Calcium in PDB 2ixt: Sphericase

The structure of Sphericase, PDB code: 2ixt was solved by O.Almog, A.Gonzalez, N.Godin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	84.52 / 0.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	46.088, 62.668, 84.874, 90.00, 95.47, 90.00
R / Rfree (%)	13.7 / 15.4

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Calcium atom in the Sphericase (pdb code 2ixt). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 12 binding sites of Calcium where determined in the Sphericase, PDB code: 2ixt:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 12 in the Sphericase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Sphericase within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1310 b:3.4 occ:1.00 OD1 A:ASP287 2.3 4.9 1.0 O A:GLY297 2.3 4.7 1.0 O A:ALA295 2.3 4.1 1.0 OD1 A:ASP299 2.3 4.4 1.0 O A:ILE288 2.3 4.0 1.0 O A:HOH2492 2.4 4.4 1.0 C A:GLY297 3.4 4.6 1.0 CG A:ASP287 3.4 4.4 1.0 C A:ILE288 3.5 3.9 1.0 CG A:ASP299 3.5 3.7 1.0 C A:ALA295 3.5 4.1 1.0 N A:GLY297 3.7 4.9 1.0 OG A:SER302 3.8 4.5 1.0 N A:ILE288 3.8 3.9 1.0 N A:ALA295 4.0 4.0 1.0 OD2 A:ASP287 4.0 6.8 1.0 C A:ILE296 4.1 4.7 1.0 CA A:GLY297 4.1 5.1 1.0 O A:HOH2493 4.2 68.3 1.0 CA A:ILE288 4.2 3.8 1.0 CB A:ASP299 4.3 4.1 1.0 CA A:ALA295 4.4 4.3 1.0 OD2 A:ASP299 4.4 4.2 1.0 N A:ILE296 4.4 4.6 1.0 CA A:ILE296 4.5 5.1 1.0 N A:LYS289 4.5 3.9 1.0 C A:ASP287 4.5 5.0 1.0 O A:GLY303 4.5 3.6 1.0 N A:ASP298 4.5 4.8 1.0 CG A:LYS289 4.5 5.8 0.5 N A:ASP299 4.5 4.0 1.0 CB A:ASP287 4.6 4.9 1.0 CA A:ASP287 4.7 4.2 1.0 CA A:LYS289 4.7 4.4 0.5 O A:ILE296 4.7 6.3 1.0 CA A:LYS289 4.7 4.0 0.5 CG A:LYS289 4.8 5.1 0.5 CB A:ILE288 4.8 3.9 1.0 C A:ASP298 4.8 4.5 1.0 CA A:ASP298 4.8 4.6 1.0

Calcium binding site 2 out of 12 in the Sphericase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Sphericase within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1311 b:4.0 occ:1.00 O A:THR214 2.3 5.2 1.0 O A:VAL219 2.3 4.9 1.0 OE1 A:GLN221 2.3 5.0 1.0 O A:HOH2487 2.3 5.1 1.0 OD1 A:ASP224 2.3 4.4 1.0 OD2 A:ASP217 2.4 6.1 1.0 CG A:ASP217 3.3 6.0 1.0 CG A:ASP224 3.3 4.1 1.0 CD A:GLN221 3.3 5.1 1.0 C A:THR214 3.5 5.1 1.0 C A:VAL219 3.5 4.7 1.0 OD1 A:ASP217 3.5 8.0 1.0 OD2 A:ASP224 3.8 6.1 1.0 NE2 A:GLN221 3.8 6.8 1.0 N A:GLN221 4.1 4.2 1.0 O A:HOH2386 4.1 17.2 1.0 CB A:THR214 4.2 5.7 1.0 N A:VAL219 4.2 5.3 1.0 CA A:THR214 4.3 5.0 1.0 CA A:ILE220 4.3 4.7 1.0 N A:ILE220 4.4 5.0 1.0 N A:ALA215 4.4 5.8 0.3 N A:ALA215 4.4 5.5 0.7 CA A:ALA215 4.4 5.9 0.3 CA A:VAL219 4.4 5.5 1.0 CA A:ALA215 4.4 5.8 0.7 OD1 A:ASP298 4.4 4.8 1.0 CB A:ASP224 4.5 3.7 1.0 CG A:GLN221 4.6 6.0 1.0 C A:ILE220 4.6 4.9 1.0 CB A:ASP217 4.7 6.9 1.0 CB A:GLN221 4.7 5.5 1.0 OG1 A:THR214 4.7 6.5 1.0 N A:ASP217 4.8 6.1 1.0 O A:HOH2488 4.8 5.0 1.0 C A:ALA215 4.8 5.6 0.7 CB A:VAL219 4.8 6.6 1.0 O A:HOH2382 4.9 38.5 1.0 N A:GLY216 4.9 5.9 1.0 CA A:GLN221 5.0 5.0 1.0

Calcium binding site 3 out of 12 in the Sphericase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Sphericase within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1312 b:4.3 occ:0.70 CA A:CA1312 0.0 4.3 0.7 CA A:CA1312 0.7 7.6 0.3 O A:HOH2123 1.7 8.2 0.3 O A:HOH2075 2.3 5.8 1.0 OD1 A:ASN29 2.3 5.6 1.0 OD2 A:ASP98 2.3 4.9 0.7 O A:HOH2122 2.4 9.2 0.5 OE1 A:GLU49 2.4 6.1 0.7 O A:HOH2264 2.4 6.4 0.7 OE2 A:GLU49 2.6 7.2 0.3 OE2 A:GLU49 2.7 10.4 0.7 OD2 A:ASP98 2.7 14.6 0.3 OE1 A:GLU49 2.8 8.0 0.3 O A:HOH2214 2.8 14.3 0.5 CD A:GLU49 2.9 6.4 0.7 CD A:GLU49 3.1 6.1 0.3 CG A:ASP98 3.1 11.8 0.3 OD1 A:ASP98 3.1 15.5 0.3 CG A:ASP98 3.4 4.2 0.7 CG A:ASN29 3.5 4.5 1.0 CB A:ASP98 3.8 3.2 0.7 O A:HOH2215 4.0 11.8 0.5 ND2 A:ASN29 4.0 5.5 1.0 CB A:ASP98 4.1 7.4 0.3 O A:HOH2030 4.4 11.5 1.0 OG1 A:THR132 4.4 4.5 0.6 NE1 A:TRP100 4.4 4.3 1.0 CG A:GLU49 4.4 5.5 0.7 OD1 A:ASP98 4.4 5.2 0.7 CG A:GLU49 4.5 5.3 0.3 O A:HOH2022 4.6 11.1 1.0 O A:HOH2119 4.6 5.6 0.5 CG2 A:THR132 4.7 8.1 0.4 O A:GLY27 4.7 5.7 1.0 CB A:ASN29 4.7 4.2 1.0 CZ2 A:TRP100 4.8 4.8 1.0 CB A:THR132 4.8 4.3 0.6 O A:HOH2124 4.9 27.5 1.0 O A:HOH2125 4.9 15.9 1.0 OG1 A:THR132 4.9 7.6 0.4 CG2 A:THR132 5.0 5.3 0.6 CE2 A:TRP100 5.0 4.2 1.0 CB A:THR132 5.0 6.6 0.4

Calcium binding site 4 out of 12 in the Sphericase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Sphericase within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1312 b:7.6 occ:0.30 CA A:CA1312 0.0 7.6 0.3 CA A:CA1312 0.7 4.3 0.7 OD2 A:ASP98 1.7 4.9 0.7 OD2 A:ASP98 2.2 14.6 0.3 O A:HOH2123 2.3 8.2 0.3 O A:HOH2122 2.3 9.2 0.5 OE1 A:GLU49 2.4 6.1 0.7 OE1 A:GLU49 2.5 8.0 0.3 O A:HOH2075 2.5 5.8 1.0 O A:HOH2214 2.5 14.3 0.5 OD1 A:ASN29 2.6 5.6 1.0 CG A:ASP98 2.6 11.8 0.3 OE2 A:GLU49 2.6 10.4 0.7 CG A:ASP98 2.7 4.2 0.7 OE2 A:GLU49 2.9 7.2 0.3 CD A:GLU49 2.9 6.4 0.7 OD1 A:ASP98 2.9 15.5 0.3 CD A:GLU49 3.0 6.1 0.3 O A:HOH2264 3.1 6.4 0.7 CB A:ASP98 3.3 3.2 0.7 O A:HOH2215 3.5 11.8 0.5 CB A:ASP98 3.6 7.4 0.3 OD1 A:ASP98 3.8 5.2 0.7 CG A:ASN29 3.8 4.5 1.0 O A:HOH2124 4.3 27.5 1.0 CG A:GLU49 4.4 5.5 0.7 ND2 A:ASN29 4.5 5.5 1.0 CG A:GLU49 4.5 5.3 0.3 O A:GLY27 4.6 5.7 1.0 O A:HOH2022 4.6 11.1 1.0 NE1 A:TRP100 4.7 4.3 1.0 O A:HOH2125 4.8 15.9 1.0 CA A:ASP98 4.8 3.4 0.7 O A:HOH2030 4.8 11.5 1.0 CB A:ASN29 4.9 4.2 1.0 C A:GLY27 4.9 5.0 1.0 CB A:GLU49 4.9 4.5 0.7 OG1 A:THR132 5.0 4.5 0.6 CA A:ASP98 5.0 5.7 0.3

Calcium binding site 5 out of 12 in the Sphericase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Sphericase within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1313 b:5.4 occ:0.70 O A:HOH2243 1.4 9.1 0.3 O A:HOH2140 2.3 6.8 1.0 O A:HOH2237 2.3 7.8 1.0 O A:HOH2136 2.4 9.2 1.0 O A:HOH2141 2.4 11.2 1.0 OD1 A:ASP115 2.4 5.6 1.0 O A:HOH2238 2.4 6.6 0.7 OD2 A:ASP115 2.6 5.6 1.0 CG A:ASP115 2.8 4.8 1.0 OD1 A:ASP114 4.2 6.1 1.0 O A:PHE54 4.3 4.2 1.0 CD1 A:TYR112 4.3 7.2 1.0 CB A:ASP115 4.4 4.3 1.0 OD2 A:ASP114 4.4 7.9 1.0 O A:THR55 4.4 7.0 1.0 O A:HOH2244 4.4 10.6 1.0 O A:HOH2041 4.5 12.4 1.0 O A:GLY56 4.5 6.5 1.0 O A:HOH2135 4.6 43.6 1.0 C A:THR55 4.6 5.1 1.0 CG A:ASP114 4.6 6.4 1.0 O A:HOH2040 4.7 20.2 1.0 CA A:THR55 4.7 4.4 1.0 CB A:TYR112 4.9 5.7 1.0 CG A:TYR112 4.9 6.5 1.0

Calcium binding site 6 out of 12 in the Sphericase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Sphericase within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1314 b:4.1 occ:0.60 O A:ALA186 2.3 4.4 1.0 O A:GLY181 2.3 3.7 1.0 O A:LEU183 2.3 4.2 1.0 O A:HOH2401 2.3 4.7 1.0 O A:HOH2405 2.4 3.7 1.0 C A:LEU183 3.4 3.7 1.0 C A:ALA186 3.4 3.6 1.0 C A:GLY181 3.5 3.8 1.0 C A:ALA182 3.7 3.5 1.0 N A:LEU183 3.7 3.8 1.0 N A:ALA188 4.0 3.2 1.0 CA A:ALA182 4.0 3.7 1.0 O A:ASP224 4.0 3.5 1.0 O A:ALA182 4.0 4.2 1.0 N A:ALA186 4.1 4.4 1.0 CA A:ALA186 4.1 3.9 1.0 CA A:LEU183 4.1 3.8 1.0 CB A:ALA188 4.2 3.9 1.0 N A:ALA182 4.2 3.7 1.0 CG2 A:ILE220 4.2 6.2 1.0 CB A:ALA186 4.2 4.8 1.0 N A:PRO184 4.3 4.1 1.0 N A:ILE187 4.3 3.6 1.0 CA A:PRO184 4.5 4.7 1.0 OE1 A:GLU226 4.5 4.0 1.0 C A:PRO184 4.5 4.6 1.0 CA A:ILE187 4.5 3.5 1.0 NH2 A:ARG276 4.5 4.0 0.6 O A:PRO184 4.6 5.6 1.0 C A:ILE187 4.6 3.2 1.0 NH2 A:ARG276 4.6 9.2 0.4 CA A:GLY181 4.6 3.8 1.0 CA A:ALA188 4.6 3.1 1.0 O A:PRO180 4.8 4.2 1.0 CB A:LEU183 4.9 4.2 1.0

Calcium binding site 7 out of 12 in the Sphericase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Sphericase within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1311 b:4.0 occ:1.00 OD1 B:ASP287 2.3 4.1 0.6 OD1 B:ASP287 2.3 7.4 0.4 O B:GLY297 2.3 5.3 1.0 O B:ALA295 2.3 4.8 1.0 O B:ILE288 2.3 4.5 0.5 OD1 B:ASP299 2.3 4.8 1.0 O B:ILE288 2.3 4.5 0.5 O B:HOH2499 2.4 4.9 1.0 CG B:ASP287 3.4 8.0 0.4 C B:ILE288 3.4 4.3 0.5 C B:GLY297 3.5 5.5 1.0 C B:ILE288 3.5 4.3 0.5 CG B:ASP287 3.5 4.4 0.6 CG B:ASP299 3.5 4.2 1.0 C B:ALA295 3.5 4.7 1.0 N B:GLY297 3.7 5.7 1.0 OG B:SER302 3.7 5.2 1.0 N B:ILE288 3.8 4.5 1.0 OD2 B:ASP287 4.0 9.4 0.4 N B:ALA295 4.0 4.7 1.0 C B:ILE296 4.1 5.7 1.0 OD2 B:ASP287 4.1 6.1 0.6 CA B:GLY297 4.2 6.1 1.0 CA B:ILE288 4.2 4.4 1.0 CB B:ASP299 4.3 4.7 1.0 C B:ASP287 4.3 4.8 0.3 C B:ASP287 4.4 5.0 0.3 CA B:ALA295 4.4 4.7 1.0 N B:ILE296 4.4 4.9 1.0 OD2 B:ASP299 4.4 4.3 1.0 CA B:ILE296 4.4 5.7 1.0 N B:LYS289 4.5 4.3 0.5 N B:LYS289 4.5 4.4 0.5 CG B:LYS289 4.5 6.2 0.5 N B:ASP299 4.5 4.5 1.0 N B:ASP298 4.5 5.5 1.0 O B:GLY303 4.5 4.1 1.0 C B:ASP287 4.6 5.6 0.3 CA B:ASP287 4.6 4.5 0.6 CB B:ASP287 4.6 5.0 0.6 CB B:ASP287 4.6 6.1 0.4 CA B:ASP287 4.7 5.7 0.4 CA B:LYS289 4.7 4.5 0.5 O B:ILE296 4.7 7.3 1.0 CA B:LYS289 4.7 4.3 0.5 CB B:ILE288 4.8 4.3 1.0 CA B:ASP298 4.8 5.1 1.0 C B:ASP298 4.8 5.2 1.0 CG B:LYS289 4.8 5.5 0.5 O B:ASP287 5.0 5.5 0.3

Calcium binding site 8 out of 12 in the Sphericase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Sphericase within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1312 b:4.3 occ:1.00 O B:THR214 2.3 5.6 1.0 O B:VAL219 2.3 5.1 1.0 OE1 B:GLN221 2.3 5.6 1.0 O B:HOH2493 2.3 2.8 0.5 OD1 B:ASP224 2.3 4.8 1.0 OD2 B:ASP217 2.4 6.0 1.0 CG B:ASP217 3.3 6.4 1.0 CD B:GLN221 3.3 5.6 1.0 CG B:ASP224 3.3 4.4 1.0 C B:THR214 3.5 5.5 1.0 C B:VAL219 3.5 5.0 1.0 OD1 B:ASP217 3.5 8.8 1.0 NE2 B:GLN221 3.8 7.2 1.0 OD2 B:ASP224 3.8 6.6 1.0 N B:GLN221 4.0 4.8 1.0 O B:HOH2392 4.1 17.7 1.0 CB B:THR214 4.2 6.0 1.0 N B:VAL219 4.2 5.7 1.0 CA B:THR214 4.3 5.2 1.0 CA B:ILE220 4.3 5.3 1.0 N B:ILE220 4.4 5.2 1.0 N B:ALA215 4.4 6.1 1.0 CA B:VAL219 4.4 5.5 1.0 CA B:ALA215 4.4 6.0 1.0 OD1 B:ASP298 4.4 5.1 1.0 CB B:ASP224 4.5 3.8 1.0 CG B:GLN221 4.5 6.4 1.0 C B:ILE220 4.6 5.5 1.0 CB B:GLN221 4.6 5.9 1.0 CB B:ASP217 4.7 7.2 1.0 OG1 B:THR214 4.7 6.5 1.0 N B:ASP217 4.8 6.2 1.0 O B:HOH2494 4.8 5.0 1.0 CB B:VAL219 4.8 6.8 1.0 C B:ALA215 4.9 6.5 1.0 N B:GLY216 4.9 6.0 1.0 N B:TYR218 5.0 6.2 1.0 CA B:GLN221 5.0 5.2 1.0

Calcium binding site 9 out of 12 in the Sphericase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Sphericase within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1313 b:4.9 occ:0.70 CA B:CA1313 0.0 4.9 0.7 CA B:CA1313 0.7 7.5 0.3 O B:HOH2112 1.4 9.2 0.3 OD1 B:ASN29 2.3 6.0 1.0 O B:HOH2077 2.3 6.5 1.0 OE1 B:GLU49 2.3 6.3 0.7 O B:HOH2264 2.4 7.1 0.7 OD2 B:ASP98 2.4 5.9 0.8 O B:HOH2118 2.4 12.4 0.7 OE2 B:GLU49 2.6 7.9 0.3 OE2 B:GLU49 2.7 9.6 0.7 OE1 B:GLU49 2.7 8.9 0.3 CD B:GLU49 2.9 6.7 0.7 CD B:GLU49 3.0 6.5 0.3 CG B:ASP98 3.4 5.0 0.8 CG B:ASN29 3.5 5.0 1.0 CB B:ASP98 3.8 3.9 0.8 O B:HOH2119 3.8 5.7 0.3 O B:HOH2208 4.0 23.8 1.0 ND2 B:ASN29 4.0 5.8 1.0 O B:HOH2032 4.4 15.5 1.0 OG1 B:THR132 4.4 2.9 0.3 NE1 B:TRP100 4.4 5.0 1.0 CG B:GLU49 4.4 5.4 0.7 OD1 B:ASP98 4.5 7.3 0.8 CG B:GLU49 4.5 5.4 0.3 O B:HOH2116 4.6 9.5 1.0 O B:HOH2023 4.6 12.2 1.0 O B:GLY27 4.6 6.4 1.0 CG2 B:THR132 4.6 7.4 0.3 CB B:ASN29 4.7 4.5 1.0 CB B:THR132 4.8 5.4 0.7 CZ2 B:TRP100 4.9 5.6 1.0 CG2 B:THR132 4.9 6.2 0.7 O B:HOH2117 5.0 10.7 1.0 OG1 B:THR132 5.0 10.6 0.7

Calcium binding site 10 out of 12 in the Sphericase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Sphericase within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1313 b:7.5 occ:0.30 CA B:CA1313 0.0 7.5 0.3 CA B:CA1313 0.7 4.9 0.7 OD2 B:ASP98 1.7 5.9 0.8 O B:HOH2112 2.0 9.2 0.3 O B:HOH2118 2.3 12.4 0.7 OE1 B:GLU49 2.4 6.3 0.7 O B:HOH2077 2.5 6.5 1.0 OE1 B:GLU49 2.5 8.9 0.3 OD1 B:ASN29 2.6 6.0 1.0 OE2 B:GLU49 2.7 9.6 0.7 CG B:ASP98 2.8 5.0 0.8 OE2 B:GLU49 2.9 7.9 0.3 CD B:GLU49 2.9 6.7 0.7 CD B:GLU49 3.0 6.5 0.3 O B:HOH2264 3.0 7.1 0.7 CB B:ASP98 3.3 3.9 0.8 O B:HOH2208 3.4 23.8 1.0 O B:HOH2119 3.7 5.7 0.3 CG B:ASN29 3.8 5.0 1.0 OD1 B:ASP98 3.8 7.3 0.8 CG B:GLU49 4.4 5.4 0.7 ND2 B:ASN29 4.5 5.8 1.0 CG B:GLU49 4.5 5.4 0.3 O B:GLY27 4.6 6.4 1.0 O B:HOH2023 4.6 12.2 1.0 NE1 B:TRP100 4.7 5.0 1.0 CA B:ASP98 4.8 4.2 1.0 O B:HOH2115 4.8 57.2 1.0 O B:HOH2117 4.8 10.7 1.0 O B:HOH2032 4.8 15.5 1.0 C B:GLY27 4.9 5.4 1.0 CB B:ASN29 4.9 4.5 1.0 CB B:GLU49 5.0 4.8 0.7 OG1 B:THR132 5.0 2.9 0.3

O.Almog, A.Gonzalez, N.Godin, M.De Leeuw, M.J.Mekel, D.Klein, S.Braun, G.Shoham, R.L.Walter. The Crystal Structures of the Psychrophilic Subtilisin S41 and the Mesophilic Subtilisin Sph Reveal the Same Calcium-Loaded State. Proteins V. 74 489 2009.
ISSN: ISSN 0887-3585
PubMed: 18655058
DOI: 10.1002/PROT.22175