Calcium in PDB 3or3: Restriction Endonuclease HPY188I in Complex with Product Dna

The structure of Restriction Endonuclease HPY188I in Complex with Product Dna, PDB code: 3or3 was solved by M.Sokolowska, H.Czapinska, M.Bochtler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.95
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	65.395, 65.395, 221.783, 90.00, 90.00, 90.00
R / Rfree (%)	16.8 / 20.1

The structure of Restriction Endonuclease HPY188I in Complex with Product Dna also contains other interesting chemical elements:

Chlorine

(Cl)

5 atoms

The binding sites of Calcium atom in the Restriction Endonuclease HPY188I in Complex with Product Dna (pdb code 3or3). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Restriction Endonuclease HPY188I in Complex with Product Dna, PDB code: 3or3:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Restriction Endonuclease HPY188I in Complex with Product Dna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Restriction Endonuclease HPY188I in Complex with Product Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca171 b:47.7 occ:1.00 OP1 E:DG1 2.5 22.2 0.5 ND1 B:HIS76 2.6 22.3 1.0 OP1 F:DG1 2.8 19.7 0.5 CD A:GLU149 3.2 33.8 1.0 OE2 A:GLU149 3.3 37.2 1.0 OE1 A:GLU149 3.4 36.6 1.0 CE1 B:HIS76 3.4 20.8 1.0 N B:HIS76 3.4 18.0 1.0 O D:HOH53 3.4 40.0 1.0 O F:HOH39 3.4 19.4 1.0 CA B:GLY75 3.6 17.9 1.0 O3' D:DA0 3.6 18.0 0.5 CG B:HIS76 3.7 20.8 1.0 O3' C:DT0 3.7 28.0 0.5 C B:GLY75 3.7 18.7 1.0 CG A:GLU149 3.8 29.8 1.0 P E:DG1 3.9 22.7 0.5 CB B:HIS76 4.0 20.1 1.0 P F:DG1 4.1 19.2 0.5 C5' E:DG1 4.1 21.8 0.5 C5' F:DG1 4.1 18.3 0.5 CA B:HIS76 4.2 19.3 1.0 OP3 F:DG1 4.3 20.1 0.5 OP3 E:DG1 4.5 23.5 0.5 O5' E:DG1 4.5 21.8 0.5 NE2 B:HIS76 4.6 23.5 1.0 O D:HOH255 4.6 41.8 1.0 CB A:GLU149 4.6 27.5 1.0 O B:GLY75 4.6 19.9 1.0 O5' F:DG1 4.6 19.1 0.5 O B:HIS76 4.7 18.8 1.0 C3' D:DA0 4.7 17.1 0.5 CD2 B:HIS76 4.7 23.6 1.0 O B:ILE74 4.8 18.8 1.0 C3' C:DT0 4.8 24.3 0.5 N B:GLY75 4.8 17.5 1.0 C B:HIS76 4.9 18.2 1.0 OP2 E:DG1 5.0 22.3 0.5

Calcium binding site 2 out of 3 in the Restriction Endonuclease HPY188I in Complex with Product Dna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Restriction Endonuclease HPY188I in Complex with Product Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca172 b:53.6 occ:1.00 OP1 F:DG1 2.5 23.6 0.5 ND1 A:HIS76 2.6 23.6 1.0 OP1 E:DG1 2.7 19.3 0.5 OE2 B:GLU149 3.1 43.6 1.0 CD B:GLU149 3.2 37.0 1.0 O C:HOH358 3.3 50.3 1.0 N A:HIS76 3.4 18.9 1.0 CE1 A:HIS76 3.4 22.7 1.0 O F:HOH52 3.5 22.7 1.0 OE1 B:GLU149 3.5 41.9 1.0 O3' C:DT0 3.5 20.7 0.5 CA A:GLY75 3.6 19.5 1.0 O3' D:DA0 3.7 26.6 0.5 CG A:HIS76 3.7 22.2 1.0 C A:GLY75 3.7 19.4 1.0 CG B:GLU149 3.8 33.1 1.0 P F:DG1 3.9 20.3 0.5 CB A:HIS76 4.1 20.3 1.0 P E:DG1 4.1 18.4 0.5 C5' F:DG1 4.2 22.6 0.5 OP3 F:DG1 4.2 21.1 0.5 C5' E:DG1 4.2 19.5 0.5 CA A:HIS76 4.2 20.2 1.0 O5' F:DG1 4.5 21.9 0.5 CB B:GLU149 4.6 30.7 1.0 NE2 A:HIS76 4.6 22.9 1.0 OP3 E:DG1 4.6 17.4 0.5 O A:GLY75 4.7 20.4 1.0 O A:HIS76 4.7 19.8 1.0 O A:ILE74 4.7 20.2 1.0 C3' D:DA0 4.7 22.6 0.5 O5' E:DG1 4.7 17.9 0.5 CD2 A:HIS76 4.8 22.6 1.0 C3' C:DT0 4.8 19.2 0.5 N A:GLY75 4.8 19.9 1.0 O C:HOH151 4.8 40.6 1.0 C A:HIS76 4.9 19.1 1.0

Calcium binding site 3 out of 3 in the Restriction Endonuclease HPY188I in Complex with Product Dna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Restriction Endonuclease HPY188I in Complex with Product Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca173 b:74.5 occ:1.00 OD1 A:ASP18 2.3 31.1 1.0 O A:HOH219 2.6 50.2 1.0 O A:HOH222 2.6 62.2 1.0 O A:HOH221 2.7 49.0 1.0 O A:HOH218 3.2 51.4 1.0 CG A:ASP18 3.3 32.0 1.0 O A:HOH220 3.4 50.6 1.0 OD2 A:ASP18 4.0 34.0 1.0 CB A:ASP18 4.2 30.8 1.0 CA A:ASP18 4.4 30.3 1.0 O A:LYS17 4.6 31.5 1.0 N A:ASP18 5.0 30.1 1.0

M.Sokolowska, H.Czapinska, M.Bochtler. HPY188I-Dna Pre- and Post-Cleavage Complexes--Snapshots of the Giy-Yig Nuclease Mediated Catalysis. Nucleic Acids Res. V. 39 1554 2011.
ISSN: ISSN 0305-1048
PubMed: 20935048
DOI: 10.1093/NAR/GKQ821