Calcium in PDB 1tlx: Thermolysin (Native)

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

The structure of Thermolysin (Native), PDB code: 1tlx 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 / 2.10
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	93.910, 93.910, 131.170, 90.00, 90.00, 120.00
R / Rfree (%)	15.3 / 21.4

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 1tlx). 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: 1tlx:
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:Ca402 b:22.6 occ:1.00 O A:HOH1014 2.6 20.0 1.0 O A:GLU187 2.6 15.4 1.0 OD2 A:ASP138 2.6 17.7 1.0 OE1 A:GLU177 2.7 20.0 1.0 OE1 A:GLU190 2.7 16.8 1.0 OE2 A:GLU190 2.7 15.8 1.0 OD1 A:ASP185 2.7 21.1 1.0 OE2 A:GLU177 3.0 18.5 1.0 CD A:GLU190 3.1 28.9 1.0 CD A:GLU177 3.2 23.0 1.0 CG A:ASP138 3.5 22.0 1.0 CG A:ASP185 3.6 28.1 1.0 C A:GLU187 3.7 22.5 1.0 CA A:CA403 3.8 25.1 1.0 OD2 A:ASP185 3.8 16.7 1.0 CB A:ASP138 4.0 17.1 1.0 N A:GLU187 4.2 21.6 1.0 O A:ASP185 4.2 23.6 1.0 CA A:ILE188 4.3 19.0 1.0 OD1 A:ASP138 4.4 19.9 1.0 N A:ILE188 4.4 20.7 1.0 CA A:GLU187 4.4 23.5 1.0 N A:GLY189 4.5 21.2 1.0 CG A:GLU190 4.6 16.2 1.0 CB A:GLU187 4.6 23.8 1.0 O A:HOH1029 4.6 21.6 1.0 CG A:GLU177 4.7 17.0 1.0 C A:ASP185 4.7 21.0 1.0 C A:ILE188 4.8 20.5 1.0 N A:ASP185 4.8 21.8 1.0 N A:GLU190 4.9 16.3 1.0 CB A:ASP185 5.0 18.6 1.0 CB A:GLU177 5.0 21.1 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:Ca403 b:25.1 occ:1.00 O A:HOH1013 2.4 21.8 1.0 OD2 A:ASP185 2.5 16.7 1.0 OE2 A:GLU177 2.6 18.5 1.0 OE2 A:GLU190 2.6 15.8 1.0 O A:ASN183 2.6 22.3 1.0 O A:HOH1030 2.6 23.1 1.0 CD A:GLU177 3.3 23.0 1.0 CG A:ASP185 3.4 28.1 1.0 CD A:GLU190 3.5 28.9 1.0 CA A:CA402 3.8 22.6 1.0 C A:ASN183 3.8 29.1 1.0 OD1 A:ASP185 3.8 21.1 1.0 OE1 A:GLU177 3.8 20.0 1.0 O A:LYS182 3.9 28.8 1.0 CG A:GLU190 4.0 16.2 1.0 N A:ASP185 4.1 21.8 1.0 C A:PRO184 4.3 28.3 1.0 CA A:PRO184 4.3 26.0 1.0 OD2 A:ASP191 4.3 25.0 1.0 OE1 A:GLU190 4.3 16.8 1.0 OD1 A:ASP191 4.4 24.0 1.0 CG A:GLU177 4.4 17.0 1.0 CB A:ASN183 4.4 33.6 1.0 N A:PRO184 4.5 28.1 1.0 CB A:ASP185 4.5 18.6 1.0 CG A:ASP191 4.7 22.6 1.0 CA A:ASN183 4.7 25.8 1.0 O A:PRO184 4.9 27.2 1.0 CA A:ASP185 4.9 20.2 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:Ca404 b:25.2 occ:1.00 O A:HOH1016 2.4 22.1 1.0 O A:GLN61 2.5 18.6 1.0 OD1 A:ASP59 2.6 21.6 1.0 OD2 A:ASP57 2.7 17.8 1.0 O A:HOH1047 2.7 23.6 1.0 OD1 A:ASP57 2.7 17.8 1.0 O A:HOH1027 2.7 19.6 1.0 CG A:ASP57 3.1 27.2 1.0 CG A:ASP59 3.6 31.1 1.0 C A:GLN61 3.6 28.8 1.0 OD2 A:ASP59 3.7 24.4 1.0 O A:HOH1052 3.8 37.3 1.0 N A:GLN61 4.0 21.0 1.0 CA A:GLN61 4.3 28.8 1.0 N A:ASP59 4.3 21.5 1.0 CB A:GLN61 4.4 27.1 1.0 CB A:ASP57 4.6 18.7 1.0 N A:ASN60 4.6 22.5 1.0 CA A:PHE62 4.7 19.8 1.0 O A:HOH1101 4.7 50.4 1.0 OD2 A:ASP67 4.7 19.5 1.0 N A:PHE62 4.7 22.7 1.0 O A:HOH1044 4.7 29.6 1.0 O A:HOH1009 4.8 18.3 1.0 CB A:ASP59 4.8 17.9 1.0 N A:ALA58 4.8 17.9 1.0 CA A:ASP59 4.9 21.9 1.0 C A:ASP59 4.9 22.9 1.0 C A:ASN60 5.0 19.6 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:Ca405 b:32.0 occ:1.00 OD1 A:ASP200 2.6 26.8 1.0 O A:TYR193 2.7 19.6 1.0 O A:THR194 2.7 23.0 1.0 O A:ILE197 2.7 35.1 1.0 OG1 A:THR194 2.7 27.6 1.0 O A:HOH1065 2.7 28.2 1.0 O A:HOH1038 2.8 37.3 1.0 C A:THR194 3.4 27.2 1.0 CG A:ASP200 3.6 26.5 1.0 C A:TYR193 3.6 25.3 1.0 OD2 A:ASP200 3.7 24.9 1.0 CB A:THR194 3.7 30.9 1.0 CA A:THR194 3.8 22.8 1.0 C A:ILE197 3.9 41.9 1.0 N A:THR194 4.0 23.8 1.0 N A:ILE197 4.2 46.0 1.0 CB A:ILE197 4.2 43.6 1.0 CA A:ILE197 4.3 43.2 1.0 N A:PRO195 4.4 27.7 1.0 O A:ASP200 4.5 24.9 1.0 N A:ASP200 4.6 27.8 1.0 CA A:SER198 4.7 40.4 1.0 CD2 A:TYR193 4.7 26.9 1.0 CA A:TYR193 4.7 23.5 1.0 O A:GLU190 4.8 22.2 1.0 N A:SER198 4.8 39.1 1.0 C A:ASP200 4.8 23.9 1.0 CA A:PRO195 4.8 33.6 1.0 CB A:TYR193 4.8 23.4 1.0 CB A:ASP200 4.8 21.5 1.0 CG2 A:THR194 4.9 23.4 1.0 C A:SER198 4.9 36.5 1.0 CG2 A:ILE197 5.0 32.4 1.0 O A:HOH1107 5.0 48.1 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