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Sodium in PDB 4rq8: Human Dna Polymerase Beta with Gapped Dna Containing An 8-Oxo-7,8- Dihydro-Guanine(8-Oxog) and Datp Soaked with MNCL2 For 35 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 MNCL2 For 35 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 MNCL2 For 35 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 MNCL2 For 35 S, PDB code: 4rq8 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) 40.79 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.220, 82.540, 54.740, 90.00, 110.89, 90.00
R / Rfree (%) 20.7 / 27

Other elements in 4rq8:

The structure of Human Dna Polymerase Beta with Gapped Dna Containing An 8-Oxo-7,8- Dihydro-Guanine(8-Oxog) and Datp Soaked with MNCL2 For 35 S also contains other interesting chemical elements:

Manganese (Mn) 6 atoms
Chlorine (Cl) 6 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 MNCL2 For 35 S (pdb code 4rq8). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 9 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 MNCL2 For 35 S, PDB code: 4rq8:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Sodium binding site 1 out of 9 in 4rq8

Go back to Sodium Binding Sites List in 4rq8
Sodium binding site 1 out of 9 in the Human Dna Polymerase Beta with Gapped Dna Containing An 8-Oxo-7,8- Dihydro-Guanine(8-Oxog) and Datp Soaked with MNCL2 For 35 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 MNCL2 For 35 S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na407

b:28.1
occ:1.00
 O A:HOH525 2.1 31.9 1.0
O A:HOH666 2.2 50.6 1.0
O A:HOH526 2.3 35.3 1.0
NE2 A:HIS340 2.9 37.8 1.0
CE1 A:HIS340 3.5 39.0 1.0
CD2 A:HIS340 3.8 37.5 1.0
O A:THR10 4.2 20.9 1.0
NZ A:LYS52 4.3 33.2 1.0
N A:GLU9 4.3 43.9 1.0
ND1 A:HIS340 4.6 38.8 1.0
CG A:HIS340 4.7 35.4 1.0

Sodium binding site 2 out of 9 in 4rq8

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Sodium binding site 2 out of 9 in the Human Dna Polymerase Beta with Gapped Dna Containing An 8-Oxo-7,8- Dihydro-Guanine(8-Oxog) and Datp Soaked with MNCL2 For 35 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 MNCL2 For 35 S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na408

b:30.9
occ:1.00
 O A:HOH548 2.2 30.3 1.0
OP1 D:DC3 2.4 27.2 1.0
O A:HOH547 2.4 31.5 1.0
O A:VAL65 2.5 26.9 1.0
O A:LEU62 2.6 29.6 1.0
O A:LYS60 2.6 29.4 1.0
P D:DC3 3.3 26.7 1.0
OP2 D:DC3 3.4 26.2 1.0
C A:LEU62 3.5 27.9 1.0
C A:VAL65 3.5 25.7 1.0
C A:LYS60 3.8 29.8 1.0
N A:VAL65 3.9 24.9 1.0
CA A:PRO63 4.1 27.0 1.0
N A:GLY64 4.1 26.0 1.0
N A:PRO63 4.2 26.5 1.0
CA A:VAL65 4.2 24.9 1.0
N A:LEU62 4.3 30.3 1.0
C A:LYS61 4.3 29.6 1.0
O3' D:DT2 4.4 24.4 1.0
O A:LYS61 4.4 26.5 1.0
CA A:LYS60 4.5 29.7 1.0
CB A:VAL65 4.5 26.1 1.0
O5' D:DC3 4.5 26.5 1.0
C A:PRO63 4.5 27.8 1.0
CA A:LEU62 4.6 27.8 1.0
N A:GLY66 4.6 23.3 1.0
CG A:LYS60 4.6 33.6 1.0
N A:LYS61 4.8 29.0 1.0
CA A:GLY66 4.9 23.9 1.0
C A:GLY64 4.9 24.3 1.0
CA A:LYS61 4.9 30.4 1.0

Sodium binding site 3 out of 9 in 4rq8

Go back to Sodium Binding Sites List in 4rq8
Sodium binding site 3 out of 9 in the Human Dna Polymerase Beta with Gapped Dna Containing An 8-Oxo-7,8- Dihydro-Guanine(8-Oxog) and Datp Soaked with MNCL2 For 35 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 Datp Soaked with MNCL2 For 35 S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na409

b:15.5
occ:1.00
 O A:HOH553 2.1 22.3 1.0
O A:THR101 2.2 16.7 1.0
O A:ILE106 2.4 19.2 1.0
O P:HOH504 2.4 20.3 1.0
OP1 P:DG9 2.5 19.8 1.0
O A:VAL103 2.5 18.1 1.0
C A:THR101 3.3 17.4 1.0
C A:VAL103 3.3 19.1 1.0
P P:DG9 3.4 19.5 1.0
C A:ILE106 3.5 18.0 1.0
OP2 P:DG9 3.6 18.2 1.0
N A:ILE106 3.8 17.4 1.0
CA A:THR101 3.9 16.9 1.0
N A:VAL103 4.0 19.6 1.0
CA A:SER104 4.0 20.0 1.0
N A:SER104 4.0 19.6 1.0
N A:GLY105 4.1 18.5 1.0
C A:ARG102 4.1 19.7 1.0
CA A:ILE106 4.2 16.4 1.0
N A:ARG102 4.2 18.7 1.0
CA A:VAL103 4.3 19.1 1.0
C A:SER104 4.4 20.1 1.0
CA A:ARG102 4.4 20.7 1.0
N A:GLY107 4.4 17.7 1.0
CB A:THR101 4.5 17.4 1.0
O3' P:DC8 4.5 20.4 1.0
O A:ARG102 4.6 20.9 1.0
O5' P:DG9 4.6 19.9 1.0
CB A:ILE106 4.6 15.9 1.0
C A:GLY105 4.7 17.7 1.0
CA A:GLY107 4.7 17.3 1.0
O A:LEU100 4.9 17.4 1.0
CA A:GLY105 4.9 18.7 1.0

Sodium binding site 4 out of 9 in 4rq8

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Sodium binding site 4 out of 9 in the Human Dna Polymerase Beta with Gapped Dna Containing An 8-Oxo-7,8- Dihydro-Guanine(8-Oxog) and Datp Soaked with MNCL2 For 35 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 Datp Soaked with MNCL2 For 35 S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na410

b:43.9
occ:1.00
 O A:HOH670 1.9 40.1 1.0
OE2 A:GLU288 2.1 39.8 1.0
ND1 A:HIS285 2.9 31.4 1.0
CD A:GLU288 3.3 38.0 1.0
O A:HOH635 3.8 35.8 1.0
CE1 A:HIS285 3.8 30.7 1.0
OE1 A:GLU288 3.8 37.8 1.0
CG A:HIS285 3.8 30.6 1.0
CB A:HIS285 4.0 28.0 1.0
CG A:GLU288 4.4 34.5 1.0
CA A:HIS285 4.4 27.4 1.0
NE2 A:HIS285 4.9 31.2 1.0
CD2 A:HIS285 5.0 31.6 1.0
NE1 A:TRP325 5.0 32.2 1.0

Sodium binding site 5 out of 9 in 4rq8

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Sodium binding site 5 out of 9 in the Human Dna Polymerase Beta with Gapped Dna Containing An 8-Oxo-7,8- Dihydro-Guanine(8-Oxog) and Datp Soaked with MNCL2 For 35 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 Datp Soaked with MNCL2 For 35 S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na411

b:18.8
occ:1.00
 OD2 A:ASP314 1.8 32.6 1.0
O A:HOH657 2.0 31.4 1.0
O A:HOH656 2.1 36.4 1.0
CG A:ASP314 2.9 30.7 1.0
CB A:ASP314 3.5 26.5 1.0
OD1 A:ASP314 4.0 32.5 1.0
O A:HOH631 4.1 35.5 1.0

Sodium binding site 6 out of 9 in 4rq8

Go back to Sodium Binding Sites List in 4rq8
Sodium binding site 6 out of 9 in the Human Dna Polymerase Beta with Gapped Dna Containing An 8-Oxo-7,8- Dihydro-Guanine(8-Oxog) and Datp Soaked with MNCL2 For 35 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 Datp Soaked with MNCL2 For 35 S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na412

b:22.7
occ:1.00
 O A:HOH586 2.1 32.8 1.0
OD2 A:ASP145 2.1 22.9 1.0
O A:HOH585 2.2 27.7 1.0
O A:HOH596 2.4 34.5 1.0
ND1 A:HIS252 2.8 24.7 1.0
CG A:ASP145 3.1 22.9 1.0
CE1 A:HIS252 3.5 23.2 1.0
OD1 A:ASP145 3.6 25.7 1.0
CG A:HIS252 3.9 22.4 1.0
N A:HIS252 4.0 23.1 1.0
CD1 A:TYR142 4.3 26.9 1.0
CB A:HIS252 4.4 22.0 1.0
CB A:ASP145 4.4 21.5 1.0
CE1 A:TYR142 4.4 27.6 1.0
CA A:PRO251 4.6 25.3 1.0
NE2 A:HIS252 4.7 23.3 1.0
O A:HOH578 4.7 25.0 1.0
C A:PRO251 4.8 24.4 1.0
CA A:HIS252 4.8 22.2 1.0
O A:TYR250 4.9 27.9 1.0
CD2 A:HIS252 4.9 22.9 1.0

Sodium binding site 7 out of 9 in 4rq8

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Sodium binding site 7 out of 9 in the Human Dna Polymerase Beta with Gapped Dna Containing An 8-Oxo-7,8- Dihydro-Guanine(8-Oxog) and Datp Soaked with MNCL2 For 35 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 Datp Soaked with MNCL2 For 35 S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na413

b:31.2
occ:1.00
 OD1 A:ASP160 1.9 33.1 1.0
O A:HOH595 2.5 29.3 1.0
CG A:ASP160 3.0 32.2 1.0
CB A:ASP160 3.5 29.8 1.0
CA A:ASP160 3.7 28.5 1.0
OD2 A:ASP160 4.1 31.5 1.0
O A:ASP160 4.3 28.5 1.0
C A:ASP160 4.5 28.9 1.0
N A:ASP160 4.9 26.8 1.0

Sodium binding site 8 out of 9 in 4rq8

Go back to Sodium Binding Sites List in 4rq8
Sodium binding site 8 out of 9 in the Human Dna Polymerase Beta with Gapped Dna Containing An 8-Oxo-7,8- Dihydro-Guanine(8-Oxog) and Datp Soaked with MNCL2 For 35 S


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Human Dna Polymerase Beta with Gapped Dna Containing An 8-Oxo-7,8- Dihydro-Guanine(8-Oxog) and Datp Soaked with MNCL2 For 35 S within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Na101

b:30.6
occ:1.00
 O T:HOH204 2.0 31.6 1.0
O T:HOH205 2.3 30.6 1.0
O T:HOH227 2.4 33.4 1.0
N7 T:DG7 2.8 20.2 1.0
N1 T:8OG6 3.6 20.1 1.0
C2 T:8OG6 3.6 21.5 1.0
C8 T:DG7 3.7 20.8 1.0
O T:HOH233 3.7 32.5 1.0
N4 T:DC8 3.8 19.9 1.0
C5 T:DG7 3.8 20.6 1.0
N2 T:8OG6 3.9 22.7 1.0
O6 T:DG7 3.9 22.6 1.0
C6 T:8OG6 4.0 19.6 1.0
N3 T:8OG6 4.0 21.2 1.0
O A:HOH531 4.1 25.6 1.0
C6 T:DG7 4.3 21.3 1.0
C4 T:8OG6 4.4 20.2 1.0
C5 T:8OG6 4.4 19.8 1.0
O6 T:8OG6 4.6 19.2 1.0
C4 T:DC8 4.7 19.5 1.0
O T:HOH203 4.7 26.9 1.0
N9 T:DG7 4.9 20.9 1.0
C4 T:DG7 5.0 20.4 1.0
C5 T:DC8 5.0 20.0 1.0

Sodium binding site 9 out of 9 in 4rq8

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Sodium binding site 9 out of 9 in the Human Dna Polymerase Beta with Gapped Dna Containing An 8-Oxo-7,8- Dihydro-Guanine(8-Oxog) and Datp Soaked with MNCL2 For 35 S


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Human Dna Polymerase Beta with Gapped Dna Containing An 8-Oxo-7,8- Dihydro-Guanine(8-Oxog) and Datp Soaked with MNCL2 For 35 S within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Na102

b:25.1
occ:1.00
 O T:HOH221 1.8 29.3 1.0
O T:HOH220 2.0 37.8 1.0
OP1 T:DA11 2.2 24.0 1.0
O T:HOH218 2.3 38.5 1.0
O T:HOH219 2.4 33.6 1.0
P T:DA11 3.4 24.8 1.0
OP2 T:DA11 3.9 23.3 1.0
O5' T:DA11 3.9 23.2 1.0
O A:LYS230 4.2 21.4 1.0
N A:LYS230 4.3 21.9 1.0
C5' T:DA11 4.6 25.1 1.0
O3' T:DC10 4.7 21.9 1.0
CA A:SER229 4.8 20.0 1.0
CB A:LYS230 4.9 27.5 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 18:19:52 2024

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