Atomistry » Sodium » PDB 4rne-4tmv » 4rq4
Atomistry »
  Sodium »
    PDB 4rne-4tmv »
      4rq4 »

Sodium in PDB 4rq4: Human Dna Polymerase Beta with Gapped Dna Containing An 8-Oxo-7,8- Dihydro-Guanine(8-Oxog) and Datp Soaked with MGCL2 For 30 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 30 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 30 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 30 S, PDB code: 4rq4 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) 40.59 / 2.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 49.160, 79.650, 55.310, 90.00, 106.35, 90.00
R / Rfree (%) 19 / 24.4

Other elements in 4rq4:

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 30 S also contains other interesting chemical elements:

Magnesium (Mg) 3 atoms
Chlorine (Cl) 5 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 30 S (pdb code 4rq4). 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 30 S, PDB code: 4rq4:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 4rq4

Go back to Sodium Binding Sites List in 4rq4
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 30 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 30 S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na404

b:20.2
occ:1.00
O A:THR101 2.2 21.0 1.0
O P:HOH201 2.3 29.9 1.0
O A:VAL103 2.4 21.7 1.0
O P:HOH202 2.4 34.8 1.0
OP1 P:DG9 2.4 28.8 1.0
O A:ILE106 2.4 25.8 1.0
C A:VAL103 3.3 22.5 1.0
C A:THR101 3.3 22.3 1.0
P P:DG9 3.4 30.9 1.0
C A:ILE106 3.5 21.0 1.0
OP2 P:DG9 3.6 30.0 1.0
N A:ILE106 3.8 19.8 1.0
CA A:SER104 4.0 22.4 1.0
N A:SER104 4.0 22.6 1.0
N A:GLY105 4.0 21.6 1.0
CA A:THR101 4.1 22.2 1.0
N A:VAL103 4.1 24.0 1.0
C A:ARG102 4.2 26.1 1.0
CA A:ILE106 4.2 20.1 1.0
CA A:VAL103 4.3 23.1 1.0
N A:ARG102 4.3 24.5 1.0
C A:SER104 4.3 22.5 1.0
N A:GLY107 4.4 20.6 1.0
O5' P:DG9 4.5 27.3 1.0
CA A:ARG102 4.5 26.6 1.0
O A:ARG102 4.5 27.6 1.0
O3' P:DC8 4.6 30.1 1.0
CB A:ILE106 4.6 20.5 1.0
CA A:GLY107 4.7 20.2 1.0
CB A:THR101 4.7 22.0 1.0
C A:GLY105 4.7 20.7 1.0
O A:LEU100 4.8 21.3 1.0
CA A:GLY105 4.9 20.9 1.0

Sodium binding site 2 out of 2 in 4rq4

Go back to Sodium Binding Sites List in 4rq4
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 30 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 30 S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na405

b:31.0
occ:1.00
O D:HOH101 2.3 43.9 1.0
O A:LEU62 2.5 35.4 1.0
O A:VAL65 2.5 30.6 1.0
O A:LYS60 2.6 35.5 1.0
OP1 D:DC3 2.6 37.8 1.0
OP2 D:DC3 3.5 37.4 1.0
P D:DC3 3.5 36.8 1.0
C A:VAL65 3.5 29.1 1.0
C A:LEU62 3.6 35.5 1.0
C A:LYS60 3.7 38.9 1.0
N A:VAL65 3.9 31.5 1.0
N A:GLY64 4.1 32.7 1.0
CA A:VAL65 4.2 29.8 1.0
CA A:PRO63 4.2 31.7 1.0
N A:LEU62 4.3 38.8 1.0
C A:LYS61 4.3 41.5 1.0
N A:PRO63 4.4 32.1 1.0
N A:GLY66 4.5 30.0 1.0
O3' D:DT2 4.5 37.0 1.0
CB A:VAL65 4.5 27.3 1.0
C A:PRO63 4.6 34.0 1.0
CA A:LYS60 4.6 38.9 1.0
CA A:LEU62 4.6 37.1 1.0
O A:LYS61 4.6 39.9 1.0
CA A:GLY66 4.7 28.9 1.0
CG A:LYS60 4.7 47.5 1.0
N A:LYS61 4.7 39.4 1.0
CA A:LYS61 4.7 42.3 1.0
O5' D:DC3 4.8 37.9 1.0
C A:GLY64 4.9 32.8 1.0
NZ A:LYS60 4.9 56.0 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 18:18:49 2024

Last articles

As in 2ILY
As in 2H79
As in 2I0K
As in 2HZE
As in 2H77
As in 2HX2
As in 2HYP
As in 2HMH
As in 2GWS
As in 2H5K
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy