Calcium in PDB 3vhq: Crystal Structure of the CA6 Site Mutant of Pro-Sa-Subtilisin

All present enzymatic activity of Crystal Structure of the CA6 Site Mutant of Pro-Sa-Subtilisin:
3.4.21.62;

The structure of Crystal Structure of the CA6 Site Mutant of Pro-Sa-Subtilisin, PDB code: 3vhq was solved by R.Uehara, Y.Takeuchi, S.Tanaka, H.Matsumura, Y.Koga, K.Takano, S.Kanaya, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.08 / 2.15
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	73.434, 92.780, 124.279, 90.00, 90.00, 90.00
R / Rfree (%)	17.1 / 24.1

The binding sites of Calcium atom in the Crystal Structure of the CA6 Site Mutant of Pro-Sa-Subtilisin (pdb code 3vhq). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Crystal Structure of the CA6 Site Mutant of Pro-Sa-Subtilisin, PDB code: 3vhq:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in the Crystal Structure of the CA6 Site Mutant of Pro-Sa-Subtilisin


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 the CA6 Site Mutant of Pro-Sa-Subtilisin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca399 b:31.0 occ:1.00 O A:VAL108 2.2 30.0 1.0 O A:ALA227 2.3 29.9 1.0 OE1 A:GLU229 2.3 24.1 1.0 OE1 A:GLN110 2.3 26.6 1.0 O A:HOH420 2.4 25.6 1.0 OE2 A:GLU229 2.5 27.6 1.0 O A:HOH413 2.6 29.5 1.0 CD A:GLU229 2.7 28.5 1.0 CD A:GLN110 3.4 32.1 1.0 C A:VAL108 3.4 28.8 1.0 C A:ALA227 3.6 29.6 1.0 NE2 A:GLN110 3.9 30.6 1.0 N A:GLN110 4.1 25.6 1.0 CG2 A:VAL108 4.1 28.3 1.0 CG A:GLU229 4.2 22.4 1.0 N A:ILE109 4.3 27.5 1.0 CA A:VAL108 4.3 29.2 1.0 N A:ALA227 4.3 28.9 1.0 C A:ASP226 4.4 29.3 1.0 CA A:ILE109 4.4 26.5 1.0 CA A:ALA227 4.5 28.5 1.0 N A:ALA228 4.5 27.5 1.0 CA A:ALA228 4.5 27.0 1.0 C A:ILE109 4.5 27.1 1.0 O A:ASP225 4.6 28.1 1.0 C A:ALA228 4.6 25.3 1.0 O A:ASP226 4.7 29.7 1.0 CG A:GLN110 4.7 24.5 1.0 CA A:ASP226 4.8 29.4 1.0 CB A:GLN110 4.8 25.7 1.0 N A:GLU229 4.8 24.6 1.0 O A:HOH564 4.8 46.8 1.0 N A:GLY221 4.8 27.5 1.0 CB A:VAL108 4.8 29.1 1.0 CA A:GLN110 5.0 25.6 1.0 O A:ASP222 5.0 31.4 1.0

Calcium binding site 2 out of 5 in the Crystal Structure of the CA6 Site Mutant of Pro-Sa-Subtilisin


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 the CA6 Site Mutant of Pro-Sa-Subtilisin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca400 b:33.0 occ:1.00 OD1 A:ASP208 2.2 31.1 1.0 OD2 A:ASP226 2.2 30.3 1.0 O A:VAL210 2.2 27.8 1.0 O A:HOH406 2.2 25.8 1.0 O A:LEU205 2.3 31.5 1.0 O A:HOH578 2.5 32.9 1.0 CG A:ASP208 3.1 33.2 1.0 CG A:ASP226 3.1 27.2 1.0 OD2 A:ASP208 3.4 33.1 1.0 C A:VAL210 3.4 28.7 1.0 C A:LEU205 3.4 30.9 1.0 OD1 A:ASP226 3.4 29.4 1.0 N A:VAL210 3.8 30.6 1.0 N A:ASP226 4.0 28.8 1.0 CA A:VAL210 4.1 29.4 1.0 N A:GLY206 4.3 31.2 1.0 O A:ALA211 4.3 27.5 1.0 CA A:GLY206 4.3 30.0 1.0 CA A:LEU205 4.4 29.3 1.0 N A:ALA227 4.4 28.9 1.0 CB A:ASP226 4.4 27.1 1.0 N A:GLY209 4.4 29.9 1.0 N A:ALA211 4.4 29.5 1.0 CB A:ASP208 4.4 30.5 1.0 OD1 A:ASP225 4.5 26.8 1.0 C A:ASP226 4.5 29.3 1.0 O A:ILE204 4.5 26.7 1.0 CA A:ASP226 4.5 29.4 1.0 N A:ASP208 4.5 30.3 1.0 C A:GLY206 4.5 29.3 1.0 CA A:ALA211 4.5 28.5 1.0 C A:ALA211 4.6 28.4 1.0 C A:ASP208 4.6 30.0 1.0 CB A:VAL210 4.7 31.3 1.0 O A:GLY206 4.7 29.6 1.0 CA A:ASP208 4.8 30.0 1.0 C A:GLY209 4.8 29.1 1.0 CB A:ASP225 4.9 27.6 1.0

Calcium binding site 3 out of 5 in the Crystal Structure of the CA6 Site Mutant of Pro-Sa-Subtilisin


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 the CA6 Site Mutant of Pro-Sa-Subtilisin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:32.8 occ:1.00 OD1 A:ASP222 2.2 29.2 1.0 O A:ILE218 2.3 28.6 1.0 OD1 A:ASP212 2.4 32.3 1.0 OD2 A:ASP225 2.4 32.2 1.0 OD2 A:ASP214 2.4 38.4 1.0 OD1 A:ASP216 2.5 31.4 1.0 CG A:ASP216 3.3 32.6 1.0 CG A:ASP222 3.4 30.3 1.0 C A:ILE218 3.5 30.0 1.0 CG A:ASP212 3.5 33.0 1.0 CG A:ASP214 3.5 35.6 1.0 CG A:ASP225 3.6 30.9 1.0 OD2 A:ASP216 3.6 30.3 1.0 OD1 A:ASP214 3.9 38.0 1.0 CA A:CA403 4.0 52.6 1.0 N A:ILE218 4.0 31.1 1.0 CB A:ASP222 4.1 27.9 1.0 CA A:ILE218 4.2 29.8 1.0 OD1 A:ASP225 4.2 26.8 1.0 OD2 A:ASP212 4.2 31.5 1.0 CA A:ASP212 4.3 31.9 1.0 N A:ASP216 4.3 34.7 1.0 CB A:ILE218 4.3 30.1 1.0 OD2 A:ASP222 4.4 29.8 1.0 CB A:ASP212 4.4 31.4 1.0 N A:ASP214 4.5 36.3 1.0 CB A:ASP216 4.5 34.3 1.0 N A:ILE219 4.5 30.1 1.0 C A:ASP212 4.6 32.8 1.0 N A:LYS213 4.6 34.8 1.0 CB A:ASP225 4.6 27.6 1.0 N A:GLY215 4.7 37.2 1.0 N A:GLY217 4.8 32.9 1.0 CB A:ASP214 4.8 35.7 1.0 CA A:ASP216 4.8 34.5 1.0 CA A:ILE219 4.9 29.9 1.0 CA A:ASP214 5.0 37.6 1.0

Calcium binding site 4 out of 5 in the Crystal Structure of the CA6 Site Mutant of Pro-Sa-Subtilisin


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 the CA6 Site Mutant of Pro-Sa-Subtilisin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:31.9 occ:1.00 O A:VAL170 2.2 28.9 1.0 OE1 A:GLN84 2.3 33.8 1.0 O A:ILE168 2.4 38.2 1.0 OD1 A:ASN166 2.4 30.8 1.0 O A:LEU164 2.5 33.6 1.0 OD1 A:ASP124 2.6 29.7 1.0 OD2 A:ASP124 2.7 33.0 1.0 CG A:ASP124 3.0 31.7 1.0 CD A:GLN84 3.3 34.9 1.0 C A:VAL170 3.3 29.2 1.0 CG A:ASN166 3.4 35.1 1.0 C A:ILE168 3.6 36.9 1.0 C A:LEU164 3.6 32.2 1.0 N A:VAL170 3.6 30.9 1.0 CG A:GLN84 3.7 37.6 1.0 ND2 A:ASN166 4.0 38.8 1.0 N A:ASN166 4.0 33.3 1.0 CA A:VAL170 4.1 30.0 1.0 C A:GLY169 4.1 32.2 1.0 CG1 A:ILE168 4.3 34.9 1.0 N A:VAL171 4.3 29.6 1.0 CA A:GLY169 4.4 33.4 1.0 N A:ILE168 4.4 39.5 1.0 CA A:LEU164 4.4 32.7 1.0 N A:GLY169 4.4 35.2 1.0 CB A:GLN84 4.5 39.5 1.0 N A:LEU164 4.5 31.6 1.0 NE2 A:GLN84 4.5 28.1 1.0 CA A:VAL171 4.5 28.9 1.0 N A:ASN165 4.5 31.3 1.0 CB A:ASP124 4.5 31.4 1.0 CA A:ILE168 4.5 37.9 1.0 CA A:ASN165 4.5 31.7 1.0 CB A:ASN166 4.6 34.0 1.0 CB A:LEU164 4.6 32.6 1.0 CA A:ASN166 4.7 35.2 1.0 C A:ASN165 4.7 32.0 1.0 C A:ASN166 4.7 36.7 1.0 O A:ASN166 4.8 37.6 1.0 CB A:VAL171 4.8 29.1 1.0 O A:GLY169 4.9 31.1 1.0 C A:ALA163 4.9 29.7 1.0

Calcium binding site 5 out of 5 in the Crystal Structure of the CA6 Site Mutant of Pro-Sa-Subtilisin


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 the CA6 Site Mutant of Pro-Sa-Subtilisin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca403 b:52.6 occ:1.00 OD2 A:ASP216 2.4 30.3 1.0 OD1 A:ASP214 2.4 38.0 1.0 OD1 A:ASP222 2.6 29.2 1.0 OD2 A:ASP224 2.7 40.2 1.0 OD2 A:ASP222 2.7 29.8 1.0 CG A:ASP222 3.0 30.3 1.0 CG A:ASP214 3.4 35.6 1.0 CG A:ASP216 3.4 32.6 1.0 CG A:ASP224 3.6 36.6 1.0 CB A:ASP224 3.7 32.7 1.0 OD2 A:ASP214 3.7 38.4 1.0 O A:HOH500 3.9 47.0 1.0 CA A:CA401 4.0 32.8 1.0 OD1 A:ASP216 4.0 31.4 1.0 CB A:ASP222 4.4 27.9 1.0 CB A:ASP216 4.5 34.3 1.0 CB A:ASP214 4.7 35.7 1.0 OD1 A:ASP224 4.7 39.8 1.0 N A:ASP224 4.8 32.3 1.0 CA A:ASP224 4.8 31.8 1.0 CD1 A:ILE218 5.0 27.7 1.0

R.Uehara, Y.Takeuchi, S.I.Tanaka, K.Takano, Y.Koga, S.Kanaya. Requirement of Ca(2+) Ions For the Hyperthermostability of Tk-Subtilisin From Thermococcus Kodakarensis Biochemistry V. 51 5369 2012.
ISSN: ISSN 0006-2960
PubMed: 22686281
DOI: 10.1021/BI300427U