Atomistry » Sodium » PDB 3bjp-3c7h » 3c2m
Atomistry »
  Sodium »
    PDB 3bjp-3c7h »
      3c2m »

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

Go back to Sodium Binding Sites List in 3c2m
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

Go back to Sodium Binding Sites List in 3c2m
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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy