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Sodium in PDB 4rq3: Precatalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Containing An 8-Oxo-7,8-Dihydro-Guanine (8-Oxog) and Datp in the Presence of CACL2

Enzymatic activity of Precatalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Containing An 8-Oxo-7,8-Dihydro-Guanine (8-Oxog) and Datp in the Presence of CACL2

All present enzymatic activity of Precatalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Containing An 8-Oxo-7,8-Dihydro-Guanine (8-Oxog) and Datp in the Presence of CACL2:
2.7.7.7;

Protein crystallography data

The structure of Precatalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Containing An 8-Oxo-7,8-Dihydro-Guanine (8-Oxog) and Datp in the Presence of CACL2, PDB code: 4rq3 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) 47.29 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 49.320, 79.680, 55.450, 90.00, 106.51, 90.00
R / Rfree (%) 19.2 / 24.6

Other elements in 4rq3:

The structure of Precatalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Containing An 8-Oxo-7,8-Dihydro-Guanine (8-Oxog) and Datp in the Presence of CACL2 also contains other interesting chemical elements:

Calcium (Ca) 2 atoms
Chlorine (Cl) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Precatalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Containing An 8-Oxo-7,8-Dihydro-Guanine (8-Oxog) and Datp in the Presence of CACL2 (pdb code 4rq3). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Precatalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Containing An 8-Oxo-7,8-Dihydro-Guanine (8-Oxog) and Datp in the Presence of CACL2, PDB code: 4rq3:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 4rq3

Go back to Sodium Binding Sites List in 4rq3
Sodium binding site 1 out of 4 in the Precatalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Containing An 8-Oxo-7,8-Dihydro-Guanine (8-Oxog) and Datp in the Presence of CACL2


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Precatalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Containing An 8-Oxo-7,8-Dihydro-Guanine (8-Oxog) and Datp in the Presence of CACL2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na404

b:49.7
occ:1.00
 O A:HOH679 2.1 37.3 1.0
O A:HOH677 2.2 40.5 1.0
O A:HOH678 2.3 44.5 1.0
O A:HOH583 3.7 39.0 1.0
OE1 A:GLU249 4.0 34.1 1.0
CE1 A:HIS252 4.1 17.9 1.0
OE1 A:GLN240 4.2 16.7 1.0
NE2 A:HIS252 4.3 17.7 1.0
OE2 A:GLU249 4.3 34.9 1.0
CD A:GLU249 4.6 34.3 1.0
O A:HOH660 5.0 45.7 1.0

Sodium binding site 2 out of 4 in 4rq3

Go back to Sodium Binding Sites List in 4rq3
Sodium binding site 2 out of 4 in the Precatalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Containing An 8-Oxo-7,8-Dihydro-Guanine (8-Oxog) and Datp in the Presence of CACL2


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Precatalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Containing An 8-Oxo-7,8-Dihydro-Guanine (8-Oxog) and Datp in the Presence of CACL2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na405

b:11.4
occ:1.00
 O A:THR101 2.2 16.8 1.0
O A:HOH504 2.3 17.3 1.0
O A:VAL103 2.3 16.6 1.0
O P:HOH102 2.4 23.0 1.0
OP1 P:DG9 2.4 24.8 1.0
O A:ILE106 2.4 16.4 1.0
C A:THR101 3.3 17.7 1.0
C A:VAL103 3.4 17.7 1.0
C A:ILE106 3.4 15.9 1.0
P P:DG9 3.4 24.1 1.0
OP2 P:DG9 3.7 24.4 1.0
N A:ILE106 3.9 16.3 1.0
CA A:THR101 3.9 16.4 1.0
N A:VAL103 4.0 18.6 1.0
CA A:SER104 4.1 17.9 1.0
N A:SER104 4.1 17.9 1.0
N A:GLY105 4.1 17.7 1.0
C A:ARG102 4.2 19.8 1.0
CA A:ILE106 4.2 15.7 1.0
N A:ARG102 4.3 19.0 1.0
CA A:VAL103 4.3 18.3 1.0
N A:GLY107 4.4 15.0 1.0
C A:SER104 4.4 17.6 1.0
CB A:THR101 4.5 15.9 1.0
O5' P:DG9 4.5 24.8 1.0
CA A:ARG102 4.5 20.7 1.0
O A:ARG102 4.5 18.6 1.0
O3' P:DC8 4.6 25.6 1.0
CB A:ILE106 4.6 15.9 1.0
CA A:GLY107 4.6 14.3 1.0
C A:GLY105 4.8 17.2 1.0
O A:LEU100 4.8 15.1 1.0
CA A:GLY105 5.0 17.6 1.0

Sodium binding site 3 out of 4 in 4rq3

Go back to Sodium Binding Sites List in 4rq3
Sodium binding site 3 out of 4 in the Precatalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Containing An 8-Oxo-7,8-Dihydro-Guanine (8-Oxog) and Datp in the Presence of CACL2


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Precatalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Containing An 8-Oxo-7,8-Dihydro-Guanine (8-Oxog) and Datp in the Presence of CACL2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na406

b:28.2
occ:1.00
 O A:HOH522 2.1 38.7 1.0
O A:VAL65 2.3 25.1 1.0
O A:LEU62 2.4 29.4 1.0
O A:LYS60 2.5 28.7 1.0
OP1 D:DC3 2.8 31.5 1.0
C A:LEU62 3.5 28.4 1.0
C A:VAL65 3.5 25.1 1.0
C A:LYS60 3.6 30.1 1.0
OP2 D:DC3 3.7 33.7 1.0
P D:DC3 3.7 32.4 1.0
N A:VAL65 3.9 25.3 1.0
CA A:VAL65 4.2 24.4 1.0
N A:LEU62 4.2 30.1 1.0
CA A:PRO63 4.2 27.2 1.0
C A:LYS61 4.2 32.4 1.0
N A:PRO63 4.2 27.6 1.0
N A:GLY64 4.3 26.3 1.0
CA A:LYS60 4.4 29.8 1.0
CB A:VAL65 4.4 23.6 1.0
CA A:LEU62 4.4 29.4 1.0
O A:LYS61 4.4 33.5 1.0
CG A:LYS60 4.5 35.6 1.0
N A:GLY66 4.5 25.7 1.0
N A:LYS61 4.6 30.9 1.0
C A:PRO63 4.6 26.6 1.0
O3' D:DT2 4.7 31.3 1.0
CA A:LYS61 4.7 33.8 1.0
CA A:GLY66 4.8 25.3 1.0
C A:GLY64 4.9 25.8 1.0
O5' D:DC3 5.0 33.1 1.0
O A:ALA59 5.0 25.8 1.0

Sodium binding site 4 out of 4 in 4rq3

Go back to Sodium Binding Sites List in 4rq3
Sodium binding site 4 out of 4 in the Precatalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Containing An 8-Oxo-7,8-Dihydro-Guanine (8-Oxog) and Datp in the Presence of CACL2


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Precatalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Containing An 8-Oxo-7,8-Dihydro-Guanine (8-Oxog) and Datp in the Presence of CACL2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na407

b:38.1
occ:1.00
 O A:HOH610 2.1 45.5 1.0
OD1 A:ASP160 2.1 20.4 1.0
O A:HOH681 2.3 30.7 1.0
O A:HOH652 2.4 14.3 0.5
CG A:ASP160 3.1 19.3 1.0
CB A:ASP160 3.5 18.6 1.0
CA A:ASP160 3.8 17.9 1.0
OD2 A:ASP160 4.2 21.7 1.0
O A:HOH667 4.3 28.2 1.0
O A:ASP160 4.3 15.7 1.0
C A:ASP160 4.6 16.9 1.0
O A:HOH617 4.7 38.1 1.0
O A:HOH607 4.7 24.6 1.0
N A:ASP160 5.0 17.9 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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