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

Sodium in PDB 4nln: Structure of Human Dna Polymerase Beta Complexed with Nicked Dna Containing A Template 8BRG and Incoming Ctp

Enzymatic activity of Structure of Human Dna Polymerase Beta Complexed with Nicked Dna Containing A Template 8BRG and Incoming Ctp

All present enzymatic activity of Structure of Human Dna Polymerase Beta Complexed with Nicked Dna Containing A Template 8BRG and Incoming Ctp:
2.7.7.7;

Protein crystallography data

The structure of Structure of Human Dna Polymerase Beta Complexed with Nicked Dna Containing A Template 8BRG and Incoming Ctp, PDB code: 4nln 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) 52.67 / 2.26
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.955, 79.075, 54.912, 90.00, 106.59, 90.00
R / Rfree (%) 21 / 27.3

Other elements in 4nln:

The structure of Structure of Human Dna Polymerase Beta Complexed with Nicked Dna Containing A Template 8BRG and Incoming Ctp also contains other interesting chemical elements:

Bromine (Br) 1 atom
Magnesium (Mg) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of Human Dna Polymerase Beta Complexed with Nicked Dna Containing A Template 8BRG and Incoming Ctp (pdb code 4nln). 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 Nicked Dna Containing A Template 8BRG and Incoming Ctp, PDB code: 4nln:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 4nln

Go back to Sodium Binding Sites List in 4nln
Sodium binding site 1 out of 2 in the Structure of Human Dna Polymerase Beta Complexed with Nicked Dna Containing A Template 8BRG and Incoming Ctp


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 Nicked Dna Containing A Template 8BRG and Incoming Ctp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na402

b:23.5
occ:1.00
O A:THR101 2.2 27.2 1.0
OP1 P:DG9 2.4 24.7 1.0
O A:ILE106 2.4 19.8 1.0
O A:VAL103 2.6 24.1 1.0
C A:THR101 3.2 26.0 1.0
C A:VAL103 3.4 25.9 1.0
P P:DG9 3.5 28.3 1.0
C A:ILE106 3.5 21.7 1.0
OP2 P:DG9 3.6 26.1 1.0
N A:ILE106 3.8 22.4 1.0
CA A:THR101 3.9 24.6 1.0
N A:SER104 3.9 25.6 1.0
CA A:SER104 4.0 25.0 1.0
N A:GLY105 4.0 22.6 1.0
N A:VAL103 4.1 24.3 1.0
CA A:ILE106 4.2 20.0 1.0
N A:ARG102 4.3 24.6 1.0
C A:ARG102 4.3 26.4 1.0
CA A:VAL103 4.4 24.4 1.0
C A:SER104 4.4 22.4 1.0
N A:GLY107 4.4 25.4 1.0
CB A:THR101 4.4 24.4 1.0
O3' P:DC8 4.5 25.4 1.0
CA A:ARG102 4.5 25.3 1.0
CA A:GLY107 4.6 27.6 1.0
C A:GLY105 4.6 23.4 1.0
CB A:ILE106 4.7 20.0 1.0
O5' P:DG9 4.7 26.8 1.0
O A:ARG102 4.8 25.9 1.0
O A:LEU100 4.8 20.7 1.0
CA A:GLY105 4.9 23.0 1.0

Sodium binding site 2 out of 2 in 4nln

Go back to Sodium Binding Sites List in 4nln
Sodium binding site 2 out of 2 in the Structure of Human Dna Polymerase Beta Complexed with Nicked Dna Containing A Template 8BRG and Incoming Ctp


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 Nicked Dna Containing A Template 8BRG and Incoming Ctp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na403

b:41.7
occ:1.00
O A:LYS60 2.2 40.3 1.0
O A:LEU62 2.5 40.1 1.0
O A:VAL65 2.5 29.3 1.0
OP1 D:DC3 2.9 38.1 1.0
C A:LYS60 3.4 39.4 1.0
C A:LEU62 3.5 37.0 1.0
C A:VAL65 3.6 30.2 1.0
C A:LYS61 3.8 35.0 1.0
N A:LEU62 3.9 35.0 1.0
P D:DC3 3.9 30.7 1.0
OP2 D:DC3 3.9 27.5 1.0
N A:VAL65 3.9 33.3 1.0
O A:LYS61 4.1 38.8 1.0
CA A:VAL65 4.2 30.1 1.0
N A:GLY64 4.2 35.5 1.0
CA A:PRO63 4.2 37.2 1.0
N A:LYS61 4.3 39.2 1.0
N A:PRO63 4.3 35.1 1.0
CA A:LYS60 4.3 36.2 1.0
CA A:LYS61 4.3 37.0 1.0
CA A:LEU62 4.3 36.6 1.0
CB A:VAL65 4.5 32.0 1.0
C A:PRO63 4.7 38.6 1.0
CG A:LYS60 4.7 39.3 1.0
N A:GLY66 4.7 25.4 1.0
O3' D:DT2 4.8 28.9 1.0
NZ A:LYS60 4.8 29.1 1.0
O A:ALA59 4.9 37.0 1.0
C A:GLY64 4.9 35.8 1.0
CE A:LYS60 5.0 32.7 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 17:14:54 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