Atomistry » Sodium » PDB 4rne-4tmv » 4rq5
Atomistry »
  Sodium »
    PDB 4rne-4tmv »
      4rq5 »

Sodium in PDB 4rq5: Human Dna Polymerase Beta with Gapped Dna Containing An 8-Oxo-7,8- Dihydro-Guanine (8-Oxog)and Datp Soaked with MGCL2 For 60 S

Enzymatic activity of Human Dna Polymerase Beta with Gapped Dna Containing An 8-Oxo-7,8- Dihydro-Guanine (8-Oxog)and Datp Soaked with MGCL2 For 60 S

All present enzymatic activity of Human Dna Polymerase Beta with Gapped Dna Containing An 8-Oxo-7,8- Dihydro-Guanine (8-Oxog)and Datp Soaked with MGCL2 For 60 S:
2.7.7.7;

Protein crystallography data

The structure of Human Dna Polymerase Beta with Gapped Dna Containing An 8-Oxo-7,8- Dihydro-Guanine (8-Oxog)and Datp Soaked with MGCL2 For 60 S, PDB code: 4rq5 was solved by R.Vyas, Z.Suo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.32
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 49.212, 79.702, 55.384, 90.00, 106.66, 90.00
R / Rfree (%) 19.6 / 26.6

Other elements in 4rq5:

The structure of Human Dna Polymerase Beta with Gapped Dna Containing An 8-Oxo-7,8- Dihydro-Guanine (8-Oxog)and Datp Soaked with MGCL2 For 60 S also contains other interesting chemical elements:

Magnesium (Mg) 3 atoms
Chlorine (Cl) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Human Dna Polymerase Beta with Gapped Dna Containing An 8-Oxo-7,8- Dihydro-Guanine (8-Oxog)and Datp Soaked with MGCL2 For 60 S (pdb code 4rq5). 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 with Gapped Dna Containing An 8-Oxo-7,8- Dihydro-Guanine (8-Oxog)and Datp Soaked with MGCL2 For 60 S, PDB code: 4rq5:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 4rq5

Go back to Sodium Binding Sites List in 4rq5
Sodium binding site 1 out of 2 in the Human Dna Polymerase Beta with Gapped Dna Containing An 8-Oxo-7,8- Dihydro-Guanine (8-Oxog)and Datp Soaked with MGCL2 For 60 S


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 with Gapped Dna Containing An 8-Oxo-7,8- Dihydro-Guanine (8-Oxog)and Datp Soaked with MGCL2 For 60 S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na403

b:35.6
occ:1.00
 OP1 P:DG9 2.1 38.3 1.0
O A:THR101 2.2 26.3 1.0
O A:HOH503 2.4 27.9 1.0
O A:ILE106 2.6 25.3 1.0
O A:VAL103 2.7 27.2 1.0
P P:DG9 3.1 37.4 1.0
O A:HOH526 3.3 14.1 0.5
C A:THR101 3.3 26.4 1.0
OP2 P:DG9 3.4 33.8 1.0
C A:ILE106 3.6 23.4 1.0
C A:VAL103 3.7 27.8 1.0
O5' P:DG9 3.9 39.1 1.0
CA A:THR101 4.0 27.4 1.0
N A:ILE106 4.1 23.9 1.0
N A:GLY105 4.1 28.8 1.0
N A:GLY107 4.3 22.8 1.0
CA A:SER104 4.3 27.1 1.0
CB A:THR101 4.4 27.6 1.0
N A:ARG102 4.4 27.7 1.0
CA A:ILE106 4.4 24.3 1.0
CA A:GLY107 4.4 22.4 1.0
N A:VAL103 4.4 28.0 1.0
O3' P:DC8 4.4 37.4 1.0
N A:SER104 4.4 26.6 1.0
C A:ARG102 4.4 29.3 1.0
CA A:ARG102 4.6 30.9 1.0
C A:SER104 4.6 28.0 1.0
CA A:VAL103 4.7 27.9 1.0
O A:ARG102 4.8 31.0 1.0
C A:GLY105 4.9 27.8 1.0
CB A:ILE106 4.9 25.0 1.0
C5' P:DG9 4.9 40.8 1.0
CA A:GLY105 5.0 28.8 1.0

Sodium binding site 2 out of 2 in 4rq5

Go back to Sodium Binding Sites List in 4rq5
Sodium binding site 2 out of 2 in the Human Dna Polymerase Beta with Gapped Dna Containing An 8-Oxo-7,8- Dihydro-Guanine (8-Oxog)and Datp Soaked with MGCL2 For 60 S


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 with Gapped Dna Containing An 8-Oxo-7,8- Dihydro-Guanine (8-Oxog)and Datp Soaked with MGCL2 For 60 S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na404

b:32.7
occ:1.00
 O A:VAL65 2.3 44.8 1.0
O A:LYS60 2.4 36.2 1.0
O A:LEU62 2.6 36.3 1.0
OP1 D:DC3 2.7 43.0 1.0
C A:VAL65 3.5 37.4 1.0
C A:LYS60 3.5 40.1 1.0
P D:DC3 3.6 45.1 1.0
OP2 D:DC3 3.6 46.0 1.0
C A:LEU62 3.7 35.6 1.0
N A:VAL65 3.9 33.6 1.0
CA A:VAL65 4.1 34.7 1.0
N A:GLY64 4.2 34.4 1.0
C A:LYS61 4.2 40.8 1.0
CA A:LYS60 4.2 39.0 1.0
CG A:LYS60 4.2 42.3 1.0
O A:LYS61 4.3 40.9 1.0
CA A:PRO63 4.4 35.0 1.0
N A:LEU62 4.4 39.3 1.0
CB A:VAL65 4.4 34.3 1.0
N A:PRO63 4.5 35.1 1.0
N A:LYS61 4.5 43.5 1.0
N A:GLY66 4.5 36.9 1.0
O3' D:DT2 4.6 41.9 1.0
CA A:LYS61 4.6 44.7 1.0
C A:PRO63 4.7 34.5 1.0
CA A:LEU62 4.7 37.5 1.0
CA A:GLY66 4.7 36.0 1.0
O5' D:DC3 4.8 45.7 1.0
NZ A:LYS60 4.8 47.5 1.0
C A:GLY64 4.9 35.1 1.0
CB A:LYS60 4.9 41.8 1.0
O A:ALA59 5.0 33.0 1.0

Reference:

R.Vyas, A.J.Reed, E.J.Tokarsky, Z.Suo. Viewing Human Dna Polymerase Beta Faithfully and Unfaithfully Bypass An Oxidative Lesion By Time-Dependent Crystallography. J.Am.Chem.Soc. V. 137 5225 2015.
ISSN: ISSN 0002-7863
PubMed: 25825995
DOI: 10.1021/JACS.5B02109
Page generated: Mon Oct 7 18:19:22 2024

Last articles

Zn in 9J0N
Zn in 9J0O
Zn in 9J0P
Zn in 9FJX
Zn in 9EKB
Zn in 9C0F
Zn in 9CAH
Zn in 9CH0
Zn in 9CH3
Zn in 9CH1
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy