Calcium in PDB 3msa: Crystal Structure of Thermolysin in Complex with 3-Bromophenol

All present enzymatic activity of Crystal Structure of Thermolysin in Complex with 3-Bromophenol:
3.4.24.27;

The structure of Crystal Structure of Thermolysin in Complex with 3-Bromophenol, PDB code: 3msa 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 / 1.66
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	93.111, 93.111, 128.726, 90.00, 90.00, 120.00
R / Rfree (%)	16.6 / 20

The structure of Crystal Structure of Thermolysin in Complex with 3-Bromophenol also contains other interesting chemical elements:

Bromine	(Br)	2 atoms
Zinc	(Zn)	1 atom

The binding sites of Calcium atom in the Crystal Structure of Thermolysin in Complex with 3-Bromophenol (pdb code 3msa). 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 3-Bromophenol, PDB code: 3msa:
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 3-Bromophenol


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 3-Bromophenol within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca601 b:13.7 occ:1.00 O A:GLU187 2.2 15.2 1.0 OD2 A:ASP138 2.4 15.4 1.0 OD1 A:ASP185 2.4 16.5 1.0 OE1 A:GLU190 2.5 14.7 1.0 O A:HOH1019 2.5 13.5 1.0 OE2 A:GLU190 2.5 15.8 1.0 OE1 A:GLU177 2.5 12.6 1.0 CD A:GLU190 2.8 13.0 1.0 OE2 A:GLU177 2.8 15.0 1.0 CD A:GLU177 3.0 13.9 1.0 C A:GLU187 3.4 12.5 1.0 CG A:ASP138 3.4 15.6 1.0 CG A:ASP185 3.4 15.6 1.0 OD2 A:ASP185 3.8 17.1 1.0 CA A:CA602 3.9 19.1 1.0 CB A:ASP138 4.0 12.2 1.0 O A:ASP185 4.1 15.1 1.0 N A:GLU187 4.2 13.0 1.0 N A:ILE188 4.2 13.7 1.0 CA A:ILE188 4.2 16.4 1.0 CA A:GLU187 4.3 14.1 1.0 CG A:GLU190 4.3 13.3 1.0 OD1 A:ASP138 4.3 16.6 1.0 N A:GLY189 4.4 14.8 1.0 O A:HOH1192 4.4 18.5 1.0 CG A:GLU177 4.5 14.8 1.0 C A:ASP185 4.6 13.9 1.0 CB A:GLU187 4.7 16.9 1.0 CB A:ASP185 4.7 13.8 1.0 N A:ASP185 4.8 18.0 1.0 C A:ILE188 4.8 13.3 1.0 N A:GLU190 5.0 14.8 1.0 CA A:ASP185 5.0 14.5 1.0 CB A:GLU177 5.0 11.1 1.0 O A:HOH1143 5.0 18.7 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of Thermolysin in Complex with 3-Bromophenol


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 3-Bromophenol within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca602 b:19.1 occ:1.00 O A:HOH1072 2.3 19.4 1.0 O A:ASN183 2.3 17.5 1.0 OE2 A:GLU190 2.3 15.8 1.0 O A:HOH1143 2.3 18.7 1.0 OD2 A:ASP185 2.4 17.1 1.0 OE2 A:GLU177 2.5 15.0 1.0 CG A:ASP185 3.3 15.6 1.0 CD A:GLU190 3.3 13.0 1.0 CD A:GLU177 3.3 13.9 1.0 C A:ASN183 3.5 17.3 1.0 CG A:GLU190 3.8 13.3 1.0 OD1 A:ASP185 3.8 16.5 1.0 OE1 A:GLU177 3.8 12.6 1.0 CA A:CA601 3.9 13.7 1.0 CA A:PRO184 4.1 12.9 1.0 CB A:ASN183 4.1 20.3 1.0 N A:ASP185 4.2 18.0 1.0 OD1 A:ASP191 4.2 20.7 1.0 OD2 A:ASP191 4.2 20.6 1.0 N A:PRO184 4.3 19.4 1.0 C A:PRO184 4.3 20.1 1.0 CG A:GLU177 4.3 14.8 1.0 O A:LYS182 4.3 30.7 1.0 OE1 A:GLU190 4.3 14.7 1.0 CA A:ASN183 4.4 19.0 1.0 CB A:ASP185 4.5 13.8 1.0 CG A:ASP191 4.5 19.8 1.0 CA A:ASP185 4.9 14.5 1.0 O A:HOH1088 5.0 40.1 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of Thermolysin in Complex with 3-Bromophenol


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 3-Bromophenol within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca603 b:13.1 occ:1.00 O A:GLN61 2.2 12.3 1.0 OD1 A:ASP57 2.3 14.0 1.0 O A:HOH1059 2.4 18.5 1.0 O A:HOH1065 2.4 15.5 1.0 O A:HOH1174 2.4 17.0 1.0 OD1 A:ASP59 2.4 13.4 1.0 OD2 A:ASP57 2.5 13.3 1.0 CG A:ASP57 2.8 11.3 1.0 C A:GLN61 3.4 9.9 1.0 CG A:ASP59 3.4 18.1 1.0 OD2 A:ASP59 3.8 16.8 1.0 O A:HOH1180 3.9 19.3 1.0 N A:GLN61 3.9 11.9 1.0 CA A:GLN61 4.2 10.8 1.0 CB A:ASP57 4.3 8.7 1.0 N A:ASP59 4.4 14.1 1.0 N A:PHE62 4.5 12.0 1.0 O A:HOH1068 4.5 17.4 1.0 CB A:GLN61 4.5 16.3 1.0 OD2 A:ASP67 4.6 12.5 1.0 O A:HOH1111 4.6 27.5 1.0 O A:HOH1005 4.6 12.4 1.0 CB A:ASP59 4.6 18.5 1.0 CA A:PHE62 4.7 12.1 1.0 N A:ASN60 4.7 12.6 1.0 N A:ALA58 4.8 11.8 1.0 O A:HOH1173 4.9 26.9 1.0 CA A:ASP59 4.9 15.5 1.0 C A:ASP59 5.0 15.2 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of Thermolysin in Complex with 3-Bromophenol


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 3-Bromophenol within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca604 b:19.4 occ:1.00 O A:ILE197 2.2 23.4 1.0 OG1 A:THR194 2.3 20.5 1.0 OD1 A:ASP200 2.3 19.8 1.0 O A:TYR193 2.4 18.4 1.0 O A:HOH1186 2.4 19.7 1.0 O A:THR194 2.4 19.8 1.0 O A:HOH1158 2.5 25.8 1.0 C A:THR194 3.2 18.9 1.0 C A:TYR193 3.4 16.8 1.0 C A:ILE197 3.4 28.7 1.0 CG A:ASP200 3.4 15.5 1.0 CB A:THR194 3.4 31.2 1.0 CA A:THR194 3.7 21.4 1.0 OD2 A:ASP200 3.8 21.5 1.0 N A:THR194 3.9 20.9 1.0 CA A:ILE197 4.1 23.0 1.0 N A:ILE197 4.1 30.4 1.0 O A:HOH1021 4.2 41.2 1.0 N A:PRO195 4.3 17.5 1.0 CB A:ILE197 4.3 24.0 1.0 O A:ASP200 4.4 23.2 1.0 N A:SER198 4.4 27.3 1.0 CA A:SER198 4.5 28.8 1.0 CA A:TYR193 4.5 16.1 1.0 N A:ASP200 4.5 18.4 1.0 O A:GLU190 4.6 18.4 1.0 CG2 A:THR194 4.7 21.9 1.0 CD2 A:TYR193 4.7 25.2 1.0 CB A:ASP200 4.7 15.4 1.0 CB A:TYR193 4.7 18.2 1.0 CA A:PRO195 4.7 32.9 1.0 C A:ASP200 4.8 15.7 1.0 C A:SER198 4.9 24.4 1.0 CA A:ASP200 4.9 17.6 1.0 C A:PRO195 4.9 27.8 1.0 N A:TYR193 5.0 15.6 1.0 N A:GLY199 5.0 32.6 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