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Sodium in PDB 4tur: Human Dna Polymerase Beta Inserting Dcmpnpp Opposite the 5'G of Cisplatin Crosslinked Gs (Pt-GG2)

Enzymatic activity of Human Dna Polymerase Beta Inserting Dcmpnpp Opposite the 5'G of Cisplatin Crosslinked Gs (Pt-GG2)

All present enzymatic activity of Human Dna Polymerase Beta Inserting Dcmpnpp Opposite the 5'G of Cisplatin Crosslinked Gs (Pt-GG2):
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), PDB code: 4tur 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) 19.83 / 2.17
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.785, 79.335, 54.786, 90.00, 107.81, 90.00
R / Rfree (%) 20.2 / 25.6

Other elements in 4tur:

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

Magnesium (Mg) 2 atoms
Platinum (Pt) 1 atom

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) (pdb code 4tur). 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), PDB code: 4tur:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 4tur

Go back to Sodium Binding Sites List in 4tur
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)


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) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na403

b:23.6
occ:1.00
OP1 P:DG9 2.3 22.7 1.0
O A:THR101 2.3 23.4 1.0
O A:ILE106 2.4 20.9 1.0
O A:HOH528 2.5 24.6 1.0
O P:HOH117 2.5 26.5 1.0
O A:VAL103 2.5 24.3 1.0
C A:THR101 3.3 24.3 1.0
O A:HOH603 3.3 32.6 1.0
C A:VAL103 3.4 23.6 1.0
P P:DG9 3.4 25.9 1.0
C A:ILE106 3.4 17.1 1.0
OP2 P:DG9 3.7 29.4 1.0
N A:ILE106 3.8 18.8 1.0
CA A:SER104 3.9 24.7 1.0
N A:GLY105 3.9 22.4 1.0
CA A:THR101 3.9 21.1 1.0
N A:SER104 4.0 25.6 1.0
CA A:ILE106 4.1 20.2 1.0
N A:VAL103 4.1 21.7 1.0
C A:ARG102 4.2 26.5 1.0
C A:SER104 4.3 21.9 1.0
N A:ARG102 4.3 23.1 1.0
O3' P:DG8 4.4 24.1 1.0
CA A:VAL103 4.4 23.5 1.0
N A:GLY107 4.5 21.1 1.0
CB A:THR101 4.5 20.9 1.0
CA A:ARG102 4.5 25.2 1.0
CB A:ILE106 4.5 20.2 1.0
O5' P:DG9 4.6 23.8 1.0
O A:ARG102 4.6 24.2 1.0
C A:GLY105 4.6 21.4 1.0
CA A:GLY107 4.7 20.4 1.0
CA A:GLY105 4.9 21.0 1.0
O A:HOH601 4.9 38.4 1.0
O A:LEU100 4.9 19.1 1.0

Sodium binding site 2 out of 2 in 4tur

Go back to Sodium Binding Sites List in 4tur
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)


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) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na404

b:38.6
occ:1.00
O A:VAL65 2.4 29.0 1.0
O A:LYS60 2.4 34.4 1.0
O A:HOH548 2.5 41.7 1.0
O A:LEU62 2.6 34.4 1.0
OP1 D:DG3 2.7 31.8 1.0
C A:VAL65 3.5 30.5 1.0
C A:LEU62 3.5 30.1 1.0
C A:LYS60 3.6 32.9 1.0
P D:DG3 3.8 34.5 1.0
OP2 D:DG3 3.9 29.9 1.0
N A:VAL65 4.0 35.0 1.0
CA A:PRO63 4.1 33.8 1.0
N A:GLY64 4.2 32.6 1.0
N A:PRO63 4.2 35.0 1.0
C A:LYS61 4.2 33.8 1.0
CA A:VAL65 4.2 31.9 1.0
N A:LEU62 4.3 35.0 1.0
CA A:LYS60 4.3 34.8 1.0
O A:LYS61 4.3 40.8 1.0
O D:HOH105 4.4 47.6 1.0
CG A:LYS60 4.4 33.6 1.0
N A:LYS61 4.5 34.1 1.0
CA A:LEU62 4.5 34.7 1.0
C A:PRO63 4.6 35.5 1.0
CB A:VAL65 4.6 33.1 1.0
N A:GLY66 4.6 27.3 1.0
CA A:LYS61 4.7 34.0 1.0
O3' D:DT2 4.7 35.5 1.0
CA A:GLY66 4.8 31.5 1.0
C A:GLY64 4.9 32.5 1.0
O5' D:DG3 5.0 36.3 1.0
CB A:LYS60 5.0 32.2 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: Tue Dec 15 07:37:45 2020

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