Calcium in PDB 5j16: Crystal Structure of Inositol Monophosphate Bound Saimpase-II

The structure of Crystal Structure of Inositol Monophosphate Bound Saimpase-II, PDB code: 5j16 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)	72.79 / 2.40
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	54.942, 78.762, 80.052, 105.46, 102.28, 109.47
R / Rfree (%)	18.1 / 23.7

The binding sites of Calcium atom in the Crystal Structure of Inositol Monophosphate Bound Saimpase-II (pdb code 5j16). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Crystal Structure of Inositol Monophosphate Bound Saimpase-II, PDB code: 5j16:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in the Crystal Structure of Inositol Monophosphate 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 Inositol Monophosphate Bound Saimpase-II within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca301 b:35.4 occ:1.00 OD2 A:ASP208 2.1 23.1 1.0 OD2 A:ASP83 2.2 30.1 1.0 O9 A:IPD303 2.3 37.2 1.0 OD1 A:ASP86 2.4 26.9 1.0 O1 A:IPD303 2.4 39.5 1.0 O A:HOH437 2.4 31.6 1.0 P1 A:IPD303 3.0 35.1 1.0 CG A:ASP208 3.2 27.5 1.0 CG A:ASP83 3.3 27.9 1.0 CG A:ASP86 3.5 26.6 1.0 C1 A:IPD303 3.6 38.4 1.0 OD1 A:ASP83 3.7 26.0 1.0 O2 A:IPD303 3.8 37.7 1.0 OD1 A:ASP208 3.8 28.8 1.0 OE1 A:GLU65 3.8 56.9 1.0 CA A:CA302 3.9 40.2 1.0 CA A:ASP86 4.0 24.9 1.0 CB A:ASP86 4.0 25.4 1.0 O8 A:IPD303 4.1 34.1 1.0 O7 A:IPD303 4.1 37.8 1.0 C6 A:IPD303 4.1 41.3 1.0 C2 A:IPD303 4.1 39.1 1.0 O6 A:IPD303 4.3 39.9 1.0 CB A:ASP208 4.5 26.9 1.0 CD1 A:TRP207 4.5 32.8 1.0 OD2 A:ASP86 4.5 24.9 1.0 CB A:ASP83 4.6 28.5 1.0 O A:ILE85 4.6 24.0 1.0 N A:GLY87 4.8 20.1 1.0 CA A:ASP208 4.8 26.7 1.0 NE1 A:TRP207 4.8 35.8 1.0 CD A:GLU65 4.9 63.0 1.0 N A:ASP86 4.9 28.6 1.0 C A:ASP86 4.9 22.7 1.0

Calcium binding site 2 out of 8 in the Crystal Structure of Inositol Monophosphate 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 Inositol Monophosphate Bound Saimpase-II within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca302 b:40.2 occ:1.00 OE1 A:GLU65 2.2 56.9 1.0 O9 A:IPD303 2.4 37.2 1.0 OD1 A:ASP83 2.4 26.0 1.0 O A:ILE85 2.5 24.0 1.0 CD A:GLU65 3.2 63.0 1.0 CG A:ASP83 3.5 27.9 1.0 C A:ILE85 3.5 29.4 1.0 OD1 A:ASP42 3.7 64.0 1.0 CG A:GLU65 3.7 67.6 1.0 OD2 A:ASP83 3.8 30.1 1.0 P1 A:IPD303 3.8 35.1 1.0 CA A:CA301 3.9 35.4 1.0 N A:ILE85 4.1 30.1 1.0 OE1 A:GLU66 4.1 96.9 1.0 O7 A:IPD303 4.2 37.8 1.0 OE2 A:GLU65 4.3 67.7 1.0 N A:ASP86 4.3 28.6 1.0 CA A:ILE85 4.3 31.4 1.0 O A:HOH437 4.3 31.6 1.0 CA A:ASP86 4.5 24.9 1.0 O8 A:IPD303 4.7 34.1 1.0 CG2 A:THR88 4.7 32.0 1.0 CD A:PRO84 4.7 31.3 1.0 CB A:ILE85 4.8 32.1 1.0 CB A:ASP83 4.8 28.5 1.0 CG A:ASP42 4.9 57.4 1.0 OG1 A:THR88 4.9 34.0 1.0 CG A:PRO84 4.9 32.1 1.0 N A:PRO84 4.9 31.1 1.0 O1 A:IPD303 4.9 39.5 1.0 CB A:GLU65 4.9 63.1 1.0

Calcium binding site 3 out of 8 in the Crystal Structure of Inositol Monophosphate 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 Inositol Monophosphate Bound Saimpase-II within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca301 b:30.0 occ:1.00 OD2 B:ASP208 2.0 37.6 1.0 O B:HOH434 2.2 22.8 1.0 OD2 B:ASP83 2.3 33.3 1.0 O1 B:IPD303 2.4 40.2 1.0 OD1 B:ASP86 2.4 21.3 1.0 O7 B:IPD303 2.6 31.7 1.0 P1 B:IPD303 3.1 36.3 1.0 CG B:ASP208 3.2 38.2 1.0 CG B:ASP83 3.5 30.5 1.0 O2 B:IPD303 3.5 36.3 1.0 C1 B:IPD303 3.6 38.5 0.7 CG B:ASP86 3.6 25.0 1.0 OD1 B:ASP208 3.9 49.7 1.0 OE2 B:GLU65 3.9 54.4 1.0 C6 B:IPD303 4.0 36.5 0.7 C2 B:IPD303 4.0 40.4 1.0 CA B:ASP86 4.0 24.9 1.0 CB B:ASP86 4.0 26.1 1.0 OD1 B:ASP83 4.1 32.0 1.0 CA B:CA302 4.1 38.9 1.0 O8 B:IPD303 4.2 37.0 1.0 O9 B:IPD303 4.2 39.1 1.0 O6 B:IPD303 4.3 36.3 0.7 CB B:ASP208 4.3 33.8 1.0 CD1 B:TRP207 4.5 29.4 1.0 CB B:ASP83 4.6 29.2 1.0 CD B:GLU65 4.6 59.8 1.0 CA B:ASP208 4.6 31.8 1.0 OE1 B:GLU65 4.7 56.7 1.0 OD2 B:ASP86 4.7 23.5 1.0 NE1 B:TRP207 4.9 29.9 1.0 N B:GLY87 4.9 24.5 1.0 O B:ILE85 5.0 31.3 1.0 N B:ASP86 5.0 24.3 1.0

Calcium binding site 4 out of 8 in the Crystal Structure of Inositol Monophosphate 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 Inositol Monophosphate Bound Saimpase-II within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca302 b:38.9 occ:1.00 OE2 B:GLU65 1.9 54.4 1.0 O B:HOH425 2.2 40.6 1.0 O B:HOH441 2.3 33.6 1.0 O7 B:IPD303 2.3 31.7 1.0 O B:ILE85 2.3 31.3 1.0 OD1 B:ASP83 2.5 32.0 1.0 CD B:GLU65 2.9 59.8 1.0 C B:ILE85 3.2 25.5 1.0 CG B:ASP83 3.4 30.5 1.0 OD2 B:ASP83 3.5 33.3 1.0 OE1 B:GLU65 3.6 56.7 1.0 P1 B:IPD303 3.7 36.3 1.0 CG B:GLU65 3.9 63.4 1.0 N B:ASP86 4.0 24.3 1.0 O9 B:IPD303 4.0 39.1 1.0 N B:ILE85 4.1 25.6 1.0 CA B:CA301 4.1 30.0 1.0 CA B:ILE85 4.2 26.8 1.0 O B:HOH434 4.2 22.8 1.0 CA B:ASP86 4.2 24.9 1.0 CG2 B:THR88 4.3 33.1 1.0 CB B:ILE85 4.5 25.9 1.0 O8 B:IPD303 4.6 37.0 1.0 CB B:GLU65 4.6 61.7 1.0 O1 B:IPD303 4.8 40.2 1.0 CD B:PRO84 4.8 30.8 1.0 CB B:ASP83 4.8 29.2 1.0

Calcium binding site 5 out of 8 in the Crystal Structure of Inositol Monophosphate Bound Saimpase-II


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of Inositol Monophosphate Bound Saimpase-II within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca301 b:30.8 occ:1.00 OD2 C:ASP83 2.1 30.9 1.0 OD2 C:ASP208 2.2 35.8 1.0 O C:HOH429 2.3 23.0 1.0 O9 C:IPD303 2.4 29.5 1.0 OD1 C:ASP86 2.4 25.8 1.0 O1 C:IPD303 2.4 33.9 1.0 P1 C:IPD303 3.0 34.3 1.0 CG C:ASP83 3.4 30.3 1.0 CG C:ASP86 3.4 26.5 1.0 CG C:ASP208 3.5 35.2 1.0 C1 C:IPD303 3.6 37.2 1.0 CB C:ASP86 3.8 27.9 1.0 O2 C:IPD303 3.8 35.9 1.0 CA C:ASP86 4.0 28.4 1.0 CA C:CA302 4.0 37.1 1.0 O7 C:IPD303 4.0 30.1 1.0 OD1 C:ASP83 4.0 30.9 1.0 C6 C:IPD303 4.1 42.1 1.0 OD1 C:ASP208 4.1 34.2 1.0 O8 C:IPD303 4.2 31.6 1.0 C2 C:IPD303 4.2 35.0 1.0 OE1 C:GLU65 4.2 55.9 1.0 CD1 C:TRP207 4.4 31.9 1.0 CB C:ASP83 4.4 30.6 1.0 OD2 C:ASP86 4.5 25.1 1.0 O6 C:IPD303 4.5 43.0 1.0 CB C:ASP208 4.5 33.9 1.0 NE1 C:TRP207 4.7 32.8 1.0 O C:ILE85 4.7 28.3 1.0 CA C:ASP208 4.7 33.5 1.0 N C:GLY87 4.9 29.0 1.0 N C:ASP86 4.9 27.8 1.0 C C:ASP86 4.9 31.2 1.0

Calcium binding site 6 out of 8 in the Crystal Structure of Inositol Monophosphate Bound Saimpase-II


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of Inositol Monophosphate Bound Saimpase-II within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca302 b:37.1 occ:1.00 O C:HOH403 2.1 22.7 1.0 OD1 C:ASP83 2.3 30.9 1.0 O9 C:IPD303 2.3 29.5 1.0 O C:ILE85 2.4 28.3 1.0 OE1 C:GLU65 2.5 55.9 1.0 O C:HOH416 2.5 42.7 1.0 CG C:ASP83 3.1 30.3 1.0 OD2 C:ASP83 3.2 30.9 1.0 C C:ILE85 3.4 30.6 1.0 CD C:GLU65 3.6 61.6 1.0 P1 C:IPD303 3.8 34.3 1.0 CA C:CA301 4.0 30.8 1.0 N C:ILE85 4.1 30.4 1.0 N C:ASP86 4.2 27.8 1.0 O8 C:IPD303 4.2 31.6 1.0 O C:HOH429 4.2 23.0 1.0 CA C:ILE85 4.3 31.3 1.0 CA C:ASP86 4.3 28.4 1.0 OE2 C:GLU66 4.3 85.8 1.0 OE2 C:GLU65 4.3 67.5 1.0 CG C:GLU65 4.4 61.0 1.0 OD2 C:ASP42 4.4 54.3 1.0 CG2 C:THR88 4.4 30.9 1.0 OD1 C:ASP42 4.4 58.5 1.0 CD C:PRO84 4.5 32.8 1.0 CB C:ASP83 4.6 30.6 1.0 O7 C:IPD303 4.6 30.1 1.0 CB C:ILE85 4.7 32.6 1.0 N C:PRO84 4.9 30.6 1.0 CG C:ASP42 4.9 50.2 1.0 O1 C:IPD303 4.9 33.9 1.0 CG C:PRO84 5.0 32.8 1.0

Calcium binding site 7 out of 8 in the Crystal Structure of Inositol Monophosphate Bound Saimpase-II


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of Inositol Monophosphate Bound Saimpase-II within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca301 b:31.1 occ:1.00 OD2 D:ASP83 2.2 23.9 1.0 OD2 D:ASP208 2.2 30.1 1.0 OD1 D:ASP86 2.3 22.1 1.0 O D:HOH403 2.4 27.1 1.0 O4 D:PO4303 2.6 40.4 1.0 O2 D:PO4303 2.6 41.5 1.0 P D:PO4303 3.1 43.1 1.0 CG D:ASP83 3.4 24.3 1.0 CG D:ASP208 3.4 31.1 1.0 CG D:ASP86 3.5 25.1 1.0 CA D:CA302 3.8 45.2 1.0 OD1 D:ASP83 3.9 22.3 1.0 CA D:ASP86 4.0 27.0 1.0 CB D:ASP86 4.0 26.8 1.0 OD1 D:ASP208 4.1 32.4 1.0 O3 D:PO4303 4.2 39.4 1.0 OE2 D:GLU65 4.2 55.9 1.0 O1 D:PO4303 4.2 45.6 1.0 OD2 D:ASP86 4.4 25.3 1.0 CD1 D:TRP207 4.4 30.0 1.0 CB D:ASP208 4.6 28.9 1.0 CB D:ASP83 4.6 24.7 1.0 O D:ILE85 4.7 33.3 1.0 CA D:ASP208 4.8 27.3 1.0 NE1 D:TRP207 4.8 31.9 1.0 N D:GLY87 4.8 28.9 1.0 N D:ASP86 5.0 30.0 1.0 C D:ASP86 5.0 28.7 1.0

Calcium binding site 8 out of 8 in the Crystal Structure of Inositol Monophosphate Bound Saimpase-II


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of Inositol Monophosphate Bound Saimpase-II within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca302 b:45.2 occ:1.00 O4 D:PO4303 2.3 40.4 1.0 O D:HOH430 2.3 34.0 1.0 O D:ILE85 2.4 33.3 1.0 OD1 D:ASP83 2.5 22.3 1.0 OE2 D:GLU65 2.5 55.9 1.0 CD D:GLU65 3.2 63.6 1.0 OE1 D:GLU65 3.3 70.5 1.0 CG D:ASP83 3.3 24.3 1.0 OD2 D:ASP83 3.4 23.9 1.0 C D:ILE85 3.4 31.9 1.0 O D:HOH403 3.6 27.1 1.0 P D:PO4303 3.7 43.1 1.0 CA D:CA301 3.8 31.1 1.0 O1 D:PO4303 4.0 45.6 1.0 N D:ASP86 4.2 30.0 1.0 CA D:ASP86 4.3 27.0 1.0 N D:ILE85 4.3 31.2 1.0 CA D:ILE85 4.4 33.1 1.0 CG2 D:THR88 4.5 32.1 1.0 O3 D:PO4303 4.5 39.4 1.0 CG D:GLU65 4.6 66.3 1.0 OD2 D:ASP42 4.6 50.6 1.0 O2 D:PO4303 4.6 41.5 1.0 CB D:ASP83 4.8 24.7 1.0 CB D:ILE85 4.9 32.3 1.0 CD D:PRO84 5.0 29.0 1.0

A.Dutta, S.Bhattacharyya, A.K.Das. Crystal Structure of Inositol Monophosphate Bound Saimpase-II To Be Published.