Calcium in PDB 1zqc: Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed with Seven Base Pairs of Dna; Soaked in the Presence of CACL2 (15 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 (15 Millimolar), PDB code: 1zqc 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 (°)	178.057, 57.638, 48.139, 90.00, 90.00, 90.00
R / Rfree (%)	17.3 / 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 (15 Millimolar) (pdb code 1zqc). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 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 (15 Millimolar), PDB code: 1zqc:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 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 (15 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 (15 Millimolar) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca340 b:93.5 occ:1.00 O P:HOH665 2.8 88.5 1.0 OD1 A:ASP190 3.2 39.0 1.0 OD2 A:ASP190 3.2 45.2 1.0 OD2 A:ASP192 3.3 63.9 1.0 O3' P:DG7 3.5 78.5 1.0 CG A:ASP190 3.5 35.9 1.0 C3' P:DG7 3.8 78.9 1.0 O A:HOH655 3.9 46.3 1.0 O A:HOH660 4.0 54.3 1.0 CG A:ASP192 4.3 47.9 1.0 CB A:ASP192 4.5 35.2 1.0 O A:HOH657 4.6 21.6 1.0 C4' P:DG7 4.7 80.0 1.0 CB A:ASP190 4.8 28.1 1.0 OD2 A:ASP256 4.8 19.3 1.0 O A:ASP190 4.9 22.9 1.0

Calcium binding site 2 out of 3 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 (15 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 (15 Millimolar) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca341 b:22.6 occ:1.00 O A:THR101 2.0 18.2 1.0 OP1 P:DT6 2.4 15.2 1.0 O A:HOH601 2.4 0.0 1.0 O A:ILE106 2.6 6.8 1.0 O A:VAL103 2.9 1.0 1.0 C A:THR101 3.3 15.2 1.0 P P:DT6 3.4 13.5 1.0 C A:VAL103 3.5 6.8 1.0 OP2 P:DT6 3.5 7.2 1.0 C A:ILE106 3.8 5.3 1.0 N A:VAL103 3.9 24.7 1.0 C A:ARG102 4.0 26.7 1.0 CA A:SER104 4.0 14.4 1.0 N A:SER104 4.0 3.9 1.0 N A:ARG102 4.2 21.4 1.0 CA A:ARG102 4.2 25.7 1.0 N A:GLY105 4.2 18.5 1.0 CA A:THR101 4.3 1.0 1.0 O5' P:DT6 4.3 1.4 1.0 CA A:VAL103 4.4 19.3 1.0 N A:ILE106 4.4 11.3 1.0 O A:ARG102 4.5 31.1 1.0 CA A:ILE106 4.5 8.4 1.0 O3' P:DA5 4.6 11.5 1.0 C A:SER104 4.7 18.0 1.0 CB A:ILE106 4.8 3.1 1.0 N A:GLY107 4.9 2.5 1.0 CG2 A:THR101 4.9 1.1 1.0

Calcium binding site 3 out of 3 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 (15 Millimolar)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 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 (15 Millimolar) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca342 b:92.7 occ:1.00 O A:LEU62 2.5 28.8 1.0 O A:LYS60 3.4 27.1 1.0 C A:LEU62 3.6 31.8 1.0 O A:VAL65 3.6 31.1 1.0 C A:LYS61 4.3 41.2 1.0 O A:LYS61 4.3 44.0 1.0 N A:PRO63 4.4 32.0 1.0 CA A:PRO63 4.4 26.6 1.0 N A:LEU62 4.4 32.1 1.0 C A:LYS60 4.6 27.9 1.0 CA A:LEU62 4.6 31.0 1.0 C A:VAL65 4.6 18.8 1.0 N A:VAL65 4.6 1.5 1.0 CA A:LYS61 4.8 43.1 1.0 N A:GLY64 4.9 27.9 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