Calcium in PDB 1zqd: Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed with Seven Base Pairs of Dna; Soaked in the Presence of CACL2 (150 Millimolar)

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 CACL2 (150 Millimolar), PDB code: 1zqd 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 / 3.50
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	178.565, 57.826, 47.988, 90.00, 90.00, 90.00
R / Rfree (%)	14.4 / n/a

The binding sites of Calcium 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 CACL2 (150 Millimolar) (pdb code 1zqd). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium 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 CACL2 (150 Millimolar), PDB code: 1zqd:
Jump to Calcium binding site number: 1; 2;

Calcium 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 CACL2 (150 Millimolar)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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 CACL2 (150 Millimolar) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca341 b:13.8 occ:1.00 O A:THR101 2.0 26.3 1.0 O P:HOH601 2.3 0.0 1.0 OP1 P:DT6 2.6 21.4 1.0 O A:ILE106 2.8 1.7 1.0 O A:VAL103 2.8 1.0 1.0 C A:THR101 3.1 24.4 1.0 P P:DT6 3.6 10.0 1.0 OP2 P:DT6 3.8 2.6 1.0 C A:VAL103 3.8 2.7 1.0 C A:ILE106 3.9 1.0 1.0 CA A:THR101 4.0 13.0 1.0 N A:ILE106 4.0 1.0 1.0 N A:ARG102 4.1 31.1 1.0 N A:VAL103 4.1 23.9 1.0 C A:ARG102 4.2 30.4 1.0 CG2 A:THR101 4.3 1.0 1.0 CA A:ARG102 4.3 31.4 1.0 CA A:ILE106 4.4 1.1 1.0 N A:GLY105 4.4 23.2 1.0 CB A:THR101 4.6 3.9 1.0 CA A:VAL103 4.6 11.2 1.0 O A:ARG102 4.7 36.4 1.0 CB A:ILE106 4.7 9.5 1.0 O3' P:DA5 4.7 1.0 1.0 N A:SER104 4.7 8.3 1.0 O5' P:DT6 4.7 4.4 1.0 CA A:SER104 4.8 22.9 1.0 N A:GLY107 5.0 1.0 1.0

Calcium 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 CACL2 (150 Millimolar)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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 CACL2 (150 Millimolar) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca342 b:66.2 occ:1.00 O A:LEU62 2.1 33.4 1.0 O A:LYS60 2.9 27.9 1.0 O A:VAL65 3.1 18.7 1.0 C A:LEU62 3.3 33.8 1.0 O A:LYS61 3.9 59.4 1.0 C A:LYS61 4.0 50.2 1.0 C A:LYS60 4.1 22.6 1.0 C A:VAL65 4.2 15.6 1.0 N A:LEU62 4.2 33.9 1.0 N A:PRO63 4.3 40.7 1.0 CA A:LEU62 4.3 25.8 1.0 CA A:PRO63 4.3 35.9 1.0 N A:VAL65 4.3 22.1 1.0 CA A:VAL65 4.6 8.1 1.0 N A:GLY64 4.7 30.9 1.0 CA A:LYS61 4.7 50.4 1.0 CB A:VAL65 4.8 1.0 1.0 C A:PRO63 4.8 24.5 1.0 N A:LYS61 4.9 34.8 1.0 CG A:LYS60 5.0 19.8 1.0

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