Calcium in PDB 8tli: Thermolysin (100% Isopropanol Soaked Crystals)

Enzymatic activity of Thermolysin (100% Isopropanol Soaked Crystals)

All present enzymatic activity of Thermolysin (100% Isopropanol Soaked Crystals):
3.4.24.27;

Protein crystallography data

The structure of Thermolysin (100% Isopropanol Soaked Crystals), PDB code: 8tli 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 / 2.20
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 93.040, 93.040, 130.420, 90.00, 90.00, 120.00
R / Rfree (%) 17.1 / 22.3

Other elements in 8tli:

The structure of Thermolysin (100% Isopropanol Soaked Crystals) also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Thermolysin (100% Isopropanol Soaked Crystals) (pdb code 8tli). 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 (100% Isopropanol Soaked Crystals), PDB code: 8tli:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 8tli

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Calcium binding site 1 out of 4 in the Thermolysin (100% 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 (100% Isopropanol Soaked Crystals) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca402

b:27.8
occ:1.00
OE2 A:GLU190 2.5 15.6 1.0
OE1 A:GLU190 2.6 20.1 1.0
OE1 A:GLU177 2.7 26.1 1.0
OD1 A:ASP185 2.7 23.6 1.0
O A:HOH1014 2.8 28.2 1.0
OD2 A:ASP138 2.9 34.7 1.0
O A:GLU187 2.9 28.3 1.0
OE2 A:GLU177 3.0 24.8 1.0
CD A:GLU190 3.1 33.3 1.0
CD A:GLU177 3.3 36.3 1.0
CG A:ASP138 3.5 31.2 1.0
CG A:ASP185 3.6 35.9 1.0
C A:GLU187 3.7 29.6 1.0
OD2 A:ASP185 3.7 20.5 1.0
CA A:CA403 3.8 31.9 1.0
N A:GLU187 4.1 29.3 1.0
OD1 A:ASP138 4.1 28.5 1.0
CB A:ASP138 4.1 18.9 1.0
O A:ASP185 4.3 29.6 1.0
CA A:GLU187 4.4 28.5 1.0
O A:HOH1029 4.5 27.3 1.0
CA A:ILE188 4.5 19.6 1.0
N A:ILE188 4.5 27.1 1.0
N A:GLY189 4.6 26.1 1.0
CG A:GLU190 4.6 18.6 1.0
CB A:GLU187 4.6 18.4 1.0
C A:ASP185 4.7 27.8 1.0
CG A:GLU177 4.7 21.6 1.0
C A:ILE188 4.9 28.9 1.0
N A:ASP185 4.9 28.9 1.0
N A:GLU190 4.9 26.3 1.0
O A:HOH1030 5.0 32.0 1.0

Calcium binding site 2 out of 4 in 8tli

Go back to Calcium Binding Sites List in 8tli
Calcium binding site 2 out of 4 in the Thermolysin (100% 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 (100% Isopropanol Soaked Crystals) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca403

b:31.9
occ:1.00
O A:HOH1013 2.5 29.8 1.0
OD2 A:ASP185 2.5 20.5 1.0
OE2 A:GLU190 2.6 15.6 1.0
OE2 A:GLU177 2.7 24.8 1.0
O A:ASN183 2.7 25.3 1.0
O A:HOH1030 2.7 32.0 1.0
CD A:GLU177 3.4 36.3 1.0
CG A:ASP185 3.4 35.9 1.0
CD A:GLU190 3.6 33.3 1.0
C A:ASN183 3.7 31.5 1.0
OD1 A:ASP185 3.8 23.6 1.0
CA A:CA402 3.8 27.8 1.0
OE1 A:GLU177 3.8 26.1 1.0
O A:LYS182 3.9 30.0 1.0
N A:ASP185 4.1 28.9 1.0
CA A:PRO184 4.2 28.7 1.0
CG A:GLU190 4.2 18.6 1.0
C A:PRO184 4.2 28.9 1.0
CB A:ASN183 4.3 27.6 1.0
OD2 A:ASP191 4.3 30.4 1.0
OE1 A:GLU190 4.4 20.1 1.0
CG A:GLU177 4.4 21.6 1.0
N A:PRO184 4.4 30.5 1.0
OD1 A:ASP191 4.4 30.6 1.0
CB A:ASP185 4.5 22.4 1.0
CA A:ASN183 4.6 30.1 1.0
CG A:ASP191 4.6 21.9 1.0
CA A:ASP185 4.9 27.6 1.0
O A:PRO184 4.9 30.2 1.0
C A:LYS182 4.9 33.5 1.0

Calcium binding site 3 out of 4 in 8tli

Go back to Calcium Binding Sites List in 8tli
Calcium binding site 3 out of 4 in the Thermolysin (100% 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 (100% Isopropanol Soaked Crystals) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca404

b:35.2
occ:1.00
O A:HOH1027 2.5 36.3 1.0
O A:GLN61 2.6 23.0 1.0
OD1 A:ASP57 2.7 28.6 1.0
OD1 A:ASP59 2.7 29.6 1.0
O A:HOH1047 2.8 46.5 1.0
O A:HOH1016 2.8 24.7 1.0
OD2 A:ASP57 2.9 29.0 1.0
CG A:ASP57 3.1 34.9 1.0
CG A:ASP59 3.6 35.7 1.0
C A:GLN61 3.7 31.8 1.0
OD2 A:ASP59 3.8 41.8 1.0
N A:GLN61 3.9 27.0 1.0
O A:HOH1052 3.9 45.9 1.0
N A:ASP59 4.2 29.9 1.0
CA A:GLN61 4.2 31.4 1.0
CB A:GLN61 4.4 35.7 1.0
CB A:ASP57 4.6 20.8 1.0
N A:ASN60 4.6 27.1 1.0
O A:HOH1009 4.6 26.6 1.0
N A:PHE62 4.7 29.5 1.0
OD2 A:ASP67 4.7 25.6 1.0
CA A:PHE62 4.7 30.4 1.0
N A:ALA58 4.7 27.7 1.0
CB A:ASP59 4.8 32.5 1.0
CA A:ASP59 4.9 29.7 1.0
C A:ASP59 5.0 31.9 1.0
O A:HOH1044 5.0 38.7 1.0

Calcium binding site 4 out of 4 in 8tli

Go back to Calcium Binding Sites List in 8tli
Calcium binding site 4 out of 4 in the Thermolysin (100% 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 (100% Isopropanol Soaked Crystals) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca405

b:35.2
occ:1.00
O A:THR194 2.4 32.9 1.0
O A:ILE197 2.4 34.3 1.0
O A:HOH1065 2.6 35.4 1.0
OD1 A:ASP200 2.7 33.8 1.0
O A:HOH1038 2.7 64.2 1.0
O A:TYR193 2.7 22.3 1.0
OG1 A:THR194 2.8 42.0 1.0
C A:THR194 3.2 34.1 1.0
C A:TYR193 3.5 25.3 1.0
C A:ILE197 3.6 40.8 1.0
CB A:THR194 3.7 39.4 1.0
CG A:ASP200 3.7 27.4 1.0
CA A:THR194 3.8 36.5 1.0
OD2 A:ASP200 4.0 29.0 1.0
N A:THR194 4.0 30.6 1.0
CA A:ILE197 4.3 44.1 1.0
N A:PRO195 4.3 37.8 1.0
N A:ILE197 4.3 45.3 1.0
CB A:ILE197 4.3 48.7 1.0
O A:ASP200 4.4 27.4 1.0
N A:ASP200 4.5 34.5 1.0
N A:SER198 4.6 41.0 1.0
CA A:PRO195 4.6 34.8 1.0
CD2 A:TYR193 4.6 32.7 1.0
CG2 A:ILE197 4.6 47.6 1.0
CA A:TYR193 4.7 24.6 1.0
O A:GLU190 4.7 27.5 1.0
CA A:SER198 4.7 40.9 1.0
CB A:TYR193 4.7 30.1 1.0
C A:ASP200 4.8 27.7 1.0
C A:PRO195 4.9 40.0 1.0
CA A:ASP200 4.9 27.9 1.0
CB A:ASP200 5.0 31.9 1.0

Reference:

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
Page generated: Sat Dec 12 08:08:13 2020

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