Calcium in PDB 3t8f: Thermolysin in Complex with UBTLN34

All present enzymatic activity of Thermolysin in Complex with UBTLN34:
3.4.24.27;

The structure of Thermolysin in Complex with UBTLN34, PDB code: 3t8f 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)	30.35 / 1.44
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	92.400, 92.400, 131.200, 90.00, 90.00, 120.00
R / Rfree (%)	14.2 / 15.9

The structure of Thermolysin in Complex with UBTLN34 also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Calcium atom in the Thermolysin in Complex with UBTLN34 (pdb code 3t8f). 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 UBTLN34, PDB code: 3t8f:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Thermolysin in Complex with UBTLN34


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 UBTLN34 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca412 b:11.0 occ:1.00 OE2 A:GLU190 2.3 9.7 1.0 O A:HOH684 2.3 13.6 1.0 O A:ASN183 2.3 11.8 1.0 O A:HOH705 2.4 13.3 1.0 OD2 A:ASP185 2.4 10.8 1.0 OE2 A:GLU177 2.4 8.5 1.0 CG A:ASP185 3.2 8.6 1.0 CD A:GLU177 3.2 7.5 1.0 CD A:GLU190 3.3 8.6 1.0 C A:ASN183 3.5 13.4 1.0 OD1 A:ASP185 3.6 9.7 1.0 OE1 A:GLU177 3.7 7.9 1.0 CA A:CA413 3.8 8.2 1.0 CG A:GLU190 3.8 10.4 1.0 CB A:ASN183 4.1 14.2 1.0 CA A:PRO184 4.1 9.4 1.0 N A:ASP185 4.2 9.7 1.0 O A:HOH875 4.2 34.4 1.0 OD2 A:ASP191 4.2 14.2 1.0 CG A:GLU177 4.2 7.9 1.0 OE1 A:GLU190 4.2 8.5 1.0 OD1 A:ASP191 4.3 12.2 1.0 C A:PRO184 4.3 12.4 1.0 N A:PRO184 4.3 10.1 1.0 CB A:ASP185 4.4 8.5 1.0 O A:LYS182 4.4 14.0 1.0 CA A:ASN183 4.5 15.1 1.0 CG A:ASP191 4.6 12.2 1.0 O A:HOH851 4.6 31.6 1.0 CA A:ASP185 4.9 8.8 1.0 O A:PRO184 5.0 12.7 1.0

Calcium binding site 2 out of 4 in the Thermolysin in Complex with UBTLN34


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 UBTLN34 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca413 b:8.2 occ:1.00 O A:GLU187 2.4 7.8 1.0 OD2 A:ASP138 2.4 7.6 1.0 O A:HOH522 2.4 8.4 1.0 OE1 A:GLU177 2.4 7.9 1.0 OD1 A:ASP185 2.4 9.7 1.0 OE1 A:GLU190 2.5 8.5 1.0 OE2 A:GLU190 2.5 9.7 1.0 OE2 A:GLU177 2.7 8.5 1.0 CD A:GLU190 2.8 8.6 1.0 CD A:GLU177 2.9 7.5 1.0 CG A:ASP138 3.4 7.5 1.0 C A:GLU187 3.4 7.9 1.0 CG A:ASP185 3.5 8.6 1.0 CA A:CA412 3.8 11.0 1.0 OD2 A:ASP185 3.8 10.8 1.0 CB A:ASP138 4.0 6.8 1.0 O A:ASP185 4.1 8.3 1.0 N A:GLU187 4.2 8.6 1.0 OD1 A:ASP138 4.2 9.6 1.0 N A:ILE188 4.3 6.2 1.0 CA A:GLU187 4.3 9.1 1.0 CA A:ILE188 4.3 6.8 1.0 CG A:GLU190 4.3 10.4 1.0 CG A:GLU177 4.4 7.9 1.0 N A:GLY189 4.4 7.9 1.0 O A:HOH717 4.4 12.1 1.0 CB A:GLU187 4.6 10.1 1.0 C A:ASP185 4.6 8.0 1.0 N A:ASP185 4.7 9.7 1.0 CB A:ASP185 4.8 8.5 1.0 C A:ILE188 4.8 8.0 1.0 CB A:GLU177 4.9 8.2 1.0 O A:HOH705 4.9 13.3 1.0 N A:GLU190 5.0 8.3 1.0 CA A:ASP185 5.0 8.8 1.0

Calcium binding site 3 out of 4 in the Thermolysin in Complex with UBTLN34


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 UBTLN34 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca414 b:11.1 occ:1.00 O A:ILE197 2.2 12.8 1.0 O A:TYR193 2.3 11.0 1.0 O A:THR194 2.4 12.1 1.0 OD1 A:ASP200 2.4 11.0 1.0 OG1 A:THR194 2.4 10.9 1.0 O A:HOH682 2.4 11.9 1.0 O A:HOH725 2.5 17.0 1.0 C A:THR194 3.2 10.8 1.0 C A:TYR193 3.3 8.7 1.0 C A:ILE197 3.4 15.2 1.0 CG A:ASP200 3.5 11.3 1.0 CB A:THR194 3.5 10.8 1.0 CA A:THR194 3.6 10.6 1.0 OD2 A:ASP200 3.8 13.4 1.0 N A:THR194 3.9 9.3 1.0 CA A:ILE197 4.2 16.1 1.0 CB A:ILE197 4.2 18.5 1.0 N A:PRO195 4.3 12.3 1.0 N A:ILE197 4.3 17.8 1.0 N A:SER198 4.5 17.3 1.0 O A:ASP200 4.5 11.3 1.0 O A:HOH546 4.5 32.8 1.0 CA A:TYR193 4.5 10.0 1.0 CD2 A:TYR193 4.6 11.8 1.0 N A:ASP200 4.6 12.5 1.0 O A:GLU190 4.6 10.1 1.0 O A:HOH864 4.6 23.0 1.0 CA A:SER198 4.6 19.4 1.0 CA A:PRO195 4.7 13.3 1.0 CB A:TYR193 4.7 10.1 1.0 O A:HOH503 4.7 39.7 1.0 CG2 A:THR194 4.7 10.8 1.0 CB A:ASP200 4.8 11.3 1.0 C A:ASP200 4.8 10.6 1.0 CG2 A:ILE197 4.9 17.6 1.0 CA A:ASP200 4.9 11.3 1.0 C A:PRO195 5.0 17.6 1.0 C A:SER198 5.0 15.3 1.0 N A:GLY199 5.0 13.8 1.0

Calcium binding site 4 out of 4 in the Thermolysin in Complex with UBTLN34


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 UBTLN34 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca415 b:8.6 occ:1.00 O A:GLN61 2.3 8.7 1.0 O A:HOH663 2.3 10.6 1.0 OD1 A:ASP59 2.4 9.1 1.0 OD1 A:ASP57 2.4 9.7 1.0 O A:HOH683 2.4 11.5 1.0 O A:HOH636 2.4 10.0 1.0 OD2 A:ASP57 2.6 8.5 1.0 CG A:ASP57 2.8 9.4 1.0 CG A:ASP59 3.4 10.4 1.0 C A:GLN61 3.4 7.6 1.0 OD2 A:ASP59 3.8 12.9 1.0 N A:GLN61 3.9 8.6 1.0 O A:HOH745 4.0 16.4 1.0 CA A:GLN61 4.1 7.2 1.0 N A:ASP59 4.3 8.6 1.0 CB A:GLN61 4.3 9.5 1.0 CB A:ASP57 4.3 8.9 1.0 N A:PHE62 4.5 7.8 1.0 O A:HOH740 4.6 16.1 1.0 CB A:ASP59 4.6 7.6 1.0 OD2 A:ASP67 4.6 9.3 1.0 O A:HOH595 4.6 8.6 1.0 N A:ASN60 4.6 7.6 1.0 O A:HOH879 4.7 24.2 1.0 N A:ALA58 4.7 8.4 1.0 CA A:PHE62 4.7 8.1 1.0 CA A:ASP59 4.8 8.9 1.0 C A:ASP59 4.9 8.9 1.0

A.Biela, M.Betz, A.Heine, G.Klebe. Water Makes the Difference: Rearrangement of Water Solvation Layer Triggers Non-Additivity of Functional Group Contributions in Protein-Ligand Binding. Chemmedchem V. 7 1423 2012.
ISSN: ISSN 1860-7179
PubMed: 22733601
DOI: 10.1002/CMDC.201200206