Calcium in PDB 4jp8: Crystal Structure of Pro-F17H/S324A

The structure of Crystal Structure of Pro-F17H/S324A, PDB code: 4jp8 was solved by K.Yuzaki, D.J.You, R.Uehara, Y.Koga, S.Kanaya, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.21
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	77.323, 92.498, 122.222, 90.00, 90.00, 90.00
R / Rfree (%)	23 / 28

The binding sites of Calcium atom in the Crystal Structure of Pro-F17H/S324A (pdb code 4jp8). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Crystal Structure of Pro-F17H/S324A, PDB code: 4jp8:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in the Crystal Structure of Pro-F17H/S324A


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 Pro-F17H/S324A within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca701 b:40.0 occ:1.00 O A:ILE168 2.1 42.4 1.0 O A:LEU164 2.2 41.1 1.0 OE1 A:GLN84 2.4 39.0 1.0 OD1 A:ASP124 2.4 48.6 1.0 OD2 A:ASP124 2.5 45.1 1.0 O A:VAL170 2.6 31.1 1.0 OD1 A:ASN166 2.8 57.4 1.0 CG A:ASP124 2.8 46.2 1.0 C A:ILE168 3.3 40.9 1.0 CG A:ASN166 3.3 51.8 1.0 C A:LEU164 3.4 40.9 1.0 ND2 A:ASN166 3.4 62.7 1.0 CD A:GLN84 3.4 36.4 1.0 C A:VAL170 3.5 30.5 1.0 N A:VAL170 3.6 30.6 1.0 CG A:GLN84 3.9 36.7 1.0 C A:GLY169 4.0 33.2 1.0 N A:ASN166 4.0 45.0 1.0 O A:ASN166 4.1 44.5 1.0 CA A:VAL170 4.1 31.9 1.0 N A:GLY169 4.2 37.5 1.0 CA A:LEU164 4.2 41.1 1.0 CA A:GLY169 4.3 35.4 1.0 CG1 A:ILE168 4.3 39.7 1.0 CA A:ILE168 4.3 41.6 1.0 N A:ASN165 4.3 42.6 1.0 N A:ILE168 4.3 43.9 1.0 CB A:ASP124 4.3 44.0 1.0 N A:LEU164 4.4 39.1 1.0 CA A:ASN165 4.5 43.7 1.0 CB A:GLN84 4.5 39.7 1.0 CB A:LEU164 4.5 41.1 1.0 N A:VAL171 4.5 33.4 1.0 C A:ASN166 4.6 45.5 1.0 CB A:ASN166 4.6 48.0 1.0 NE2 A:GLN84 4.6 37.0 1.0 CA A:ASN166 4.6 46.3 1.0 O A:GLY169 4.7 33.8 1.0 C A:ASN165 4.7 44.4 1.0 CA A:VAL171 4.8 30.3 1.0 CB A:VAL171 4.8 34.4 1.0 C A:ALA163 4.9 38.5 1.0 CB A:ILE168 4.9 40.1 1.0

Calcium binding site 2 out of 6 in the Crystal Structure of Pro-F17H/S324A


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 Pro-F17H/S324A within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca702 b:55.0 occ:1.00 O A:VAL210 1.7 48.6 1.0 OD2 A:ASP226 2.1 36.9 1.0 O A:LEU205 2.5 41.7 1.0 OD1 A:ASP208 2.7 46.1 1.0 C A:VAL210 2.8 47.9 1.0 O A:ALA211 3.2 52.4 1.0 CG A:ASP226 3.3 39.1 1.0 OD2 A:ASP208 3.4 48.3 1.0 CG A:ASP208 3.4 46.5 1.0 C A:LEU205 3.5 38.7 1.0 N A:ALA211 3.6 47.1 1.0 C A:ALA211 3.7 50.3 1.0 CA A:ALA211 3.7 47.6 1.0 N A:ASP226 3.9 39.6 1.0 OD1 A:ASP226 3.9 37.5 1.0 CA A:VAL210 3.9 46.7 1.0 N A:VAL210 4.0 46.5 1.0 O A:ILE204 4.1 39.6 1.0 CA A:GLY206 4.2 38.1 1.0 N A:GLY206 4.2 37.3 1.0 CA A:LEU205 4.3 40.2 1.0 CA A:ASP226 4.4 37.9 1.0 CB A:ASP226 4.4 37.9 1.0 N A:ALA227 4.4 34.7 1.0 CB A:VAL210 4.5 47.8 1.0 C A:ASP226 4.5 38.6 1.0 OD1 A:ASP225 4.5 41.0 1.0 CB A:ASP208 4.7 46.1 1.0 C A:GLY206 4.7 36.7 1.0 N A:GLY209 4.9 47.1 1.0 N A:ASP212 4.9 49.1 1.0 C A:ASP225 5.0 41.3 1.0 C A:GLY209 5.0 46.5 1.0 CB A:ASP225 5.0 42.4 1.0

Calcium binding site 3 out of 6 in the Crystal Structure of Pro-F17H/S324A


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 Pro-F17H/S324A within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca703 b:44.9 occ:1.00 OD2 A:ASP225 1.9 41.8 1.0 O A:ILE218 2.0 45.5 1.0 OD2 A:ASP214 2.1 62.0 1.0 OD1 A:ASP216 2.2 39.6 1.0 CG A:ASP214 2.4 58.8 1.0 OD1 A:ASP214 2.4 58.9 1.0 OD1 A:ASP212 2.7 50.0 1.0 OD1 A:ASP222 2.8 46.0 1.0 CG A:ASP216 3.1 45.5 1.0 CG A:ASP225 3.1 44.9 1.0 C A:ILE218 3.2 46.7 1.0 OD2 A:ASP216 3.5 35.3 1.0 CG A:ASP222 3.6 47.0 1.0 CG A:ASP212 3.7 48.6 1.0 CB A:ASP214 3.7 56.2 1.0 N A:ILE218 3.7 47.6 1.0 OD1 A:ASP225 3.8 41.0 1.0 CB A:ASP222 3.9 45.6 1.0 CA A:ILE218 3.9 47.0 1.0 N A:ASP216 4.1 51.8 1.0 CA A:CA704 4.2 63.7 1.0 CB A:ASP216 4.2 50.3 1.0 CB A:ASP225 4.2 42.4 1.0 N A:ILE219 4.3 45.6 1.0 CB A:ILE218 4.3 47.9 1.0 OD2 A:ASP212 4.3 45.8 1.0 CA A:ASP212 4.3 47.6 1.0 N A:ASP214 4.4 54.8 1.0 N A:GLY217 4.5 51.9 1.0 CA A:ASP214 4.5 55.5 1.0 OD2 A:ASP222 4.5 44.3 1.0 CB A:ASP212 4.5 46.5 1.0 CA A:ILE219 4.5 45.1 1.0 CA A:ASP216 4.5 51.4 1.0 N A:GLY215 4.5 53.5 1.0 C A:ASP212 4.7 47.6 1.0 C A:ASP216 4.7 51.9 1.0 C A:ASP214 4.8 54.9 1.0 C A:GLY217 4.9 50.1 1.0 N A:LYS213 4.9 49.9 1.0

Calcium binding site 4 out of 6 in the Crystal Structure of Pro-F17H/S324A


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 Pro-F17H/S324A within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca704 b:63.7 occ:1.00 OD1 A:ASP222 2.0 46.0 1.0 OD2 A:ASP224 2.4 47.5 1.0 OD2 A:ASP216 2.6 35.3 1.0 OD1 A:ASP214 2.7 58.9 1.0 CG A:ASP222 2.7 47.0 1.0 OD2 A:ASP222 2.8 44.3 1.0 CG A:ASP224 3.3 50.9 1.0 CB A:ASP224 3.5 46.6 1.0 CG A:ASP216 3.5 45.5 1.0 CG A:ASP214 3.6 58.8 1.0 CB A:ASP214 3.9 56.2 1.0 CB A:ASP222 4.1 45.6 1.0 CA A:CA703 4.2 44.9 1.0 OD1 A:ASP216 4.2 39.6 1.0 CB A:ASP216 4.4 50.3 1.0 OD1 A:ASP224 4.5 50.6 1.0 N A:ASP224 4.6 44.0 1.0 CA A:ASP224 4.7 46.3 1.0 OD2 A:ASP214 4.7 62.0 1.0 OD2 A:ASP225 4.9 41.8 1.0

Calcium binding site 5 out of 6 in the Crystal Structure of Pro-F17H/S324A


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 Pro-F17H/S324A within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca705 b:36.5 occ:1.00 O A:VAL108 1.9 39.4 1.0 O A:ALA227 2.0 33.8 1.0 OE1 A:GLN110 2.1 33.6 1.0 OE1 A:GLU229 2.2 33.0 1.0 OE2 A:GLU229 2.5 49.5 1.0 O A:HOH803 2.6 43.5 1.0 CD A:GLU229 2.7 44.9 1.0 C A:VAL108 3.2 39.7 1.0 CD A:GLN110 3.2 41.8 1.0 C A:ALA227 3.2 36.0 1.0 NE2 A:GLN110 3.7 44.3 1.0 CG2 A:VAL108 4.0 33.9 1.0 N A:ALA227 4.1 34.7 1.0 N A:GLN110 4.1 37.4 1.0 N A:ILE109 4.1 39.7 1.0 N A:ALA228 4.1 36.5 1.0 CA A:VAL108 4.2 38.7 1.0 CG A:GLU229 4.2 46.4 1.0 CA A:ALA227 4.2 34.0 1.0 C A:ASP226 4.3 38.6 1.0 CA A:ILE109 4.3 38.0 1.0 CA A:ALA228 4.4 37.7 1.0 O A:ASP226 4.4 36.2 1.0 CG A:GLN110 4.4 38.5 1.0 C A:ILE109 4.5 38.9 1.0 C A:ALA228 4.5 37.9 1.0 CB A:GLN110 4.6 38.9 1.0 N A:GLU229 4.7 40.0 1.0 CB A:VAL108 4.7 41.0 1.0 N A:GLY221 4.7 44.5 1.0 O A:ASP225 4.7 41.0 1.0 O A:ASP222 4.8 45.8 1.0 CB A:ALA227 4.9 33.2 1.0 CA A:ASP226 4.9 37.9 1.0 CA A:GLN110 5.0 37.2 1.0

Calcium binding site 6 out of 6 in the Crystal Structure of Pro-F17H/S324A


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 Pro-F17H/S324A within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca706 b:70.4 occ:1.00 OD1 A:ASP372 2.2 46.8 1.0 O A:PRO375 2.2 56.0 1.0 O A:LEU373 2.3 51.0 1.0 O A:GLY377 2.4 54.9 1.0 OD1 A:ASP379 3.0 52.5 1.0 CG A:ASP372 3.2 47.9 1.0 C A:PRO375 3.4 56.2 1.0 C A:LEU373 3.5 49.7 1.0 C A:GLY377 3.5 54.8 1.0 N A:LEU373 3.6 47.5 1.0 OD2 A:ASP372 3.8 50.2 1.0 N A:GLY377 3.9 55.7 1.0 CG A:ASP379 3.9 52.8 1.0 CB A:ASP379 3.9 50.5 1.0 C A:THR376 4.0 57.3 1.0 C A:GLY374 4.1 52.2 1.0 N A:PRO375 4.2 53.1 1.0 O A:GLY374 4.2 51.8 1.0 CA A:LEU373 4.2 49.1 1.0 CA A:THR376 4.3 58.7 1.0 C A:ASP372 4.3 47.7 1.0 N A:THR376 4.3 57.4 1.0 N A:ASP379 4.3 51.2 1.0 O A:GLY383 4.3 51.2 1.0 CA A:GLY377 4.3 54.7 1.0 CA A:PRO375 4.4 54.8 1.0 CB A:ASP372 4.4 47.8 1.0 CA A:ASP372 4.4 47.7 1.0 N A:GLY374 4.5 50.4 1.0 C A:TRP378 4.5 51.4 1.0 N A:TRP378 4.5 52.9 1.0 O A:THR376 4.5 57.3 1.0 CA A:GLY374 4.7 50.6 1.0 CA A:TRP378 4.7 51.5 1.0 CA A:ASP379 4.8 51.0 1.0 CD A:PRO375 4.9 52.7 1.0 O A:TYR384 4.9 48.6 1.0 CB A:PRO375 5.0 54.9 1.0

K.Yuzaki, Y.Sanda, D.J.You, R.Uehara, Y.Koga, S.Kanaya. Increase in Activation Rate of Pro-Tk-Subtilisin By A Single Nonpolar-to-Polar Amino Acid Substitution at the Hydrophobic Core of the Propeptide Domain Protein Sci. V. 22 1711 2013.
ISSN: ISSN 0961-8368
PubMed: 24115021
DOI: 10.1002/PRO.2371