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Sodium in PDB 4tus: Human Dna Polymerase Beta Inserting Dcmpnpp Opposite the 5'G of Cisplatin Crosslinked Gs (Pt-GG2) with Manganese in the Active Site.

Enzymatic activity of Human Dna Polymerase Beta Inserting Dcmpnpp Opposite the 5'G of Cisplatin Crosslinked Gs (Pt-GG2) with Manganese in the Active Site.

All present enzymatic activity of Human Dna Polymerase Beta Inserting Dcmpnpp Opposite the 5'G of Cisplatin Crosslinked Gs (Pt-GG2) with Manganese in the Active Site.:
2.7.7.7;

Protein crystallography data

The structure of Human Dna Polymerase Beta Inserting Dcmpnpp Opposite the 5'G of Cisplatin Crosslinked Gs (Pt-GG2) with Manganese in the Active Site., PDB code: 4tus was solved by M.C.Koag, S.Lee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.81 / 2.42
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.878, 78.417, 54.803, 90.00, 112.80, 90.00
R / Rfree (%) 20 / 24.3

Other elements in 4tus:

The structure of Human Dna Polymerase Beta Inserting Dcmpnpp Opposite the 5'G of Cisplatin Crosslinked Gs (Pt-GG2) with Manganese in the Active Site. also contains other interesting chemical elements:

Platinum (Pt) 1 atom
Manganese (Mn) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Human Dna Polymerase Beta Inserting Dcmpnpp Opposite the 5'G of Cisplatin Crosslinked Gs (Pt-GG2) with Manganese in the Active Site. (pdb code 4tus). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Human Dna Polymerase Beta Inserting Dcmpnpp Opposite the 5'G of Cisplatin Crosslinked Gs (Pt-GG2) with Manganese in the Active Site., PDB code: 4tus:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 4tus

Go back to Sodium Binding Sites List in 4tus
Sodium binding site 1 out of 2 in the Human Dna Polymerase Beta Inserting Dcmpnpp Opposite the 5'G of Cisplatin Crosslinked Gs (Pt-GG2) 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 Human Dna Polymerase Beta Inserting Dcmpnpp Opposite the 5'G of Cisplatin Crosslinked Gs (Pt-GG2) with Manganese in the Active Site. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na403

b:31.9
occ:1.00
O A:THR101 2.3 30.1 1.0
OP1 P:DG9 2.3 29.3 1.0
O A:VAL103 2.4 25.6 1.0
O A:ILE106 2.5 26.8 1.0
O P:HOH109 2.5 30.7 1.0
O A:HOH521 2.6 35.8 1.0
C A:THR101 3.3 24.4 1.0
C A:VAL103 3.4 28.6 1.0
P P:DG9 3.4 29.3 1.0
C A:ILE106 3.5 27.2 1.0
OP2 P:DG9 3.6 33.9 1.0
N A:ILE106 3.8 22.0 1.0
CA A:THR101 3.8 25.8 1.0
CA A:SER104 3.9 24.0 1.0
N A:GLY105 4.0 26.2 1.0
N A:SER104 4.0 28.2 1.0
CA A:ILE106 4.1 26.6 1.0
N A:VAL103 4.2 30.9 1.0
N A:ARG102 4.4 25.7 1.0
C A:SER104 4.4 26.9 1.0
CA A:VAL103 4.4 28.2 1.0
CB A:THR101 4.4 22.9 1.0
C A:ARG102 4.4 29.5 1.0
O3' P:DG8 4.4 27.1 1.0
N A:GLY107 4.5 29.2 1.0
O5' P:DG9 4.6 24.9 1.0
CB A:ILE106 4.6 25.1 1.0
CA A:ARG102 4.7 29.3 1.0
C A:GLY105 4.7 28.8 1.0
CA A:GLY107 4.7 25.2 1.0
O A:LEU100 4.8 28.5 1.0
O A:ARG102 4.9 30.0 1.0
CA A:GLY105 5.0 26.1 1.0

Sodium binding site 2 out of 2 in 4tus

Go back to Sodium Binding Sites List in 4tus
Sodium binding site 2 out of 2 in the Human Dna Polymerase Beta Inserting Dcmpnpp Opposite the 5'G of Cisplatin Crosslinked Gs (Pt-GG2) 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 Human Dna Polymerase Beta Inserting Dcmpnpp Opposite the 5'G of Cisplatin Crosslinked Gs (Pt-GG2) with Manganese in the Active Site. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na404

b:42.4
occ:1.00
O A:LYS60 2.4 37.5 1.0
OP1 D:DG3 2.4 32.6 1.0
O A:HOH547 2.4 34.8 1.0
O A:VAL65 2.4 37.4 1.0
O A:LEU62 2.6 36.5 1.0
C A:LYS60 3.5 37.5 1.0
C A:LEU62 3.5 36.0 1.0
C A:VAL65 3.6 36.0 1.0
P D:DG3 3.6 32.5 1.0
OP2 D:DG3 4.0 40.6 1.0
C A:LYS61 4.1 38.9 1.0
N A:LEU62 4.1 39.4 1.0
N A:VAL65 4.1 31.6 1.0
CA A:PRO63 4.2 36.3 1.0
N A:PRO63 4.2 38.6 1.0
O A:LYS61 4.2 40.3 1.0
CA A:LYS60 4.2 37.6 1.0
CA A:VAL65 4.3 30.1 1.0
CG A:LYS60 4.4 39.8 1.0
N A:GLY64 4.4 39.8 1.0
CA A:LEU62 4.4 37.5 1.0
N A:LYS61 4.4 43.1 1.0
O5' D:DG3 4.5 32.2 1.0
CB A:VAL65 4.6 36.3 1.0
N A:GLY66 4.6 36.6 1.0
CA A:LYS61 4.6 41.3 1.0
NZ A:LYS60 4.7 41.3 1.0
O3' D:DT2 4.8 40.4 1.0
C A:PRO63 4.8 41.6 1.0
CA A:GLY66 4.8 28.7 1.0
CB A:LYS60 4.9 35.9 1.0
O A:ALA59 4.9 36.4 1.0

Reference:

M.C.Koag, L.Lai, S.Lee. Structural Basis For the Inefficient Nucleotide Incorporation Opposite Cisplatin-Dna Lesion By Human Dna Polymerase Beta J.Biol.Chem. 2014.
ISSN: ESSN 1083-351X
PubMed: 25237188
DOI: 10.1074/JBC.M114.605451
Page generated: Thu Oct 29 05:11:27 2020

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