Calcium in PDB 1ea7: Sphericase

The structure of Sphericase, PDB code: 1ea7 was solved by O.Almog, A.Gonzalez, D.Klein, S.Braun, G.Shoham, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.30 / 0.93
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	46.280, 62.380, 46.120, 90.00, 114.31, 90.00
R / Rfree (%)	9.7 / 11.6

The binding sites of Calcium atom in the Sphericase (pdb code 1ea7). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Sphericase, PDB code: 1ea7:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 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:Ca311 b:3.5 occ:1.00 OD1 A:ASP287 2.3 5.1 1.0 O A:GLY297 2.3 4.9 1.0 O A:ALA295 2.3 4.3 1.0 OD1 A:ASP299 2.3 4.2 1.0 O A:ILE288 2.3 3.8 1.0 O A:HOH2665 2.4 4.7 1.0 H A:ALA295 3.3 4.8 1.0 C A:GLY297 3.4 4.5 1.0 CG A:ASP287 3.5 5.2 1.0 H A:ILE288 3.5 4.8 1.0 C A:ILE288 3.5 3.6 1.0 CG A:ASP299 3.5 3.6 1.0 C A:ALA295 3.5 3.8 1.0 H A:GLY297 3.6 5.9 1.0 N A:GLY297 3.7 4.9 1.0 OG A:SER302 3.7 4.7 1.0 N A:ILE288 3.8 4.0 1.0 HB3 A:ASP299 3.9 4.7 1.0 HA A:LYS289 4.0 4.2 1.0 N A:ALA295 4.0 4.0 1.0 OD2 A:ASP287 4.1 6.9 1.0 HG2 A:LYS289 4.1 6.9 1.0 HA A:ILE296 4.1 5.2 1.0 C A:ILE296 4.1 4.7 1.0 CA A:GLY297 4.1 6.3 1.0 CA A:ILE288 4.2 3.9 1.0 HB A:ILE288 4.2 4.3 1.0 HA A:ASP287 4.3 5.5 1.0 CB A:ASP299 4.3 4.0 1.0 H A:ASP299 4.3 4.6 1.0 CA A:ALA295 4.4 3.9 1.0 HG3 A:LYS289 4.4 6.9 1.0 OD2 A:ASP299 4.4 4.0 1.0 N A:ILE296 4.4 4.3 1.0 HA A:ASP298 4.4 5.3 1.0 C A:ASP287 4.4 5.2 1.0 CA A:ILE296 4.5 4.4 1.0 N A:LYS289 4.5 3.7 1.0 O A:GLY303 4.5 3.9 1.0 N A:ASP298 4.5 5.0 1.0 N A:ASP299 4.5 3.8 1.0 HA2 A:GLY297 4.6 7.5 1.0 HB3 A:ALA294 4.6 6.9 1.0 CB A:ASP287 4.6 5.5 1.0 CA A:ASP287 4.6 4.6 1.0 HB2 A:ALA295 4.6 7.2 1.0 CA A:LYS289 4.7 3.5 1.0 CG A:LYS289 4.7 5.8 1.0 O A:ILE296 4.7 6.5 1.0 CB A:ILE288 4.8 3.6 1.0 CA A:ASP298 4.8 4.4 1.0 C A:ASP298 4.8 4.5 1.0 HA A:ALA294 4.9 4.6 1.0 HA3 A:GLY297 4.9 7.5 1.0

Calcium binding site 2 out of 6 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:Ca312 b:4.2 occ:1.00 O A:THR214 2.3 5.7 1.0 O A:VAL219 2.3 4.9 1.0 OE1 A:GLN221 2.3 5.5 1.0 OD1 A:ASP224 2.3 4.8 1.0 O A:HOH2662 2.4 5.2 1.0 OD2 A:ASP217 2.4 5.9 1.0 CG A:ASP217 3.3 5.7 1.0 H A:GLN221 3.3 5.5 1.0 CG A:ASP224 3.3 4.1 1.0 CD A:GLN221 3.4 5.0 1.0 HB A:THR214 3.4 7.0 1.0 C A:THR214 3.5 5.0 1.0 OD1 A:ASP217 3.5 8.2 1.0 C A:VAL219 3.5 4.8 1.0 H A:VAL219 3.5 6.3 1.0 HE22 A:GLN221 3.5 8.2 1.0 HA A:ILE220 3.6 5.8 1.0 HA A:ALA215 3.7 7.0 1.0 OD2 A:ASP224 3.8 6.5 1.0 NE2 A:GLN221 3.8 6.8 1.0 H A:ASP217 4.0 6.8 1.0 N A:GLN221 4.1 4.6 1.0 HB2 A:GLN221 4.1 6.7 1.0 O A:HOH2542 4.2 15.2 1.0 CB A:THR214 4.2 5.8 1.0 N A:VAL219 4.2 5.3 1.0 HB A:VAL219 4.2 8.5 1.0 CA A:THR214 4.3 5.3 1.0 CA A:ILE220 4.3 4.8 1.0 N A:ALA215 4.4 5.7 1.0 N A:ILE220 4.4 5.0 1.0 HA A:THR214 4.4 6.3 1.0 CA A:ALA215 4.4 5.8 1.0 CA A:VAL219 4.4 5.7 1.0 HD11 A:ILE220 4.5 9.7 1.0 HB3 A:ASP224 4.5 4.7 1.0 OD1 A:ASP298 4.5 5.1 1.0 H A:GLY216 4.5 7.1 1.0 CB A:ASP224 4.5 3.9 1.0 CG A:GLN221 4.6 6.7 1.0 C A:ILE220 4.6 4.8 1.0 CB A:ASP217 4.6 6.5 1.0 HE21 A:GLN221 4.7 8.2 1.0 CB A:GLN221 4.7 5.6 1.0 HB2 A:ASP224 4.7 4.7 1.0 H A:TYR218 4.7 6.8 1.0 OG1 A:THR214 4.8 6.6 1.0 N A:ASP217 4.8 5.7 1.0 O A:HOH2661 4.8 4.9 1.0 HE1 A:PHE304 4.8 7.7 1.0 CB A:VAL219 4.9 7.1 1.0 C A:ALA215 4.9 5.8 1.0 N A:GLY216 4.9 5.9 1.0 CA A:GLN221 5.0 5.0 1.0 N A:TYR218 5.0 5.7 1.0

Calcium binding site 3 out of 6 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:Ca313 b:4.8 occ:0.77 CA A:CA313 0.0 4.8 0.8 CA A:CA313 0.9 4.9 0.2 O A:HOH2186 1.8 5.7 0.3 O A:HOH2120 2.3 6.1 1.0 OD2 A:ASP98 2.3 5.7 0.8 OD1 A:ASN29 2.3 6.3 1.0 OE1 A:GLU49 2.4 5.9 0.8 O A:HOH2189 2.4 15.1 1.0 O A:HOH2185 2.4 6.7 0.7 OE1 A:GLU49 2.6 7.9 0.2 OE2 A:GLU49 2.6 6.5 0.2 OE2 A:GLU49 2.8 11.6 0.8 CD A:GLU49 2.9 6.1 0.2 CD A:GLU49 2.9 6.2 0.8 OD2 A:ASP98 3.0 11.4 0.2 OD1 A:ASP98 3.2 10.1 0.2 CG A:ASP98 3.3 11.2 0.2 CG A:ASP98 3.4 4.9 0.8 CG A:ASN29 3.5 4.7 1.0 HE1 A:TRP100 3.7 5.2 1.0 HD22 A:ASN29 3.7 7.6 1.0 CB A:ASP98 3.8 9.0 0.2 CB A:ASP98 3.8 4.3 0.8 O A:HOH2341 3.9 20.4 1.0 HG22 A:THR132 4.0 12.5 1.0 ND2 A:ASN29 4.0 6.3 1.0 HZ2 A:TRP100 4.2 5.8 1.0 O A:HOH2066 4.4 15.8 1.0 NE1 A:TRP100 4.4 4.3 1.0 O A:HOH2183 4.4 16.1 0.5 OD1 A:ASP98 4.4 5.7 0.8 CG A:GLU49 4.4 5.5 0.8 CG A:GLU49 4.4 4.8 0.2 O A:HOH2188 4.5 4.8 0.5 HB A:THR132 4.5 8.1 1.0 OG1 A:THR132 4.5 11.1 1.0 O A:GLY27 4.6 5.7 1.0 O A:HOH2044 4.6 11.3 1.0 CB A:ASN29 4.7 4.0 1.0 HA2 A:GLY27 4.7 6.9 1.0 O A:HOH2067 4.8 45.0 1.0 HB3 A:ASN29 4.8 4.8 1.0 CG2 A:THR132 4.8 8.3 1.0 CZ2 A:TRP100 4.9 4.8 1.0 HD21 A:ASN29 4.9 7.6 1.0 CB A:THR132 4.9 6.7 1.0 HA A:ASN29 4.9 4.2 1.0 O A:HOH2181 4.9 5.5 0.5 CE2 A:TRP100 5.0 4.0 1.0

Calcium binding site 4 out of 6 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:Ca313 b:4.9 occ:0.23 CA A:CA313 0.0 4.9 0.2 CA A:CA313 0.9 4.8 0.8 OD2 A:ASP98 1.5 5.7 0.8 OD2 A:ASP98 2.2 11.4 0.2 OE1 A:GLU49 2.3 7.9 0.2 OD1 A:ASP98 2.4 10.1 0.2 OE1 A:GLU49 2.4 5.9 0.8 O A:HOH2189 2.4 15.1 1.0 CG A:ASP98 2.5 11.2 0.2 O A:HOH2120 2.5 6.1 1.0 CG A:ASP98 2.5 4.9 0.8 O A:HOH2186 2.6 5.7 0.3 OD1 A:ASN29 2.6 6.3 1.0 OE2 A:GLU49 2.7 11.6 0.8 OE2 A:GLU49 2.9 6.5 0.2 CD A:GLU49 3.0 6.2 0.8 CD A:GLU49 3.0 6.1 0.2 CB A:ASP98 3.2 9.0 0.2 CB A:ASP98 3.2 4.3 0.8 O A:HOH2185 3.3 6.7 0.7 O A:HOH2341 3.3 20.4 1.0 OD1 A:ASP98 3.6 5.7 0.8 CG A:ASN29 3.8 4.7 1.0 HE1 A:TRP100 4.0 5.2 1.0 O A:HOH2183 4.1 16.1 0.5 HA2 A:GLY27 4.3 6.9 1.0 HD22 A:ASN29 4.3 7.6 1.0 O A:HOH2343 4.4 18.3 0.5 CG A:GLU49 4.4 5.5 0.8 CG A:GLU49 4.4 4.8 0.2 O A:GLY27 4.5 5.7 1.0 ND2 A:ASN29 4.5 6.3 1.0 HG22 A:THR132 4.6 12.5 1.0 CA A:ASP98 4.7 4.3 1.0 O A:HOH2044 4.7 11.3 1.0 NE1 A:TRP100 4.7 4.3 1.0 HA A:ASN29 4.8 4.2 1.0 O A:HOH2181 4.8 5.5 0.5 C A:GLY27 4.8 5.0 1.0 H A:ASP98 4.9 5.0 1.0 CB A:ASN29 4.9 4.0 1.0 O A:HOH2331 4.9 4.0 0.5 CB A:GLU49 4.9 4.8 0.8 HZ2 A:TRP100 4.9 5.8 1.0 CB A:GLU49 4.9 4.2 0.2 O A:HOH2342 5.0 9.9 0.5

Calcium binding site 5 out of 6 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:Ca314 b:7.0 occ:1.00 O A:HOH2374 2.3 7.8 1.0 O A:HOH2214 2.3 6.5 1.0 O A:HOH2210 2.4 10.3 1.0 O A:HOH2212 2.4 11.1 1.0 OD1 A:ASP115 2.4 5.4 1.0 O A:HOH2372 2.4 8.4 1.0 OD2 A:ASP115 2.6 5.3 1.0 CG A:ASP115 2.8 4.5 1.0 HD1 A:TYR112 3.7 8.3 1.0 HA A:THR55 3.9 4.4 1.0 HB2 A:TYR112 4.1 6.5 1.0 O A:HOH2378 4.2 23.2 0.5 OD1 A:ASP114 4.2 6.3 1.0 CD1 A:TYR112 4.3 6.9 1.0 O A:PHE54 4.3 4.0 1.0 CB A:ASP115 4.4 4.0 1.0 OD2 A:ASP114 4.4 8.5 1.0 O A:THR55 4.4 6.4 1.0 O A:HOH2079 4.5 12.0 1.0 O A:HOH2379 4.5 4.1 0.5 O A:GLY56 4.5 5.3 1.0 O A:HOH2077 4.6 17.9 1.0 C A:THR55 4.6 4.3 1.0 CG A:ASP114 4.6 5.9 1.0 CA A:THR55 4.7 3.6 1.0 O A:HOH2147 4.7 32.4 1.0 HB3 A:ASP115 4.7 4.8 1.0 HB2 A:ASP115 4.8 4.8 1.0 CB A:TYR112 4.9 5.5 1.0 H A:ASP115 4.9 4.9 1.0 CG A:TYR112 4.9 6.2 1.0 HE1 A:TYR112 5.0 10.9 1.0 HB3 A:TYR112 5.0 6.5 1.0

Calcium binding site 6 out of 6 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:Ca315 b:7.6 occ:1.00 O A:ALA186 2.3 4.6 1.0 O A:GLY181 2.3 4.0 1.0 O A:LEU183 2.3 4.1 1.0 O A:HOH2564 2.3 4.9 1.0 O A:HOH2566 2.4 3.8 1.0 C A:LEU183 3.4 3.8 1.0 C A:ALA186 3.4 4.0 1.0 HB3 A:ALA188 3.4 5.9 1.0 H A:ALA188 3.4 3.8 1.0 C A:GLY181 3.5 3.8 1.0 HB3 A:ALA186 3.5 7.7 1.0 H A:ALA186 3.6 5.3 1.0 HA A:ALA182 3.6 4.5 1.0 C A:ALA182 3.7 3.8 1.0 N A:LEU183 3.7 3.9 1.0 HG23 A:ILE220 3.7 9.6 1.0 H A:LEU183 3.8 4.7 1.0 N A:ALA188 4.0 3.1 1.0 CA A:ALA182 4.0 3.8 1.0 HH22 A:ARG276 4.0 7.5 1.0 O A:ASP224 4.0 3.8 1.0 O A:ALA182 4.0 4.2 1.0 HA A:PRO184 4.1 6.1 1.0 HA A:ILE187 4.1 3.9 1.0 CA A:ALA186 4.1 4.2 1.0 N A:ALA186 4.1 4.4 1.0 CA A:LEU183 4.1 4.0 1.0 HG22 A:ILE220 4.1 9.6 1.0 CB A:ALA188 4.2 3.9 1.0 N A:ALA182 4.2 3.8 1.0 HB1 A:ALA188 4.2 5.9 1.0 CB A:ALA186 4.2 5.1 1.0 CG2 A:ILE220 4.3 6.4 1.0 N A:PRO184 4.3 4.5 1.0 N A:ILE187 4.4 3.7 1.0 HG21 A:ILE220 4.4 9.6 1.0 HH21 A:ARG276 4.4 7.5 1.0 HA2 A:GLY181 4.4 5.0 1.0 CA A:PRO184 4.5 5.1 1.0 OE1 A:GLU226 4.5 4.5 1.0 C A:PRO184 4.5 4.7 1.0 NH2 A:ARG276 4.5 6.2 1.0 HB2 A:LEU183 4.5 4.9 1.0 CA A:ILE187 4.5 3.3 1.0 O A:PRO184 4.6 5.7 1.0 C A:ILE187 4.6 2.8 1.0 CA A:GLY181 4.6 4.2 1.0 CA A:ALA188 4.6 3.1 1.0 HB1 A:ALA186 4.6 7.7 1.0 O A:PRO180 4.8 4.4 1.0 HA A:LEU183 4.9 4.7 1.0 HD12 A:ILE177 4.9 6.5 1.0 H A:GLY223 4.9 4.9 1.0 HA A:ALA188 4.9 3.7 1.0 CB A:LEU183 5.0 4.1 1.0 HB2 A:GLU226 5.0 4.8 1.0 HB2 A:ALA188 5.0 5.9 1.0 H A:ASP224 5.0 4.5 1.0 HB2 A:ALA186 5.0 7.7 1.0

O.Almog, A.Gonzalez, D.Klein, H.M.Greenblat, S.Braun, G.Shoham. The 0.93A Crystal Structure of Sphericase: A Calcium-Loaded Serine Protease From Bacillus Sphaericus J.Mol.Biol. V. 332 1071 2003.
ISSN: ISSN 0022-2836
PubMed: 14499610
DOI: 10.1016/J.JMB.2003.07.011