Calcium in PDB 3ls7: Crystal Structure of Thermolysin in Complex with Xenon

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

The structure of Crystal Structure of Thermolysin in Complex with Xenon, PDB code: 3ls7 was solved by J.Behnen, G.Klebe, A.Heine, B.Brumshtein, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.00 / 1.98
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	93.100, 93.100, 130.200, 90.00, 90.00, 120.00
R / Rfree (%)	17.6 / 23.4

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

Xenon	(Xe)	1 atom
Zinc	(Zn)	1 atom

The binding sites of Calcium atom in the Crystal Structure of Thermolysin in Complex with Xenon (pdb code 3ls7). 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 Xenon, PDB code: 3ls7:
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 Xenon


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 Xenon within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca601 b:19.0 occ:1.00 O A:HOH1081 2.3 18.0 1.0 O A:HOH1020 2.3 19.1 1.0 O A:GLN61 2.3 15.6 1.0 OD1 A:ASP59 2.3 20.0 1.0 OD2 A:ASP57 2.4 19.4 1.0 OD1 A:ASP57 2.4 20.3 1.0 O A:HOH1001 2.4 20.1 1.0 CG A:ASP57 2.7 16.9 1.0 CG A:ASP59 3.4 19.9 1.0 C A:GLN61 3.5 16.3 1.0 OD2 A:ASP59 3.8 20.3 1.0 O A:HOH1109 4.0 19.3 1.0 N A:GLN61 4.0 15.9 1.0 CA A:GLN61 4.1 19.7 1.0 CB A:ASP57 4.2 18.1 1.0 N A:ASP59 4.3 20.8 1.0 CB A:GLN61 4.3 24.1 1.0 O A:HOH1098 4.4 24.8 1.0 O A:HOH1082 4.5 16.6 1.0 N A:PHE62 4.6 14.7 1.0 CB A:ASP59 4.6 19.7 1.0 N A:ASN60 4.6 19.9 1.0 N A:ALA58 4.7 17.1 1.0 OD2 A:ASP67 4.7 22.4 1.0 CA A:PHE62 4.8 22.6 1.0 CA A:ASP59 4.8 19.5 1.0 C A:ASP59 4.9 21.5 1.0 CA A:ASP57 5.0 18.1 1.0

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


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 Xenon within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca602 b:23.2 occ:1.00 O A:ILE197 2.2 22.7 1.0 O A:TYR193 2.3 19.8 1.0 O A:HOH1002 2.3 25.8 1.0 OG1 A:THR194 2.4 34.1 1.0 O A:HOH1016 2.4 22.5 1.0 O A:THR194 2.4 25.4 1.0 OD1 A:ASP200 2.4 16.0 1.0 C A:THR194 3.2 29.6 1.0 C A:TYR193 3.3 20.4 1.0 CB A:THR194 3.3 31.7 1.0 C A:ILE197 3.4 29.1 1.0 CG A:ASP200 3.4 17.8 1.0 CA A:THR194 3.6 25.3 1.0 OD2 A:ASP200 3.7 25.2 1.0 N A:THR194 3.9 23.5 1.0 CA A:ILE197 4.1 29.6 1.0 N A:ILE197 4.2 40.0 1.0 CB A:ILE197 4.2 35.5 1.0 N A:PRO195 4.3 25.5 1.0 N A:SER198 4.4 32.2 1.0 O A:ASP200 4.5 25.4 1.0 CA A:SER198 4.5 35.6 1.0 CA A:TYR193 4.5 16.9 1.0 CD2 A:TYR193 4.6 34.0 1.0 CG2 A:THR194 4.6 24.3 1.0 O A:GLU190 4.6 27.7 1.0 CA A:PRO195 4.7 29.8 1.0 N A:ASP200 4.7 20.8 1.0 CB A:TYR193 4.7 19.5 1.0 CB A:ASP200 4.8 17.8 1.0 CG2 A:ILE197 4.8 23.9 1.0 C A:ASP200 4.8 26.0 1.0 O A:HOH1072 4.9 26.0 1.0 C A:PRO195 4.9 32.0 1.0 C A:SER198 5.0 29.0 1.0 CG A:TYR193 5.0 26.0 1.0

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


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 Xenon within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca603 b:22.9 occ:1.00 OE2 A:GLU190 2.2 18.2 1.0 O A:HOH1003 2.2 22.2 1.0 O A:HOH1191 2.3 37.9 1.0 OD2 A:ASP185 2.4 21.6 1.0 O A:ASN183 2.4 25.1 1.0 OE1 A:GLU177 2.5 19.8 1.0 CD A:GLU190 3.2 16.6 1.0 CD A:GLU177 3.2 24.6 1.0 CG A:ASP185 3.3 15.2 1.0 C A:ASN183 3.6 19.8 1.0 OE2 A:GLU177 3.7 15.4 1.0 OD1 A:ASP185 3.8 16.1 1.0 CG A:GLU190 3.8 25.9 1.0 CA A:CA604 3.8 20.3 1.0 OD1 A:ASP191 4.1 31.7 1.0 OD2 A:ASP191 4.1 20.1 1.0 N A:ASP185 4.1 19.5 1.0 CB A:ASN183 4.2 28.5 1.0 CA A:PRO184 4.2 15.2 1.0 OE1 A:GLU190 4.2 14.7 1.0 O A:LYS182 4.3 24.5 1.0 CG A:GLU177 4.3 17.7 1.0 O A:HOH1208 4.3 35.7 1.0 C A:PRO184 4.3 25.2 1.0 N A:PRO184 4.4 18.7 1.0 CG A:ASP191 4.4 22.5 1.0 CB A:ASP185 4.5 17.1 1.0 CA A:ASN183 4.5 18.2 1.0 CA A:ASP185 4.9 17.6 1.0

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


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 Xenon within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca604 b:20.3 occ:1.00 O A:GLU187 2.3 14.2 1.0 OE2 A:GLU177 2.4 15.4 1.0 OD2 A:ASP138 2.4 24.2 1.0 OE1 A:GLU190 2.5 14.7 1.0 O A:HOH1032 2.5 15.5 1.0 OD1 A:ASP185 2.5 16.1 1.0 OE2 A:GLU190 2.6 18.2 1.0 OE1 A:GLU177 2.8 19.8 1.0 CD A:GLU190 2.9 16.6 1.0 CD A:GLU177 2.9 24.6 1.0 C A:GLU187 3.4 13.6 1.0 CG A:ASP138 3.4 31.0 1.0 CG A:ASP185 3.5 15.2 1.0 OD2 A:ASP185 3.8 21.6 1.0 CA A:CA603 3.8 22.9 1.0 CB A:ASP138 4.1 19.5 1.0 N A:GLU187 4.1 23.3 1.0 O A:ASP185 4.2 23.2 1.0 N A:ILE188 4.2 12.8 1.0 CA A:GLU187 4.2 25.6 1.0 CA A:ILE188 4.3 15.8 1.0 OD1 A:ASP138 4.3 26.8 1.0 CG A:GLU190 4.4 25.9 1.0 CG A:GLU177 4.4 17.7 1.0 O A:HOH1045 4.4 24.0 1.0 N A:GLY189 4.5 15.4 1.0 CB A:GLU187 4.6 28.7 1.0 C A:ASP185 4.6 23.9 1.0 N A:ASP185 4.7 19.5 1.0 CB A:ASP185 4.8 17.1 1.0 C A:ILE188 4.8 17.6 1.0 N A:GLU190 4.9 18.8 1.0 O A:HOH1003 4.9 22.2 1.0 CA A:ASP185 4.9 17.6 1.0 CB A:GLU177 5.0 15.6 1.0

J.Behnen, H.Krueger, L.Toker, B.Brumshtein, I.Silman, J.L.Sussman, G.Klebe, A.Heine. Old Acquantance Rediscovered, Use of Xenon/Protein Complexes As A Generic Tool For Sad Phasing of in House Data To Be Published.