Calcium in PDB 2fkc: Crystal Form I of Pre-Reactive Complex of Restriction Endonuclease HINP1I with Cognate Dna and Calcium Ion

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

The structure of Crystal Form I of Pre-Reactive Complex of Restriction Endonuclease HINP1I with Cognate Dna and Calcium Ion, PDB code: 2fkc 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)	19.89 / 2.39
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	105.104, 105.104, 130.360, 90.00, 90.00, 120.00
R / Rfree (%)	22.2 / 26

The binding sites of Calcium atom in the Crystal Form I of Pre-Reactive Complex of Restriction Endonuclease HINP1I with Cognate Dna and Calcium Ion (pdb code 2fkc). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Crystal Form I of Pre-Reactive Complex of Restriction Endonuclease HINP1I with Cognate Dna and Calcium Ion, PDB code: 2fkc:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Crystal Form I of Pre-Reactive Complex of Restriction Endonuclease HINP1I with Cognate Dna and Calcium Ion


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Form I of Pre-Reactive Complex of Restriction Endonuclease HINP1I with Cognate Dna and Calcium Ion within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca52 b:61.5 occ:1.00 OD1 A:ASP62 2.5 58.5 1.0 O C:HOH54 2.6 55.5 1.0 OE1 A:GLU18 2.6 60.7 1.0 O3' C:DG4 2.6 51.1 1.0 OP1 C:DC5 2.9 49.9 1.0 P C:DC5 3.3 48.3 1.0 C5' C:DC5 3.6 41.8 1.0 CG A:ASP62 3.7 59.1 1.0 CD A:GLU18 3.7 60.3 1.0 C3' C:DG4 3.8 52.3 1.0 O5' C:DC5 4.0 46.6 1.0 C4' C:DG4 4.1 54.4 1.0 OE2 A:GLU18 4.2 61.5 1.0 CA A:CA248 4.2 50.5 1.0 O A:HOH249 4.4 36.0 1.0 OD2 A:ASP62 4.4 59.2 1.0 CB A:ASP62 4.6 59.3 1.0 OP2 C:DC5 4.6 48.7 1.0 CE2 A:PHE15 4.7 48.8 1.0 C2' C:DG4 4.9 50.6 1.0 C5' C:DG4 5.0 59.0 1.0

Calcium binding site 2 out of 3 in the Crystal Form I of Pre-Reactive Complex of Restriction Endonuclease HINP1I with Cognate Dna and Calcium Ion


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Form I of Pre-Reactive Complex of Restriction Endonuclease HINP1I with Cognate Dna and Calcium Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca248 b:50.5 occ:1.00 OP1 C:DC5 2.1 49.9 1.0 O C:HOH53 2.4 35.1 1.0 O A:VAL82 2.4 46.4 1.0 OD2 A:ASP62 2.5 59.2 1.0 OE1 A:GLN81 2.5 44.8 1.0 CG A:ASP62 3.2 59.1 1.0 OD1 A:ASP62 3.3 58.5 1.0 P C:DC5 3.4 48.3 1.0 CD A:GLN81 3.4 44.2 1.0 C A:VAL82 3.6 45.4 1.0 NE2 A:GLN81 3.8 43.5 1.0 O5' C:DC5 4.0 46.6 1.0 N A:VAL82 4.0 45.2 1.0 OP2 C:DC5 4.1 48.7 1.0 OE1 A:GLU18 4.2 60.7 1.0 CA C:CA52 4.2 61.5 1.0 OP2 C:DG6 4.2 39.1 1.0 CA A:VAL82 4.3 45.5 1.0 C5' C:DC5 4.4 41.8 1.0 CG A:GLN81 4.5 44.1 1.0 O3' C:DG4 4.5 51.1 1.0 CB A:ASP62 4.6 59.3 1.0 N A:LYS83 4.6 45.4 1.0 CA A:LYS83 4.7 45.5 1.0 CG A:LYS83 4.7 46.9 1.0 CB A:VAL82 4.8 46.0 1.0 NZ A:LYS83 5.0 50.4 1.0

Calcium binding site 3 out of 3 in the Crystal Form I of Pre-Reactive Complex of Restriction Endonuclease HINP1I with Cognate Dna and Calcium Ion


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Form I of Pre-Reactive Complex of Restriction Endonuclease HINP1I with Cognate Dna and Calcium Ion within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca248 b:57.6 occ:1.00 OP1 E:DC5 2.1 46.5 1.0 O B:VAL82 2.2 46.7 1.0 OD2 B:ASP62 2.3 63.5 1.0 O E:HOH12 2.4 40.7 1.0 OE1 B:GLN81 2.5 48.0 1.0 CG B:ASP62 3.1 63.8 1.0 OD1 B:ASP62 3.4 64.4 1.0 CD B:GLN81 3.4 47.2 1.0 C B:VAL82 3.4 46.0 1.0 P E:DC5 3.5 45.9 1.0 N B:VAL82 3.9 45.6 1.0 NE2 B:GLN81 3.9 47.3 1.0 O5' E:DC5 4.0 45.1 1.0 CA B:VAL82 4.1 46.0 1.0 OE1 B:GLU18 4.2 69.0 1.0 OP2 E:DC5 4.3 44.7 1.0 OP2 E:DG6 4.4 42.9 1.0 N B:LYS83 4.4 46.6 1.0 CB B:ASP62 4.5 63.5 1.0 C5' E:DC5 4.5 43.7 1.0 CG B:GLN81 4.5 46.3 1.0 CG B:LYS83 4.5 46.9 1.0 O3' E:DG4 4.6 48.5 1.0 CA B:LYS83 4.6 47.0 1.0 CB B:VAL82 4.7 45.7 1.0 NZ B:LYS83 4.8 49.5 1.0 C B:GLN81 4.9 45.4 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