Calcium in PDB 5tli: Thermolysin (60% Isopropanol Soaked Crystals)

All present enzymatic activity of Thermolysin (60% Isopropanol Soaked Crystals):
3.4.24.27;

The structure of Thermolysin (60% Isopropanol Soaked Crystals), PDB code: 5tli 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)	30.00 / 2.10
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	94.230, 94.230, 131.030, 90.00, 90.00, 120.00
R / Rfree (%)	15.7 / 19.2

The structure of Thermolysin (60% Isopropanol Soaked Crystals) also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Calcium atom in the Thermolysin (60% Isopropanol Soaked Crystals) (pdb code 5tli). 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 (60% Isopropanol Soaked Crystals), PDB code: 5tli:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Thermolysin (60% Isopropanol Soaked Crystals)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Thermolysin (60% Isopropanol Soaked Crystals) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca318 b:21.9 occ:1.00 O A:GLU187 2.6 16.9 1.0 OD2 A:ASP138 2.6 18.3 1.0 O A:HOH1014 2.6 18.2 1.0 OE1 A:GLU177 2.6 18.6 1.0 OE2 A:GLU190 2.7 16.1 1.0 OD1 A:ASP185 2.7 21.8 1.0 OE1 A:GLU190 2.7 17.7 1.0 OE2 A:GLU177 2.9 17.1 1.0 CD A:GLU190 3.2 28.2 1.0 CD A:GLU177 3.2 22.9 1.0 CG A:ASP138 3.5 22.8 1.0 CG A:ASP185 3.6 29.6 1.0 C A:GLU187 3.6 21.5 1.0 CA A:CA319 3.8 22.8 1.0 OD2 A:ASP185 3.8 20.6 1.0 CB A:ASP138 4.0 16.9 1.0 N A:GLU187 4.2 18.7 1.0 O A:ASP185 4.2 22.2 1.0 CA A:ILE188 4.3 15.3 1.0 N A:ILE188 4.3 17.9 1.0 OD1 A:ASP138 4.4 18.9 1.0 CA A:GLU187 4.4 22.3 1.0 N A:GLY189 4.4 14.5 1.0 O A:HOH1126 4.4 45.0 1.0 CB A:GLU187 4.6 21.8 1.0 CG A:GLU177 4.6 15.7 1.0 CG A:GLU190 4.6 16.5 1.0 O A:HOH1029 4.6 20.9 1.0 C A:ASP185 4.7 22.6 1.0 N A:ASP185 4.8 21.7 1.0 C A:ILE188 4.8 18.9 1.0 O A:HOH1030 4.9 22.2 1.0 CB A:ASP185 5.0 17.0 1.0 N A:GLU190 5.0 15.3 1.0 CB A:GLU177 5.0 17.6 1.0

Calcium binding site 2 out of 4 in the Thermolysin (60% Isopropanol Soaked Crystals)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Thermolysin (60% Isopropanol Soaked Crystals) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca319 b:22.8 occ:1.00 O A:HOH1030 2.4 22.2 1.0 O A:HOH1013 2.5 19.8 1.0 OE2 A:GLU190 2.6 16.1 1.0 OE2 A:GLU177 2.6 17.1 1.0 O A:ASN183 2.6 19.8 1.0 OD2 A:ASP185 2.6 20.6 1.0 CD A:GLU177 3.3 22.9 1.0 CG A:ASP185 3.4 29.6 1.0 CD A:GLU190 3.5 28.2 1.0 C A:ASN183 3.7 26.4 1.0 OE1 A:GLU177 3.8 18.6 1.0 CA A:CA318 3.8 21.9 1.0 OD1 A:ASP185 3.8 21.8 1.0 O A:LYS182 3.8 30.9 1.0 CG A:GLU190 4.1 16.5 1.0 N A:ASP185 4.1 21.7 1.0 CA A:PRO184 4.2 22.7 1.0 OD2 A:ASP191 4.2 20.3 1.0 C A:PRO184 4.2 24.9 1.0 OD1 A:ASP191 4.3 24.2 1.0 CB A:ASN183 4.3 39.3 1.0 CG A:GLU177 4.4 15.7 1.0 OE1 A:GLU190 4.4 17.7 1.0 N A:PRO184 4.4 26.6 1.0 CB A:ASP185 4.5 17.0 1.0 CG A:ASP191 4.6 22.1 1.0 CA A:ASN183 4.7 26.9 1.0 O A:HOH1126 4.7 45.0 1.0 CA A:ASP185 4.9 20.2 1.0 O A:PRO184 4.9 22.6 1.0 C A:LYS182 5.0 30.0 1.0

Calcium binding site 3 out of 4 in the Thermolysin (60% Isopropanol Soaked Crystals)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Thermolysin (60% Isopropanol Soaked Crystals) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca320 b:24.1 occ:1.00 O A:HOH1016 2.5 28.6 1.0 OD1 A:ASP59 2.6 20.9 1.0 O A:GLN61 2.6 16.2 1.0 OD1 A:ASP57 2.6 16.4 1.0 O A:HOH1047 2.7 21.4 1.0 OD2 A:ASP57 2.7 20.4 1.0 O A:HOH1027 2.8 19.9 1.0 CG A:ASP57 3.1 25.4 1.0 CG A:ASP59 3.5 29.1 1.0 OD2 A:ASP59 3.7 26.4 1.0 C A:GLN61 3.7 25.0 1.0 O A:HOH1052 3.8 39.4 1.0 N A:GLN61 3.8 17.1 1.0 CA A:GLN61 4.2 24.6 1.0 N A:ASP59 4.2 20.2 1.0 CB A:GLN61 4.5 23.1 1.0 N A:ASN60 4.6 23.2 1.0 CB A:ASP57 4.6 16.0 1.0 O A:HOH1009 4.6 21.2 1.0 O A:HOH1044 4.7 29.8 1.0 CA A:PHE62 4.7 17.8 1.0 N A:PHE62 4.7 20.0 1.0 OD2 A:ASP67 4.7 20.0 1.0 O A:HOH1101 4.7 52.7 1.0 CB A:ASP59 4.7 16.1 1.0 N A:ALA58 4.8 17.4 1.0 CA A:ASP59 4.8 21.0 1.0 C A:ASP59 4.9 22.2 1.0 C A:ASN60 5.0 20.1 1.0

Calcium binding site 4 out of 4 in the Thermolysin (60% Isopropanol Soaked Crystals)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Thermolysin (60% Isopropanol Soaked Crystals) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca321 b:28.3 occ:1.00 O A:ILE197 2.3 36.8 1.0 OD1 A:ASP200 2.6 26.2 1.0 O A:HOH1038 2.6 36.9 1.0 O A:THR194 2.6 22.2 1.0 O A:TYR193 2.7 19.8 1.0 OG1 A:THR194 2.7 25.1 1.0 O A:HOH1065 2.9 27.6 1.0 C A:THR194 3.4 26.4 1.0 C A:ILE197 3.4 39.0 1.0 CG A:ASP200 3.6 20.4 1.0 C A:TYR193 3.7 22.9 1.0 CB A:THR194 3.7 31.0 1.0 OD2 A:ASP200 3.8 22.2 1.0 CA A:THR194 3.8 23.6 1.0 N A:THR194 4.0 24.3 1.0 CA A:ILE197 4.2 38.2 1.0 CB A:ILE197 4.2 40.8 1.0 N A:ILE197 4.2 41.6 1.0 N A:PRO195 4.4 26.3 1.0 N A:SER198 4.5 36.9 1.0 O A:ASP200 4.6 24.2 1.0 N A:ASP200 4.6 27.0 1.0 CA A:SER198 4.6 37.1 1.0 O A:GLU190 4.6 18.2 1.0 CA A:TYR193 4.7 20.4 1.0 CD2 A:TYR193 4.7 25.3 1.0 CB A:TYR193 4.8 21.9 1.0 CA A:PRO195 4.8 29.8 1.0 CB A:ASP200 4.9 20.1 1.0 C A:ASP200 4.9 23.7 1.0 C A:SER198 4.9 34.3 1.0 CG2 A:THR194 5.0 23.9 1.0 C A:PRO195 5.0 35.0 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