Atomistry » Sodium » PDB 4njk-4nwh » 4nm2
Atomistry »
  Sodium »
    PDB 4njk-4nwh »
      4nm2 »

Sodium in PDB 4nm2: Structure of Human Dna Polymerase Beta Complexed with A Nicked Dna Containing A 8BRG-G 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-G 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-G 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-G at N-1 Position and G-C at N Position, PDB code: 4nm2 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) 52.81 / 2.52
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.731, 80.202, 55.109, 90.00, 106.60, 90.00
R / Rfree (%) 20 / 27.7

Other elements in 4nm2:

The structure of Structure of Human Dna Polymerase Beta Complexed with A Nicked Dna Containing A 8BRG-G at N-1 Position and G-C at N Position also contains other interesting chemical elements:

Bromine (Br) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of Human Dna Polymerase Beta Complexed with A Nicked Dna Containing A 8BRG-G at N-1 Position and G-C at N Position (pdb code 4nm2). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Structure of Human Dna Polymerase Beta Complexed with A Nicked Dna Containing A 8BRG-G at N-1 Position and G-C at N Position, PDB code: 4nm2:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 4nm2

Go back to Sodium Binding Sites List in 4nm2
Sodium binding site 1 out of 2 in the Structure of Human Dna Polymerase Beta Complexed with A Nicked Dna Containing A 8BRG-G at N-1 Position and G-C at N Position


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Human Dna Polymerase Beta Complexed with A Nicked Dna Containing A 8BRG-G at N-1 Position and G-C at N Position within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na401

b:44.1
occ:1.00
O A:THR101 2.9 32.8 1.0
NA A:NA402 3.5 32.9 1.0
C A:THR101 3.8 30.0 1.0
CA A:ARG102 4.2 30.8 1.0
N A:ARG102 4.4 29.7 1.0
OG1 A:THR101 4.6 25.2 1.0
C A:ARG102 4.7 33.1 1.0
O A:ARG102 4.7 34.3 1.0
NZ A:LYS27 4.7 37.1 1.0
CB A:THR101 4.9 26.2 1.0
OP2 P:DG9 4.9 29.3 1.0
OP1 P:DG9 4.9 30.0 1.0
CA A:THR101 5.0 28.3 1.0

Sodium binding site 2 out of 2 in 4nm2

Go back to Sodium Binding Sites List in 4nm2
Sodium binding site 2 out of 2 in the Structure of Human Dna Polymerase Beta Complexed with A Nicked Dna Containing A 8BRG-G at N-1 Position and G-C at N Position


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of Human Dna Polymerase Beta Complexed with A Nicked Dna Containing A 8BRG-G at N-1 Position and G-C at N Position within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na402

b:32.9
occ:1.00
O A:THR101 2.2 32.8 1.0
OP1 P:DG9 2.3 30.0 1.0
O A:ILE106 2.3 27.1 1.0
O A:VAL103 2.5 32.8 1.0
C A:THR101 3.2 30.0 1.0
C A:ILE106 3.3 26.9 1.0
C A:VAL103 3.4 30.6 1.0
P P:DG9 3.4 30.3 1.0
NA A:NA401 3.5 44.1 1.0
N A:ILE106 3.7 25.5 1.0
OP2 P:DG9 3.7 29.3 1.0
CA A:SER104 3.8 25.8 1.0
N A:GLY105 3.8 25.5 1.0
CA A:THR101 3.9 28.3 1.0
N A:SER104 4.0 28.1 1.0
CA A:ILE106 4.0 26.3 1.0
N A:VAL103 4.1 30.7 1.0
C A:SER104 4.2 25.7 1.0
C A:ARG102 4.2 33.1 1.0
N A:GLY107 4.3 28.3 1.0
N A:ARG102 4.3 29.7 1.0
CA A:VAL103 4.4 30.0 1.0
CB A:ILE106 4.5 26.3 1.0
O5' P:DG9 4.5 33.4 1.0
O3' P:DC8 4.5 29.7 1.0
CB A:THR101 4.5 26.2 1.0
CA A:ARG102 4.5 30.8 1.0
CA A:GLY107 4.6 29.4 1.0
C A:GLY105 4.6 26.3 1.0
O A:ARG102 4.6 34.3 1.0
CA A:GLY105 4.7 24.6 1.0
O A:LEU100 4.9 35.2 1.0
CB A:SER104 5.0 25.2 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 Oct 7 17:16:15 2024

Last articles

Fe in 5XTE
Fe in 5XNM
Fe in 5XNL
Fe in 5XNT
Fe in 5XNH
Fe in 5XFA
Fe in 5XF9
Fe in 5XNF
Fe in 5XNC
Fe in 5XLH
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy