Calcium in PDB 2tlx: Thermolysin (Native)

All present enzymatic activity of Thermolysin (Native):
3.4.24.27;

The structure of Thermolysin (Native), PDB code: 2tlx was solved by A.C.English, S.H.Done, C.R.Groom, R.E.Hubbard, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.65
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	94.145, 94.145, 131.616, 90.00, 90.00, 120.00
R / Rfree (%)	16.3 / 18.7

The structure of Thermolysin (Native) also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

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

Calcium binding site 1 out of 4 in the Thermolysin (Native)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Thermolysin (Native) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca323 b:11.2 occ:1.00 OD2 A:ASP138 2.5 12.0 1.0 O A:GLU187 2.5 13.3 1.0 O A:HOH340 2.5 14.9 1.0 OE1 A:GLU177 2.5 11.7 1.0 OD1 A:ASP185 2.6 14.7 1.0 OE1 A:GLU190 2.6 12.4 1.0 OE2 A:GLU190 2.6 17.2 1.0 OE2 A:GLU177 2.8 15.0 1.0 CD A:GLU190 3.0 16.9 1.0 CD A:GLU177 3.1 14.2 1.0 CG A:ASP138 3.5 14.6 1.0 C A:GLU187 3.6 11.8 1.0 CG A:ASP185 3.6 21.2 1.0 CA A:CA324 3.8 13.9 1.0 OD2 A:ASP185 3.9 16.7 1.0 CB A:ASP138 4.1 10.6 1.0 O A:ASP185 4.2 15.9 1.0 O A:HOH469 4.2 33.7 1.0 N A:GLU187 4.2 13.4 1.0 OD1 A:ASP138 4.3 14.6 1.0 CA A:ILE188 4.4 11.4 1.0 CA A:GLU187 4.4 12.8 1.0 N A:ILE188 4.4 11.9 1.0 CG A:GLU190 4.5 13.9 1.0 N A:GLY189 4.5 12.2 1.0 CG A:GLU177 4.5 11.8 1.0 O A:HOH355 4.6 19.4 1.0 CB A:GLU187 4.7 16.6 1.0 C A:ASP185 4.7 13.6 1.0 N A:ASP185 4.8 12.6 1.0 C A:ILE188 4.8 11.4 1.0 CB A:ASP185 4.9 13.8 1.0 O A:HOH356 4.9 25.0 1.0 N A:GLU190 4.9 11.5 1.0 CB A:GLU177 5.0 10.8 1.0

Calcium binding site 2 out of 4 in the Thermolysin (Native)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Thermolysin (Native) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca324 b:13.9 occ:1.00 O A:HOH356 2.4 25.0 1.0 O A:HOH339 2.4 24.7 1.0 OE2 A:GLU177 2.5 15.0 1.0 OD2 A:ASP185 2.5 16.7 1.0 OE2 A:GLU190 2.5 17.2 1.0 O A:ASN183 2.6 19.8 1.0 CG A:ASP185 3.3 21.2 1.0 CD A:GLU177 3.4 14.2 1.0 CD A:GLU190 3.5 16.9 1.0 OD1 A:ASP185 3.6 14.7 1.0 C A:ASN183 3.7 20.1 1.0 CA A:CA323 3.8 11.2 1.0 OE1 A:GLU177 3.9 11.7 1.0 O A:LYS182 3.9 26.4 1.0 CG A:GLU190 3.9 13.9 1.0 O A:HOH485 4.0 41.6 1.0 N A:ASP185 4.2 12.6 1.0 CB A:ASN183 4.2 23.6 1.0 CA A:PRO184 4.2 16.2 1.0 OD2 A:ASP191 4.3 19.6 1.0 C A:PRO184 4.3 18.7 1.0 OD1 A:ASP191 4.3 17.6 1.0 CG A:GLU177 4.3 11.8 1.0 OE1 A:GLU190 4.3 12.4 1.0 N A:PRO184 4.4 18.6 1.0 O A:HOH469 4.5 33.7 1.0 CB A:ASP185 4.5 13.8 1.0 CA A:ASN183 4.6 19.3 1.0 CG A:ASP191 4.7 19.7 1.0 C A:LYS182 5.0 23.7 1.0 CA A:ASP185 5.0 13.0 1.0 O A:PRO184 5.0 20.6 1.0

Calcium binding site 3 out of 4 in the Thermolysin (Native)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Thermolysin (Native) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca325 b:12.4 occ:1.00 O A:HOH342 2.4 23.4 1.0 O A:HOH353 2.4 16.2 1.0 O A:GLN61 2.4 14.5 1.0 OD1 A:ASP57 2.5 13.9 1.0 OD1 A:ASP59 2.5 15.7 1.0 O A:HOH373 2.5 25.4 1.0 OD2 A:ASP57 2.7 14.8 1.0 CG A:ASP57 3.0 14.5 1.0 CG A:ASP59 3.6 20.7 1.0 C A:GLN61 3.6 13.4 1.0 OD2 A:ASP59 3.8 19.6 1.0 O A:HOH378 4.0 26.0 1.0 N A:GLN61 4.0 12.2 1.0 CA A:GLN61 4.2 11.5 1.0 N A:ASP59 4.3 14.1 1.0 O A:HOH426 4.4 59.3 1.0 CB A:GLN61 4.4 16.0 1.0 CB A:ASP57 4.5 10.1 1.0 O A:HOH335 4.6 13.0 1.0 N A:PHE62 4.6 11.6 1.0 O A:HOH370 4.6 19.8 1.0 N A:ASN60 4.7 11.3 1.0 OD2 A:ASP67 4.7 12.4 1.0 CB A:ASP59 4.7 14.5 1.0 CA A:PHE62 4.7 12.7 1.0 N A:ALA58 4.8 11.9 1.0 CA A:ASP59 4.9 13.3 1.0 C A:ASP59 4.9 13.0 1.0

Calcium binding site 4 out of 4 in the Thermolysin (Native)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Thermolysin (Native) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca326 b:17.4 occ:1.00 O A:HOH391 2.4 22.6 1.0 O A:HOH364 2.4 58.5 1.0 O A:ILE197 2.5 27.0 1.0 O A:TYR193 2.5 16.3 1.0 OD1 A:ASP200 2.6 18.0 1.0 O A:THR194 2.6 21.1 1.0 OG1 A:THR194 2.6 18.9 1.0 C A:THR194 3.4 21.3 1.0 C A:TYR193 3.6 17.1 1.0 CG A:ASP200 3.6 18.6 1.0 C A:ILE197 3.6 32.0 1.0 CB A:THR194 3.7 21.6 1.0 CA A:THR194 3.8 20.7 1.0 OD2 A:ASP200 3.9 21.7 1.0 N A:THR194 4.0 18.5 1.0 CB A:ILE197 4.2 34.4 1.0 CA A:ILE197 4.2 31.4 1.0 N A:ILE197 4.3 34.7 1.0 N A:PRO195 4.4 22.8 1.0 O A:ASP200 4.5 19.3 1.0 N A:SER198 4.6 31.8 1.0 N A:ASP200 4.6 21.6 1.0 O A:GLU190 4.6 15.5 1.0 CA A:SER198 4.6 33.3 1.0 CG2 A:ILE197 4.7 28.1 1.0 CA A:TYR193 4.7 14.9 1.0 CD2 A:TYR193 4.7 22.4 1.0 O A:HOH432 4.8 35.0 1.0 CB A:TYR193 4.8 16.3 1.0 CA A:PRO195 4.8 26.4 1.0 C A:ASP200 4.9 16.5 1.0 CB A:ASP200 4.9 18.9 1.0 CG2 A:THR194 4.9 19.0 1.0 C A:SER198 5.0 31.7 1.0

A.C.English, S.H.Done, L.S.Caves, C.R.Groom, R.E.Hubbard. Locating Interaction Sites on Proteins: the Crystal Structure of Thermolysin Soaked in 2% to 100% Isopropanol. Proteins V. 37 628 1999.
ISSN: ISSN 0887-3585
PubMed: 10651278
DOI: 10.1002/(SICI)1097-0134(19991201)37:4<628::AID-PROT13>3.3.CO;2-7