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

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

Resolution Low / High (Å) 44.19 / 2.19
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 49.410, 79.320, 55.410, 90.00, 106.20, 90.00
R / Rfree (%) 19.5 / 25.1

Other elements in 4rpz:

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

Magnesium (Mg) 3 atoms
Chlorine (Cl) 3 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 Dctp Soaked with MGCL2 For 60 S (pdb code 4rpz). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 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 Dctp Soaked with MGCL2 For 60 S, PDB code: 4rpz:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 4rpz

Go back to Sodium Binding Sites List in 4rpz
Sodium binding site 1 out of 4 in the Human Dna Polymerase Beta with Gapped Dna Containing An 8-Oxo-7,8- Dihydro-Guanine (8-Oxog)and Dctp 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 Dctp Soaked with MGCL2 For 60 S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na403

b:24.9
occ:1.00
 O A:VAL65 2.2 23.3 1.0
O D:HOH202 2.2 26.4 1.0
O A:HOH589 2.2 29.1 1.0
O A:LEU62 2.3 25.6 1.0
O A:LYS60 2.3 25.6 1.0
OP1 D:DC3 2.3 24.9 1.0
C A:VAL65 3.3 22.7 1.0
C A:LEU62 3.4 25.7 1.0
C A:LYS60 3.4 26.9 1.0
P D:DC3 3.6 24.4 1.0
N A:VAL65 3.7 21.8 1.0
CA A:VAL65 3.9 22.1 1.0
OP2 D:DC3 4.0 24.3 1.0
N A:LEU62 4.0 27.2 1.0
C A:LYS61 4.1 28.9 1.0
N A:GLY64 4.1 23.9 1.0
N A:PRO63 4.2 24.8 1.0
CA A:PRO63 4.2 24.8 1.0
CB A:VAL65 4.2 22.1 1.0
CD A:LYS60 4.2 31.9 1.0
CA A:LYS60 4.3 27.0 1.0
O A:LYS61 4.3 30.5 1.0
CA A:LEU62 4.3 26.5 1.0
N A:LYS61 4.4 28.8 1.0
CE A:LYS60 4.4 33.0 1.0
N A:GLY66 4.4 21.9 1.0
C A:PRO63 4.4 24.7 1.0
O3' D:DT2 4.5 22.7 1.0
CA A:LYS61 4.5 30.2 1.0
C A:GLY64 4.7 22.5 1.0
O5' D:DC3 4.7 24.2 1.0
CA A:GLY66 4.8 21.4 1.0
O A:ALA59 4.8 24.8 1.0
CG A:LYS60 4.9 30.8 1.0
CA A:GLY64 5.0 23.1 1.0

Sodium binding site 2 out of 4 in 4rpz

Go back to Sodium Binding Sites List in 4rpz
Sodium binding site 2 out of 4 in the Human Dna Polymerase Beta with Gapped Dna Containing An 8-Oxo-7,8- Dihydro-Guanine (8-Oxog)and Dctp 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 Dctp Soaked with MGCL2 For 60 S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na404

b:19.6
occ:1.00
 O A:THR101 2.2 18.5 1.0
OP1 P:DG9 2.2 21.3 1.0
O P:HOH208 2.2 23.6 1.0
O A:HOH517 2.2 18.5 1.0
O A:ILE106 2.3 18.9 1.0
O A:VAL103 2.3 19.5 1.0
C A:THR101 3.3 19.0 1.0
P P:DG9 3.3 23.8 1.0
C A:ILE106 3.3 18.8 1.0
C A:VAL103 3.3 19.0 1.0
OP2 P:DG9 3.5 22.3 1.0
N A:ILE106 3.6 19.0 1.0
N A:GLY105 3.9 18.6 1.0
CA A:THR101 4.0 18.9 1.0
CA A:SER104 4.0 19.1 1.0
CA A:ILE106 4.0 18.9 1.0
N A:SER104 4.0 19.1 1.0
N A:VAL103 4.1 18.8 1.0
C A:ARG102 4.2 19.8 1.0
O3' P:DC8 4.3 24.1 1.0
N A:ARG102 4.3 19.6 1.0
N A:GLY107 4.3 17.9 1.0
C A:SER104 4.3 18.6 1.0
CA A:VAL103 4.3 19.0 1.0
O5' P:DG9 4.5 22.8 1.0
CA A:ARG102 4.5 20.3 1.0
CB A:ILE106 4.5 19.5 1.0
C A:GLY105 4.5 19.0 1.0
CA A:GLY107 4.6 17.4 1.0
CB A:THR101 4.6 18.7 1.0
O A:ARG102 4.6 19.4 1.0
O A:LEU100 4.8 18.1 1.0
CA A:GLY105 4.8 18.7 1.0
C5' P:DG9 5.0 24.4 1.0

Sodium binding site 3 out of 4 in 4rpz

Go back to Sodium Binding Sites List in 4rpz
Sodium binding site 3 out of 4 in the Human Dna Polymerase Beta with Gapped Dna Containing An 8-Oxo-7,8- Dihydro-Guanine (8-Oxog)and Dctp 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 3 of Human Dna Polymerase Beta with Gapped Dna Containing An 8-Oxo-7,8- Dihydro-Guanine (8-Oxog)and Dctp Soaked with MGCL2 For 60 S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na405

b:35.8
occ:1.00
 O A:HOH593 2.2 33.6 1.0
OD1 A:ASP318 2.3 33.8 1.0
OD2 A:ASP321 2.3 33.8 1.0
CG A:ASP321 3.4 32.0 1.0
CG A:ASP318 3.5 31.6 1.0
O A:HOH608 3.5 35.0 1.0
N A:ASP318 3.8 28.6 1.0
CA A:ASP318 3.9 29.2 1.0
CG A:LYS317 4.0 33.7 1.0
CD A:LYS317 4.1 35.1 1.0
OD1 A:ASP321 4.1 31.4 1.0
NZ A:LYS317 4.1 36.4 1.0
C A:LYS317 4.2 29.5 1.0
CB A:LYS317 4.3 32.9 1.0
O A:HOH585 4.3 16.7 0.5
CB A:ASP318 4.3 30.3 1.0
OG A:SER315 4.4 30.1 1.0
CB A:ASP321 4.4 31.3 1.0
OD2 A:ASP318 4.4 32.5 1.0
O A:LYS317 4.5 29.2 1.0
CE A:LYS317 4.7 35.8 1.0
CA A:LYS317 4.9 30.9 1.0

Sodium binding site 4 out of 4 in 4rpz

Go back to Sodium Binding Sites List in 4rpz
Sodium binding site 4 out of 4 in the Human Dna Polymerase Beta with Gapped Dna Containing An 8-Oxo-7,8- Dihydro-Guanine (8-Oxog)and Dctp 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 4 of Human Dna Polymerase Beta with Gapped Dna Containing An 8-Oxo-7,8- Dihydro-Guanine (8-Oxog)and Dctp Soaked with MGCL2 For 60 S within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na102

b:33.5
occ:1.00
 O1B D:DCP101 2.0 38.0 0.8
O2G D:DCP101 2.2 35.2 0.8
O D:HOH209 2.2 31.1 0.5
O D:HOH208 2.3 21.2 0.5
O D:HOH210 3.0 37.8 1.0
PB D:DCP101 3.2 34.9 0.8
PG D:DCP101 3.3 35.6 0.8
O3B D:DCP101 3.4 36.6 0.8
O1G D:DCP101 3.9 36.1 0.8
O2B D:DCP101 4.3 34.9 0.8
O3A D:DCP101 4.4 38.7 0.8
O3G D:DCP101 4.5 34.5 0.8

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 18:17:50 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy