Calcium in PDB 3zdc: Structure of E. Coli Exoix in Complex with the Palindromic 5OV4 Dna Oligonucleotide, Potassium and Calcium

The structure of Structure of E. Coli Exoix in Complex with the Palindromic 5OV4 Dna Oligonucleotide, Potassium and Calcium, PDB code: 3zdc was solved by G.R.Hemsworth, C.S.Anstey-Gilbert, C.S.Flemming, M.R.G.Hodskinson, J.Zhang, S.E.Sedelnikova, T.J.Stillman, J.R.Sayers, P.J.Artymiuk, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.53 / 1.53
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	66.178, 152.688, 34.530, 90.00, 90.00, 90.00
R / Rfree (%)	20.485 / 22.865

The structure of Structure of E. Coli Exoix in Complex with the Palindromic 5OV4 Dna Oligonucleotide, Potassium and Calcium also contains other interesting chemical elements:

Potassium

(K)

1 atom

The binding sites of Calcium atom in the Structure of E. Coli Exoix in Complex with the Palindromic 5OV4 Dna Oligonucleotide, Potassium and Calcium (pdb code 3zdc). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Structure of E. Coli Exoix in Complex with the Palindromic 5OV4 Dna Oligonucleotide, Potassium and Calcium, PDB code: 3zdc:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Structure of E. Coli Exoix in Complex with the Palindromic 5OV4 Dna Oligonucleotide, Potassium and Calcium


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of E. Coli Exoix in Complex with the Palindromic 5OV4 Dna Oligonucleotide, Potassium and Calcium within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1252 b:28.2 occ:0.75 O A:HOH2094 2.4 36.1 1.0 OD1 A:ASP127 2.4 25.6 1.0 OD2 A:ASP127 2.4 31.7 1.0 O A:HOH2095 2.6 40.0 1.0 O A:HOH2125 2.7 42.2 1.0 CG A:ASP127 2.8 25.9 1.0 O A:HOH2058 2.9 47.2 1.0 CB A:ASP127 4.3 19.2 1.0 O A:HOH2076 4.3 29.7 1.0 O A:HOH2099 4.4 33.2 1.0 N A:GLY129 4.4 15.6 1.0 CA A:GLY129 4.5 16.0 1.0 O A:HOH2057 4.7 37.0 1.0 O A:HOH2093 4.8 30.2 1.0 OD2 A:ASP104 5.0 33.4 1.0

Calcium binding site 2 out of 2 in the Structure of E. Coli Exoix in Complex with the Palindromic 5OV4 Dna Oligonucleotide, Potassium and Calcium


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of E. Coli Exoix in Complex with the Palindromic 5OV4 Dna Oligonucleotide, Potassium and Calcium within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1253 b:23.0 occ:0.60 K A:K1251 1.9 24.0 0.4 OP1 X:DC10 2.1 34.7 1.0 O A:HOH2121 2.3 41.9 1.0 O A:HOH2123 2.3 32.1 1.0 O A:ALA172 2.3 21.4 1.0 O A:ILE185 2.6 30.6 1.0 P X:DC10 3.3 31.3 1.0 C A:ALA172 3.4 20.3 1.0 OP2 X:DC10 3.7 35.8 1.0 C A:ILE185 3.7 27.9 1.0 CA A:ALA172 4.0 22.6 1.0 CA A:GLY186 4.1 19.4 1.0 O A:PRO180 4.2 26.8 1.0 O5' X:DC10 4.3 33.3 1.0 N A:GLY186 4.3 20.5 1.0 O3' X:DA9 4.4 28.0 1.0 O A:HOH2052 4.4 39.6 1.0 N A:GLY173 4.4 22.9 1.0 O A:HOH2122 4.5 36.7 1.0 O A:VAL182 4.5 25.5 1.0 O A:HOH2124 4.6 38.7 1.0 C3' X:DA9 4.6 22.5 1.0 O A:LEU171 4.7 22.6 1.0 CA A:GLY173 4.7 23.0 1.0 N A:ILE185 4.8 24.4 1.0 CB A:ALA172 4.8 20.2 1.0 CA A:ILE185 4.8 23.6 1.0 O X:HOH2009 4.9 44.5 1.0

C.S.Anstey-Gilbert, G.R.Hemsworth, C.S.Flemming, M.R.G.Hodskinson, J.Zhang, S.E.Sedelnikova, T.J.Stillman, J.R.Sayers, P.J.Artymiuk. The Structure of E. Coli Exoix - Implications For Dna Binding and Catalysis in Flap Endonucleases Nucleic Acids Res. V. 41 8357 2013.
ISSN: ISSN 0305-1048
PubMed: 23821668
DOI: 10.1093/NAR/GKT591