Calcium in PDB 3msn: Crystal Structure of Thermolysin in Complex with N-Methylurea

All present enzymatic activity of Crystal Structure of Thermolysin in Complex with N-Methylurea:
3.4.24.27;

The structure of Crystal Structure of Thermolysin in Complex with N-Methylurea, PDB code: 3msn 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 / 1.97
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	93.088, 93.088, 129.149, 90.00, 90.00, 120.00
R / Rfree (%)	17.6 / 23.1

The structure of Crystal Structure of Thermolysin in Complex with N-Methylurea 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 N-Methylurea (pdb code 3msn). 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 N-Methylurea, PDB code: 3msn:
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 N-Methylurea


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 N-Methylurea within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca501 b:21.7 occ:1.00 O A:GLU187 2.3 20.6 1.0 OD1 A:ASP185 2.3 18.8 1.0 OE2 A:GLU190 2.5 18.7 1.0 OD2 A:ASP138 2.5 21.4 1.0 O A:HOH1016 2.5 15.8 1.0 OE1 A:GLU190 2.6 17.3 1.0 OE1 A:GLU177 2.7 22.1 1.0 OE2 A:GLU177 2.8 17.0 1.0 CD A:GLU190 2.9 19.3 1.0 CD A:GLU177 3.1 20.2 1.0 CG A:ASP185 3.3 16.2 1.0 C A:GLU187 3.3 21.8 1.0 CG A:ASP138 3.5 22.4 1.0 OD2 A:ASP185 3.7 22.6 1.0 CA A:CA502 3.9 22.9 1.0 O A:ASP185 4.1 18.1 1.0 CB A:ASP138 4.1 16.5 1.0 N A:ILE188 4.1 22.1 1.0 CA A:ILE188 4.2 20.9 1.0 N A:GLU187 4.2 19.3 1.0 CA A:GLU187 4.2 26.0 1.0 CG A:GLU190 4.4 18.1 1.0 OD1 A:ASP138 4.4 22.6 1.0 N A:GLY189 4.5 17.4 1.0 C A:ASP185 4.5 24.6 1.0 CG A:GLU177 4.5 18.4 1.0 CB A:GLU187 4.6 24.8 1.0 CB A:ASP185 4.6 19.0 1.0 O A:HOH1095 4.6 24.9 1.0 N A:ASP185 4.7 20.7 1.0 C A:ILE188 4.7 23.1 1.0 CA A:ASP185 4.9 21.0 1.0 CB A:GLU177 5.0 16.3 1.0

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


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 N-Methylurea within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca502 b:22.9 occ:1.00 O A:HOH1157 2.2 22.7 1.0 O A:ASN183 2.3 18.7 1.0 OE2 A:GLU190 2.3 18.7 1.0 OE2 A:GLU177 2.4 17.0 1.0 OD2 A:ASP185 2.4 22.6 1.0 O A:HOH1167 2.4 19.3 1.0 CD A:GLU177 3.2 20.2 1.0 CG A:ASP185 3.3 16.2 1.0 CD A:GLU190 3.3 19.3 1.0 C A:ASN183 3.4 20.1 1.0 OD1 A:ASP185 3.8 18.8 1.0 OE1 A:GLU177 3.8 22.1 1.0 CG A:GLU190 3.8 18.1 1.0 CA A:CA501 3.9 21.7 1.0 CA A:PRO184 4.0 12.8 1.0 OD2 A:ASP191 4.0 22.8 1.0 CB A:ASN183 4.0 29.8 1.0 OD1 A:ASP191 4.1 24.1 1.0 N A:ASP185 4.1 20.7 1.0 N A:PRO184 4.2 19.5 1.0 O A:LYS182 4.2 31.7 1.0 C A:PRO184 4.3 18.1 1.0 CG A:GLU177 4.3 18.4 1.0 CG A:ASP191 4.4 22.0 1.0 CA A:ASN183 4.4 26.6 1.0 OE1 A:GLU190 4.4 17.3 1.0 CB A:ASP185 4.5 19.0 1.0 CA A:ASP185 4.9 21.0 1.0

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


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 N-Methylurea within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:18.5 occ:1.00 O A:HOH1169 2.2 24.3 1.0 O A:GLN61 2.3 16.3 1.0 OD1 A:ASP57 2.3 22.4 1.0 O A:HOH1155 2.3 17.3 1.0 OD1 A:ASP59 2.4 23.4 1.0 O A:HOH1098 2.5 25.0 1.0 OD2 A:ASP57 2.6 16.7 1.0 CG A:ASP57 2.8 18.1 1.0 C A:GLN61 3.4 17.0 1.0 CG A:ASP59 3.4 22.7 1.0 N A:GLN61 3.8 20.3 1.0 OD2 A:ASP59 3.8 18.8 1.0 O A:HOH1060 3.9 26.6 1.0 CA A:GLN61 4.0 23.2 1.0 N A:ASP59 4.2 18.8 1.0 CB A:ASP57 4.3 11.6 1.0 CB A:GLN61 4.3 33.9 1.0 O A:HOH1036 4.5 18.4 1.0 N A:PHE62 4.5 12.9 1.0 OD2 A:ASP67 4.5 19.5 1.0 O A:HOH1168 4.6 32.6 1.0 O A:HOH1112 4.6 17.4 1.0 N A:ALA58 4.6 17.0 1.0 N A:ASN60 4.6 14.8 1.0 CB A:ASP59 4.6 22.6 1.0 O A:HOH1140 4.7 51.4 1.0 CA A:PHE62 4.7 20.3 1.0 CA A:ASP59 4.8 15.9 1.0 C A:ASP59 4.9 19.4 1.0 C A:ASN60 5.0 21.5 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of Thermolysin in Complex with N-Methylurea


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 N-Methylurea within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca504 b:24.7 occ:1.00 O A:ILE197 2.3 32.7 1.0 O A:TYR193 2.4 16.3 1.0 OG1 A:THR194 2.4 22.8 1.0 O A:THR194 2.4 24.9 1.0 O A:HOH1004 2.4 22.2 1.0 OD1 A:ASP200 2.5 26.6 1.0 O A:HOH1077 2.7 28.0 1.0 C A:THR194 3.1 23.4 1.0 C A:TYR193 3.3 19.3 1.0 CB A:THR194 3.4 27.2 1.0 C A:ILE197 3.5 30.8 1.0 CG A:ASP200 3.5 20.7 1.0 CA A:THR194 3.6 26.2 1.0 OD2 A:ASP200 3.8 21.1 1.0 N A:THR194 3.8 20.7 1.0 N A:PRO195 4.2 20.0 1.0 CA A:ILE197 4.2 32.3 1.0 N A:ILE197 4.2 34.5 1.0 CB A:ILE197 4.3 37.7 1.0 CA A:TYR193 4.5 18.2 1.0 N A:SER198 4.5 27.4 1.0 O A:ASP200 4.5 21.5 1.0 CA A:SER198 4.5 31.6 1.0 O A:GLU190 4.5 19.4 1.0 CA A:PRO195 4.6 23.3 1.0 CD2 A:TYR193 4.6 19.1 1.0 CB A:TYR193 4.6 24.4 1.0 CG2 A:THR194 4.7 26.7 1.0 N A:ASP200 4.7 20.7 1.0 O A:HOH1061 4.8 39.3 1.0 CG2 A:ILE197 4.8 25.0 1.0 CB A:ASP200 4.8 20.1 1.0 C A:ASP200 4.9 31.6 1.0 C A:PRO195 4.9 27.8 1.0 C A:SER198 4.9 27.1 1.0 N A:TYR193 4.9 18.7 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