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Sodium in PDB 6u6b: Structure of Human Dna Polymerase Beta Misinserting Dampnpp Opposite the 5'G of the Cisplatin Pt-Gg Intrastrand Crosslink with Manganese in the Active Site

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

All present enzymatic activity of Structure of Human Dna Polymerase Beta Misinserting Dampnpp Opposite the 5'G of the Cisplatin Pt-Gg Intrastrand Crosslink with Manganese in the Active Site:
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 with Manganese in the Active Site, PDB code: 6u6b 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) 44.14 / 3.11
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 53.430, 78.216, 53.965, 90.00, 110.57, 90.00
R / Rfree (%) 22.2 / 26.8

Other elements in 6u6b:

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

Manganese (Mn) 2 atoms
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 with Manganese in the Active Site (pdb code 6u6b). 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 with Manganese in the Active Site, PDB code: 6u6b:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 6u6b

Go back to Sodium Binding Sites List in 6u6b
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 with Manganese in the Active Site


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 with Manganese in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na403

b:46.5
occ:1.00
 O A:THR101 2.6 41.8 1.0
OP1 P:DG9 3.3 46.3 1.0
HA A:ARG102 3.4 38.4 1.0
O A:VAL103 3.6 41.7 1.0
C A:THR101 3.7 39.6 1.0
HA A:SER104 3.7 36.8 1.0
O A:ARG102 4.0 37.4 1.0
C A:ARG102 4.0 34.1 1.0
CA A:ARG102 4.0 32.0 1.0
P P:DG9 4.2 29.2 1.0
C A:VAL103 4.2 38.4 1.0
OP2 P:DG9 4.3 39.6 1.0
N A:ARG102 4.3 34.9 1.0
O A:ILE106 4.5 40.3 1.0
HB A:THR101 4.6 56.1 1.0
O5' P:DG9 4.6 37.8 1.0
CA A:SER104 4.6 30.6 1.0
N A:VAL103 4.7 36.4 1.0
N A:SER104 4.7 42.5 1.0
H A:GLY105 4.8 37.2 1.0
CA A:THR101 4.9 41.1 1.0
HA A:THR101 4.9 49.4 1.0
H3' P:DG9 4.9 63.1 1.0

Sodium binding site 2 out of 2 in 6u6b

Go back to Sodium Binding Sites List in 6u6b
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 with Manganese in the Active Site


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 with Manganese in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na404

b:53.7
occ:1.00
 OP1 D:DG3 2.5 58.0 1.0
O A:LYS60 2.5 49.5 1.0
O A:LEU62 2.6 55.0 1.0
O A:VAL65 3.0 67.0 1.0
HA A:PRO63 3.2 71.1 1.0
H A:VAL65 3.4 63.4 1.0
C A:LEU62 3.5 50.6 1.0
H A:GLY64 3.7 66.2 1.0
C A:LYS60 3.7 48.8 1.0
P D:DG3 3.8 60.9 1.0
CA A:PRO63 3.9 59.2 1.0
C A:LYS61 4.0 57.4 1.0
C A:VAL65 4.1 60.6 1.0
HA A:LYS61 4.1 71.7 1.0
O A:LYS61 4.1 53.2 1.0
N A:VAL65 4.1 52.8 1.0
N A:GLY64 4.1 55.1 1.0
N A:PRO63 4.1 55.3 1.0
O5' D:DG3 4.1 62.5 1.0
N A:LEU62 4.2 56.0 1.0
HB A:VAL65 4.2 74.4 1.0
HG2 A:LYS60 4.4 62.2 1.0
C A:PRO63 4.4 54.1 1.0
CA A:LYS61 4.4 59.8 1.0
HA A:LYS60 4.4 64.5 1.0
CA A:LEU62 4.5 44.8 1.0
H A:LEU62 4.5 67.2 1.0
N A:LYS61 4.5 47.1 1.0
CA A:VAL65 4.6 56.0 1.0
OP2 D:DG3 4.6 67.2 1.0
HA2 A:GLY66 4.7 60.6 1.0
CA A:LYS60 4.7 53.8 1.0
H5'' D:DG3 4.7 73.1 1.0
O3' D:DT2 4.9 64.6 1.0
CB A:VAL65 4.9 62.0 1.0
C A:GLY64 5.0 47.2 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 Oct 8 14:07:49 2024

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