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Sodium in PDB 1tva: Human Dna Polymerase Beta Complexed with Nicked Dna Containing A Mismatched Template Thymidine and Incoming Cytidine

Enzymatic activity of Human Dna Polymerase Beta Complexed with Nicked Dna Containing A Mismatched Template Thymidine and Incoming Cytidine

All present enzymatic activity of Human Dna Polymerase Beta Complexed with Nicked Dna Containing A Mismatched Template Thymidine and Incoming Cytidine:
2.7.7.7;

Protein crystallography data

The structure of Human Dna Polymerase Beta Complexed with Nicked Dna Containing A Mismatched Template Thymidine and Incoming Cytidine, PDB code: 1tva was solved by J.M.Krahn, W.A.Beard, S.H.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.600, 79.700, 54.600, 90.00, 106.40, 90.00
R / Rfree (%) 21.2 / 28.2

Other elements in 1tva:

The structure of Human Dna Polymerase Beta Complexed with Nicked Dna Containing A Mismatched Template Thymidine and Incoming Cytidine also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Human Dna Polymerase Beta Complexed with Nicked Dna Containing A Mismatched Template Thymidine and Incoming Cytidine (pdb code 1tva). 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 Complexed with Nicked Dna Containing A Mismatched Template Thymidine and Incoming Cytidine, PDB code: 1tva:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 1tva

Go back to Sodium Binding Sites List in 1tva
Sodium binding site 1 out of 2 in the Human Dna Polymerase Beta Complexed with Nicked Dna Containing A Mismatched Template Thymidine and Incoming Cytidine


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 Complexed with Nicked Dna Containing A Mismatched Template Thymidine and Incoming Cytidine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na341

b:16.2
occ:1.00
O A:THR101 2.3 18.8 1.0
OP1 P:DG9 2.4 15.5 1.0
O P:HOH346 2.4 17.7 1.0
O A:VAL103 2.4 18.7 1.0
O A:ILE106 2.4 16.6 1.0
O P:HOH347 2.5 20.4 1.0
C A:THR101 3.3 16.0 1.0
C A:VAL103 3.4 17.0 1.0
C A:ILE106 3.5 15.8 1.0
P P:DG9 3.5 13.5 1.0
O A:HOH492 3.6 16.0 1.0
OP2 P:DG9 3.8 12.4 1.0
N A:ILE106 3.8 18.6 1.0
CA A:SER104 3.9 15.7 1.0
N A:VAL103 4.0 15.1 1.0
CA A:THR101 4.0 14.7 1.0
N A:SER104 4.0 17.1 1.0
N A:GLY105 4.1 17.8 1.0
CA A:ILE106 4.2 16.5 1.0
C A:ARG102 4.3 18.6 1.0
N A:ARG102 4.3 17.2 1.0
CA A:VAL103 4.4 15.0 1.0
C A:SER104 4.4 16.6 1.0
N A:GLY107 4.4 14.6 1.0
CB A:THR101 4.5 13.1 1.0
O5' P:DG9 4.5 18.1 1.0
CA A:ARG102 4.6 16.1 1.0
O3' P:DC8 4.6 15.2 1.0
CB A:ILE106 4.6 16.9 1.0
CA A:GLY107 4.7 14.4 1.0
C A:GLY105 4.7 18.7 1.0
O A:ARG102 4.8 20.1 1.0
O A:LEU100 5.0 18.1 1.0
O A:HOH468 5.0 28.1 1.0

Sodium binding site 2 out of 2 in 1tva

Go back to Sodium Binding Sites List in 1tva
Sodium binding site 2 out of 2 in the Human Dna Polymerase Beta Complexed with Nicked Dna Containing A Mismatched Template Thymidine and Incoming Cytidine


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 Complexed with Nicked Dna Containing A Mismatched Template Thymidine and Incoming Cytidine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na342

b:30.8
occ:1.00
O D:HOH348 2.4 29.3 1.0
O A:HOH349 2.4 31.7 1.0
O A:VAL65 2.4 27.9 1.0
O A:LEU62 2.4 29.3 1.0
O A:LYS60 2.4 31.4 1.0
OP1 D:DC3 2.5 29.1 1.0
C A:VAL65 3.5 24.6 1.0
C A:LEU62 3.5 28.7 1.0
C A:LYS60 3.6 29.4 1.0
P D:DC3 3.6 28.2 1.0
N A:VAL65 3.8 27.0 1.0
OP2 D:DC3 3.9 23.7 1.0
CA A:VAL65 4.1 25.1 1.0
N A:GLY64 4.1 31.4 1.0
N A:LEU62 4.2 30.4 1.0
C A:LYS61 4.2 31.7 1.0
N A:PRO63 4.3 29.2 1.0
CA A:PRO63 4.3 30.3 1.0
CA A:LYS60 4.4 27.0 1.0
O A:LYS61 4.4 34.3 1.0
O3' D:DT2 4.4 25.2 1.0
CA A:LEU62 4.5 28.3 1.0
CB A:VAL65 4.5 24.2 1.0
N A:GLY66 4.5 25.1 1.0
N A:LYS61 4.5 30.2 1.0
CG A:LYS60 4.6 25.5 1.0
CA A:LYS61 4.7 31.0 1.0
C A:PRO63 4.7 31.1 1.0
CA A:GLY66 4.8 23.5 1.0
C A:GLY64 4.8 28.8 1.0
O5' D:DC3 4.9 22.7 1.0

Reference:

J.M.Krahn, W.A.Beard, S.H.Wilson. Structural Insights Into Dna Polymerase Beta Deterrents For Misincorporation Support An Induced-Fit Mechanism For Fidelity Structure V. 12 1823 2004.
ISSN: ISSN 0969-2126
PubMed: 15458631
DOI: 10.1016/J.STR.2004.08.001
Page generated: Sun Oct 6 22:41:46 2024

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