Calcium in PDB 3nn7: Crystal Structure of Thermolysin in Complex with 2-Bromoacetate

All present enzymatic activity of Crystal Structure of Thermolysin in Complex with 2-Bromoacetate:
3.4.24.27;

The structure of Crystal Structure of Thermolysin in Complex with 2-Bromoacetate, PDB code: 3nn7 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 / 2.05
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	92.947, 92.947, 129.951, 90.00, 90.00, 120.00
R / Rfree (%)	17.3 / 25.4

The structure of Crystal Structure of Thermolysin in Complex with 2-Bromoacetate also contains other interesting chemical elements:

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

The binding sites of Calcium atom in the Crystal Structure of Thermolysin in Complex with 2-Bromoacetate (pdb code 3nn7). 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 2-Bromoacetate, PDB code: 3nn7:
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 2-Bromoacetate


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 2-Bromoacetate within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca501 b:24.9 occ:1.00 O A:GLU187 2.2 17.3 1.0 OD2 A:ASP138 2.4 21.7 1.0 OE2 A:GLU190 2.4 20.9 1.0 O A:HOH1089 2.6 19.9 1.0 OD1 A:ASP185 2.6 24.7 1.0 OE1 A:GLU190 2.6 20.1 1.0 OE1 A:GLU177 2.8 26.2 1.0 CD A:GLU190 2.8 21.2 1.0 OE2 A:GLU177 2.9 24.4 1.0 CD A:GLU177 3.1 23.8 1.0 C A:GLU187 3.2 24.0 1.0 CG A:ASP138 3.4 24.1 1.0 CG A:ASP185 3.5 26.5 1.0 OD2 A:ASP185 3.8 30.5 1.0 CA A:CA504 4.0 43.2 1.0 CB A:ASP138 4.0 22.9 1.0 N A:GLU187 4.1 28.6 1.0 N A:ILE188 4.1 21.9 1.0 CA A:GLU187 4.1 30.1 1.0 CA A:ILE188 4.2 28.3 1.0 O A:ASP185 4.2 21.5 1.0 OD1 A:ASP138 4.2 22.7 1.0 CG A:GLU190 4.3 26.2 1.0 N A:GLY189 4.4 25.9 1.0 O A:HOH1062 4.4 29.6 1.0 CB A:GLU187 4.5 36.1 1.0 CG A:GLU177 4.6 21.7 1.0 C A:ASP185 4.7 24.7 1.0 C A:ILE188 4.7 27.7 1.0 N A:ASP185 4.8 20.0 1.0 CB A:ASP185 4.8 26.5 1.0 N A:GLU190 4.9 17.1 1.0

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


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 2-Bromoacetate within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca502 b:22.3 occ:1.00 O A:GLN61 2.2 13.6 1.0 OD1 A:ASP57 2.4 20.3 1.0 O A:HOH1003 2.4 21.5 1.0 OD1 A:ASP59 2.4 19.9 1.0 O A:HOH1044 2.5 29.7 1.0 OD2 A:ASP57 2.6 19.4 1.0 O A:HOH1128 2.7 21.8 1.0 CG A:ASP57 2.8 18.7 1.0 C A:GLN61 3.4 19.7 1.0 CG A:ASP59 3.4 20.6 1.0 OD2 A:ASP59 3.8 26.3 1.0 N A:GLN61 3.8 19.0 1.0 O A:HOH1060 3.9 23.4 1.0 CA A:GLN61 4.1 20.0 1.0 CB A:ASP57 4.3 18.1 1.0 O A:HOH1111 4.3 41.7 1.0 N A:ASP59 4.4 16.8 1.0 CB A:GLN61 4.4 22.6 1.0 N A:PHE62 4.5 17.9 1.0 OD2 A:ASP67 4.5 20.3 1.0 N A:ASN60 4.6 13.3 1.0 CB A:ASP59 4.7 15.0 1.0 N A:ALA58 4.7 15.6 1.0 O A:HOH1091 4.7 20.2 1.0 CA A:PHE62 4.7 24.0 1.0 CA A:ASP59 4.9 12.6 1.0 C A:ASP59 4.9 16.6 1.0 C A:ASN60 4.9 17.6 1.0

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


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 2-Bromoacetate within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:27.3 occ:1.00 OG1 A:THR194 2.3 30.7 1.0 O A:TYR193 2.4 17.1 1.0 O A:ILE197 2.4 27.9 1.0 OD1 A:ASP200 2.4 22.4 1.0 O A:THR194 2.5 33.3 1.0 O A:HOH1068 2.5 24.4 1.0 C A:THR194 3.2 31.0 1.0 C A:TYR193 3.2 20.7 1.0 CG A:ASP200 3.4 22.7 1.0 CB A:THR194 3.4 18.6 1.0 C A:ILE197 3.5 28.5 1.0 OD2 A:ASP200 3.6 24.8 1.0 CA A:THR194 3.6 25.7 1.0 N A:THR194 3.7 20.5 1.0 N A:ILE197 4.0 46.0 1.0 CA A:ILE197 4.1 36.2 1.0 CB A:ILE197 4.3 40.8 1.0 N A:PRO195 4.3 25.0 1.0 O A:ASP200 4.4 23.9 1.0 CA A:TYR193 4.4 24.2 1.0 CD2 A:TYR193 4.5 20.5 1.0 N A:SER198 4.6 29.3 1.0 O A:GLU190 4.6 28.1 1.0 CA A:SER198 4.6 34.2 1.0 CB A:TYR193 4.6 25.6 1.0 CG2 A:THR194 4.7 21.0 1.0 N A:ASP200 4.7 24.6 1.0 CB A:ASP200 4.7 22.7 1.0 CA A:PRO195 4.8 25.9 1.0 C A:ASP200 4.8 23.8 1.0 C A:PRO195 4.9 33.9 1.0 CG A:TYR193 4.9 25.2 1.0 C A:SER198 4.9 30.8 1.0 N A:TYR193 5.0 17.4 1.0 CA A:ASP200 5.0 17.5 1.0

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


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 2-Bromoacetate within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca504 b:43.2 occ:1.00 OE2 A:GLU190 2.3 20.9 1.0 OD2 A:ASP185 2.5 30.5 1.0 OE2 A:GLU177 2.7 24.4 1.0 O A:ASN183 2.7 23.9 1.0 CD A:GLU190 3.2 21.2 1.0 CD A:GLU177 3.4 23.8 1.0 CG A:ASP185 3.5 26.5 1.0 CG A:GLU190 3.7 26.2 1.0 OD1 A:ASP191 3.7 26.9 1.0 OE1 A:GLU177 3.9 26.2 1.0 C A:ASN183 3.9 27.7 1.0 CA A:CA501 4.0 24.9 1.0 OD1 A:ASP185 4.0 24.7 1.0 CA A:PRO184 4.3 19.2 1.0 OD2 A:ASP191 4.3 28.1 1.0 N A:ASP185 4.3 20.0 1.0 CG A:ASP191 4.3 23.7 1.0 OE1 A:GLU190 4.4 20.1 1.0 CG A:GLU177 4.4 21.7 1.0 C A:PRO184 4.5 22.9 1.0 CB A:ASN183 4.5 31.1 1.0 O A:LYS182 4.5 39.7 1.0 N A:PRO184 4.6 28.3 1.0 CB A:ASP185 4.6 26.5 1.0 O A:HOH1062 4.8 29.6 1.0 CA A:ASN183 4.9 30.1 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