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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

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