Calcium in PDB 3tli: Thermolysin (10% Isopropanol Soaked Crystals)

All present enzymatic activity of Thermolysin (10% Isopropanol Soaked Crystals):
3.4.24.27;

The structure of Thermolysin (10% Isopropanol Soaked Crystals), PDB code: 3tli 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 / 1.95
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	93.990, 93.990, 130.880, 90.00, 90.00, 120.00
R / Rfree (%)	16.6 / 21.2

The structure of Thermolysin (10% Isopropanol Soaked Crystals) also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Calcium atom in the Thermolysin (10% Isopropanol Soaked Crystals) (pdb code 3tli). 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 (10% Isopropanol Soaked Crystals), PDB code: 3tli:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Thermolysin (10% 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 (10% Isopropanol Soaked Crystals) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca318 b:21.7 occ:1.00 O A:GLU187 2.5 17.6 1.0 OD2 A:ASP138 2.6 20.0 1.0 OE1 A:GLU190 2.6 17.6 1.0 OD1 A:ASP185 2.6 18.5 1.0 OE1 A:GLU177 2.6 19.0 1.0 OE2 A:GLU190 2.7 18.4 1.0 O A:HOH1014 2.7 19.8 1.0 OE2 A:GLU177 2.9 18.9 1.0 CD A:GLU190 3.1 27.0 1.0 CD A:GLU177 3.2 22.5 1.0 CG A:ASP138 3.5 25.9 1.0 C A:GLU187 3.6 21.4 1.0 CG A:ASP185 3.6 32.0 1.0 CA A:CA319 3.8 24.7 1.0 OD2 A:ASP185 3.8 18.9 1.0 CB A:ASP138 4.1 17.3 1.0 N A:GLU187 4.2 23.3 1.0 CA A:ILE188 4.3 17.8 1.0 O A:ASP185 4.3 22.7 1.0 N A:ILE188 4.3 15.7 1.0 OD1 A:ASP138 4.3 20.1 1.0 CA A:GLU187 4.4 21.5 1.0 N A:GLY189 4.5 22.1 1.0 CG A:GLU190 4.5 21.0 1.0 CB A:GLU187 4.6 22.2 1.0 CG A:GLU177 4.6 17.2 1.0 O A:HOH1029 4.6 27.4 1.0 C A:ASP185 4.7 22.6 1.0 C A:ILE188 4.8 20.3 1.0 N A:ASP185 4.8 20.7 1.0 N A:GLU190 4.9 16.8 1.0 CB A:ASP185 4.9 19.8 1.0

Calcium binding site 2 out of 4 in the Thermolysin (10% 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 (10% Isopropanol Soaked Crystals) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca319 b:24.7 occ:1.00 OD2 A:ASP185 2.5 18.9 1.0 OE2 A:GLU190 2.5 18.4 1.0 O A:HOH1013 2.5 21.1 1.0 O A:HOH1030 2.5 24.4 1.0 OE2 A:GLU177 2.6 18.9 1.0 O A:ASN183 2.6 23.5 1.0 CG A:ASP185 3.4 32.0 1.0 CD A:GLU177 3.4 22.5 1.0 CD A:GLU190 3.4 27.0 1.0 OD1 A:ASP185 3.7 18.5 1.0 C A:ASN183 3.7 27.8 1.0 O A:LYS182 3.8 33.9 1.0 CA A:CA318 3.8 21.7 1.0 OE1 A:GLU177 3.8 19.0 1.0 CG A:GLU190 4.0 21.0 1.0 N A:ASP185 4.2 20.7 1.0 CA A:PRO184 4.2 25.7 1.0 O A:HOH1135 4.2 43.5 1.0 OE1 A:GLU190 4.3 17.6 1.0 C A:PRO184 4.3 27.7 1.0 OD1 A:ASP191 4.3 23.1 1.0 OD2 A:ASP191 4.3 23.9 1.0 CG A:GLU177 4.4 17.2 1.0 N A:PRO184 4.4 27.1 1.0 CB A:ASN183 4.4 38.6 1.0 CB A:ASP185 4.4 19.8 1.0 CG A:ASP191 4.6 26.1 1.0 CA A:ASN183 4.7 25.8 1.0 C A:LYS182 4.9 29.4 1.0 CA A:ASP185 4.9 20.8 1.0 O A:PRO184 4.9 23.0 1.0

Calcium binding site 3 out of 4 in the Thermolysin (10% 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 (10% Isopropanol Soaked Crystals) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca320 b:23.0 occ:1.00 O A:HOH1027 2.5 19.7 1.0 O A:GLN61 2.6 20.6 1.0 OD1 A:ASP59 2.6 18.7 1.0 OD1 A:ASP57 2.6 20.6 1.0 O A:HOH1016 2.6 25.4 1.0 O A:HOH1047 2.7 25.2 1.0 OD2 A:ASP57 2.7 20.2 1.0 CG A:ASP57 3.1 24.4 1.0 CG A:ASP59 3.6 29.2 1.0 C A:GLN61 3.7 23.9 1.0 OD2 A:ASP59 3.8 24.8 1.0 N A:GLN61 4.0 19.5 1.0 O A:HOH1052 4.0 35.2 1.0 CA A:GLN61 4.3 24.7 1.0 N A:ASP59 4.3 22.8 1.0 O A:HOH1044 4.5 26.2 1.0 CB A:GLN61 4.5 28.3 1.0 CB A:ASP57 4.5 18.3 1.0 N A:PHE62 4.6 18.2 1.0 N A:ASN60 4.6 20.6 1.0 CA A:PHE62 4.7 17.2 1.0 OD2 A:ASP67 4.7 19.9 1.0 O A:HOH1102 4.7 47.3 1.0 O A:HOH1009 4.7 20.9 1.0 CB A:ASP59 4.8 19.4 1.0 N A:ALA58 4.8 19.5 1.0 CA A:ASP59 4.8 22.0 1.0 C A:ASP59 4.9 23.1 1.0

Calcium binding site 4 out of 4 in the Thermolysin (10% 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 (10% Isopropanol Soaked Crystals) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca321 b:26.2 occ:1.00 O A:HOH1038 2.6 32.8 1.0 OD1 A:ASP200 2.6 23.0 1.0 O A:HOH1065 2.6 25.5 1.0 O A:ILE197 2.6 29.2 1.0 O A:TYR193 2.6 19.2 1.0 O A:THR194 2.6 25.9 1.0 OG1 A:THR194 2.7 26.2 1.0 C A:THR194 3.4 26.7 1.0 CG A:ASP200 3.6 22.2 1.0 C A:TYR193 3.6 23.7 1.0 CB A:THR194 3.7 28.1 1.0 OD2 A:ASP200 3.7 24.6 1.0 CA A:THR194 3.8 23.9 1.0 C A:ILE197 3.8 37.5 1.0 N A:THR194 4.0 22.3 1.0 CB A:ILE197 4.2 40.8 1.0 N A:ILE197 4.2 40.4 1.0 CA A:ILE197 4.3 38.8 1.0 N A:PRO195 4.4 26.6 1.0 O A:ASP200 4.5 24.4 1.0 N A:ASP200 4.6 25.9 1.0 CD2 A:TYR193 4.7 27.5 1.0 O A:GLU190 4.7 21.2 1.0 CA A:SER198 4.7 37.5 1.0 CA A:TYR193 4.7 18.4 1.0 N A:SER198 4.7 36.7 1.0 CB A:TYR193 4.8 19.1 1.0 C A:ASP200 4.9 22.2 1.0 CA A:PRO195 4.9 30.7 1.0 CB A:ASP200 4.9 22.4 1.0 CG2 A:THR194 4.9 25.1 1.0 C A:SER198 4.9 38.0 1.0 CG2 A:ILE197 4.9 36.3 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