Sodium in PDB 8icl: 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 NICL2 (5 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 NICL2 (5 Millimolar), PDB code: 8icl 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 / 3.10
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 178.721, 57.784, 48.382, 90.00, 90.00, 90.00
R / Rfree (%) 16.4 / n/a

Other elements in 8icl:

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 NICL2 (5 Millimolar) also contains other interesting chemical elements:

Nickel (Ni) 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 NICL2 (5 Millimolar) (pdb code 8icl). 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 NICL2 (5 Millimolar), PDB code: 8icl:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 8icl

Go back to Sodium Binding Sites List in 8icl
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 NICL2 (5 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 NICL2 (5 Millimolar) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na341

b:2.4
occ:1.00
O A:THR101 2.1 14.8 1.0
OP1 P:DT6 2.2 13.2 1.0
O A:VAL103 2.5 5.1 1.0
O A:ILE106 2.6 8.2 1.0
O A:HOH601 2.7 99.0 1.0
C A:THR101 3.3 14.1 1.0
C A:VAL103 3.3 6.5 1.0
P P:DT6 3.3 15.0 1.0
O A:ARG102 3.3 24.5 1.0
C A:ARG102 3.5 22.5 1.0
OP2 P:DT6 3.6 17.3 1.0
C A:ILE106 3.6 1.0 1.0
N A:ILE106 3.7 1.0 1.0
N A:VAL103 3.9 21.1 1.0
N A:GLY105 3.9 6.2 1.0
N A:SER104 4.1 7.3 1.0
CA A:ARG102 4.1 21.6 1.0
CA A:ILE106 4.1 1.0 1.0
CA A:SER104 4.1 12.6 1.0
N A:ARG102 4.2 14.9 1.0
CA A:VAL103 4.2 13.5 1.0
O5' P:DT6 4.2 9.3 1.0
CA A:THR101 4.3 7.7 1.0
CB A:ILE106 4.3 5.0 1.0
C A:SER104 4.4 12.7 1.0
C A:GLY105 4.6 3.6 1.0
N A:GLY107 4.7 1.0 1.0
O3' P:DA5 4.7 7.7 1.0
O A:LEU100 4.7 16.1 1.0
CA A:GLY105 4.9 1.9 1.0
CG2 A:ILE106 5.0 8.7 1.0

Sodium binding site 2 out of 2 in 8icl

Go back to Sodium Binding Sites List in 8icl
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 NICL2 (5 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 NICL2 (5 Millimolar) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na342

b:37.3
occ:1.00
O A:LEU62 2.0 34.2 1.0
O A:LYS60 2.6 17.5 1.0
O A:HOH656 3.1 25.6 1.0
O A:VAL65 3.2 13.0 1.0
C A:LEU62 3.2 31.0 1.0
C A:LYS60 3.8 19.6 1.0
C A:LYS61 4.0 24.0 1.0
N A:LEU62 4.0 16.6 1.0
N A:VAL65 4.0 3.6 1.0
C A:VAL65 4.1 10.1 1.0
N A:PRO63 4.1 34.6 1.0
CG2 A:VAL65 4.1 21.5 1.0
O A:LYS61 4.1 20.5 1.0
CA A:LEU62 4.2 18.6 1.0
CA A:PRO63 4.2 32.7 1.0
CA A:VAL65 4.4 8.4 1.0
CA A:LYS61 4.5 33.2 1.0
N A:GLY64 4.6 40.5 1.0
N A:LYS61 4.6 26.2 1.0
C A:PRO63 4.7 35.6 1.0
CG A:LYS60 4.7 9.3 1.0
CA A:LYS60 4.9 20.7 1.0
CB A:VAL65 4.9 15.5 1.0
CE A:LYS60 5.0 37.7 1.0

Reference:

H.Pelletier, M.R.Sawaya, W.Wolfle, S.H.Wilson, J.Kraut. A Structural Basis For Metal Ion Mutagenicity and Nucleotide Selectivity in Human Dna Polymerase Beta. Biochemistry V. 35 12762 1996.
ISSN: ISSN 0006-2960
PubMed: 8841119
DOI: 10.1021/BI9529566
Page generated: Tue Dec 15 18:25:59 2020

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