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Sodium in PDB 4rq2: Human Dna Polymerase Beta with Gapped Dna Containing An 8-Oxo-7,8- Dihydro-Guanine (8-Oxog)and Dctp 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 Dctp 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 Dctp 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 Dctp Soaked with MNCL2 For 35 S, PDB code: 4rq2 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) 46.64 / 2.20
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 49.850, 82.290, 54.680, 90.00, 110.68, 90.00
R / Rfree (%) 19.4 / 26.9

Other elements in 4rq2:

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

Manganese (Mn) 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 Dctp Soaked with MNCL2 For 35 S (pdb code 4rq2). 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 MNCL2 For 35 S, PDB code: 4rq2:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7;

Sodium binding site 1 out of 7 in 4rq2

Go back to Sodium Binding Sites List in 4rq2
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 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 Dctp Soaked with MNCL2 For 35 S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na407

b:38.3
occ:1.00
 O A:HOH597 2.3 29.8 1.0
OD2 A:ASP145 2.4 30.8 1.0
ND1 A:HIS252 3.1 30.6 1.0
CG A:ASP145 3.4 31.5 1.0
CE1 A:HIS252 3.7 29.0 1.0
OD1 A:ASP145 3.8 35.3 1.0
CG A:HIS252 4.3 27.5 1.0
N A:HIS252 4.3 27.1 1.0
CD1 A:TYR142 4.6 30.1 1.0
CB A:ASP145 4.7 29.6 1.0
CE1 A:TYR142 4.7 29.4 1.0
CB A:HIS252 4.7 26.3 1.0
CA A:PRO251 4.7 31.2 1.0
NE2 A:HIS252 4.9 29.3 1.0

Sodium binding site 2 out of 7 in 4rq2

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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 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 Dctp Soaked with MNCL2 For 35 S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na408

b:18.6
occ:1.00
 O A:HOH520 2.1 27.5 1.0
O A:THR101 2.1 20.7 1.0
OP1 P:DG9 2.2 25.3 1.0
O P:HOH201 2.3 16.0 1.0
O A:ILE106 2.3 19.7 1.0
O A:VAL103 2.6 20.0 1.0
P P:DG9 3.3 25.9 1.0
C A:THR101 3.3 20.0 1.0
C A:ILE106 3.3 19.4 1.0
OP2 P:DG9 3.4 23.7 1.0
C A:VAL103 3.6 19.8 1.0
N A:ILE106 3.8 19.1 1.0
CA A:THR101 3.9 19.4 1.0
N A:GLY105 4.1 17.9 1.0
CA A:ILE106 4.1 18.9 1.0
CA A:SER104 4.1 20.3 1.0
N A:VAL103 4.2 20.4 1.0
N A:GLY107 4.2 20.1 1.0
O3' P:DC8 4.3 26.2 1.0
N A:ARG102 4.3 20.7 1.0
N A:SER104 4.3 19.4 1.0
C A:ARG102 4.3 22.0 1.0
CA A:GLY107 4.4 21.4 1.0
C A:SER104 4.4 19.5 1.0
O5' P:DG9 4.5 24.8 1.0
CB A:THR101 4.5 19.6 1.0
CA A:ARG102 4.5 22.7 1.0
CB A:ILE106 4.5 18.8 1.0
CA A:VAL103 4.6 19.7 1.0
C A:GLY105 4.7 19.6 1.0
O A:LEU100 4.8 19.6 1.0
O A:ARG102 4.9 24.0 1.0
CA A:GLY105 5.0 18.6 1.0

Sodium binding site 3 out of 7 in 4rq2

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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 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 Dctp Soaked with MNCL2 For 35 S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na409

b:39.4
occ:1.00
 O A:HOH614 2.2 35.3 0.5
OE2 A:GLU288 2.2 46.9 1.0
O A:HOH613 2.2 39.6 0.5
ND1 A:HIS285 2.3 39.4 1.0
CE1 A:HIS285 3.1 40.3 1.0
CG A:HIS285 3.3 39.1 1.0
CD A:GLU288 3.5 51.9 1.0
CB A:HIS285 3.7 33.9 1.0
NE2 A:HIS285 4.1 40.1 1.0
CD2 A:HIS285 4.3 40.5 1.0
CA A:HIS285 4.3 33.6 1.0
OE1 A:GLU288 4.3 53.2 1.0
CG A:GLU288 4.4 47.8 1.0
NE1 A:TRP325 4.9 45.1 1.0

Sodium binding site 4 out of 7 in 4rq2

Go back to Sodium Binding Sites List in 4rq2
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 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 Dctp Soaked with MNCL2 For 35 S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na410

b:34.3
occ:1.00
 O A:HOH593 2.2 38.2 1.0
OD2 A:ASP314 2.2 38.5 1.0
O A:HOH592 2.2 42.3 1.0
CG A:ASP314 3.1 40.8 1.0
CB A:ASP314 3.4 34.5 1.0
O A:HOH566 3.9 30.3 1.0
OD1 A:ASP314 4.2 45.0 1.0
CA A:ASP314 4.9 31.5 1.0

Sodium binding site 5 out of 7 in 4rq2

Go back to Sodium Binding Sites List in 4rq2
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 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 Dctp Soaked with MNCL2 For 35 S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na411

b:40.8
occ:1.00
 O A:LYS60 2.3 37.6 1.0
O A:VAL65 2.5 32.8 1.0
OP1 D:DC3 2.6 32.2 1.0
O A:LEU62 2.6 35.9 1.0
C A:LYS60 3.5 37.5 1.0
P D:DC3 3.5 38.6 1.0
OP2 D:DC3 3.5 38.3 1.0
C A:LEU62 3.6 36.8 1.0
C A:VAL65 3.6 34.7 1.0
N A:VAL65 3.9 35.6 1.0
C A:LYS61 4.1 42.9 1.0
N A:GLY64 4.1 38.0 1.0
CA A:PRO63 4.1 34.8 1.0
O A:LYS61 4.2 42.2 1.0
N A:PRO63 4.3 34.7 1.0
CA A:LYS60 4.3 37.1 1.0
N A:LEU62 4.3 42.4 1.0
CA A:VAL65 4.3 33.0 1.0
CG A:LYS60 4.4 37.2 1.0
N A:LYS61 4.4 40.3 1.0
C A:PRO63 4.5 38.3 1.0
CA A:LYS61 4.5 43.5 1.0
CA A:LEU62 4.6 38.8 1.0
O3' D:DT2 4.6 36.3 1.0
CB A:VAL65 4.6 31.5 1.0
N A:GLY66 4.6 34.8 1.0
O5' D:DC3 4.7 33.0 1.0
CA A:GLY66 4.9 34.0 1.0
C A:GLY64 4.9 38.3 1.0
NZ A:LYS60 4.9 33.7 1.0
O A:ALA59 5.0 37.8 1.0
CB A:LYS60 5.0 39.5 1.0

Sodium binding site 6 out of 7 in 4rq2

Go back to Sodium Binding Sites List in 4rq2
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 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 Dctp Soaked with MNCL2 For 35 S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na412

b:46.5
occ:1.00
 O A:HOH524 2.0 37.9 1.0
O A:HOH585 2.2 22.2 1.0
O A:THR10 3.3 39.3 1.0
CD2 A:HIS340 3.6 66.2 1.0
N A:ASN12 3.9 31.6 1.0
NE2 A:HIS340 3.9 72.7 1.0
O A:HOH504 4.1 16.8 1.0
N A:GLY13 4.1 31.8 1.0
NZ A:LYS52 4.3 57.9 1.0
CA A:ASN12 4.4 31.3 1.0
C A:THR10 4.5 35.5 1.0
CG A:HIS340 4.5 62.6 1.0
O A:HOH556 4.6 45.0 1.0
CA A:LEU11 4.7 32.6 1.0
C A:LEU11 4.7 30.4 1.0
C A:ASN12 4.8 31.8 1.0
CE1 A:HIS340 4.9 70.8 1.0

Sodium binding site 7 out of 7 in 4rq2

Go back to Sodium Binding Sites List in 4rq2
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 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 Dctp Soaked with MNCL2 For 35 S within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Na101

b:28.0
occ:1.00
 O T:HOH223 1.9 25.1 1.0
O T:HOH214 2.0 27.8 1.0
O T:HOH225 2.1 31.2 1.0
O T:HOH215 2.2 53.6 1.0
OP1 T:DA11 2.3 26.8 1.0
O T:HOH227 2.4 15.9 0.5
P T:DA11 3.6 30.7 1.0
O T:HOH226 4.1 34.1 1.0
O5' T:DA11 4.1 27.8 1.0
N A:LYS230 4.2 27.9 1.0
OP2 T:DA11 4.3 26.5 1.0
O A:LYS230 4.4 33.4 1.0
C5' T:DA11 4.5 30.5 1.0
CA A:SER229 4.5 25.4 1.0
O3' T:DC10 4.7 25.7 1.0
C A:SER229 4.8 27.3 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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