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Sodium in PDB 1tv9: Human Dna Polymerase Beta Complexed with Nicked Dna Containing A Mismatched Template Adenine and Incoming Cytidine

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

All present enzymatic activity of Human Dna Polymerase Beta Complexed with Nicked Dna Containing A Mismatched Template Adenine 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 Adenine and Incoming Cytidine, PDB code: 1tv9 was solved by J.M.Krahn, W.M.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 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.680, 79.650, 54.670, 90.00, 106.77, 90.00
R / Rfree (%) 17.9 / 23.9

Other elements in 1tv9:

The structure of Human Dna Polymerase Beta Complexed with Nicked Dna Containing A Mismatched Template Adenine 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 Adenine and Incoming Cytidine (pdb code 1tv9). 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 Adenine and Incoming Cytidine, PDB code: 1tv9:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 1tv9

Go back to Sodium Binding Sites List in 1tv9
Sodium binding site 1 out of 2 in the Human Dna Polymerase Beta Complexed with Nicked Dna Containing A Mismatched Template Adenine 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 Adenine and Incoming Cytidine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na784

b:9.9
occ:1.00
 O A:THR101 2.3 11.9 1.0
O A:ILE106 2.4 11.0 1.0
O P:HOH19 2.4 15.3 1.0
OP1 P:DG9 2.4 12.1 1.0
O A:VAL103 2.5 9.9 1.0
O A:HOH822 2.6 18.4 1.0
C A:THR101 3.3 11.5 1.0
C A:ILE106 3.4 10.9 1.0
C A:VAL103 3.4 11.2 1.0
P P:DG9 3.5 13.8 1.0
O A:HOH884 3.6 24.9 1.0
OP2 P:DG9 3.7 14.5 1.0
N A:ILE106 3.7 8.0 1.0
CA A:THR101 3.9 12.1 1.0
CA A:SER104 4.0 9.5 1.0
N A:GLY105 4.0 9.8 1.0
N A:SER104 4.1 10.4 1.0
CA A:ILE106 4.1 8.8 1.0
N A:VAL103 4.1 9.4 1.0
C A:ARG102 4.3 8.9 1.0
N A:GLY107 4.3 11.6 1.0
C A:SER104 4.3 10.3 1.0
N A:ARG102 4.4 11.8 1.0
CB A:THR101 4.4 12.1 1.0
CA A:VAL103 4.4 8.9 1.0
O3' P:DC8 4.5 9.7 1.0
CB A:ILE106 4.6 9.7 1.0
CA A:GLY107 4.6 10.1 1.0
CA A:ARG102 4.6 9.4 1.0
C A:GLY105 4.6 8.0 1.0
O5' P:DG9 4.6 13.0 1.0
O A:ARG102 4.8 13.2 1.0
O A:LEU100 4.9 12.4 1.0
O A:HOH828 4.9 19.1 1.0
CA A:GLY105 4.9 9.2 1.0

Sodium binding site 2 out of 2 in 1tv9

Go back to Sodium Binding Sites List in 1tv9
Sodium binding site 2 out of 2 in the Human Dna Polymerase Beta Complexed with Nicked Dna Containing A Mismatched Template Adenine 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 Adenine and Incoming Cytidine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na785

b:24.2
occ:1.00
 O A:LYS60 2.3 23.8 1.0
O A:VAL65 2.3 15.0 1.0
O A:HOH821 2.4 18.1 1.0
O A:LEU62 2.5 19.3 1.0
O A:HOH913 2.7 28.5 1.0
OP1 D:DC3 2.8 17.4 1.0
C A:LYS60 3.5 26.1 1.0
C A:LEU62 3.5 21.0 1.0
C A:VAL65 3.5 16.2 1.0
P D:DC3 3.8 16.0 1.0
OP2 D:DC3 3.9 17.9 1.0
N A:VAL65 3.9 17.3 1.0
O D:HOH17 4.0 33.2 1.0
N A:LEU62 4.1 23.8 1.0
C A:LYS61 4.1 24.8 1.0
CA A:VAL65 4.2 15.3 1.0
N A:PRO63 4.2 18.3 1.0
CA A:PRO63 4.2 19.9 1.0
CA A:LYS60 4.3 23.1 1.0
N A:GLY64 4.3 18.3 1.0
CB A:VAL65 4.4 17.3 1.0
CA A:LEU62 4.4 21.4 1.0
O A:LYS61 4.4 25.7 1.0
N A:LYS61 4.4 23.7 1.0
O A:HOH1115 4.4 45.9 1.0
N A:GLY66 4.5 15.1 1.0
NZ A:LYS60 4.5 20.8 1.0
CA A:LYS61 4.6 24.7 1.0
C A:PRO63 4.7 20.5 1.0
O3' D:DT2 4.7 18.2 1.0
CD A:LYS60 4.7 23.9 1.0
CG A:LYS60 4.7 30.0 1.0
CA A:GLY66 4.8 14.8 1.0
O A:ALA59 4.8 21.0 1.0
C A:GLY64 5.0 16.6 1.0

Reference:

J.M.Krahn, W.M.Beard, S.H.Wilson. Structural Insights Into Dna Polymerase Beta Deterrents For Misincorporation Support of 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: Tue Dec 15 05:36:39 2020

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