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Sodium in PDB 1zqs: Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed with Seven Base Pairs of Dna; Soaked in the Presence of Tlcl (0.5 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 Tlcl (0.5 Millimolar), PDB code: 1zqs 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 / 3.30
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 178.430, 57.723, 48.314, 90.00, 90.00, 90.00
R / Rfree (%) 16.5 / n/a

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 Tlcl (0.5 Millimolar) (pdb code 1zqs). 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 Tlcl (0.5 Millimolar), PDB code: 1zqs:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 1zqs

Go back to Sodium Binding Sites List in 1zqs
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 Tlcl (0.5 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 Tlcl (0.5 Millimolar) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na341

b:1.0
occ:1.00
O A:THR101 2.1 16.3 1.0
OP1 P:DT6 2.1 14.3 1.0
O A:HOH601 2.2 84.5 1.0
O A:ILE106 2.5 6.5 1.0
O A:VAL103 2.9 3.6 1.0
C A:THR101 3.3 14.8 1.0
P P:DT6 3.4 6.7 1.0
C A:ILE106 3.6 8.4 1.0
C A:VAL103 3.6 5.5 1.0
OP2 P:DT6 3.7 12.5 1.0
N A:ILE106 3.9 13.1 1.0
N A:GLY105 3.9 8.9 1.0
CA A:SER104 4.0 13.3 1.0
C A:ARG102 4.1 28.8 1.0
N A:VAL103 4.1 22.9 1.0
CA A:ILE106 4.1 5.4 1.0
N A:SER104 4.1 10.6 1.0
N A:ARG102 4.2 21.7 1.0
CA A:THR101 4.3 6.6 1.0
CA A:ARG102 4.3 28.8 1.0
CB A:ILE106 4.4 1.0 1.0
O5' P:DT6 4.4 2.5 1.0
O A:ARG102 4.4 27.8 1.0
O3' P:DA5 4.5 1.0 1.0
C A:SER104 4.5 10.3 1.0
CA A:VAL103 4.5 11.5 1.0
N A:GLY107 4.7 7.3 1.0
C A:GLY105 4.8 11.0 1.0
CA A:GLY105 4.9 7.9 1.0
CG2 A:THR101 4.9 2.0 1.0
CB A:THR101 5.0 1.0 1.0

Sodium binding site 2 out of 2 in 1zqs

Go back to Sodium Binding Sites List in 1zqs
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 Tlcl (0.5 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 Tlcl (0.5 Millimolar) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na342

b:19.5
occ:1.00
O A:LEU62 1.9 32.7 1.0
C A:LEU62 3.1 32.4 1.0
O A:LYS60 3.2 25.6 1.0
O A:VAL65 3.5 19.1 1.0
CA A:PRO63 3.9 25.4 1.0
N A:PRO63 3.9 35.3 1.0
C A:LYS61 4.1 43.0 1.0
O A:LYS61 4.1 52.4 1.0
N A:LEU62 4.1 28.9 1.0
CA A:LEU62 4.2 25.5 1.0
N A:VAL65 4.2 27.6 1.0
N A:GLY64 4.3 36.6 1.0
C A:LYS60 4.4 25.6 1.0
C A:VAL65 4.4 18.4 1.0
C A:PRO63 4.6 19.8 1.0
CA A:VAL65 4.7 20.6 1.0
CD A:PRO63 4.8 37.4 1.0
CA A:LYS61 4.8 45.3 1.0
CB A:VAL65 5.0 19.5 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 05:44:44 2020

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