Calcium in PDB 4d9w: Thermolysin in Complex with UBTLN32

All present enzymatic activity of Thermolysin in Complex with UBTLN32:
3.4.24.27;

The structure of Thermolysin in Complex with UBTLN32, PDB code: 4d9w was solved by A.Biela, A.Heine, G.Klebe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	22.30 / 1.38
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	93.100, 93.100, 130.900, 90.00, 90.00, 120.00
R / Rfree (%)	10.9 / 14

The structure of Thermolysin in Complex with UBTLN32 also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Calcium atom in the Thermolysin in Complex with UBTLN32 (pdb code 4d9w). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Thermolysin in Complex with UBTLN32, PDB code: 4d9w:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Thermolysin in Complex with UBTLN32


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Thermolysin in Complex with UBTLN32 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca409 b:8.4 occ:1.00 OD2 A:ASP138 2.3 8.0 1.0 O A:GLU187 2.3 8.6 1.0 O A:HOH792 2.4 9.0 1.0 OD1 A:ASP185 2.5 9.5 1.0 OE1 A:GLU190 2.5 8.8 1.0 OE1 A:GLU177 2.5 9.0 1.0 OE2 A:GLU190 2.5 9.5 1.0 OE2 A:GLU177 2.7 9.1 1.0 CD A:GLU190 2.8 9.0 1.0 CD A:GLU177 2.9 8.3 1.0 CG A:ASP138 3.4 7.8 1.0 C A:GLU187 3.4 9.6 1.0 CG A:ASP185 3.5 10.2 1.0 HB3 A:ASP138 3.6 8.6 1.0 HA A:ILE188 3.6 10.1 1.0 H A:GLU187 3.7 12.7 1.0 H A:GLY189 3.8 11.2 1.0 CA A:CA410 3.8 10.9 1.0 OD2 A:ASP185 3.8 11.7 1.0 HB2 A:GLU187 3.9 14.4 1.0 CB A:ASP138 4.0 7.2 1.0 O A:ASP185 4.1 9.4 1.0 H A:ASP185 4.2 11.7 1.0 H A:GLU190 4.2 10.9 1.0 N A:GLU187 4.2 10.6 1.0 N A:ILE188 4.3 8.8 1.0 O A:HOH633 4.3 23.4 1.0 HB2 A:ASP138 4.3 8.6 1.0 OD1 A:ASP138 4.3 9.9 1.0 CA A:GLU187 4.3 10.9 1.0 CA A:ILE188 4.3 8.4 1.0 HD13 A:ILE188 4.3 13.4 1.0 CG A:GLU190 4.3 9.6 1.0 CG A:GLU177 4.4 8.4 1.0 N A:GLY189 4.4 9.3 1.0 O A:HOH539 4.4 14.9 1.0 CB A:GLU187 4.6 12.0 1.0 HG3 A:GLU190 4.6 11.6 1.0 C A:ASP185 4.6 9.4 1.0 HB2 A:GLU177 4.7 10.2 1.0 HB3 A:GLU177 4.7 10.2 1.0 N A:ASP185 4.8 9.8 1.0 C A:ILE188 4.8 9.4 1.0 CB A:ASP185 4.8 10.0 1.0 HG2 A:GLU190 4.8 11.6 1.0 HG2 A:GLU177 4.8 10.1 1.0 HA A:THR174 4.9 8.0 1.0 CB A:GLU177 4.9 8.5 1.0 HG3 A:GLU177 4.9 10.1 1.0 O A:HOH798 4.9 13.2 1.0 HB3 A:GLU190 5.0 11.9 1.0 N A:GLU190 5.0 9.1 1.0

Calcium binding site 2 out of 4 in the Thermolysin in Complex with UBTLN32


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Thermolysin in Complex with UBTLN32 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca410 b:10.9 occ:1.00 O A:ASN183 2.3 12.5 1.0 OE2 A:GLU190 2.3 9.5 1.0 OD2 A:ASP185 2.4 11.7 1.0 O A:HOH798 2.4 13.2 1.0 O A:HOH797 2.4 12.4 1.0 OE2 A:GLU177 2.4 9.1 1.0 CG A:ASP185 3.2 10.2 1.0 CD A:GLU177 3.2 8.3 1.0 CD A:GLU190 3.3 9.0 1.0 C A:ASN183 3.5 13.2 1.0 HA A:PRO184 3.5 13.9 1.0 HG3 A:GLU190 3.6 11.6 1.0 OD1 A:ASP185 3.6 9.5 1.0 OE1 A:GLU177 3.7 9.0 1.0 HB2 A:ASN183 3.7 21.0 1.0 HG2 A:GLU190 3.8 11.6 1.0 HB3 A:ASN183 3.8 21.0 1.0 CG A:GLU190 3.8 9.6 1.0 CA A:CA409 3.8 8.4 1.0 H A:ASP185 4.0 11.7 1.0 CA A:PRO184 4.1 11.6 1.0 N A:ASP185 4.1 9.8 1.0 CB A:ASN183 4.1 17.5 1.0 O A:HOH733 4.2 30.7 1.0 OD2 A:ASP191 4.2 13.5 1.0 C A:PRO184 4.2 11.7 1.0 OD1 A:ASP191 4.3 13.8 1.0 OE1 A:GLU190 4.3 8.8 1.0 CG A:GLU177 4.3 8.4 1.0 HG2 A:GLU177 4.3 10.1 1.0 N A:PRO184 4.3 12.0 1.0 O A:LYS182 4.3 15.3 1.0 HG3 A:GLU177 4.4 10.1 1.0 HB3 A:ASP185 4.4 12.0 1.0 CB A:ASP185 4.4 10.0 1.0 CA A:ASN183 4.5 15.6 1.0 O A:HOH633 4.5 23.4 1.0 CG A:ASP191 4.5 12.5 1.0 O A:HOH770 4.6 31.2 1.0 CA A:ASP185 4.9 9.9 1.0 O A:PRO184 4.9 13.2 1.0

Calcium binding site 3 out of 4 in the Thermolysin in Complex with UBTLN32


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Thermolysin in Complex with UBTLN32 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca411 b:12.9 occ:1.00 O A:ILE197 2.3 16.2 1.0 OG1 A:THR194 2.3 12.8 1.0 O A:TYR193 2.3 12.2 1.0 O A:THR194 2.4 13.4 1.0 OD1 A:ASP200 2.4 12.9 1.0 O A:HOH795 2.4 13.3 1.0 O A:HOH799 2.4 16.8 1.0 C A:THR194 3.2 13.2 1.0 C A:TYR193 3.3 12.0 1.0 CB A:THR194 3.4 13.0 1.0 CG A:ASP200 3.5 14.2 1.0 HB A:ILE197 3.5 24.6 1.0 C A:ILE197 3.5 17.8 1.0 CA A:THR194 3.6 12.3 1.0 H A:ILE197 3.7 23.2 1.0 HB A:THR194 3.7 15.6 1.0 OD2 A:ASP200 3.8 15.6 1.0 N A:THR194 3.9 11.8 1.0 H A:ASP200 3.9 18.8 1.0 HD2 A:TYR193 4.0 15.4 1.0 HB3 A:TYR193 4.1 14.0 1.0 HA A:SER198 4.1 25.1 0.3 HA A:SER198 4.1 25.4 0.7 CB A:ILE197 4.2 20.5 1.0 CA A:ILE197 4.2 18.6 1.0 N A:PRO195 4.3 15.2 1.0 HA A:PRO195 4.3 19.9 1.0 N A:ILE197 4.3 19.4 1.0 HG22 A:ILE197 4.4 23.9 1.0 O A:HOH898 4.4 34.4 1.0 O A:ASP200 4.5 13.4 1.0 N A:SER198 4.5 19.7 1.0 CA A:TYR193 4.6 11.2 1.0 HA A:THR194 4.6 14.7 1.0 CD2 A:TYR193 4.6 12.8 1.0 O A:GLU190 4.6 11.0 1.0 O A:HOH671 4.7 28.4 1.0 CA A:SER198 4.7 21.0 0.3 CA A:PRO195 4.7 16.6 1.0 N A:ASP200 4.7 15.6 1.0 CA A:SER198 4.7 21.2 0.7 CB A:TYR193 4.7 11.6 1.0 CG2 A:THR194 4.7 13.1 1.0 H A:THR194 4.7 14.2 1.0 H A:GLY199 4.8 22.6 1.0 CB A:ASP200 4.8 14.7 1.0 C A:ASP200 4.8 13.3 1.0 HG23 A:THR194 4.8 15.8 1.0 CG2 A:ILE197 4.9 19.9 1.0 H A:TYR193 4.9 12.6 1.0 HG21 A:THR194 5.0 15.8 1.0 C A:PRO195 5.0 18.6 1.0 C A:SER198 5.0 20.8 1.0 CA A:ASP200 5.0 14.6 1.0

Calcium binding site 4 out of 4 in the Thermolysin in Complex with UBTLN32


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Thermolysin in Complex with UBTLN32 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca412 b:9.2 occ:1.00 O A:GLN61 2.3 9.0 1.0 O A:HOH794 2.3 12.1 1.0 OD1 A:ASP59 2.3 9.4 1.0 O A:HOH796 2.4 11.2 1.0 OD1 A:ASP57 2.4 9.3 1.0 O A:HOH793 2.4 10.6 1.0 OD2 A:ASP57 2.5 9.0 1.0 CG A:ASP57 2.8 8.7 1.0 H A:GLN61 3.3 11.3 0.6 H A:GLN61 3.3 11.3 0.4 CG A:ASP59 3.4 10.6 1.0 C A:GLN61 3.5 8.8 1.0 H A:ASP59 3.6 11.0 1.0 HB2 A:GLN61 3.6 13.7 0.4 HB2 A:GLN61 3.6 13.0 0.6 OD2 A:ASP59 3.8 13.0 1.0 N A:GLN61 3.9 9.5 1.0 O A:HOH562 4.0 15.4 1.0 HA A:PHE62 4.0 9.7 1.0 CA A:GLN61 4.1 9.6 0.4 CA A:GLN61 4.1 9.3 0.6 H A:ASN60 4.3 10.5 1.0 CB A:ASP57 4.3 7.9 1.0 CB A:GLN61 4.3 11.4 0.4 CB A:GLN61 4.3 10.9 0.6 N A:ASP59 4.3 9.2 1.0 H A:ALA58 4.4 10.3 1.0 O A:HOH538 4.5 13.8 1.0 N A:PHE62 4.5 8.1 1.0 CB A:ASP59 4.6 10.0 1.0 O A:HOH664 4.6 20.6 1.0 N A:ASN60 4.6 8.8 1.0 O A:HOH507 4.6 8.8 1.0 OD2 A:ASP67 4.7 9.3 1.0 HB2 A:ASP57 4.7 9.5 1.0 O A:HOH674 4.7 25.6 1.0 HB3 A:ASP57 4.7 9.5 1.0 CA A:PHE62 4.8 8.1 1.0 CA A:ASP59 4.8 9.5 1.0 N A:ALA58 4.8 8.6 1.0 HB3 A:GLN61 4.8 13.7 0.4 H A:PHE63 4.8 10.8 1.0 HA A:ASP57 4.9 9.6 1.0 C A:ASP59 4.9 9.3 1.0 HB3 A:ASP59 4.9 11.9 1.0 HB3 A:GLN61 5.0 13.0 0.6 HG2 A:GLN61 5.0 17.4 0.6

A.Biela, N.Nasief, A.Heine, D.Hangauer, G.Klebe. Thermolysin Inhibition To Be Published.