Atomistry » Sodium » PDB 6tos-6u6b » 6u2o
Atomistry »
  Sodium »
    PDB 6tos-6u6b »
      6u2o »

Sodium in PDB 6u2o: Structure of Human Dna Polymerase Beta Misinserting Dampnpp Opposite the 5'G of the Cisplatin Pt-Gg Intrastrand Crosslink

Enzymatic activity of Structure of Human Dna Polymerase Beta Misinserting Dampnpp Opposite the 5'G of the Cisplatin Pt-Gg Intrastrand Crosslink

All present enzymatic activity of Structure of Human Dna Polymerase Beta Misinserting Dampnpp Opposite the 5'G of the Cisplatin Pt-Gg Intrastrand Crosslink:
2.7.7.7;

Protein crystallography data

The structure of Structure of Human Dna Polymerase Beta Misinserting Dampnpp Opposite the 5'G of the Cisplatin Pt-Gg Intrastrand Crosslink, PDB code: 6u2o was solved by H.Ouzon-Shubeita, C.K.Vilas, S.Lee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.52 / 2.30
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 53.990, 79.184, 54.587, 90.00, 107.60, 90.00
R / Rfree (%) 20.1 / 24.8

Other elements in 6u2o:

The structure of Structure of Human Dna Polymerase Beta Misinserting Dampnpp Opposite the 5'G of the Cisplatin Pt-Gg Intrastrand Crosslink also contains other interesting chemical elements:

Magnesium (Mg) 1 atom
Platinum (Pt) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of Human Dna Polymerase Beta Misinserting Dampnpp Opposite the 5'G of the Cisplatin Pt-Gg Intrastrand Crosslink (pdb code 6u2o). 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 Misinserting Dampnpp Opposite the 5'G of the Cisplatin Pt-Gg Intrastrand Crosslink, PDB code: 6u2o:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 6u2o

Go back to Sodium Binding Sites List in 6u2o
Sodium binding site 1 out of 2 in the Structure of Human Dna Polymerase Beta Misinserting Dampnpp Opposite the 5'G of the Cisplatin Pt-Gg Intrastrand Crosslink


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 Misinserting Dampnpp Opposite the 5'G of the Cisplatin Pt-Gg Intrastrand Crosslink within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na402

b:24.4
occ:1.00
 O A:THR101 2.0 29.4 1.0
O P:HOH106 2.3 26.0 1.0
OP1 P:DG9 2.3 27.9 1.0
O A:ILE106 2.3 25.0 1.0
O A:VAL103 2.6 27.8 1.0
C A:THR101 3.1 26.2 1.0
C A:ILE106 3.4 23.2 1.0
C A:VAL103 3.5 26.5 1.0
P P:DG9 3.5 26.6 1.0
OP2 P:DG9 3.7 27.2 1.0
CA A:THR101 3.8 24.6 1.0
N A:ILE106 3.9 25.8 1.0
N A:GLY105 4.0 23.8 1.0
N A:SER104 4.0 26.2 1.0
CA A:SER104 4.1 25.2 1.0
N A:VAL103 4.1 25.1 1.0
CA A:ILE106 4.2 23.8 1.0
C A:ARG102 4.2 24.9 1.0
N A:ARG102 4.2 28.7 1.0
CB A:THR101 4.3 23.9 1.0
N A:GLY107 4.3 23.9 1.0
C A:SER104 4.4 23.9 1.0
O3' P:DG8 4.4 24.3 1.0
CA A:VAL103 4.5 25.1 1.0
CA A:ARG102 4.5 26.1 1.0
O A:ARG102 4.5 24.0 1.0
CA A:GLY107 4.6 25.0 1.0
CB A:ILE106 4.6 21.9 1.0
O5' P:DG9 4.7 24.7 1.0
O A:HOH519 4.7 29.4 1.0
C A:GLY105 4.7 26.5 1.0
O A:LEU100 4.8 25.8 1.0
CA A:GLY105 4.9 26.3 1.0

Sodium binding site 2 out of 2 in 6u2o

Go back to Sodium Binding Sites List in 6u2o
Sodium binding site 2 out of 2 in the Structure of Human Dna Polymerase Beta Misinserting Dampnpp Opposite the 5'G of the Cisplatin Pt-Gg Intrastrand Crosslink


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 Misinserting Dampnpp Opposite the 5'G of the Cisplatin Pt-Gg Intrastrand Crosslink within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na101

b:46.4
occ:1.00
 O A:VAL65 2.7 37.8 1.0
O A:LYS60 2.9 57.6 1.0
O A:HOH537 3.0 46.1 1.0
OP1 D:DG3 3.0 39.1 1.0
OP2 D:DG3 3.0 35.1 1.0
P D:DG3 3.5 41.3 1.0
C A:VAL65 3.9 34.1 1.0
O A:LEU62 3.9 57.4 1.0
C A:LYS60 4.1 52.5 1.0
CG A:LYS60 4.1 52.9 1.0
CA A:GLY66 4.5 31.9 1.0
O3' D:DT2 4.6 38.4 1.0
N A:GLY66 4.6 33.2 1.0
CA A:LYS60 4.7 50.1 1.0
O5' D:DG3 4.7 39.5 1.0
NZ A:LYS60 4.9 56.1 1.0
N A:VAL65 4.9 35.7 1.0
C A:LEU62 4.9 53.4 1.0
CA A:VAL65 4.9 34.5 1.0
CB A:LYS60 5.0 50.6 1.0

Reference:

H.Ouzon-Shubeita, C.K.Vilas, S.Lee. Structures of the Mutagenic Bypass of the Major Cisplatin-Dna Lesion By Human Dna Polymerase Beta Reveal Insights Into Cisplatin-Induced Mutagenesis To Be Published.
Page generated: Tue Dec 15 14:28:54 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy