Calcium in PDB 3n21: Crystal Structure of Thermolysin in Complex with S-1,2-Propandiol

All present enzymatic activity of Crystal Structure of Thermolysin in Complex with S-1,2-Propandiol:
3.4.24.27;

The structure of Crystal Structure of Thermolysin in Complex with S-1,2-Propandiol, PDB code: 3n21 was solved by J.Behnen, A.Heine, G.Klebe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.00 / 1.87
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	93.138, 93.138, 128.620, 90.00, 90.00, 120.00
R / Rfree (%)	18.2 / 23.2

The structure of Crystal Structure of Thermolysin in Complex with S-1,2-Propandiol also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Calcium atom in the Crystal Structure of Thermolysin in Complex with S-1,2-Propandiol (pdb code 3n21). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of Thermolysin in Complex with S-1,2-Propandiol, PDB code: 3n21:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of Thermolysin in Complex with S-1,2-Propandiol


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 Thermolysin in Complex with S-1,2-Propandiol within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca501 b:18.1 occ:1.00 O A:GLU187 2.3 19.1 1.0 OE2 A:GLU190 2.4 19.9 1.0 O A:HOH1166 2.4 20.0 1.0 OE1 A:GLU177 2.4 15.8 1.0 OD2 A:ASP138 2.5 22.8 1.0 OE1 A:GLU190 2.5 17.0 1.0 OD1 A:ASP185 2.5 17.1 1.0 CD A:GLU190 2.7 17.4 1.0 OE2 A:GLU177 2.7 18.6 1.0 CD A:GLU177 2.9 20.0 1.0 CG A:ASP185 3.4 22.2 1.0 C A:GLU187 3.4 19.2 1.0 CG A:ASP138 3.5 22.8 1.0 OD2 A:ASP185 3.7 20.4 1.0 CA A:CA502 3.8 20.8 1.0 CB A:ASP138 4.1 17.6 1.0 O A:ASP185 4.2 21.0 1.0 CG A:GLU190 4.2 18.6 1.0 CA A:ILE188 4.3 22.6 1.0 N A:GLU187 4.3 23.3 1.0 N A:ILE188 4.3 22.1 1.0 CA A:GLU187 4.4 27.4 1.0 CG A:GLU177 4.4 15.4 1.0 OD1 A:ASP138 4.4 17.6 1.0 N A:GLY189 4.5 18.4 1.0 O A:HOH1168 4.5 26.4 1.0 C A:ASP185 4.6 26.0 1.0 CB A:ASP185 4.7 19.3 1.0 N A:ASP185 4.7 18.4 1.0 C A:ILE188 4.8 22.8 1.0 CB A:GLU187 4.9 25.3 1.0 CB A:GLU177 4.9 17.7 1.0 CA A:ASP185 4.9 19.8 1.0 N A:GLU190 5.0 18.5 1.0 O A:HOH1165 5.0 17.3 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of Thermolysin in Complex with S-1,2-Propandiol


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 Thermolysin in Complex with S-1,2-Propandiol within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca502 b:20.8 occ:1.00 O A:HOH1167 2.2 23.4 1.0 OD2 A:ASP185 2.2 20.4 1.0 O A:ASN183 2.3 21.6 1.0 O A:HOH1165 2.4 17.3 1.0 OE2 A:GLU190 2.4 19.9 1.0 OE2 A:GLU177 2.5 18.6 1.0 CG A:ASP185 3.2 22.2 1.0 CD A:GLU190 3.3 17.4 1.0 CD A:GLU177 3.3 20.0 1.0 C A:ASN183 3.5 18.3 1.0 OD1 A:ASP185 3.7 17.1 1.0 CG A:GLU190 3.7 18.6 1.0 CA A:CA501 3.8 18.1 1.0 OE1 A:GLU177 3.9 15.8 1.0 OD2 A:ASP191 4.0 23.5 1.0 N A:ASP185 4.1 18.4 1.0 CA A:PRO184 4.1 18.6 1.0 CB A:ASN183 4.2 21.3 1.0 C A:PRO184 4.2 21.8 1.0 OD1 A:ASP191 4.2 21.4 1.0 O A:LYS182 4.3 28.0 1.0 CG A:GLU177 4.3 15.4 1.0 CB A:ASP185 4.3 19.3 1.0 N A:PRO184 4.3 20.1 1.0 OE1 A:GLU190 4.3 17.0 1.0 O A:HOH1169 4.4 36.7 1.0 CG A:ASP191 4.4 23.8 1.0 CA A:ASN183 4.5 22.5 1.0 CA A:ASP185 4.8 19.8 1.0 O A:PRO184 5.0 22.8 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of Thermolysin in Complex with S-1,2-Propandiol


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 Thermolysin in Complex with S-1,2-Propandiol within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:18.4 occ:1.00 OD1 A:ASP57 2.2 16.4 1.0 O A:GLN61 2.3 18.2 1.0 O A:HOH1170 2.3 21.8 1.0 OD1 A:ASP59 2.3 18.9 1.0 O A:HOH1172 2.4 17.9 1.0 O A:HOH1096 2.4 21.1 1.0 OD2 A:ASP57 2.5 18.8 1.0 CG A:ASP57 2.7 20.7 1.0 CG A:ASP59 3.4 19.8 1.0 C A:GLN61 3.4 13.1 1.0 OD2 A:ASP59 3.8 18.1 1.0 O A:HOH1171 3.9 20.8 1.0 N A:GLN61 3.9 13.4 1.0 CA A:GLN61 4.1 15.9 1.0 CB A:ASP57 4.2 15.5 1.0 N A:ASP59 4.2 18.9 1.0 CB A:GLN61 4.4 17.5 1.0 O A:HOH1035 4.4 16.7 1.0 N A:PHE62 4.5 14.7 1.0 CB A:ASP59 4.5 20.1 1.0 N A:ASN60 4.6 16.9 1.0 OD2 A:ASP67 4.6 15.6 1.0 O A:HOH1137 4.6 43.5 1.0 N A:ALA58 4.6 18.0 1.0 O A:HOH1004 4.7 16.6 1.0 CA A:PHE62 4.7 22.7 1.0 CA A:ASP59 4.8 21.3 1.0 C A:ASP59 4.8 21.7 1.0 CA A:ASP57 5.0 14.3 1.0 C A:ASN60 5.0 17.2 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of Thermolysin in Complex with S-1,2-Propandiol


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 Thermolysin in Complex with S-1,2-Propandiol within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca504 b:21.7 occ:1.00 O A:HOH1173 2.2 29.4 1.0 O A:HOH1148 2.3 19.6 1.0 O A:TYR193 2.3 20.1 1.0 O A:ILE197 2.3 21.1 1.0 O A:THR194 2.3 23.0 1.0 OD1 A:ASP200 2.4 26.3 1.0 OG1 A:THR194 2.5 21.6 1.0 C A:THR194 3.2 19.3 1.0 C A:TYR193 3.3 24.6 1.0 CG A:ASP200 3.5 25.8 1.0 C A:ILE197 3.5 27.2 1.0 CB A:THR194 3.5 16.4 1.0 CA A:THR194 3.7 21.9 1.0 N A:THR194 3.8 23.0 1.0 OD2 A:ASP200 3.9 23.8 1.0 N A:PRO195 4.2 18.8 1.0 N A:ILE197 4.3 25.3 1.0 CA A:ILE197 4.3 24.0 1.0 O A:ASP200 4.3 20.9 1.0 CB A:ILE197 4.4 29.6 1.0 CA A:TYR193 4.5 19.9 1.0 N A:SER198 4.5 20.7 1.0 O A:GLU190 4.5 23.1 1.0 CA A:SER198 4.6 24.3 1.0 CD2 A:TYR193 4.6 19.6 1.0 CA A:PRO195 4.6 27.3 1.0 CB A:TYR193 4.6 23.1 1.0 N A:ASP200 4.7 21.7 1.0 CG2 A:THR194 4.8 22.7 1.0 CB A:ASP200 4.8 21.9 1.0 C A:ASP200 4.8 22.1 1.0 C A:PRO195 4.9 32.5 1.0 C A:SER198 5.0 18.2 1.0 CG A:TYR193 5.0 21.8 1.0

J.Behnen, H.Koster, G.Neudert, T.Craan, A.Heine, G.Klebe. Experimental and Computational Active Site Mapping As A Starting Point to Fragment-Based Lead Discovery. Chemmedchem V. 7 248 2012.
ISSN: ISSN 1860-7179
PubMed: 22213702
DOI: 10.1002/CMDC.201100490