO4101 3.5 44.0 1.0
N A:ASP190 3.7 21.1 1.0
C A:ASP190 3.7 22.1 1.0
OD1 A:ASP192 3.8 23.0 1.0
OD2 A:ASP190 3.8 32.6 1.0
P P:DC11 4.0 31.0 1.0
CA A:ASP190 4.1 23.1 1.0
CB A:ASP190 4.2 25.9 1.0
O A:HOH568 4.3 15.8 1.0
MG A:MG402 4.3 46.1 1.0
O1 P:PO4101 4.4 37.0 1.0
O5' P:DC11 4.5 29.2 1.0
OG A:SER180 4.6 16.6 1.0
N A:MET191 4.6 20.8 1.0
N A:SER180 4.7 16.6 1.0
C5' P:DC11 4.7 22.7 1.0
CB A:ASP192 4.7 19.7 1.0
N A:GLY189 4.7 21.5 1.0
C A:GLY189 4.7 21.1 1.0
CA A:GLY179 4.7 16.2 1.0
N A:ASP192 4.9 20.6 1.0
OP2 P:DC11 4.9 31.2 1.0
O P:HOH205 4.9 14.8 1.0
O3' P:DC10 4.9 29.5 1.0

Magnesium binding site 2 out of 2 in 4nm1

Go back to Magnesium Binding Sites List in 4nm1
Magnesium binding site 2 out of 2 in the Structure of Human Dna Polymerase Beta Complexed with A Nicked Dna Containing A 8BRG-C at N-1 Position and G-C at N Position


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 A Nicked Dna Containing A 8BRG-C at N-1 Position and G-C at N Position within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:46.1
occ:1.00
 OD2 A:ASP190 2.1 32.6 1.0
OD2 A:ASP256 2.3 19.6 1.0
OD1 A:ASP192 2.6 23.0 1.0
CG A:ASP190 2.7 28.7 1.0
OD1 A:ASP190 3.1 29.6 1.0
CG A:ASP256 3.2 19.7 1.0
O3' P:DC10 3.5 29.5 1.0
OP1 P:DC11 3.5 27.9 1.0
CB A:ASP256 3.6 19.7 1.0
CB A:ASP190 3.7 25.9 1.0
CG A:ASP192 3.7 21.2 1.0
C5' P:DC10 4.1 24.1 1.0
P P:DC11 4.1 31.0 1.0
OD1 A:ASP256 4.1 20.9 1.0
O A:MET191 4.1 20.9 1.0
OD2 A:ASP192 4.1 21.5 1.0
NH2 A:ARG254 4.2 13.3 1.0
C4' P:DC10 4.2 26.4 1.0
MG A:MG401 4.3 48.5 1.0
C3' P:DC10 4.4 27.6 1.0
N A:ASP256 4.5 15.9 1.0
CZ A:ARG254 4.6 13.4 1.0
C A:MET191 4.6 20.4 1.0
CA A:ASP256 4.7 17.3 1.0
N A:MET191 4.7 20.8 1.0
NH1 A:ARG254 4.7 13.2 1.0
O A:ARG254 4.8 14.1 1.0
C A:ILE255 4.8 15.2 1.0
CA A:ASP190 4.8 23.1 1.0
C A:ASP190 4.8 22.1 1.0
OP1 P:DC10 4.8 23.0 1.0
CB A:ASP192 4.9 19.7 1.0
CB A:ARG254 4.9 13.0 1.0
OP2 P:DC11 5.0 31.2 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 23:43:31 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