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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

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