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Sodium in PDB 5vez: Dna Polymerase Beta Substrate Complex with 8-Oxog:A at the Primer Terminus and Incoming Dctp Analog

Enzymatic activity of Dna Polymerase Beta Substrate Complex with 8-Oxog:A at the Primer Terminus and Incoming Dctp Analog

All present enzymatic activity of Dna Polymerase Beta Substrate Complex with 8-Oxog:A at the Primer Terminus and Incoming Dctp Analog:
2.7.7.7;

Protein crystallography data

The structure of Dna Polymerase Beta Substrate Complex with 8-Oxog:A at the Primer Terminus and Incoming Dctp Analog, PDB code: 5vez was solved by B.D.Freudenthal, M.A.Schaich, A.M.Whitaker, M.R.Smith, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 31.84 / 2.04
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.469, 79.712, 55.523, 90.00, 107.50, 90.00
R / Rfree (%) 18.7 / 23.2

Other elements in 5vez:

The structure of Dna Polymerase Beta Substrate Complex with 8-Oxog:A at the Primer Terminus and Incoming Dctp Analog also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Dna Polymerase Beta Substrate Complex with 8-Oxog:A at the Primer Terminus and Incoming Dctp Analog (pdb code 5vez). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Dna Polymerase Beta Substrate Complex with 8-Oxog:A at the Primer Terminus and Incoming Dctp Analog, PDB code: 5vez:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 5vez

Go back to Sodium Binding Sites List in 5vez
Sodium binding site 1 out of 3 in the Dna Polymerase Beta Substrate Complex with 8-Oxog:A at the Primer Terminus and Incoming Dctp Analog


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Dna Polymerase Beta Substrate Complex with 8-Oxog:A at the Primer Terminus and Incoming Dctp Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Na101

b:30.0
occ:1.00
 O A:HOH570 2.2 36.0 1.0
O A:HOH599 2.2 36.0 1.0
O A:HOH687 2.2 36.0 1.0
O1G A:XC5404 4.0 31.3 1.0
O2A A:XC5404 4.2 20.0 1.0
OP2 P:8OG10 4.4 37.2 1.0
O A:HOH589 4.6 37.6 1.0
OP1 P:8OG10 4.6 33.2 1.0
O A:HOH698 4.6 35.9 1.0
O3G A:XC5404 4.6 23.2 1.0
OD2 A:ASP190 4.7 29.5 1.0
O A:HOH634 4.8 41.5 1.0
O A:HOH507 4.8 39.5 1.0
PG A:XC5404 5.0 21.0 1.0

Sodium binding site 2 out of 3 in 5vez

Go back to Sodium Binding Sites List in 5vez
Sodium binding site 2 out of 3 in the Dna Polymerase Beta Substrate Complex with 8-Oxog:A at the Primer Terminus and Incoming Dctp Analog


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Dna Polymerase Beta Substrate Complex with 8-Oxog:A at the Primer Terminus and Incoming Dctp Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na402

b:27.6
occ:1.00
 OP1 P:DG9 2.3 29.8 1.0
O A:ILE106 2.3 24.3 1.0
O A:THR101 2.3 29.8 1.0
O P:HOH202 2.4 36.0 1.0
O A:VAL103 2.4 25.1 1.0
O A:HOH682 3.0 32.8 1.0
C A:ILE106 3.3 23.6 1.0
C A:THR101 3.3 25.4 1.0
P P:DG9 3.3 25.4 1.0
C A:VAL103 3.4 25.8 1.0
OP2 P:DG9 3.5 24.8 1.0
N A:ILE106 3.6 26.4 1.0
CA A:THR101 3.9 27.4 1.0
N A:GLY105 3.9 25.7 1.0
CA A:ILE106 4.0 23.6 1.0
CA A:SER104 4.0 28.0 1.0
N A:SER104 4.1 25.4 1.0
N A:VAL103 4.2 28.1 1.0
N A:GLY107 4.2 28.5 1.0
O3' P:DC8 4.2 28.1 1.0
C A:SER104 4.3 28.5 1.0
C A:ARG102 4.3 30.2 1.0
N A:ARG102 4.4 28.6 1.0
CB A:ILE106 4.4 29.6 1.0
CB A:THR101 4.4 28.9 1.0
CA A:VAL103 4.5 28.3 1.0
C A:GLY105 4.5 28.3 1.0
CA A:GLY107 4.5 26.7 1.0
O5' P:DG9 4.6 29.9 1.0
CA A:ARG102 4.6 32.0 1.0
O A:ARG102 4.7 31.9 1.0
CA A:GLY105 4.7 27.8 1.0
O A:LEU100 4.8 25.4 1.0

Sodium binding site 3 out of 3 in 5vez

Go back to Sodium Binding Sites List in 5vez
Sodium binding site 3 out of 3 in the Dna Polymerase Beta Substrate Complex with 8-Oxog:A at the Primer Terminus and Incoming Dctp Analog


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Dna Polymerase Beta Substrate Complex with 8-Oxog:A at the Primer Terminus and Incoming Dctp Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na403

b:37.5
occ:1.00
 O A:LYS60 2.3 42.6 1.0
O A:LEU62 2.3 40.3 1.0
O D:HOH106 2.4 30.0 1.0
O A:VAL65 2.5 42.3 1.0
O D:HOH103 2.6 40.7 1.0
OP1 D:DC3 2.6 35.4 1.0
C A:LEU62 3.3 35.4 1.0
C A:LYS60 3.4 38.9 1.0
C A:VAL65 3.7 32.8 1.0
P D:DC3 3.7 36.6 1.0
OP2 D:DC3 3.9 33.9 1.0
C A:LYS61 4.0 38.7 1.0
N A:LEU62 4.0 38.0 1.0
CA A:PRO63 4.0 38.2 1.0
O A:LYS61 4.1 44.4 1.0
N A:VAL65 4.1 35.1 1.0
N A:PRO63 4.1 35.2 1.0
CA A:LYS60 4.2 36.5 1.0
CG A:LYS60 4.2 46.6 1.0
N A:GLY64 4.3 28.8 1.0
CA A:LEU62 4.3 40.6 1.0
CA A:VAL65 4.3 34.5 1.0
N A:LYS61 4.4 36.0 1.0
CA A:LYS61 4.5 39.1 1.0
C A:PRO63 4.6 40.6 1.0
CB A:VAL65 4.6 31.9 1.0
N A:GLY66 4.7 31.1 1.0
O3' D:DT2 4.7 38.9 1.0
O5' D:DC3 4.8 43.8 1.0
CB A:LYS60 4.9 42.2 1.0
O A:ALA59 4.9 36.4 1.0

Reference:

A.M.Whitaker, M.R.Smith, M.A.Schaich, B.D.Freudenthal. Capturing A Mammalian Dna Polymerase Extending From An Oxidized Nucleotide. Nucleic Acids Res. V. 45 6934 2017.
ISSN: ESSN 1362-4962
PubMed: 28449123
DOI: 10.1093/NAR/GKX293
Page generated: Tue Oct 8 00:48:02 2024

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