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Sodium in PDB 4rpy: Human Dna Polymerase Beta with Gapped Dna Containing An 8-Oxo-7,8- Dihydro-Guanine(8-Oxog) and Dctp 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 Dctp 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 Dctp 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 Dctp Soaked with MGCL2 For 30 S, PDB code: 4rpy 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) 31.23 / 1.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 49.440, 79.530, 55.520, 90.00, 106.61, 90.00
R / Rfree (%) 19 / 23

Other elements in 4rpy:

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 30 S also contains other interesting chemical elements:

Magnesium (Mg) 3 atoms
Chlorine (Cl) 4 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 30 S (pdb code 4rpy). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 7 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 30 S, PDB code: 4rpy:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7;

Sodium binding site 1 out of 7 in 4rpy

Go back to Sodium Binding Sites List in 4rpy
Sodium binding site 1 out of 7 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 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 Dctp Soaked with MGCL2 For 30 S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na403

b:46.4
occ:1.00
 O A:HOH562 2.1 38.0 1.0
O A:HOH640 2.3 37.4 1.0
O A:HOH546 2.4 44.4 1.0
OE1 A:GLU249 3.2 32.5 1.0
O A:HOH535 3.4 35.4 1.0
OE2 A:GLU249 3.5 34.1 1.0
CD A:GLU249 3.8 34.0 1.0
CE1 A:HIS252 4.0 15.8 1.0
NE2 A:HIS252 4.7 16.2 1.0
O A:HOH587 4.7 27.8 1.0
OE1 A:GLN240 4.8 17.1 1.0
NE2 A:GLN240 4.9 16.4 1.0

Sodium binding site 2 out of 7 in 4rpy

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Sodium binding site 2 out of 7 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 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 Dctp Soaked with MGCL2 For 30 S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na404

b:18.5
occ:1.00
 O D:HOH202 2.3 25.4 1.0
O A:HOH536 2.3 23.1 1.0
O A:VAL65 2.4 16.5 1.0
O A:LYS60 2.4 19.7 1.0
O A:LEU62 2.5 20.2 1.0
OP1 D:DC3 2.6 17.8 1.0
C A:LEU62 3.5 20.1 1.0
C A:VAL65 3.5 15.9 1.0
C A:LYS60 3.5 21.2 1.0
P D:DC3 3.6 17.8 1.0
OP2 D:DC3 3.8 17.9 1.0
O D:HOH212 3.8 29.0 1.0
N A:VAL65 3.9 16.0 1.0
N A:LEU62 4.1 20.3 1.0
C A:LYS61 4.1 22.0 1.0
CA A:VAL65 4.2 15.6 1.0
CA A:PRO63 4.3 20.2 1.0
N A:GLY64 4.3 18.1 1.0
N A:PRO63 4.3 20.0 1.0
CA A:LYS60 4.3 21.3 1.0
O A:LYS61 4.3 21.9 1.0
CB A:VAL65 4.4 15.1 1.0
CA A:LEU62 4.5 20.5 1.0
N A:LYS61 4.5 21.3 1.0
O3' D:DT2 4.5 16.8 1.0
CG A:LYS60 4.5 25.8 1.0
N A:GLY66 4.6 16.0 1.0
CA A:LYS61 4.6 23.2 1.0
C A:PRO63 4.7 19.2 1.0
CA A:GLY66 4.9 16.4 1.0
O5' D:DC3 4.9 18.8 1.0
C A:GLY64 4.9 16.5 1.0

Sodium binding site 3 out of 7 in 4rpy

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Sodium binding site 3 out of 7 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 30 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 30 S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na405

b:46.0
occ:1.00
 OD1 A:ASP160 2.3 19.4 1.0
O A:HOH660 2.3 13.9 0.5
O A:HOH689 2.4 31.1 1.0
O A:HOH688 2.6 33.7 1.0
CG A:ASP160 3.3 18.3 1.0
CB A:ASP160 3.8 17.8 1.0
CA A:ASP160 3.8 17.1 1.0
O A:ASP160 4.3 16.4 1.0
OD2 A:ASP160 4.4 20.3 1.0
C A:ASP160 4.6 16.8 1.0
O A:HOH610 4.6 25.0 1.0
N A:ASP160 5.0 16.7 1.0

Sodium binding site 4 out of 7 in 4rpy

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Sodium binding site 4 out of 7 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 30 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 30 S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na406

b:42.3
occ:1.00
 O A:HOH568 2.6 27.6 1.0
OD2 A:ASP321 2.7 32.6 1.0
OD1 A:ASP318 2.8 25.3 1.0
O A:HOH678 2.8 36.2 1.0
CG A:ASP321 3.8 29.3 1.0
O A:HOH684 3.9 33.4 1.0
CG A:LYS317 4.0 30.2 1.0
CG A:ASP318 4.0 24.8 1.0
CD A:LYS317 4.0 31.7 1.0
O A:HOH677 4.0 33.2 1.0
NZ A:LYS317 4.2 33.2 1.0
N A:ASP318 4.2 24.5 1.0
CB A:LYS317 4.3 28.3 1.0
CA A:ASP318 4.4 23.9 1.0
OG A:SER315 4.4 22.9 1.0
OD1 A:ASP321 4.4 29.8 1.0
C A:LYS317 4.5 25.9 1.0
CE A:LYS317 4.7 32.8 1.0
O A:LYS317 4.7 27.5 1.0
CB A:ASP318 4.8 24.7 1.0
CB A:ASP321 4.9 28.2 1.0
OD2 A:ASP318 4.9 25.8 1.0

Sodium binding site 5 out of 7 in 4rpy

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Sodium binding site 5 out of 7 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 30 S


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Human Dna Polymerase Beta with Gapped Dna Containing An 8-Oxo-7,8- Dihydro-Guanine(8-Oxog) and Dctp Soaked with MGCL2 For 30 S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na407

b:12.7
occ:1.00
 O A:THR101 2.3 11.9 1.0
O A:HOH503 2.4 14.5 1.0
OP1 P:DG9 2.4 18.4 1.0
O A:VAL103 2.4 11.5 1.0
O P:HOH202 2.5 21.1 1.0
O A:ILE106 2.5 12.4 1.0
C A:THR101 3.3 12.5 1.0
C A:VAL103 3.4 12.4 1.0
P P:DG9 3.4 18.8 1.0
C A:ILE106 3.5 11.5 1.0
OP2 P:DG9 3.6 18.7 1.0
N A:ILE106 3.8 10.7 1.0
CA A:THR101 4.0 11.8 1.0
CA A:SER104 4.0 12.2 1.0
N A:GLY105 4.0 11.5 1.0
N A:SER104 4.1 12.3 1.0
N A:VAL103 4.1 13.5 1.0
C A:ARG102 4.2 14.2 1.0
CA A:ILE106 4.2 11.1 1.0
N A:ARG102 4.3 13.1 1.0
C A:SER104 4.4 11.9 1.0
CA A:VAL103 4.4 13.3 1.0
N A:GLY107 4.4 11.7 1.0
O A:ARG102 4.4 14.4 1.0
O3' P:DC8 4.5 19.2 1.0
CA A:ARG102 4.5 14.9 1.0
CB A:THR101 4.6 11.6 1.0
O5' P:DG9 4.6 20.2 1.0
CB A:ILE106 4.6 10.8 1.0
C A:GLY105 4.7 11.2 1.0
CA A:GLY107 4.7 12.1 1.0
O A:LEU100 4.8 10.9 1.0
CA A:GLY105 4.9 11.3 1.0
O A:HOH682 4.9 33.7 1.0

Sodium binding site 6 out of 7 in 4rpy

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Sodium binding site 6 out of 7 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 30 S


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Human Dna Polymerase Beta with Gapped Dna Containing An 8-Oxo-7,8- Dihydro-Guanine(8-Oxog) and Dctp Soaked with MGCL2 For 30 S within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na101

b:33.1
occ:1.00
 O1G T:DCP101 1.9 28.1 0.7
O1B T:DCP101 2.1 26.3 0.7
O T:HOH235 2.1 35.5 1.0
PG T:DCP101 3.2 28.4 0.7
PB T:DCP101 3.2 26.5 0.7
O3B T:DCP101 3.4 27.3 0.7
O2B T:DCP101 3.9 25.8 0.7
O2G T:DCP101 4.1 28.6 0.7
O3G T:DCP101 4.2 27.4 0.7
O3A T:DCP101 4.5 26.2 0.7

Sodium binding site 7 out of 7 in 4rpy

Go back to Sodium Binding Sites List in 4rpy
Sodium binding site 7 out of 7 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 30 S


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Human Dna Polymerase Beta with Gapped Dna Containing An 8-Oxo-7,8- Dihydro-Guanine(8-Oxog) and Dctp Soaked with MGCL2 For 30 S within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Na102

b:44.0
occ:1.00
 O A:HOH663 2.0 28.6 1.0
O T:HOH231 2.1 32.4 1.0
OP1 T:DA11 2.3 20.4 1.0
O T:HOH232 2.5 40.9 1.0
P T:DA11 3.6 19.6 1.0
OP2 T:DA11 4.2 19.3 1.0
O A:LYS230 4.3 19.3 1.0
N A:LYS230 4.3 17.1 1.0
O5' T:DA11 4.4 20.7 1.0
C5' T:DA11 4.6 22.5 1.0
O3' T:DC10 4.8 18.4 1.0
CA A:SER229 4.8 15.4 1.0
O T:HOH207 4.8 44.6 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 18:17:50 2024

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