Calcium in PDB 3msf: Crystal Structure of Thermolysin in Complex with Urea

All present enzymatic activity of Crystal Structure of Thermolysin in Complex with Urea:
3.4.24.27;

The structure of Crystal Structure of Thermolysin in Complex with Urea, PDB code: 3msf 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 / 2.09
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	92.614, 92.614, 128.701, 90.00, 90.00, 120.00
R / Rfree (%)	18.4 / 24.8

The structure of Crystal Structure of Thermolysin in Complex with Urea 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 Urea (pdb code 3msf). 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 Urea, PDB code: 3msf:
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 Urea


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 Urea within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca501 b:24.2 occ:1.00 O A:GLU187 2.3 19.9 1.0 O A:HOH1094 2.3 15.4 1.0 OD1 A:ASP185 2.4 31.6 1.0 OE1 A:GLU177 2.4 25.5 1.0 OE2 A:GLU190 2.5 17.6 1.0 OD2 A:ASP138 2.5 23.2 1.0 OE1 A:GLU190 2.7 22.0 1.0 OE2 A:GLU177 2.8 21.6 1.0 CD A:GLU177 2.9 22.1 1.0 CD A:GLU190 3.0 20.7 1.0 CG A:ASP185 3.4 30.9 1.0 CG A:ASP138 3.4 24.1 1.0 C A:GLU187 3.4 27.0 1.0 OD2 A:ASP185 3.8 29.8 1.0 CA A:CA502 3.9 31.0 1.0 CB A:ASP138 4.0 21.8 1.0 O A:ASP185 4.1 23.0 1.0 N A:ILE188 4.3 28.8 1.0 N A:GLU187 4.3 25.8 1.0 CA A:ILE188 4.3 25.1 1.0 OD1 A:ASP138 4.3 22.3 1.0 CA A:GLU187 4.3 28.8 1.0 O A:HOH1030 4.4 29.7 1.0 CG A:GLU177 4.4 17.1 1.0 N A:GLY189 4.5 23.6 1.0 CG A:GLU190 4.5 17.4 1.0 C A:ASP185 4.5 24.1 1.0 CB A:GLU187 4.6 31.1 1.0 CB A:ASP185 4.7 32.9 1.0 N A:ASP185 4.7 21.8 1.0 C A:ILE188 4.8 31.9 1.0 CB A:GLU177 4.9 20.9 1.0 CA A:ASP185 4.9 26.9 1.0 OG1 A:THR174 5.0 22.1 1.0

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


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 Urea within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca502 b:31.0 occ:1.00 O A:ASN183 2.2 30.4 1.0 O A:HOH1150 2.3 26.8 1.0 OE2 A:GLU190 2.4 17.6 1.0 OD2 A:ASP185 2.5 29.8 1.0 O A:HOH1095 2.5 24.8 1.0 OE2 A:GLU177 2.5 21.6 1.0 CG A:ASP185 3.2 30.9 1.0 CD A:GLU177 3.3 22.1 1.0 C A:ASN183 3.4 27.5 1.0 CD A:GLU190 3.4 20.7 1.0 OD1 A:ASP185 3.6 31.6 1.0 CA A:CA501 3.9 24.2 1.0 CG A:GLU190 3.9 17.4 1.0 OE1 A:GLU177 3.9 25.5 1.0 CA A:PRO184 4.0 23.1 1.0 OD2 A:ASP191 4.1 24.2 1.0 CB A:ASN183 4.1 33.1 1.0 N A:PRO184 4.2 24.3 1.0 OD1 A:ASP191 4.2 29.9 1.0 N A:ASP185 4.2 21.8 1.0 C A:PRO184 4.2 25.2 1.0 O A:LYS182 4.3 27.5 1.0 CG A:GLU177 4.4 17.1 1.0 CB A:ASP185 4.4 32.9 1.0 CA A:ASN183 4.4 29.4 1.0 CG A:ASP191 4.4 27.4 1.0 OE1 A:GLU190 4.5 22.0 1.0 O A:HOH1117 4.8 36.7 1.0 O A:HOH1030 4.9 29.7 1.0 O A:PRO184 4.9 25.2 1.0 CA A:ASP185 4.9 26.9 1.0

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


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 Urea within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:24.7 occ:1.00 O A:HOH1151 2.2 20.0 1.0 O A:GLN61 2.3 25.7 1.0 OD1 A:ASP57 2.3 23.7 1.0 OD1 A:ASP59 2.4 31.1 1.0 O A:HOH1096 2.5 20.9 1.0 O A:HOH1097 2.5 21.1 1.0 OD2 A:ASP57 2.6 19.5 1.0 CG A:ASP57 2.7 21.6 1.0 CG A:ASP59 3.3 27.1 1.0 C A:GLN61 3.4 27.9 1.0 OD2 A:ASP59 3.7 19.5 1.0 O A:HOH1011 3.9 25.4 1.0 N A:GLN61 4.0 25.3 1.0 CA A:GLN61 4.1 28.9 1.0 O A:HOH1061 4.2 33.0 1.0 CB A:ASP57 4.3 18.3 1.0 N A:ASP59 4.4 26.2 1.0 CB A:GLN61 4.4 29.9 1.0 N A:PHE62 4.5 22.7 1.0 CB A:ASP59 4.6 26.1 1.0 OD2 A:ASP67 4.6 20.6 1.0 N A:ASN60 4.7 24.5 1.0 O A:HOH1135 4.7 21.9 1.0 N A:ALA58 4.8 23.3 1.0 CA A:PHE62 4.8 23.7 1.0 CA A:ASP59 4.8 26.8 1.0 C A:ASP59 4.9 26.1 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of Thermolysin in Complex with Urea


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 Urea within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca504 b:25.7 occ:1.00 OG1 A:THR194 2.1 29.5 1.0 O A:HOH1109 2.1 37.3 1.0 O A:ILE197 2.2 28.9 1.0 O A:TYR193 2.3 24.1 1.0 O A:THR194 2.4 27.5 1.0 OD1 A:ASP200 2.4 32.2 1.0 O A:HOH1098 2.4 23.8 1.0 C A:THR194 3.0 26.1 1.0 CB A:THR194 3.3 34.9 1.0 C A:TYR193 3.3 31.2 1.0 C A:ILE197 3.4 32.8 1.0 CG A:ASP200 3.4 34.0 1.0 CA A:THR194 3.5 30.2 1.0 N A:THR194 3.8 33.9 1.0 OD2 A:ASP200 3.9 32.9 1.0 N A:PRO195 4.1 18.6 1.0 CA A:ILE197 4.2 38.8 1.0 N A:ILE197 4.3 43.8 1.0 CB A:ILE197 4.4 42.5 1.0 N A:SER198 4.4 30.5 1.0 CG2 A:THR194 4.5 52.6 1.0 CA A:SER198 4.5 35.6 1.0 CA A:TYR193 4.5 25.2 1.0 CD2 A:TYR193 4.5 29.9 1.0 O A:ASP200 4.5 25.2 1.0 CA A:PRO195 4.6 25.6 1.0 N A:ASP200 4.6 35.0 1.0 O A:GLU190 4.7 35.6 1.0 CB A:TYR193 4.7 24.9 1.0 CB A:ASP200 4.7 28.5 1.0 C A:ASP200 4.8 25.2 1.0 C A:SER198 4.8 29.2 1.0 C A:PRO195 4.9 40.6 1.0 CA A:ASP200 5.0 25.4 1.0 CG A:TYR193 5.0 26.6 1.0 N A:TYR193 5.0 22.4 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