Calcium in PDB 3fgd: Drugscore Fp: Thermoylsin in Complex with Fragment.

All present enzymatic activity of Drugscore Fp: Thermoylsin in Complex with Fragment.:
3.4.24.27;

The structure of Drugscore Fp: Thermoylsin in Complex with Fragment., PDB code: 3fgd was solved by L.Englert, 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 / 1.33
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	92.600, 92.600, 128.673, 90.00, 90.00, 120.00
R / Rfree (%)	14.8 / 21.7

The structure of Drugscore Fp: Thermoylsin in Complex with Fragment. also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Calcium atom in the Drugscore Fp: Thermoylsin in Complex with Fragment. (pdb code 3fgd). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Drugscore Fp: Thermoylsin in Complex with Fragment., PDB code: 3fgd:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Drugscore Fp: Thermoylsin in Complex with Fragment.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Drugscore Fp: Thermoylsin in Complex with Fragment. within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca317 b:9.4 occ:1.00 O A:GLU187 2.3 11.3 1.0 OD2 A:ASP138 2.4 10.3 1.0 O A:HOH1470 2.4 10.8 1.0 OE1 A:GLU177 2.5 9.3 1.0 OD1 A:ASP185 2.5 10.6 1.0 OE2 A:GLU190 2.5 11.5 1.0 OE1 A:GLU190 2.5 10.6 1.0 OE2 A:GLU177 2.8 11.9 1.0 CD A:GLU190 2.8 10.2 1.0 CD A:GLU177 2.9 10.6 1.0 C A:GLU187 3.4 9.7 1.0 CG A:ASP138 3.4 10.0 1.0 CG A:ASP185 3.5 10.5 1.0 CA A:CA318 3.8 14.2 1.0 OD2 A:ASP185 3.8 13.0 1.0 CB A:ASP138 4.0 8.4 1.0 O A:ASP185 4.1 10.8 1.0 O A:HOH1600 4.2 20.9 1.0 N A:GLU187 4.2 11.4 1.0 N A:ILE188 4.3 9.7 1.0 CA A:GLU187 4.3 10.8 1.0 OD1 A:ASP138 4.3 13.6 1.0 CA A:ILE188 4.3 9.2 1.0 CG A:GLU190 4.3 11.7 1.0 CG A:GLU177 4.4 10.1 1.0 O A:HOH1444 4.5 15.7 1.0 N A:GLY189 4.5 9.7 1.0 C A:ASP185 4.5 10.4 1.0 CB A:GLU187 4.6 13.0 1.0 N A:ASP185 4.7 11.2 1.0 CB A:ASP185 4.8 11.6 1.0 C A:ILE188 4.8 8.9 1.0 CB A:GLU177 4.9 9.2 1.0 CA A:ASP185 4.9 10.9 1.0 N A:GLU190 5.0 10.0 1.0 O A:HOH1673 5.0 15.8 1.0

Calcium binding site 2 out of 4 in the Drugscore Fp: Thermoylsin in Complex with Fragment.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Drugscore Fp: Thermoylsin in Complex with Fragment. within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca318 b:14.2 occ:1.00 OE2 A:GLU190 2.3 11.5 1.0 O A:HOH1675 2.3 18.7 1.0 O A:HOH1673 2.3 15.8 1.0 O A:ASN183 2.3 13.3 1.0 OD2 A:ASP185 2.4 13.0 1.0 OE2 A:GLU177 2.5 11.9 1.0 CD A:GLU177 3.2 10.6 1.0 CG A:ASP185 3.2 10.5 1.0 CD A:GLU190 3.3 10.2 1.0 C A:ASN183 3.5 12.8 1.0 OD1 A:ASP185 3.6 10.6 1.0 OE1 A:GLU177 3.7 9.3 1.0 CG A:GLU190 3.7 11.7 1.0 CA A:CA317 3.8 9.4 1.0 CA A:PRO184 4.1 11.9 1.0 N A:ASP185 4.1 11.2 1.0 OD2 A:ASP191 4.1 15.3 1.0 CB A:ASN183 4.2 16.8 1.0 C A:PRO184 4.2 12.4 1.0 OD1 A:ASP191 4.2 17.7 1.0 OE1 A:GLU190 4.2 10.6 1.0 CG A:GLU177 4.3 10.1 1.0 N A:PRO184 4.3 11.9 1.0 O A:LYS182 4.4 16.4 1.0 CB A:ASP185 4.4 11.6 1.0 O A:HOH1600 4.4 20.9 1.0 O A:HOH1654 4.4 34.5 1.0 CG A:ASP191 4.4 15.5 1.0 CA A:ASN183 4.5 15.1 1.0 CA A:ASP185 4.9 10.9 1.0 O A:PRO184 4.9 14.4 1.0

Calcium binding site 3 out of 4 in the Drugscore Fp: Thermoylsin in Complex with Fragment.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Drugscore Fp: Thermoylsin in Complex with Fragment. within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca319 b:9.4 occ:1.00 O A:HOH1603 2.3 12.1 1.0 O A:GLN61 2.3 9.4 1.0 OD2 A:ASP57 2.4 9.1 1.0 O A:HOH1436 2.4 12.6 1.0 OD1 A:ASP59 2.4 9.8 1.0 O A:HOH1604 2.4 10.2 1.0 OD1 A:ASP57 2.6 9.5 1.0 CG A:ASP57 2.8 8.8 1.0 CG A:ASP59 3.4 9.9 1.0 C A:GLN61 3.5 7.9 1.0 OD2 A:ASP59 3.8 14.3 1.0 O A:HOH1601 3.9 14.3 1.0 N A:GLN61 3.9 9.1 1.0 CA A:GLN61 4.2 9.4 1.0 N A:ASP59 4.3 10.5 1.0 CB A:ASP57 4.3 10.0 1.0 CB A:GLN61 4.3 11.8 1.0 O A:HOH1602 4.5 18.1 1.0 N A:PHE62 4.6 8.2 1.0 N A:ASN60 4.6 8.9 1.0 OD2 A:ASP67 4.6 8.9 1.0 CB A:ASP59 4.6 9.7 1.0 O A:HOH1414 4.6 9.7 1.0 O A:HOH1616 4.7 26.3 1.0 O A:HOH1563 4.7 29.6 1.0 N A:ALA58 4.7 9.3 1.0 CA A:PHE62 4.8 7.6 1.0 CA A:ASP59 4.8 9.4 1.0 C A:ASP59 4.8 8.7 1.0

Calcium binding site 4 out of 4 in the Drugscore Fp: Thermoylsin in Complex with Fragment.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Drugscore Fp: Thermoylsin in Complex with Fragment. within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca320 b:13.8 occ:1.00 O A:HOH1517 2.3 18.4 1.0 O A:ILE197 2.3 18.0 1.0 O A:TYR193 2.4 13.0 1.0 OG1 A:THR194 2.4 15.5 1.0 O A:HOH1606 2.4 14.8 1.0 OD1 A:ASP200 2.4 14.1 1.0 O A:THR194 2.4 16.2 1.0 C A:THR194 3.2 14.5 1.0 C A:TYR193 3.4 13.1 1.0 CB A:THR194 3.5 14.5 1.0 C A:ILE197 3.5 19.5 1.0 CG A:ASP200 3.5 15.0 1.0 CA A:THR194 3.7 14.4 1.0 OD2 A:ASP200 3.9 15.3 1.0 N A:THR194 3.9 13.4 1.0 CA A:ILE197 4.2 21.2 1.0 N A:PRO195 4.3 16.8 1.0 CB A:ILE197 4.3 21.1 1.0 N A:ILE197 4.3 23.5 1.0 O A:ASP200 4.5 13.8 1.0 N A:SER198 4.5 19.9 1.0 CA A:TYR193 4.5 11.5 1.0 CA A:SER198 4.5 18.7 0.6 N A:ASP200 4.6 14.0 1.0 CB A:TYR193 4.6 12.0 1.0 O A:HOH1605 4.6 31.6 1.0 CD2 A:TYR193 4.6 14.5 1.0 CA A:SER198 4.6 19.1 0.4 CA A:PRO195 4.7 19.8 1.0 O A:GLU190 4.7 12.4 1.0 CG2 A:THR194 4.8 16.4 1.0 CB A:ASP200 4.8 14.1 1.0 CG2 A:ILE197 4.9 23.3 1.0 C A:ASP200 4.9 11.1 1.0 C A:SER198 4.9 18.7 1.0 N A:GLY199 4.9 16.1 1.0 CG A:TYR193 5.0 13.3 1.0 C A:PRO195 5.0 22.6 1.0 CA A:ASP200 5.0 14.2 1.0

P.Pfeffer, G.Neudert, L.Englert, T.Ritschel, B.Baum, G.Klebe. Drugscore Fp: Profiling Protein-Ligand Interactions Using Fingerprint Simplicity Paired with Knowledge-Based Potential Fields To Be Published.