Calcium in PDB 8hrf: Catalytic Domain of Vibrio Parahaemolyticus Chitinase 1

The structure of Catalytic Domain of Vibrio Parahaemolyticus Chitinase 1, PDB code: 8hrf was solved by A.Nakamura, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.70 / 2.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	48.804, 159.996, 75.489, 90, 92.68, 90
R / Rfree (%)	16.1 / 24.5

The binding sites of Calcium atom in the Catalytic Domain of Vibrio Parahaemolyticus Chitinase 1 (pdb code 8hrf). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Catalytic Domain of Vibrio Parahaemolyticus Chitinase 1, PDB code: 8hrf:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Catalytic Domain of Vibrio Parahaemolyticus Chitinase 1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Catalytic Domain of Vibrio Parahaemolyticus Chitinase 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca602 b:15.5 occ:1.00 O A:HOH730 2.1 12.0 1.0 OD2 A:ASP373 2.3 12.1 1.0 O A:HOH765 2.5 17.9 1.0 O A:HOH890 2.5 15.6 1.0 O A:HOH785 2.5 9.4 1.0 O A:ASP369 2.6 14.3 1.0 O A:HOH1039 3.1 13.9 1.0 O A:HOH1029 3.3 12.8 1.0 CG A:ASP373 3.4 13.7 1.0 C A:ASP369 3.6 14.2 1.0 OD1 A:ASP373 3.9 11.7 1.0 CB A:ASP369 4.3 12.7 1.0 OD2 A:ASP369 4.3 16.9 1.0 O A:GLY318 4.4 14.6 1.0 CA A:ASP369 4.4 12.6 1.0 N A:LYS370 4.5 10.2 1.0 O A:HOH1072 4.5 13.4 1.0 OE2 A:GLU372 4.5 15.9 1.0 O A:HOH1052 4.5 16.9 1.0 CD A:LYS370 4.6 8.8 1.0 CB A:ASP373 4.6 15.3 1.0 CA A:LYS370 4.6 9.7 1.0 C A:GLY318 4.6 12.8 1.0 O A:GLY319 4.7 13.1 1.0 CG A:ASP369 4.8 14.8 1.0 O A:HOH758 4.8 17.6 1.0 CA A:GLY318 4.8 11.1 1.0 O A:PRO317 4.9 8.9 1.0

Calcium binding site 2 out of 3 in the Catalytic Domain of Vibrio Parahaemolyticus Chitinase 1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Catalytic Domain of Vibrio Parahaemolyticus Chitinase 1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca602 b:15.2 occ:1.00 O B:ASP369 2.2 9.9 1.0 O B:HOH783 2.2 10.1 1.0 O B:HOH741 2.3 10.8 1.0 O B:HOH777 2.4 14.1 1.0 O B:HOH846 2.4 17.6 1.0 OD2 B:ASP373 2.4 17.5 1.0 O B:HOH959 2.6 14.5 1.0 C B:ASP369 3.4 14.8 1.0 CG B:ASP373 3.4 17.1 1.0 OD1 B:ASP373 3.9 14.8 1.0 O B:HOH983 3.9 14.6 1.0 CB B:ASP369 4.2 13.5 1.0 CA B:ASP369 4.2 16.6 1.0 CD B:LYS370 4.4 16.8 1.0 N B:LYS370 4.4 14.6 1.0 O B:GLY318 4.4 15.2 1.0 OD2 B:ASP369 4.5 30.2 1.0 CA B:LYS370 4.6 13.9 1.0 CB B:ASP373 4.6 9.1 1.0 O B:GLY319 4.6 13.5 1.0 C B:GLY318 4.7 12.3 1.0 OE2 B:GLU372 4.7 21.0 1.0 CG B:ASP369 4.8 17.1 1.0 CA B:GLY318 4.8 11.2 1.0 O B:HOH1008 4.8 22.0 1.0 O B:HOH834 4.9 14.1 1.0 O B:PRO317 4.9 10.7 1.0

Calcium binding site 3 out of 3 in the Catalytic Domain of Vibrio Parahaemolyticus Chitinase 1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Catalytic Domain of Vibrio Parahaemolyticus Chitinase 1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca603 b:28.8 occ:1.00 OE1 B:GLU342 2.6 11.2 1.0 OD1 B:ASP291 2.7 6.7 1.0 O B:HOH1003 3.1 9.5 1.0 C B:ARG290 3.1 10.7 1.0 N B:ASP291 3.1 6.4 1.0 O B:ARG290 3.2 10.6 1.0 CA B:ASP291 3.2 8.4 1.0 CD B:GLU342 3.3 10.4 1.0 CB B:ARG290 3.5 9.1 1.0 CG B:GLU342 3.6 4.1 1.0 CG B:ASP291 3.7 12.8 1.0 CB B:GLU342 3.7 6.2 1.0 CG2 B:VAL294 3.8 7.2 1.0 CA B:ARG290 3.9 11.1 1.0 CB B:VAL294 4.0 13.3 1.0 CB B:ASP291 4.0 13.0 1.0 OE2 B:GLU342 4.2 10.6 1.0 C B:ASP291 4.4 8.8 1.0 NZ B:LYS287 4.5 7.2 1.0 O B:LYS287 4.5 12.1 1.0 CD B:LYS287 4.7 10.1 1.0 O B:HOH916 4.7 16.1 1.0 CG1 B:VAL294 4.7 7.6 1.0 O B:ASP291 4.8 13.4 1.0 NE B:ARG290 4.8 7.6 1.0 OD2 B:ASP291 4.8 12.1 1.0 O B:HOH881 4.9 5.6 1.0 CG B:ARG290 5.0 11.1 1.0

A.Nakamura, A.Nakamura. N/A N/A.