Calcium in PDB 3d43: The Crystal Structure of Sph at 0.8A

The structure of The Crystal Structure of Sph at 0.8A, PDB code: 3d43 was solved by O.Almog, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.01 / 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 (%)	14.7 / 16.6

Pages:

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

Binding sites:

The binding sites of Calcium atom in the The Crystal Structure of Sph at 0.8A (pdb code 3d43). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 12 binding sites of Calcium where determined in the The Crystal Structure of Sph at 0.8A, PDB code: 3d43:
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 The Crystal Structure of Sph at 0.8A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of The Crystal Structure of Sph at 0.8A within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca312 b:4.4 occ:1.00 O A:ALA295 2.3 4.8 1.0 OD1 A:ASP287 2.3 5.7 1.0 O A:GLY297 2.3 5.3 1.0 O A:ILE288 2.3 4.7 1.0 OD1 A:ASP299 2.3 4.8 1.0 O A:HOH321 2.4 4.8 1.0 C A:GLY297 3.4 5.2 1.0 CG A:ASP287 3.5 5.5 1.0 C A:ILE288 3.5 4.6 1.0 CG A:ASP299 3.5 4.4 1.0 C A:ALA295 3.5 4.6 1.0 N A:GLY297 3.7 5.6 1.0 OG A:SER302 3.7 5.2 1.0 N A:ILE288 3.8 4.6 1.0 N A:ALA295 4.0 4.5 1.0 OD2 A:ASP287 4.1 7.8 1.0 C A:ILE296 4.1 5.2 1.0 CA A:GLY297 4.1 5.7 1.0 CA A:ILE288 4.2 4.5 1.0 CB A:ASP299 4.3 4.8 1.0 OD2 A:ASP299 4.4 5.1 1.0 CA A:ALA295 4.4 4.7 1.0 N A:ILE296 4.4 5.2 1.0 CA A:ILE296 4.4 5.5 1.0 N A:LYS289 4.5 4.7 1.0 C A:ASP287 4.5 5.7 1.0 O A:GLY303 4.5 4.1 1.0 N A:ASP298 4.5 5.2 1.0 N A:ASP299 4.5 5.0 1.0 CG A:LYS289 4.5 6.0 0.5 CB A:ASP287 4.6 5.4 1.0 CA A:LYS289 4.7 4.9 0.5 CA A:ASP287 4.7 4.9 1.0 O A:ILE296 4.7 6.7 1.0 CA A:LYS289 4.7 4.7 0.5 CB A:ILE288 4.8 4.6 1.0 C A:ASP298 4.8 5.0 1.0 CA A:ASP298 4.8 5.2 1.0 CG A:LYS289 4.8 5.3 0.5

Calcium binding site 2 out of 12 in the The Crystal Structure of Sph at 0.8A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of The Crystal Structure of Sph at 0.8A within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca313 b:4.9 occ:1.00 O A:THR214 2.3 5.7 1.0 O A:VAL219 2.3 5.5 1.0 OE1 A:GLN221 2.3 5.5 1.0 OD1 A:ASP224 2.3 5.0 1.0 O A:HOH317 2.3 5.9 1.0 OD2 A:ASP217 2.4 6.5 1.0 CG A:ASP217 3.3 7.5 1.0 CG A:ASP224 3.3 4.8 1.0 CD A:GLN221 3.3 5.5 1.0 C A:THR214 3.5 5.8 1.0 C A:VAL219 3.5 5.1 1.0 OD1 A:ASP217 3.5 8.7 1.0 OD2 A:ASP224 3.8 7.0 1.0 NE2 A:GLN221 3.8 7.4 1.0 N A:GLN221 4.0 4.8 1.0 O A:HOH553 4.1 17.8 1.0 N A:VAL219 4.2 5.9 1.0 CB A:THR214 4.2 6.4 1.0 CA A:THR214 4.3 5.6 1.0 CA A:ILE220 4.3 5.2 1.0 N A:ILE220 4.3 5.5 1.0 N A:ALA215 4.4 6.2 0.7 CA A:VAL219 4.4 6.0 1.0 CA A:ALA215 4.4 6.5 0.3 N A:ALA215 4.4 7.0 0.3 OD1 A:ASP298 4.4 5.5 1.0 CA A:ALA215 4.4 6.4 0.7 CB A:ASP224 4.5 4.2 1.0 CG A:GLN221 4.6 6.6 1.0 C A:ILE220 4.6 5.6 1.0 CB A:GLN221 4.6 6.4 1.0 CB A:ASP217 4.6 7.5 1.0 OG1 A:THR214 4.7 7.5 1.0 N A:ASP217 4.8 6.7 1.0 C A:ALA215 4.8 6.1 0.7 O A:HOH332 4.8 5.7 1.0 CB A:VAL219 4.8 7.5 1.0 N A:GLY216 4.9 6.5 1.0 CA A:GLN221 5.0 5.5 1.0 N A:TYR218 5.0 6.4 1.0

Calcium binding site 3 out of 12 in the The Crystal Structure of Sph at 0.8A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of The Crystal Structure of Sph at 0.8A within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca314 b:4.9 occ:0.73 CA A:CA314 0.0 4.9 0.7 CA A:CA314 0.8 6.9 0.3 O A:HOH385 1.6 6.4 0.3 OD1 A:ASN29 2.3 5.6 1.0 O A:HOH347 2.3 6.9 1.0 OD2 A:ASP98 2.4 9.2 0.2 OD2 A:ASP98 2.4 6.7 0.8 OE1 A:GLU49 2.4 7.3 0.8 O A:HOH384 2.4 6.6 0.7 O A:HOH476 2.4 8.6 0.5 OE2 A:GLU49 2.6 8.0 0.2 OE1 A:GLU49 2.7 9.9 0.2 OE2 A:GLU49 2.7 11.9 0.8 OD1 A:ASP98 2.9 16.6 0.2 CG A:ASP98 2.9 10.5 0.2 CD A:GLU49 2.9 7.1 0.8 CD A:GLU49 3.0 7.6 0.2 O A:HOH477 3.2 26.1 0.5 CG A:ASP98 3.4 4.9 0.8 CG A:ASN29 3.5 5.1 1.0 CB A:ASP98 3.8 4.8 0.8 CB A:ASP98 3.8 6.2 0.2 O A:HOH682 4.0 13.4 0.7 ND2 A:ASN29 4.0 6.2 1.0 O A:HOH486 4.4 13.6 1.0 OG1 A:THR132 4.4 4.7 0.6 NE1 A:TRP100 4.4 4.7 1.0 OD1 A:ASP98 4.4 6.2 0.8 CG A:GLU49 4.4 6.0 0.8 CG A:GLU49 4.5 5.4 0.2 O A:HOH447 4.6 13.1 1.0 O A:HOH411 4.6 5.7 0.5 O A:GLY27 4.7 6.3 1.0 CB A:ASN29 4.7 4.7 1.0 CB A:THR132 4.8 4.7 0.6 CG2 A:THR132 4.8 6.6 0.4 CZ2 A:TRP100 4.9 5.4 1.0 OG1 A:THR132 4.9 6.1 0.4 CG2 A:THR132 4.9 8.3 0.6 CE2 A:TRP100 5.0 5.0 1.0

Calcium binding site 4 out of 12 in the The Crystal Structure of Sph at 0.8A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of The Crystal Structure of Sph at 0.8A within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca314 b:6.9 occ:0.27 CA A:CA314 0.0 6.9 0.3 CA A:CA314 0.8 4.9 0.7 OD2 A:ASP98 1.6 6.7 0.8 OD2 A:ASP98 1.7 9.2 0.2 O A:HOH385 2.3 6.4 0.3 CG A:ASP98 2.4 10.5 0.2 O A:HOH476 2.4 8.6 0.5 OE1 A:GLU49 2.4 9.9 0.2 OE1 A:GLU49 2.4 7.3 0.8 O A:HOH347 2.5 6.9 1.0 OD1 A:ASN29 2.6 5.6 1.0 OD1 A:ASP98 2.6 16.6 0.2 OE2 A:GLU49 2.7 11.9 0.8 CG A:ASP98 2.7 4.9 0.8 O A:HOH477 2.8 26.1 0.5 OE2 A:GLU49 2.9 8.0 0.2 CD A:GLU49 2.9 7.1 0.8 CD A:GLU49 3.1 7.6 0.2 O A:HOH384 3.1 6.6 0.7 CB A:ASP98 3.3 6.2 0.2 CB A:ASP98 3.3 4.8 0.8 O A:HOH682 3.4 13.4 0.7 OD1 A:ASP98 3.7 6.2 0.8 CG A:ASN29 3.8 5.1 1.0 CG A:GLU49 4.4 6.0 0.8 ND2 A:ASN29 4.5 6.2 1.0 CG A:GLU49 4.5 5.4 0.2 O A:GLY27 4.6 6.3 1.0 O A:HOH447 4.6 13.1 1.0 NE1 A:TRP100 4.7 4.7 1.0 CA A:ASP98 4.8 4.8 0.2 CA A:ASP98 4.8 4.6 0.8 C A:GLY27 4.9 5.6 1.0 CB A:ASN29 4.9 4.7 1.0 O A:HOH486 4.9 13.6 1.0 CB A:GLU49 5.0 5.0 0.8

Calcium binding site 5 out of 12 in the The Crystal Structure of Sph at 0.8A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of The Crystal Structure of Sph at 0.8A within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca315 b:6.1 occ:0.70 O A:HOH379 2.3 7.6 1.0 O A:HOH403 2.3 8.9 1.0 OD1 A:ASP115 2.4 6.5 1.0 O A:HOH456 2.4 12.6 1.0 O A:HOH422 2.4 7.5 1.0 O A:HOH414 2.5 11.0 1.0 OD2 A:ASP115 2.5 6.2 1.0 CG A:ASP115 2.8 5.3 1.0 OD1 A:ASP114 4.2 7.2 1.0 O A:PHE54 4.3 5.0 1.0 CD1 A:TYR112 4.3 8.4 1.0 CB A:ASP115 4.3 5.0 1.0 OD2 A:ASP114 4.4 10.3 1.0 O A:HOH521 4.4 17.7 1.0 O A:HOH425 4.4 12.7 1.0 O A:THR55 4.4 8.0 1.0 O A:HOH601 4.5 23.6 1.0 O A:GLY56 4.5 7.2 1.0 C A:THR55 4.6 5.7 1.0 CG A:ASP114 4.6 7.2 1.0 O A:HOH624 4.7 52.3 1.0 CA A:THR55 4.7 4.9 1.0 CB A:TYR112 4.9 6.1 1.0 CG A:TYR112 5.0 7.3 1.0

Calcium binding site 6 out of 12 in the The Crystal Structure of Sph at 0.8A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of The Crystal Structure of Sph at 0.8A within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca316 b:5.3 occ:0.66 O A:ALA186 2.3 5.1 1.0 O A:LEU183 2.3 4.7 1.0 O A:GLY181 2.3 4.4 1.0 O A:HOH322 2.3 5.5 1.0 O A:HOH318 2.4 4.2 1.0 C A:LEU183 3.4 4.6 1.0 C A:ALA186 3.4 4.2 1.0 C A:GLY181 3.5 4.4 1.0 C A:ALA182 3.7 4.1 1.0 N A:LEU183 3.7 4.3 1.0 N A:ALA188 4.0 4.1 1.0 CA A:ALA182 4.0 4.4 1.0 O A:ASP224 4.0 4.0 1.0 O A:ALA182 4.0 4.8 1.0 N A:ALA186 4.1 4.9 1.0 CA A:ALA186 4.1 4.3 1.0 CA A:LEU183 4.1 4.2 1.0 CB A:ALA188 4.2 4.6 1.0 N A:ALA182 4.2 4.5 1.0 CB A:ALA186 4.2 5.5 1.0 CG2 A:ILE220 4.2 6.6 1.0 N A:PRO184 4.3 4.9 1.0 N A:ILE187 4.3 4.2 1.0 CA A:PRO184 4.4 5.3 1.0 OE1 A:GLU226 4.5 4.8 1.0 C A:PRO184 4.5 4.9 1.0 NH2 A:ARG276 4.5 4.5 0.5 CA A:ILE187 4.5 3.8 1.0 O A:PRO184 4.5 6.1 1.0 C A:ILE187 4.6 4.1 1.0 CA A:GLY181 4.6 4.5 1.0 NH2 A:ARG276 4.6 4.9 0.5 CA A:ALA188 4.6 3.7 1.0 O A:PRO180 4.8 5.1 1.0 CB A:LEU183 4.9 4.6 1.0

Calcium binding site 7 out of 12 in the The Crystal Structure of Sph at 0.8A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of The Crystal Structure of Sph at 0.8A within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca312 b:5.0 occ:1.00 OD1 B:ASP287 2.2 5.0 0.4 O B:GLY297 2.3 5.8 1.0 O B:ALA295 2.3 5.3 1.0 OD1 B:ASP287 2.3 5.4 0.6 OD1 B:ASP299 2.3 5.2 1.0 O B:ILE288 2.3 2.9 0.5 O B:HOH333 2.4 5.3 1.0 O B:ILE288 2.4 4.3 0.5 CG B:ASP287 3.4 4.3 0.4 C B:ILE288 3.5 4.8 0.5 C B:GLY297 3.5 5.9 1.0 CG B:ASP287 3.5 5.4 0.6 C B:ILE288 3.5 4.7 0.5 CG B:ASP299 3.5 5.0 1.0 C B:ALA295 3.5 5.0 1.0 N B:GLY297 3.7 6.5 1.0 OG B:SER302 3.7 6.2 1.0 N B:ILE288 3.8 5.1 1.0 N B:ALA295 4.0 5.0 1.0 OD2 B:ASP287 4.1 5.0 0.4 C B:ILE296 4.1 7.0 1.0 OD2 B:ASP287 4.1 6.7 0.6 C B:ASP287 4.1 3.8 0.1 CA B:GLY297 4.2 7.3 1.0 CA B:ILE288 4.2 5.1 1.0 CB B:ASP299 4.3 5.2 1.0 C B:ASP287 4.4 6.1 0.6 CA B:ALA295 4.4 5.2 1.0 OD2 B:ASP299 4.4 5.1 1.0 N B:ILE296 4.4 5.7 1.0 N B:LYS289 4.4 4.1 0.4 CA B:ILE296 4.5 6.0 1.0 N B:LYS289 4.5 5.8 0.6 N B:ASP299 4.5 5.3 1.0 N B:ASP298 4.5 6.2 1.0 O B:GLY303 4.5 4.6 1.0 CG B:LYS289 4.5 6.5 0.4 CB B:ASP287 4.6 5.2 0.4 C B:ASP287 4.6 5.9 0.3 CB B:ASP287 4.6 5.8 0.6 CA B:ASP287 4.6 5.1 0.6 CA B:ASP287 4.7 6.3 0.4 O B:ILE296 4.7 8.4 1.0 CA B:LYS289 4.7 4.9 0.4 CA B:LYS289 4.7 5.1 0.6 CB B:ILE288 4.8 5.0 1.0 O B:ASP287 4.8 2.2 0.1 CA B:ASP298 4.8 5.5 1.0 C B:ASP298 4.8 5.6 1.0 CG B:LYS289 4.8 5.6 0.6

Calcium binding site 8 out of 12 in the The Crystal Structure of Sph at 0.8A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of The Crystal Structure of Sph at 0.8A within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca313 b:5.1 occ:1.00 O B:THR214 2.3 6.2 1.0 O B:VAL219 2.3 5.8 1.0 OE1 B:GLN221 2.3 6.5 1.0 OD1 B:ASP224 2.3 5.6 1.0 O B:HOH317 2.3 2.4 0.5 OD2 B:ASP217 2.4 6.4 1.0 CG B:ASP217 3.3 7.6 1.0 CD B:GLN221 3.3 6.2 1.0 CG B:ASP224 3.3 5.0 1.0 C B:THR214 3.4 6.4 1.0 C B:VAL219 3.5 5.5 1.0 OD1 B:ASP217 3.5 9.3 1.0 OD2 B:ASP224 3.8 7.2 1.0 NE2 B:GLN221 3.8 7.7 1.0 N B:GLN221 4.0 5.3 1.0 O B:HOH566 4.1 22.1 1.0 CB B:THR214 4.2 6.6 1.0 N B:VAL219 4.2 6.3 1.0 CA B:THR214 4.3 5.7 1.0 CA B:ILE220 4.3 5.8 1.0 N B:ILE220 4.4 6.0 1.0 N B:ALA215 4.4 7.3 1.0 CA B:VAL219 4.4 6.1 1.0 CA B:ALA215 4.4 6.5 1.0 OD1 B:ASP298 4.4 5.7 1.0 CB B:ASP224 4.5 4.5 1.0 CG B:GLN221 4.5 6.9 1.0 C B:ILE220 4.6 6.2 1.0 CB B:GLN221 4.6 6.9 1.0 CB B:ASP217 4.7 7.6 1.0 OG1 B:THR214 4.8 7.5 1.0 N B:ASP217 4.8 6.7 1.0 O B:HOH321 4.8 5.8 1.0 CB B:VAL219 4.8 7.9 1.0 N B:GLY216 4.9 6.7 1.0 C B:ALA215 4.9 7.0 1.0 N B:TYR218 5.0 6.7 1.0 CA B:GLN221 5.0 6.1 1.0

Calcium binding site 9 out of 12 in the The Crystal Structure of Sph at 0.8A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of The Crystal Structure of Sph at 0.8A within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca314 b:5.5 occ:0.76 CA B:CA314 0.0 5.5 0.8 CA B:CA314 0.8 6.3 0.2 O B:HOH383 1.4 6.6 0.3 OE1 B:GLU49 2.3 7.1 0.7 OD1 B:ASN29 2.3 6.1 1.0 O B:HOH352 2.3 7.1 1.0 OD2 B:ASP98 2.3 8.1 1.0 O B:HOH464 2.4 11.7 0.7 O B:HOH382 2.4 7.5 0.7 OE2 B:GLU49 2.6 8.2 0.3 OE2 B:GLU49 2.7 10.9 0.7 OE1 B:GLU49 2.7 8.2 0.3 CD B:GLU49 2.9 7.2 0.7 CD B:GLU49 3.1 6.6 0.3 CG B:ASP98 3.4 6.8 1.0 CG B:ASN29 3.5 5.9 1.0 CB B:ASP98 3.8 5.4 1.0 O B:HOH659 3.8 22.8 1.0 O B:HOH465 3.8 8.7 0.3 ND2 B:ASN29 4.0 6.0 1.0 O B:HOH517 4.4 15.8 1.0 CG B:GLU49 4.4 5.9 0.7 NE1 B:TRP100 4.4 5.6 1.0 OG1 B:THR132 4.4 5.7 0.6 OD1 B:ASP98 4.4 9.3 1.0 O B:HOH574 4.5 45.2 1.0 CG B:GLU49 4.5 6.2 0.3 O B:HOH472 4.6 13.5 1.0 O B:GLY27 4.6 7.0 1.0 O B:HOH400 4.6 12.2 1.0 CB B:ASN29 4.7 5.1 1.0 CG2 B:THR132 4.8 12.2 0.4 CB B:THR132 4.9 5.8 0.6 CZ2 B:TRP100 4.9 6.3 1.0 CG2 B:THR132 4.9 7.0 0.6 O B:HOH651 4.9 32.4 1.0

Calcium binding site 10 out of 12 in the The Crystal Structure of Sph at 0.8A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of The Crystal Structure of Sph at 0.8A within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca314 b:6.3 occ:0.24 CA B:CA314 0.0 6.3 0.2 CA B:CA314 0.8 5.5 0.8 OD2 B:ASP98 1.6 8.1 1.0 O B:HOH383 2.1 6.6 0.3 O B:HOH464 2.4 11.7 0.7 OE1 B:GLU49 2.4 7.1 0.7 O B:HOH352 2.5 7.1 1.0 OE1 B:GLU49 2.5 8.2 0.3 OD1 B:ASN29 2.6 6.1 1.0 CG B:ASP98 2.6 6.8 1.0 OE2 B:GLU49 2.7 10.9 0.7 CD B:GLU49 2.9 7.2 0.7 OE2 B:GLU49 3.0 8.2 0.3 CD B:GLU49 3.1 6.6 0.3 O B:HOH382 3.1 7.5 0.7 O B:HOH659 3.2 22.8 1.0 CB B:ASP98 3.3 5.4 1.0 O B:HOH465 3.6 8.7 0.3 OD1 B:ASP98 3.7 9.3 1.0 CG B:ASN29 3.8 5.9 1.0 O B:HOH574 4.0 45.2 1.0 CG B:GLU49 4.4 5.9 0.7 O B:GLY27 4.5 7.0 1.0 ND2 B:ASN29 4.5 6.0 1.0 CG B:GLU49 4.6 6.2 0.3 O B:HOH472 4.6 13.5 1.0 CA B:ASP98 4.7 4.6 1.0 NE1 B:TRP100 4.8 5.6 1.0 C B:GLY27 4.8 6.3 1.0 O B:HOH651 4.8 32.4 1.0 O B:HOH517 4.9 15.8 1.0 CB B:ASN29 4.9 5.1 1.0 CA B:GLY27 5.0 7.6 1.0 CB B:GLU49 5.0 5.4 0.7 CB B:GLU49 5.0 5.6 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