Sodium in PDB 6uol: Y271G Dna Polymerase Beta Substrate Complex with A Templating Cytosine and Incoming Rgtp

Enzymatic activity of Y271G Dna Polymerase Beta Substrate Complex with A Templating Cytosine and Incoming Rgtp

All present enzymatic activity of Y271G Dna Polymerase Beta Substrate Complex with A Templating Cytosine and Incoming Rgtp:
2.7.7.7;

Protein crystallography data

The structure of Y271G Dna Polymerase Beta Substrate Complex with A Templating Cytosine and Incoming Rgtp, PDB code: 6uol was solved by M.R.Smith, B.D.Freudenthal, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.09 / 1.94
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.800, 80.400, 55.500, 90.00, 107.90, 90.00
R / Rfree (%) 18.7 / 25

Other elements in 6uol:

The structure of Y271G Dna Polymerase Beta Substrate Complex with A Templating Cytosine and Incoming Rgtp also contains other interesting chemical elements:

Manganese (Mn) 5 atoms
Chlorine (Cl) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Y271G Dna Polymerase Beta Substrate Complex with A Templating Cytosine and Incoming Rgtp (pdb code 6uol). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Y271G Dna Polymerase Beta Substrate Complex with A Templating Cytosine and Incoming Rgtp, PDB code: 6uol:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 6uol

Go back to Sodium Binding Sites List in 6uol
Sodium binding site 1 out of 3 in the Y271G Dna Polymerase Beta Substrate Complex with A Templating Cytosine and Incoming Rgtp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Y271G Dna Polymerase Beta Substrate Complex with A Templating Cytosine and Incoming Rgtp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na405

b:40.7
occ:1.00
 O A:HOH605 2.2 25.8 1.0
O P:HOH117 2.3 37.0 1.0
O A:HOH641 2.5 30.8 1.0
O A:HOH546 3.6 33.7 1.0
O3G A:GTP409 3.9 19.4 1.0
O P:HOH107 4.5 21.1 1.0
CA A:GLY189 4.6 9.4 1.0
OD2 A:ASP190 4.8 15.4 1.0
C A:GLY189 4.8 16.4 1.0
O A:GLY189 4.8 11.6 1.0

Sodium binding site 2 out of 3 in 6uol

Go back to Sodium Binding Sites List in 6uol
Sodium binding site 2 out of 3 in the Y271G Dna Polymerase Beta Substrate Complex with A Templating Cytosine and Incoming Rgtp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Y271G Dna Polymerase Beta Substrate Complex with A Templating Cytosine and Incoming Rgtp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na406

b:15.1
occ:1.00
 O A:THR101 2.3 14.8 1.0
OP1 P:DG9 2.4 14.2 1.0
O P:HOH104 2.4 16.7 1.0
O A:HOH624 2.4 17.3 1.0
O A:VAL103 2.6 11.2 1.0
O A:ILE106 2.6 18.1 1.0
C A:THR101 3.3 15.6 1.0
P P:DG9 3.4 14.0 1.0
C A:VAL103 3.4 14.7 1.0
C A:ILE106 3.6 16.6 1.0
OP2 P:DG9 3.6 12.2 1.0
N A:ILE106 3.8 12.8 1.0
N A:GLY105 3.9 11.5 1.0
CA A:THR101 4.0 12.4 1.0
CA A:SER104 4.0 11.8 1.0
N A:VAL103 4.1 15.0 1.0
N A:SER104 4.1 11.9 1.0
CA A:ILE106 4.2 9.7 1.0
C A:ARG102 4.3 15.6 1.0
C A:SER104 4.3 16.9 1.0
N A:ARG102 4.4 15.7 1.0
CA A:VAL103 4.4 15.2 1.0
O3' P:DC8 4.4 12.4 1.0
N A:GLY107 4.5 16.7 1.0
CB A:THR101 4.5 12.6 1.0
O5' P:DG9 4.6 13.3 1.0
CA A:ARG102 4.6 14.1 1.0
C A:GLY105 4.6 16.9 1.0
CB A:ILE106 4.6 12.9 1.0
CA A:GLY107 4.7 16.2 1.0
O A:ARG102 4.8 15.5 1.0
CA A:GLY105 4.8 14.5 1.0
O A:LEU100 4.9 12.4 1.0

Sodium binding site 3 out of 3 in 6uol

Go back to Sodium Binding Sites List in 6uol
Sodium binding site 3 out of 3 in the Y271G Dna Polymerase Beta Substrate Complex with A Templating Cytosine and Incoming Rgtp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Y271G Dna Polymerase Beta Substrate Complex with A Templating Cytosine and Incoming Rgtp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na407

b:22.1
occ:1.00
 O A:LEU62 2.4 21.7 1.0
O A:VAL65 2.4 19.9 1.0
O A:LYS60 2.4 22.1 1.0
OP1 D:DC3 2.6 19.1 1.0
O D:HOH103 2.8 32.6 1.0
C A:LEU62 3.3 20.2 1.0
C A:LYS60 3.5 27.6 1.0
C A:VAL65 3.5 18.5 1.0
P D:DC3 3.6 25.2 1.0
OP2 D:DC3 3.8 23.7 1.0
N A:VAL65 3.9 23.9 1.0
N A:LEU62 4.0 26.2 1.0
CA A:PRO63 4.0 29.9 1.0
N A:PRO63 4.0 25.5 1.0
N A:GLY64 4.1 24.6 1.0
C A:LYS61 4.1 31.6 1.0
CA A:LYS60 4.2 20.5 1.0
CA A:VAL65 4.2 18.0 1.0
CG A:LYS60 4.2 22.5 1.0
CA A:LEU62 4.3 20.1 1.0
C A:PRO63 4.4 27.4 1.0
O A:LYS61 4.4 28.9 1.0
N A:LYS61 4.5 24.4 1.0
CB A:VAL65 4.5 18.2 1.0
N A:GLY66 4.6 17.9 1.0
O3' D:DT2 4.6 24.5 1.0
CA A:LYS61 4.7 24.3 1.0
NZ A:LYS60 4.8 33.9 1.0
C A:GLY64 4.8 25.6 1.0
O5' D:DC3 4.8 25.1 1.0
CB A:LYS60 4.8 25.0 1.0
CA A:GLY66 4.9 21.6 1.0
O A:ALA59 4.9 22.4 1.0

Reference:

M.R.Smith, K.S.Alnajjar, N.M.Hoitsma, J.B.Sweasy, B.D.Freudenthal. Molecular Characterization of Oxidized Ribonucleotide Insertion By Human Dna Polymerase Beta J.Biol.Chem. 2020.
ISSN: ESSN 1083-351X
Page generated: Tue Dec 15 14:32:55 2020

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