Calcium in PDB 5dw8: Crystal Structure of 2'Amp Bound Saimpase-II

All present enzymatic activity of Crystal Structure of 2'Amp Bound Saimpase-II:
3.1.3.25;

The structure of Crystal Structure of 2'Amp Bound Saimpase-II, PDB code: 5dw8 was solved by A.Dutta, S.Bhattacharyya, A.K.Das, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.68 / 2.40
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	49.008, 105.687, 53.313, 90.00, 101.91, 90.00
R / Rfree (%)	20.6 / 26.6

The binding sites of Calcium atom in the Crystal Structure of 2'Amp Bound Saimpase-II (pdb code 5dw8). 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 2'Amp Bound Saimpase-II, PDB code: 5dw8:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of 2'Amp Bound Saimpase-II


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 2'Amp Bound Saimpase-II within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca301 b:45.6 occ:1.00 OD1 A:ASP83 2.3 19.6 1.0 O A:ILE85 2.3 19.3 1.0 O3P A:2AM302 2.4 41.6 1.0 CG A:ASP83 3.0 20.4 1.0 OD2 A:ASP83 3.1 22.0 1.0 C A:ILE85 3.2 19.5 1.0 CA A:CA303 3.3 70.7 1.0 CG A:GLU65 3.4 22.6 1.0 CD A:GLU65 3.6 26.5 1.0 OE1 A:GLU65 3.9 28.8 1.0 P A:2AM302 3.9 40.5 1.0 N A:ILE85 4.0 17.7 1.0 CA A:ILE85 4.1 19.0 1.0 N A:ASP86 4.1 19.2 1.0 OE2 A:GLU65 4.1 25.7 1.0 CB A:GLU65 4.2 20.5 1.0 OD2 A:ASP42 4.2 31.4 1.0 OD1 A:ASP42 4.3 30.4 1.0 CG2 A:THR88 4.3 18.4 1.0 CA A:ASP86 4.4 19.0 1.0 CB A:ASP83 4.5 18.2 1.0 CD A:PRO84 4.5 17.6 1.0 CB A:ILE85 4.6 19.9 1.0 CG A:ASP42 4.7 29.8 1.0 O1P A:2AM302 4.7 40.5 1.0 O2P A:2AM302 4.8 45.1 1.0 N A:PRO84 4.8 17.0 1.0 O2' A:2AM302 4.9 46.0 1.0 C A:ASP83 5.0 16.8 1.0 CA A:ASP83 5.0 17.3 1.0 O A:HOH443 5.0 16.0 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of 2'Amp Bound Saimpase-II


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 2'Amp Bound Saimpase-II within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca303 b:70.7 occ:1.00 OD2 A:ASP83 2.2 22.0 1.0 OD2 A:ASP208 2.3 19.6 1.0 O3P A:2AM302 2.4 41.6 1.0 O2' A:2AM302 2.6 46.0 1.0 P A:2AM302 2.9 40.5 1.0 O A:HOH443 3.0 16.0 1.0 OD1 A:ASP86 3.0 20.6 1.0 CG A:ASP208 3.2 19.6 1.0 CG A:ASP83 3.3 20.4 1.0 CA A:CA301 3.3 45.6 1.0 OD1 A:ASP208 3.5 21.2 1.0 OD1 A:ASP83 3.8 19.6 1.0 C2' A:2AM302 3.9 45.0 1.0 CG A:ASP86 4.0 20.6 1.0 CD1 A:TRP207 4.0 13.8 1.0 O2P A:2AM302 4.1 45.1 1.0 NE1 A:TRP207 4.1 13.9 1.0 O1P A:2AM302 4.1 40.5 1.0 CA A:ASP86 4.2 19.0 1.0 O A:ILE85 4.3 19.3 1.0 CB A:ASP86 4.4 20.3 1.0 C1' A:2AM302 4.5 47.8 1.0 CB A:ASP83 4.5 18.2 1.0 O3' A:2AM302 4.5 37.4 1.0 CB A:ASP208 4.6 18.3 1.0 C3' A:2AM302 4.7 42.7 1.0 CG A:GLU65 4.8 22.6 1.0 N A:ASP86 4.8 19.2 1.0 C A:ILE85 4.9 19.5 1.0 N9 A:2AM302 4.9 55.5 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of 2'Amp Bound Saimpase-II


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 2'Amp Bound Saimpase-II within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca301 b:22.5 occ:1.00 OD2 B:ASP83 2.1 15.3 1.0 OD2 B:ASP208 2.2 13.7 1.0 OD1 B:ASP86 2.5 14.9 1.0 O2' B:2AM303 2.5 33.3 1.0 O2P B:2AM303 2.7 28.4 1.0 P B:2AM303 3.1 31.1 1.0 CG B:ASP83 3.2 14.4 1.0 CG B:ASP208 3.4 12.9 1.0 O B:HOH408 3.5 27.8 1.0 CG B:ASP86 3.6 14.8 1.0 CA B:CA302 3.6 31.1 1.0 C2' B:2AM303 3.8 37.9 1.0 OD1 B:ASP83 3.8 14.4 1.0 O3' B:2AM303 3.9 33.0 1.0 CB B:ASP86 4.0 14.5 1.0 CA B:ASP86 4.1 14.1 1.0 OD1 B:ASP208 4.1 14.6 1.0 O3P B:2AM303 4.2 30.1 1.0 C1' B:2AM303 4.2 41.3 1.0 O1P B:2AM303 4.3 29.5 1.0 CB B:ASP83 4.4 13.9 1.0 C3' B:2AM303 4.4 36.8 1.0 OE2 B:GLU65 4.5 32.2 1.0 CB B:ASP208 4.5 12.2 1.0 CD1 B:TRP207 4.6 9.7 1.0 O B:ILE85 4.6 15.1 1.0 OD2 B:ASP86 4.6 15.3 1.0 CA B:ASP208 4.7 11.3 1.0 N B:GLY87 4.9 14.3 1.0 NE1 B:TRP207 5.0 9.8 1.0 N B:ASP86 5.0 14.0 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of 2'Amp Bound Saimpase-II


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 2'Amp Bound Saimpase-II within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca302 b:31.1 occ:1.00 O2P B:2AM303 2.0 28.4 1.0 O B:HOH403 2.1 41.4 1.0 O B:ILE85 2.3 15.1 1.0 OE2 B:GLU65 2.5 32.2 1.0 OD1 B:ASP83 2.6 14.4 1.0 CD B:GLU65 3.3 32.4 1.0 CG B:ASP83 3.4 14.4 1.0 C B:ILE85 3.4 14.6 1.0 OD2 B:ASP83 3.4 15.3 1.0 P B:2AM303 3.4 31.1 1.0 OE1 B:GLU65 3.5 36.9 1.0 CA B:CA301 3.6 22.5 1.0 CG2 B:THR88 3.9 17.9 1.0 O1P B:2AM303 4.2 29.5 1.0 N B:ASP86 4.2 14.0 1.0 CA B:ASP86 4.2 14.1 1.0 O3P B:2AM303 4.3 30.1 1.0 N B:ILE85 4.4 14.7 1.0 CA B:ILE85 4.4 14.2 1.0 O2' B:2AM303 4.5 33.3 1.0 CG B:GLU65 4.6 30.3 1.0 CB B:ILE85 4.7 14.4 1.0 OG1 B:THR88 4.7 17.5 1.0 OD2 B:ASP42 4.8 34.6 1.0 CB B:ASP83 4.8 13.9 1.0 CB B:THR88 4.9 17.9 1.0

A.Dutta, S.Bhattacharyya, A.K.Das. Crystal Structure of 2'Amp Bound Saimpase-II To Be Published.