Atomistry » Sodium » PDB 1b7s-1c82 » 1bpx
Atomistry »
  Sodium »
    PDB 1b7s-1c82 »
      1bpx »

Sodium in PDB 1bpx: Dna Polymerase Beta/Dna Complex

Enzymatic activity of Dna Polymerase Beta/Dna Complex

All present enzymatic activity of Dna Polymerase Beta/Dna Complex:
2.7.7.7;

Protein crystallography data

The structure of Dna Polymerase Beta/Dna Complex, PDB code: 1bpx was solved by M.R.Sawaya, R.Prasad, S.H.Wilson, J.Kraut, H.Pelletier, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.40
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 52.767, 79.395, 54.622, 90.00, 106.35, 90.00
R / Rfree (%) 25.3 / n/a

Sodium Binding Sites:

The binding sites of Sodium atom in the Dna Polymerase Beta/Dna Complex (pdb code 1bpx). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Dna Polymerase Beta/Dna Complex, PDB code: 1bpx:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 1bpx

Go back to Sodium Binding Sites List in 1bpx
Sodium binding site 1 out of 2 in the Dna Polymerase Beta/Dna Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Dna Polymerase Beta/Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na342

b:54.2
occ:1.00
O A:HOH502 1.8 76.8 1.0
O A:LEU62 2.4 34.4 1.0
O A:VAL65 2.5 60.7 1.0
OP1 D:DC3 2.5 33.1 1.0
O A:LYS60 2.6 44.1 1.0
OP2 D:DC3 2.8 34.4 1.0
P D:DC3 3.1 44.3 1.0
C A:LEU62 3.6 27.9 1.0
C A:VAL65 3.6 49.3 1.0
C A:LYS60 3.9 40.0 1.0
N A:GLY64 3.9 59.3 1.0
CG A:LYS60 4.0 55.5 1.0
O3' D:DT2 4.1 53.0 1.0
CA A:PRO63 4.1 33.8 1.0
N A:VAL65 4.1 50.1 1.0
N A:PRO63 4.2 22.8 1.0
CA A:VAL65 4.3 42.5 1.0
O5' D:DC3 4.5 41.2 1.0
C A:PRO63 4.5 52.5 1.0
N A:GLY66 4.6 50.8 1.0
CA A:GLY66 4.6 47.7 1.0
C A:LYS61 4.6 54.0 1.0
N A:LEU62 4.6 47.3 1.0
CB A:VAL65 4.7 42.9 1.0
O A:LYS61 4.7 59.9 1.0
CA A:LYS60 4.7 40.0 1.0
CA A:LEU62 4.8 36.4 1.0
C A:GLY64 4.8 55.8 1.0
CD A:LYS60 4.8 63.5 1.0
N A:LYS61 4.9 39.7 1.0
C3' D:DT2 4.9 41.6 1.0

Sodium binding site 2 out of 2 in 1bpx

Go back to Sodium Binding Sites List in 1bpx
Sodium binding site 2 out of 2 in the Dna Polymerase Beta/Dna Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Dna Polymerase Beta/Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na341

b:29.9
occ:1.00
OP1 P:DG9 2.0 48.7 1.0
O A:THR101 2.0 37.6 1.0
O A:ILE106 2.1 28.2 1.0
O P:HOH501 2.6 42.3 1.0
O A:HOH500 2.7 36.0 1.0
O A:VAL103 2.8 53.6 1.0
P P:DG9 3.2 46.4 1.0
C A:THR101 3.2 41.4 1.0
C A:ILE106 3.2 38.3 1.0
OP2 P:DG9 3.4 45.9 1.0
C A:VAL103 3.4 47.7 1.0
O A:HOH539 3.5 70.8 1.0
CA A:THR101 3.8 43.6 1.0
N A:ILE106 3.8 27.6 1.0
N A:SER104 4.0 41.4 1.0
CA A:SER104 4.0 32.3 1.0
N A:GLY105 4.0 38.8 1.0
CA A:ILE106 4.0 32.6 1.0
C A:ARG102 4.2 33.6 1.0
N A:VAL103 4.2 35.9 1.0
O5' P:DG9 4.3 38.2 1.0
O A:ARG102 4.3 36.2 1.0
N A:GLY107 4.3 35.3 1.0
O3' P:DC8 4.3 43.2 1.0
N A:ARG102 4.4 28.0 1.0
CA A:VAL103 4.4 45.1 1.0
CB A:THR101 4.4 35.0 1.0
CB A:ILE106 4.4 37.5 1.0
C A:SER104 4.5 41.0 1.0
CA A:GLY107 4.6 47.8 1.0
C A:GLY105 4.7 34.8 1.0
CA A:ARG102 4.7 27.5 1.0
O A:LEU100 4.8 41.3 1.0
CG2 A:ILE106 5.0 33.8 1.0
CA A:GLY105 5.0 25.4 1.0

Reference:

M.R.Sawaya, R.Prasad, S.H.Wilson, J.Kraut, H.Pelletier. Crystal Structures of Human Dna Polymerase Beta Complexed with Gapped and Nicked Dna: Evidence For An Induced Fit Mechanism. Biochemistry V. 36 11205 1997.
ISSN: ISSN 0006-2960
PubMed: 9287163
DOI: 10.1021/BI9703812
Page generated: Tue Dec 15 05:22:11 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy