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Sodium in PDB 3c2m: Ternary Complex of Dna Polymerase Beta with A G:Dapcpp Mismatch in the Active Site

Enzymatic activity of Ternary Complex of Dna Polymerase Beta with A G:Dapcpp Mismatch in the Active Site

All present enzymatic activity of Ternary Complex of Dna Polymerase Beta with A G:Dapcpp Mismatch in the Active Site:
2.7.7.7;

Protein crystallography data

The structure of Ternary Complex of Dna Polymerase Beta with A G:Dapcpp Mismatch in the Active Site, PDB code: 3c2m was solved by V.K.Batra, W.A.Beard, D.D.Shock, L.C.Pedersen, S.H.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 22.35 / 2.15
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.750, 78.370, 55.170, 90.00, 113.36, 90.00
R / Rfree (%) 21.4 / 27

Other elements in 3c2m:

The structure of Ternary Complex of Dna Polymerase Beta with A G:Dapcpp Mismatch in the Active Site also contains other interesting chemical elements:

Manganese (Mn) 7 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Ternary Complex of Dna Polymerase Beta with A G:Dapcpp Mismatch in the Active Site (pdb code 3c2m). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the Ternary Complex of Dna Polymerase Beta with A G:Dapcpp Mismatch in the Active Site, PDB code: 3c2m:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in 3c2m

Go back to Sodium Binding Sites List in 3c2m
Sodium binding site 1 out of 6 in the Ternary Complex of Dna Polymerase Beta with A G:Dapcpp Mismatch in the Active Site


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Ternary Complex of Dna Polymerase Beta with A G:Dapcpp Mismatch in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Na358

b:46.5
occ:1.00
 O T:HOH290 2.0 41.4 1.0
N7 T:DG15 4.7 31.0 1.0
N7 T:DA14 4.7 31.6 1.0
C8 T:DA14 4.8 32.0 1.0
N4 T:DC16 4.8 25.7 1.0
OP2 T:DA14 4.9 40.7 1.0

Sodium binding site 2 out of 6 in 3c2m

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Sodium binding site 2 out of 6 in the Ternary Complex of Dna Polymerase Beta with A G:Dapcpp Mismatch in the Active Site


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Ternary Complex of Dna Polymerase Beta with A G:Dapcpp Mismatch in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Na357

b:46.5
occ:1.00
 O P:HOH378 2.0 31.6 1.0
N7 P:DG4 2.7 33.4 1.0
O6 P:DG4 3.5 28.9 1.0
C5 P:DG4 3.6 32.0 1.0
C8 P:DG4 3.7 36.1 1.0
C6 P:DG4 3.9 29.7 1.0
C2' P:DT3 4.0 42.0 1.0
N6 P:DA5 4.2 32.4 1.0
C6 P:DT3 4.6 37.3 1.0
C4 P:DG4 4.8 33.6 1.0
O4 T:DT12 4.9 26.0 1.0
N1 P:DT3 4.9 38.1 1.0
N9 P:DG4 4.9 36.9 1.0
C1' P:DT3 4.9 39.8 1.0
OP2 P:DG4 4.9 48.3 1.0
O P:HOH379 4.9 39.6 1.0

Sodium binding site 3 out of 6 in 3c2m

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Sodium binding site 3 out of 6 in the Ternary Complex of Dna Polymerase Beta with A G:Dapcpp Mismatch in the Active Site


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Ternary Complex of Dna Polymerase Beta with A G:Dapcpp Mismatch in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na354

b:34.1
occ:1.00
 O A:THR101 2.3 16.0 1.0
O A:HOH378 2.4 42.2 1.0
O P:HOH360 2.5 28.5 1.0
O A:VAL103 2.6 18.0 1.0
OP1 P:DG9 2.7 26.8 1.0
O A:ILE106 3.0 14.6 1.0
C A:VAL103 3.4 18.1 1.0
C A:THR101 3.4 15.8 1.0
P P:DG9 3.7 23.9 1.0
OP2 P:DG9 3.8 22.0 1.0
CA A:SER104 3.9 19.2 1.0
N A:SER104 3.9 16.8 1.0
C A:ILE106 3.9 16.5 1.0
N A:VAL103 4.0 14.7 1.0
CA A:THR101 4.1 17.9 1.0
N A:GLY105 4.1 17.3 1.0
N A:ILE106 4.1 14.3 1.0
C A:ARG102 4.3 14.8 1.0
CA A:VAL103 4.4 16.0 1.0
N A:ARG102 4.4 15.7 1.0
C A:SER104 4.4 19.7 1.0
CA A:ILE106 4.6 15.6 1.0
CA A:ARG102 4.6 16.4 1.0
CB A:THR101 4.6 17.4 1.0
O5' P:DG9 4.7 25.2 1.0
O A:ARG102 4.7 15.8 1.0
O3' P:DC8 4.8 22.0 1.0
N A:GLY107 4.8 14.9 1.0
CB A:ILE106 4.9 15.4 1.0
O A:LEU100 5.0 15.4 1.0

Sodium binding site 4 out of 6 in 3c2m

Go back to Sodium Binding Sites List in 3c2m
Sodium binding site 4 out of 6 in the Ternary Complex of Dna Polymerase Beta with A G:Dapcpp Mismatch in the Active Site


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Ternary Complex of Dna Polymerase Beta with A G:Dapcpp Mismatch in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na355

b:31.2
occ:1.00
 O A:VAL65 2.4 23.6 1.0
O A:LEU62 2.4 23.8 1.0
O A:LYS60 2.4 27.9 1.0
OP1 D:DC3 2.4 23.8 1.0
O A:HOH407 2.6 25.3 1.0
O D:HOH17 2.7 22.1 1.0
C A:LEU62 3.4 24.5 1.0
C A:VAL65 3.4 23.1 1.0
C A:LYS60 3.5 28.1 1.0
P D:DC3 3.6 21.1 1.0
N A:VAL65 3.8 22.3 1.0
OP2 D:DC3 3.9 23.0 1.0
C A:LYS61 4.0 28.1 1.0
N A:LEU62 4.0 26.5 1.0
CA A:VAL65 4.1 22.7 1.0
N A:PRO63 4.1 26.1 1.0
O A:LYS61 4.1 29.1 1.0
CA A:PRO63 4.1 26.5 1.0
N A:GLY64 4.2 23.8 1.0
CA A:LYS60 4.3 27.2 1.0
CA A:LEU62 4.3 24.1 1.0
CB A:VAL65 4.4 22.8 1.0
N A:GLY66 4.4 22.8 1.0
N A:LYS61 4.4 28.3 1.0
CD A:LYS60 4.4 34.0 1.0
CA A:LYS61 4.6 28.3 1.0
O3' D:DT2 4.6 22.1 1.0
C A:PRO63 4.6 24.5 1.0
CA A:GLY66 4.7 20.5 1.0
O A:ALA59 4.7 21.0 1.0
O5' D:DC3 4.7 22.7 1.0
CE A:LYS60 4.8 33.3 1.0
CG A:LYS60 4.8 31.8 1.0
C A:GLY64 4.9 24.3 1.0

Sodium binding site 5 out of 6 in 3c2m

Go back to Sodium Binding Sites List in 3c2m
Sodium binding site 5 out of 6 in the Ternary Complex of Dna Polymerase Beta with A G:Dapcpp Mismatch in the Active Site


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Ternary Complex of Dna Polymerase Beta with A G:Dapcpp Mismatch in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na356

b:48.4
occ:1.00
 O A:HOH590 2.5 40.2 1.0
O A:HOH589 2.9 28.4 1.0
OD1 A:ASP92 3.0 33.6 0.5
OD1 A:ASP92 3.4 28.1 0.5
CG A:ASP92 3.7 33.4 0.5
OD2 A:ASP92 4.1 33.3 0.5
CG A:ASP92 4.3 27.6 0.5
O A:HOH588 4.4 44.4 1.0
CB A:ASP92 4.7 32.4 0.5
CB A:ASP92 4.8 29.2 0.5

Sodium binding site 6 out of 6 in 3c2m

Go back to Sodium Binding Sites List in 3c2m
Sodium binding site 6 out of 6 in the Ternary Complex of Dna Polymerase Beta with A G:Dapcpp Mismatch in the Active Site


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Ternary Complex of Dna Polymerase Beta with A G:Dapcpp Mismatch in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na359

b:42.6
occ:1.00
 O A:HOH467 2.3 32.9 1.0
O P:HOH374 3.9 35.4 1.0
O1G A:F2A338 4.1 29.8 1.0
O3G A:F2A338 4.1 27.2 1.0
O P:HOH359 4.6 17.1 1.0
CA A:GLY189 4.6 18.9 1.0
C A:GLY189 4.8 19.7 1.0
PG A:F2A338 4.8 29.0 1.0
OD2 A:ASP190 4.8 20.8 1.0
O A:HOH466 4.9 53.0 1.0
O A:GLY189 4.9 19.0 1.0
O2A A:F2A338 4.9 22.5 1.0
OP2 P:DC10 5.0 33.9 1.0

Reference:

V.K.Batra, W.A.Beard, D.D.Shock, L.C.Pedersen, S.H.Wilson. Structures of Dna Polymerase Beta with Active-Site Mismatches Suggest A Transient Abasic Site Intermediate During Misincorporation. Mol.Cell V. 30 315 2008.
ISSN: ISSN 1097-2765
PubMed: 18471977
DOI: 10.1016/J.MOLCEL.2008.02.025
Page generated: Mon Oct 7 06:08:21 2024

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