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Sodium in PDB 4rpx: Precatalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Containing An 8-Oxo-7,8-Dihydro-Guanine (8-Oxog) and Dctp 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 Dctp 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 Dctp 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 Dctp in the Presence of CACL2, PDB code: 4rpx 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) 31.43 / 1.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 49.660, 79.360, 55.650, 90.00, 106.34, 90.00
R / Rfree (%) 18.9 / 22.7

Other elements in 4rpx:

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 Dctp in the Presence of CACL2 also contains other interesting chemical elements:

Calcium (Ca) 2 atoms
Chlorine (Cl) 3 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 Dctp in the Presence of CACL2 (pdb code 4rpx). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 7 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 Dctp in the Presence of CACL2, PDB code: 4rpx:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7;

Sodium binding site 1 out of 7 in 4rpx

Go back to Sodium Binding Sites List in 4rpx
Sodium binding site 1 out of 7 in the Precatalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Containing An 8-Oxo-7,8-Dihydro-Guanine (8-Oxog) and Dctp 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 Dctp in the Presence of CACL2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na404

b:49.8
occ:1.00
 OD2 A:ASP321 2.4 29.4 1.0
OD1 A:ASP318 2.8 23.6 1.0
O A:HOH571 2.9 33.3 1.0
CG A:ASP321 3.6 27.6 1.0
CG A:ASP318 4.0 24.5 1.0
NA A:NA408 4.2 37.0 1.0
NZ A:LYS317 4.3 32.9 1.0
CA A:ASP318 4.3 23.7 1.0
CG A:LYS317 4.4 29.4 1.0
N A:ASP318 4.4 23.6 1.0
CB A:ASP321 4.4 26.3 1.0
OD1 A:ASP321 4.5 28.6 1.0
CD A:LYS317 4.5 30.8 1.0
C A:LYS317 4.7 24.4 1.0
CB A:ASP318 4.8 24.2 1.0
CB A:LYS317 4.8 27.6 1.0
OD2 A:ASP318 4.8 25.2 1.0
OG A:SER315 4.8 25.7 1.0
O A:LYS317 5.0 25.2 1.0

Sodium binding site 2 out of 7 in 4rpx

Go back to Sodium Binding Sites List in 4rpx
Sodium binding site 2 out of 7 in the Precatalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Containing An 8-Oxo-7,8-Dihydro-Guanine (8-Oxog) and Dctp 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 Dctp in the Presence of CACL2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na405

b:12.8
occ:1.00
 O A:HOH504 2.2 19.1 1.0
O A:THR101 2.3 15.4 1.0
OP1 P:DG9 2.3 21.6 1.0
O A:ILE106 2.4 15.9 1.0
O P:HOH202 2.4 24.3 1.0
O A:VAL103 2.5 15.0 1.0
C A:THR101 3.3 16.4 1.0
P P:DG9 3.4 22.3 1.0
C A:VAL103 3.4 16.0 1.0
C A:ILE106 3.5 15.2 1.0
OP2 P:DG9 3.5 21.6 1.0
N A:ILE106 3.8 14.4 1.0
CA A:THR101 4.0 15.6 1.0
CA A:SER104 4.0 15.0 1.0
N A:GLY105 4.0 14.6 1.0
N A:SER104 4.1 15.4 1.0
N A:VAL103 4.1 17.0 1.0
CA A:ILE106 4.2 14.9 1.0
C A:ARG102 4.2 18.2 1.0
N A:ARG102 4.4 17.4 1.0
O3' P:DC8 4.4 22.8 1.0
C A:SER104 4.4 14.6 1.0
CA A:VAL103 4.4 17.0 1.0
N A:GLY107 4.4 15.2 1.0
CB A:THR101 4.6 15.4 1.0
O5' P:DG9 4.6 22.6 1.0
CA A:ARG102 4.6 19.2 1.0
O A:ARG102 4.6 18.0 1.0
CA A:GLY107 4.6 15.3 1.0
CB A:ILE106 4.6 14.8 1.0
C A:GLY105 4.7 14.9 1.0
O A:LEU100 4.9 13.3 1.0
CA A:GLY105 4.9 14.7 1.0

Sodium binding site 3 out of 7 in 4rpx

Go back to Sodium Binding Sites List in 4rpx
Sodium binding site 3 out of 7 in the Precatalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Containing An 8-Oxo-7,8-Dihydro-Guanine (8-Oxog) and Dctp 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 Dctp in the Presence of CACL2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na406

b:37.8
occ:1.00
 O A:HOH565 2.2 37.4 1.0
O A:HOH553 2.2 40.5 1.0
O A:HOH547 2.3 30.6 1.0
O A:HOH650 2.3 37.2 1.0
O A:HOH605 2.3 34.6 1.0
OE2 A:GLU249 2.6 33.9 1.0
O A:HOH535 3.0 37.4 1.0
OE1 A:GLU249 3.0 32.8 1.0
CD A:GLU249 3.2 33.4 1.0
CE1 A:HIS252 4.7 18.2 1.0
CG A:GLU249 4.7 30.6 1.0
OE1 A:GLN240 4.7 18.6 1.0
O A:HOH595 4.9 31.9 1.0
NE2 A:GLN240 5.0 19.3 1.0
O A:HOH593 5.0 60.2 1.0

Sodium binding site 4 out of 7 in 4rpx

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

b:19.2
occ:1.00
 O D:HOH202 2.2 25.7 1.0
O A:HOH537 2.3 24.2 1.0
O A:VAL65 2.3 18.0 1.0
O A:LYS60 2.4 20.1 1.0
O A:LEU62 2.5 18.5 1.0
OP1 D:DC3 2.5 18.9 1.0
C A:VAL65 3.4 17.6 1.0
C A:LEU62 3.5 19.6 1.0
C A:LYS60 3.5 21.6 1.0
P D:DC3 3.6 19.4 1.0
OP2 D:DC3 3.7 19.4 1.0
N A:VAL65 3.8 16.9 1.0
O D:HOH213 4.1 29.2 1.0
CA A:VAL65 4.1 17.4 1.0
N A:LEU62 4.1 20.3 1.0
C A:LYS61 4.1 21.8 1.0
N A:GLY64 4.2 18.4 1.0
CA A:PRO63 4.2 19.6 1.0
N A:PRO63 4.3 19.7 1.0
CA A:LYS60 4.3 21.6 1.0
O A:LYS61 4.4 21.9 1.0
CB A:VAL65 4.4 17.1 1.0
CA A:LEU62 4.5 20.0 1.0
O3' D:DT2 4.5 18.1 1.0
CG A:LYS60 4.5 25.6 1.0
N A:LYS61 4.5 21.8 1.0
N A:GLY66 4.5 18.1 1.0
C A:PRO63 4.6 19.1 1.0
CA A:LYS61 4.6 22.8 1.0
CA A:GLY66 4.8 17.9 1.0
C A:GLY64 4.8 17.4 1.0
O5' D:DC3 4.8 19.7 1.0
O A:ALA59 5.0 18.2 1.0
CB A:LYS60 5.0 23.9 1.0

Sodium binding site 5 out of 7 in 4rpx

Go back to Sodium Binding Sites List in 4rpx
Sodium binding site 5 out of 7 in the Precatalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Containing An 8-Oxo-7,8-Dihydro-Guanine (8-Oxog) and Dctp 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 5 of Precatalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Containing An 8-Oxo-7,8-Dihydro-Guanine (8-Oxog) and Dctp in the Presence of CACL2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na408

b:37.0
occ:1.00
 O A:HOH637 2.3 46.6 1.0
OD2 A:ASP318 2.4 25.2 1.0
OD1 A:ASP314 2.5 38.6 1.0
OD1 A:ASP318 2.7 23.6 1.0
O A:HOH572 2.8 41.2 1.0
CG A:ASP318 2.9 24.5 1.0
CG A:ASP314 3.5 35.6 1.0
OD2 A:ASP314 3.9 39.8 1.0
NA A:NA404 4.2 49.8 1.0
CB A:ASP318 4.4 24.2 1.0
OG A:SER315 4.6 25.7 1.0
O A:HOH571 4.7 33.3 1.0
N A:ASP314 4.8 27.5 1.0
CB A:ASP314 4.8 32.4 1.0
C A:ASP314 5.0 27.8 1.0

Sodium binding site 6 out of 7 in 4rpx

Go back to Sodium Binding Sites List in 4rpx
Sodium binding site 6 out of 7 in the Precatalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Containing An 8-Oxo-7,8-Dihydro-Guanine (8-Oxog) and Dctp 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 6 of Precatalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Containing An 8-Oxo-7,8-Dihydro-Guanine (8-Oxog) and Dctp in the Presence of CACL2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na409

b:41.6
occ:1.00
 O A:HOH672 2.3 23.9 0.5
OD1 A:ASP160 2.4 25.2 1.0
CG A:ASP160 3.5 24.4 1.0
CA A:ASP160 3.9 21.4 1.0
CB A:ASP160 4.0 23.1 1.0
O A:ASP160 4.4 19.5 1.0
OD2 A:ASP160 4.6 27.0 1.0
C A:ASP160 4.7 20.8 1.0
O A:HOH621 4.7 24.4 1.0

Sodium binding site 7 out of 7 in 4rpx

Go back to Sodium Binding Sites List in 4rpx
Sodium binding site 7 out of 7 in the Precatalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Containing An 8-Oxo-7,8-Dihydro-Guanine (8-Oxog) and Dctp 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 7 of Precatalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Containing An 8-Oxo-7,8-Dihydro-Guanine (8-Oxog) and Dctp in the Presence of CACL2 within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Na101

b:40.4
occ:1.00
 O T:HOH115 2.2 56.0 1.0
O P:HOH207 2.2 38.6 1.0
O P:HOH206 2.7 33.7 1.0
O T:HOH106 2.8 31.2 1.0
O6 T:DG9 2.9 15.3 1.0
O6 P:DG7 2.9 19.8 1.0
N4 T:DC10 3.9 17.7 1.0
C6 T:DG9 4.0 15.3 1.0
N4 P:DC8 4.0 20.0 1.0
C6 P:DG7 4.0 21.2 1.0
O4 P:DT6 4.3 24.1 1.0
N7 P:DG7 4.6 22.4 1.0
N7 T:DG9 4.6 15.7 1.0
C5 T:DG9 4.6 15.2 1.0
C5 P:DG7 4.7 22.1 1.0
C7 P:DT6 4.7 24.2 1.0
C4 P:DT6 4.7 24.0 1.0
O T:HOH114 4.8 31.0 1.0
C4 T:DC8 4.8 19.9 1.0
N4 T:DC8 4.8 20.3 1.0
C5 T:DC8 4.9 19.9 1.0
N1 T:DG9 5.0 14.8 1.0
C5 P:DT6 5.0 24.3 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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