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Sodium in PDB 8ice: Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed with Seven Base Pairs of Dna; Soaked in the Presence of Datp (1 Millimolar) and CDCL2 (1 Millimolar)

Protein crystallography data

The structure of Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed with Seven Base Pairs of Dna; Soaked in the Presence of Datp (1 Millimolar) and CDCL2 (1 Millimolar), PDB code: 8ice was solved by H.Pelletier, M.R.Sawaya, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 3.20
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 178.260, 57.756, 48.255, 90.00, 90.00, 90.00
R / Rfree (%) 17.1 / n/a

Other elements in 8ice:

The structure of Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed with Seven Base Pairs of Dna; Soaked in the Presence of Datp (1 Millimolar) and CDCL2 (1 Millimolar) also contains other interesting chemical elements:

Cadmium (Cd) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed with Seven Base Pairs of Dna; Soaked in the Presence of Datp (1 Millimolar) and CDCL2 (1 Millimolar) (pdb code 8ice). 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 (Pol B) (E.C.2.7.7.7) Complexed with Seven Base Pairs of Dna; Soaked in the Presence of Datp (1 Millimolar) and CDCL2 (1 Millimolar), PDB code: 8ice:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 8ice

Go back to Sodium Binding Sites List in 8ice
Sodium binding site 1 out of 2 in the Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed with Seven Base Pairs of Dna; Soaked in the Presence of Datp (1 Millimolar) and CDCL2 (1 Millimolar)


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 (Pol B) (E.C.2.7.7.7) Complexed with Seven Base Pairs of Dna; Soaked in the Presence of Datp (1 Millimolar) and CDCL2 (1 Millimolar) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na341

b:8.1
occ:1.00
OP1 P:DT6 1.5 8.2 1.0
O A:VAL103 2.2 12.3 1.0
O A:THR101 2.8 4.3 1.0
O A:ILE106 2.9 1.0 1.0
P P:DT6 3.0 9.9 1.0
O A:HOH601 3.1 57.6 1.0
C A:VAL103 3.3 13.6 1.0
N A:GLY105 3.3 18.4 1.0
N A:ILE106 3.5 1.2 1.0
C A:ILE106 3.6 1.0 1.0
O A:ARG102 3.7 20.3 1.0
CA A:SER104 3.7 15.9 1.0
OP2 P:DT6 3.9 1.0 1.0
C A:SER104 3.9 16.7 1.0
C A:THR101 3.9 8.7 1.0
O5' P:DT6 3.9 10.7 1.0
O3' P:DA5 3.9 14.7 1.0
N A:SER104 3.9 13.7 1.0
C A:ARG102 3.9 21.0 1.0
CA A:ILE106 4.0 1.0 1.0
C A:GLY105 4.0 9.1 1.0
CA A:GLY105 4.2 16.3 1.0
N A:VAL103 4.3 20.4 1.0
CA A:VAL103 4.3 16.0 1.0
N A:GLY107 4.5 4.5 1.0
CB A:ILE106 4.6 1.0 1.0
CA A:ARG102 4.6 20.6 1.0
N A:ARG102 4.7 15.6 1.0
CA A:THR101 4.8 6.6 1.0
O A:GLY105 4.9 12.0 1.0
O A:SER104 5.0 11.2 1.0
CA A:GLY107 5.0 6.7 1.0
CB A:SER104 5.0 12.6 1.0

Sodium binding site 2 out of 2 in 8ice

Go back to Sodium Binding Sites List in 8ice
Sodium binding site 2 out of 2 in the Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed with Seven Base Pairs of Dna; Soaked in the Presence of Datp (1 Millimolar) and CDCL2 (1 Millimolar)


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 (Pol B) (E.C.2.7.7.7) Complexed with Seven Base Pairs of Dna; Soaked in the Presence of Datp (1 Millimolar) and CDCL2 (1 Millimolar) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na342

b:37.7
occ:1.00
O A:LEU62 2.9 18.6 1.0
O A:LYS60 3.4 20.8 1.0
O A:VAL65 3.6 13.7 1.0
C A:LEU62 3.9 29.7 1.0
CE A:LYS60 4.2 63.4 1.0
CG A:LYS60 4.6 42.0 1.0
N A:PRO63 4.6 38.7 1.0
C A:LYS60 4.6 27.2 1.0
C A:VAL65 4.6 17.8 1.0
CA A:PRO63 4.7 43.2 1.0
N A:LEU62 4.8 38.8 1.0
C A:LYS61 4.8 42.7 1.0
N A:VAL65 4.9 26.5 1.0
CA A:LEU62 4.9 32.1 1.0
O A:LYS61 5.0 42.9 1.0
N A:GLY64 5.0 43.8 1.0

Reference:

H.Pelletier, M.R.Sawaya. Characterization of the Metal Ion Binding Helix-Hairpin-Helix Motifs in Human Dna Polymerase Beta By X-Ray Structural Analysis. Biochemistry V. 35 12778 1996.
ISSN: ISSN 0006-2960
PubMed: 8841120
DOI: 10.1021/BI960790I
Page generated: Tue Dec 15 18:22:22 2020

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