Calcium in PDB 2fkh: Crystal Form II of Pre-Reactive Complex of Restriction Endonuclease HINP1I with Cognate Dna and Calcium Ions

All present enzymatic activity of Crystal Form II of Pre-Reactive Complex of Restriction Endonuclease HINP1I with Cognate Dna and Calcium Ions:
3.1.21.4;

The structure of Crystal Form II of Pre-Reactive Complex of Restriction Endonuclease HINP1I with Cognate Dna and Calcium Ions, PDB code: 2fkh was solved by J.R.Horton, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	31.51 / 3.09
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	109.134, 109.134, 113.269, 90.00, 90.00, 120.00
R / Rfree (%)	22 / 31.3

The binding sites of Calcium atom in the Crystal Form II of Pre-Reactive Complex of Restriction Endonuclease HINP1I with Cognate Dna and Calcium Ions (pdb code 2fkh). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Form II of Pre-Reactive Complex of Restriction Endonuclease HINP1I with Cognate Dna and Calcium Ions, PDB code: 2fkh:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Form II of Pre-Reactive Complex of Restriction Endonuclease HINP1I with Cognate Dna and Calcium Ions


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Form II of Pre-Reactive Complex of Restriction Endonuclease HINP1I with Cognate Dna and Calcium Ions within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca22 b:80.4 occ:1.00 OD1 B:ASP62 2.5 37.1 1.0 O3' E:DG4 2.6 33.2 1.0 OP1 E:DC5 2.8 34.6 1.0 P E:DC5 3.1 33.7 1.0 CG B:ASP62 3.4 37.0 1.0 C3' E:DG4 3.6 34.6 1.0 O B:TYR59 3.6 42.4 1.0 OD2 B:ASP62 3.7 35.9 1.0 OP2 E:DC5 3.8 32.5 1.0 C4' E:DG4 4.0 35.3 1.0 NE2 B:GLN81 4.3 33.9 1.0 CA B:CA248 4.3 36.6 1.0 O B:SER61 4.4 37.1 1.0 O5' E:DC5 4.6 30.8 1.0 CB B:ASP62 4.6 36.9 1.0 C5' E:DG4 4.7 38.9 1.0 C B:SER61 4.7 36.7 1.0 C B:TYR59 4.8 42.3 1.0 CA B:ASP62 4.8 36.7 1.0 C2' E:DG4 4.9 34.5 1.0 C B:LYS60 4.9 39.5 1.0 OE1 B:GLN81 4.9 34.5 1.0 N B:ASP62 4.9 37.0 1.0 C5' E:DC5 5.0 28.3 1.0

Calcium binding site 2 out of 2 in the Crystal Form II of Pre-Reactive Complex of Restriction Endonuclease HINP1I with Cognate Dna and Calcium Ions


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Form II of Pre-Reactive Complex of Restriction Endonuclease HINP1I with Cognate Dna and Calcium Ions within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca248 b:36.6 occ:1.00 O B:VAL82 2.2 31.4 1.0 OP1 E:DC5 2.2 34.6 1.0 OE1 B:GLN81 2.5 34.5 1.0 OD2 B:ASP62 2.6 35.9 1.0 O B:HOH249 2.8 41.2 1.0 C B:VAL82 3.4 31.8 1.0 P E:DC5 3.4 33.7 1.0 CD B:GLN81 3.5 34.0 1.0 CG B:ASP62 3.6 37.0 1.0 OP2 E:DC5 3.8 32.5 1.0 OD1 B:ASP62 3.9 37.1 1.0 NE2 B:GLN81 3.9 33.9 1.0 CG B:LYS83 4.0 30.8 1.0 OP2 E:DG6 4.1 25.7 1.0 NZ B:LYS83 4.1 32.4 1.0 O5' E:DC5 4.1 30.8 1.0 N B:VAL82 4.2 33.4 1.0 CA E:CA22 4.3 80.4 1.0 CA B:VAL82 4.3 32.4 1.0 N B:LYS83 4.3 31.2 1.0 CA B:LYS83 4.5 30.4 1.0 C5' E:DC5 4.6 28.3 1.0 O3' E:DG4 4.7 33.2 1.0 OE1 B:GLU18 4.7 41.5 1.0 CG B:GLN81 4.8 34.4 1.0 CB B:ASP62 4.9 36.9 1.0 C3' E:DC5 4.9 25.9 1.0 CB B:LYS83 4.9 29.9 1.0 CE B:LYS83 4.9 31.6 1.0 P E:DG6 5.0 26.8 1.0 CB B:VAL82 5.0 33.2 1.0 O3' E:DC5 5.0 26.6 1.0

J.R.Horton, X.Zhang, R.Maunus, Z.Yang, G.G.Wilson, R.J.Roberts, X.Cheng. Dna Nicking By HINP1I Endonuclease: Bending, Base Flipping and Minor Groove Expansion. Nucleic Acids Res. V. 34 939 2006.
ISSN: ISSN 0305-1048
PubMed: 16473850
DOI: 10.1093/NAR/GKJ484