Calcium in PDB 6eko: Crystal Structure of Type Iip Restriction Endonuclease Pfoi with Cognate Dna

All present enzymatic activity of Crystal Structure of Type Iip Restriction Endonuclease Pfoi with Cognate Dna:
3.1.21.4;

The structure of Crystal Structure of Type Iip Restriction Endonuclease Pfoi with Cognate Dna, PDB code: 6eko was solved by G.Tamulaitiene, E.Manakova, V.Jovaisaite, S.Grazulis, V.Siksnys, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.96 / 2.28
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	56.279, 91.663, 152.742, 90.00, 90.00, 90.00
R / Rfree (%)	20.5 / 24.8

The binding sites of Calcium atom in the Crystal Structure of Type Iip Restriction Endonuclease Pfoi with Cognate Dna (pdb code 6eko). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of Type Iip Restriction Endonuclease Pfoi with Cognate Dna, PDB code: 6eko:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of Type Iip Restriction Endonuclease Pfoi with Cognate Dna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Type Iip Restriction Endonuclease Pfoi with Cognate Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:27.0 occ:1.00 OP1 F:DC5 2.2 25.0 1.0 O A:ALA186 2.3 23.2 1.0 O A:HOH529 2.4 23.1 1.0 OD2 A:ASP169 2.4 27.5 1.0 O F:HOH102 2.5 20.3 1.0 CG A:ASP169 3.1 36.3 1.0 OD1 A:ASP169 3.1 32.7 1.0 P F:DC5 3.4 25.6 1.0 C A:ALA186 3.4 20.4 1.0 N A:ALA186 3.8 19.9 1.0 O5' F:DC5 4.0 29.0 1.0 OP2 F:DC5 4.0 25.5 1.0 OE2 A:GLU167 4.0 41.3 1.0 CA A:ALA186 4.1 23.3 1.0 C5' F:DC5 4.2 17.8 1.0 O A:HOH507 4.4 28.9 1.0 O F:HOH115 4.4 20.4 1.0 O A:HOH602 4.4 39.4 1.0 N A:ALA187 4.5 16.2 1.0 CB A:ASP169 4.5 21.1 1.0 OP2 F:DC6 4.5 27.8 1.0 O3' F:DT4 4.6 22.6 1.0 CD A:GLU167 4.7 48.5 1.0 CB A:ALA186 4.8 14.6 1.0 CA A:ALA187 4.8 18.6 1.0 C A:SER185 4.8 22.9 1.0 CB A:ALA187 5.0 19.3 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of Type Iip Restriction Endonuclease Pfoi with Cognate Dna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Type Iip Restriction Endonuclease Pfoi with Cognate Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:40.9 occ:1.00 OE1 A:GLN15 2.3 28.9 1.0 OD2 A:ASP131 2.6 22.9 1.0 CD A:GLN15 3.5 23.5 1.0 CG A:ASP131 3.5 27.1 1.0 CB A:ASP131 3.8 24.3 1.0 NE2 A:GLN15 4.4 23.1 1.0 CG A:GLN15 4.4 22.9 1.0 CB A:GLN15 4.5 24.0 1.0 OD1 A:ASP131 4.7 28.6 1.0 N A:ASP16 4.8 22.9 1.0 O A:ASP131 4.8 24.4 1.0 CA A:GLN15 4.9 26.5 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of Type Iip Restriction Endonuclease Pfoi with Cognate Dna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Type Iip Restriction Endonuclease Pfoi with Cognate Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca403 b:48.8 occ:1.00 OE1 A:GLU28 2.4 47.4 1.0 CD A:GLU28 3.1 43.2 1.0 OE2 A:GLU28 3.2 46.1 1.0 CG A:GLU28 4.4 38.2 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of Type Iip Restriction Endonuclease Pfoi with Cognate Dna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Type Iip Restriction Endonuclease Pfoi with Cognate Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca401 b:24.1 occ:1.00 OP1 E:DC5 2.2 22.4 1.0 O B:ALA186 2.2 19.4 1.0 OD2 B:ASP169 2.4 27.9 1.0 O B:HOH552 2.5 26.1 1.0 O E:HOH101 2.5 22.8 1.0 CG B:ASP169 3.2 29.0 1.0 OD1 B:ASP169 3.3 28.4 1.0 P E:DC5 3.4 25.7 1.0 C B:ALA186 3.4 22.9 1.0 N B:ALA186 3.8 21.9 1.0 O5' E:DC5 3.9 29.1 1.0 OP2 E:DC5 3.9 23.4 1.0 CA B:ALA186 4.1 24.9 1.0 OE2 B:GLU167 4.2 40.5 1.0 C5' E:DC5 4.4 20.0 1.0 N B:ALA187 4.5 23.8 1.0 OP2 E:DC6 4.5 34.6 1.0 O E:HOH107 4.5 24.8 1.0 O B:HOH512 4.5 30.8 1.0 CB B:ASP169 4.5 25.4 1.0 O3' E:DT4 4.6 19.4 1.0 CA B:ALA187 4.7 26.4 1.0 C B:SER185 4.8 21.4 1.0 CB B:ALA186 4.8 23.2 1.0

G.Tamulaitiene, E.Manakova, V.Jovaisaite, G.Tamulaitis, S.Grazulis, M.Bochtler, V.Siksnys. Unique Mechanism of Target Recognition By Pfoi Restriction Endonuclease of the Ccgg-Family. Nucleic Acids Res. V. 47 997 2019.
ISSN: ESSN 1362-4962
PubMed: 30445642
DOI: 10.1093/NAR/GKY1137