Atomistry » Sodium » PDB 6u6u-6v04 » 6uom
Atomistry »
  Sodium »
    PDB 6u6u-6v04 »
      6uom »

Sodium in PDB 6uom: Y271G Dna Polymerase Beta Ternary Complex with Templating Adenine and Incoming R8-Oxo-Gtp

Enzymatic activity of Y271G Dna Polymerase Beta Ternary Complex with Templating Adenine and Incoming R8-Oxo-Gtp

All present enzymatic activity of Y271G Dna Polymerase Beta Ternary Complex with Templating Adenine and Incoming R8-Oxo-Gtp:
2.7.7.7;

Protein crystallography data

The structure of Y271G Dna Polymerase Beta Ternary Complex with Templating Adenine and Incoming R8-Oxo-Gtp, PDB code: 6uom 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) 25.00 / 2.05
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 (%) 19.4 / 24.4

Other elements in 6uom:

The structure of Y271G Dna Polymerase Beta Ternary Complex with Templating Adenine and Incoming R8-Oxo-Gtp also contains other interesting chemical elements:

Manganese (Mn) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Y271G Dna Polymerase Beta Ternary Complex with Templating Adenine and Incoming R8-Oxo-Gtp (pdb code 6uom). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Y271G Dna Polymerase Beta Ternary Complex with Templating Adenine and Incoming R8-Oxo-Gtp, PDB code: 6uom:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 6uom

Go back to Sodium Binding Sites List in 6uom
Sodium binding site 1 out of 4 in the Y271G Dna Polymerase Beta Ternary Complex with Templating Adenine and Incoming R8-Oxo-Gtp


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 Ternary Complex with Templating Adenine and Incoming R8-Oxo-Gtp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na401

b:21.6
occ:1.00
 O A:THR101 2.3 23.1 1.0
OP1 P:DG9 2.3 19.1 1.0
O A:ILE106 2.5 16.7 1.0
O P:HOH208 2.5 24.4 1.0
O A:HOH645 2.6 23.9 1.0
O A:VAL103 2.6 18.1 1.0
C A:THR101 3.3 22.8 1.0
P P:DG9 3.4 21.3 1.0
C A:ILE106 3.5 19.9 1.0
C A:VAL103 3.5 22.0 1.0
OP2 P:DG9 3.5 22.9 1.0
N A:ILE106 3.9 19.5 1.0
CA A:THR101 3.9 18.7 1.0
CA A:SER104 4.0 21.2 1.0
N A:GLY105 4.1 20.3 1.0
N A:VAL103 4.1 20.9 1.0
N A:SER104 4.1 17.3 1.0
CA A:ILE106 4.2 13.9 1.0
C A:ARG102 4.3 21.1 1.0
N A:ARG102 4.4 18.2 1.0
C A:SER104 4.4 21.1 1.0
N A:GLY107 4.4 20.4 1.0
O5' P:DG9 4.5 24.8 1.0
CA A:VAL103 4.5 21.2 1.0
O3' P:DC8 4.5 18.6 1.0
CB A:THR101 4.5 21.8 1.0
CB A:ILE106 4.6 16.6 1.0
CA A:ARG102 4.6 22.5 0.5
CA A:ARG102 4.6 22.6 0.5
CA A:GLY107 4.7 21.4 1.0
C A:GLY105 4.7 21.5 1.0
O A:ARG102 4.8 23.0 1.0
O A:LEU100 4.9 19.7 1.0
CA A:GLY105 4.9 22.2 1.0

Sodium binding site 2 out of 4 in 6uom

Go back to Sodium Binding Sites List in 6uom
Sodium binding site 2 out of 4 in the Y271G Dna Polymerase Beta Ternary Complex with Templating Adenine and Incoming R8-Oxo-Gtp


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 Ternary Complex with Templating Adenine and Incoming R8-Oxo-Gtp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na402

b:27.9
occ:1.00
 O A:LYS60 2.4 32.3 1.0
O A:VAL65 2.4 27.9 1.0
O A:LEU62 2.4 31.7 1.0
O D:HOH212 2.5 35.6 1.0
OP1 D:DC3 2.5 24.1 1.0
O D:HOH205 2.6 37.7 1.0
C A:LEU62 3.4 26.3 1.0
C A:LYS60 3.5 35.4 1.0
C A:VAL65 3.5 23.7 1.0
P D:DC3 3.6 30.5 1.0
OP2 D:DC3 3.8 34.4 1.0
N A:VAL65 3.9 25.4 1.0
CA A:PRO63 4.0 31.9 1.0
N A:LEU62 4.1 28.0 1.0
N A:PRO63 4.1 32.8 1.0
N A:GLY64 4.2 28.7 1.0
CA A:VAL65 4.2 21.7 1.0
CA A:LYS60 4.2 30.6 1.0
C A:LYS61 4.2 34.7 1.0
CG A:LYS60 4.2 30.6 1.0
CA A:LEU62 4.4 24.8 1.0
N A:LYS61 4.5 31.2 1.0
CB A:VAL65 4.5 28.9 1.0
C A:PRO63 4.5 29.6 1.0
O A:LYS61 4.5 32.8 1.0
O3' D:DT2 4.6 27.9 1.0
N A:GLY66 4.6 24.3 1.0
CA A:LYS61 4.6 31.1 1.0
NZ A:LYS60 4.8 39.5 1.0
CB A:LYS60 4.8 33.8 1.0
C A:GLY64 4.8 29.7 1.0
O5' D:DC3 4.8 31.2 1.0
CA A:GLY66 4.9 26.3 1.0
O A:ALA59 5.0 25.5 1.0

Sodium binding site 3 out of 4 in 6uom

Go back to Sodium Binding Sites List in 6uom
Sodium binding site 3 out of 4 in the Y271G Dna Polymerase Beta Ternary Complex with Templating Adenine and Incoming R8-Oxo-Gtp


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 Ternary Complex with Templating Adenine and Incoming R8-Oxo-Gtp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na405

b:12.5
occ:1.00
 OD2 A:ASP145 2.1 24.8 1.0
O A:HOH586 2.2 28.5 1.0
O A:HOH594 2.3 25.5 1.0
O A:HOH649 2.4 33.0 1.0
ND1 A:HIS252 2.4 20.9 1.0
CE1 A:HIS252 3.1 20.9 1.0
CG A:ASP145 3.2 28.4 1.0
CG A:HIS252 3.6 24.1 1.0
OD1 A:ASP145 3.7 31.3 1.0
N A:HIS252 4.1 20.9 1.0
CB A:HIS252 4.1 20.3 1.0
NE2 A:HIS252 4.3 19.9 1.0
CD1 A:TYR142 4.4 20.4 1.0
CB A:ASP145 4.5 27.8 1.0
CD2 A:HIS252 4.6 21.3 1.0
CE1 A:TYR142 4.7 20.9 1.0
O A:HOH512 4.7 36.4 1.0
OE1 A:GLU249 4.8 37.9 1.0
CA A:HIS252 4.8 22.7 1.0
O A:TYR250 4.8 25.6 1.0
C A:PRO251 5.0 22.3 1.0
CA A:PRO251 5.0 23.8 1.0

Sodium binding site 4 out of 4 in 6uom

Go back to Sodium Binding Sites List in 6uom
Sodium binding site 4 out of 4 in the Y271G Dna Polymerase Beta Ternary Complex with Templating Adenine and Incoming R8-Oxo-Gtp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Y271G Dna Polymerase Beta Ternary Complex with Templating Adenine and Incoming R8-Oxo-Gtp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na406

b:37.8
occ:1.00
 O A:HOH653 2.4 39.6 1.0
O A:HOH648 2.4 31.9 1.0
O2G A:8GT407 2.4 35.1 1.0
PG A:8GT407 3.7 27.8 1.0
O A:HOH654 4.0 30.5 1.0
O1G A:8GT407 4.0 28.6 1.0
O1A A:8GT407 4.2 30.2 1.0
O3B A:8GT407 4.3 27.6 1.0
CA A:GLY189 4.6 19.9 1.0
O2A A:8GT407 4.8 27.0 1.0
O3G A:8GT407 4.9 21.2 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 Oct 8 14:12:25 2024

Last articles

Fe in 2YXO
Fe in 2YRS
Fe in 2YXC
Fe in 2YNM
Fe in 2YVJ
Fe in 2YP1
Fe in 2YU2
Fe in 2YU1
Fe in 2YQB
Fe in 2YOO
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy