Calcium in PDB 7tli: Thermolysin (90% Isopropanol Soaked Crystals)

Enzymatic activity of Thermolysin (90% Isopropanol Soaked Crystals)

All present enzymatic activity of Thermolysin (90% Isopropanol Soaked Crystals):
3.4.24.27;

Protein crystallography data

The structure of Thermolysin (90% Isopropanol Soaked Crystals), PDB code: 7tli 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 (°) 93.270, 93.270, 130.360, 90.00, 90.00, 120.00
R / Rfree (%) 17.1 / 21.3

Other elements in 7tli:

The structure of Thermolysin (90% 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 (90% Isopropanol Soaked Crystals) (pdb code 7tli). 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 (90% Isopropanol Soaked Crystals), PDB code: 7tli:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 7tli

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Calcium binding site 1 out of 4 in the Thermolysin (90% 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 (90% Isopropanol Soaked Crystals) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca402

b:21.6
occ:1.00
OE2 A:GLU190 2.6 17.1 1.0
OE1 A:GLU177 2.6 19.0 1.0
OE1 A:GLU190 2.6 18.1 1.0
OD1 A:ASP185 2.6 19.0 1.0
OD2 A:ASP138 2.7 21.0 1.0
O A:GLU187 2.7 19.4 1.0
O A:HOH1014 2.7 24.1 1.0
OE2 A:GLU177 2.9 16.1 1.0
CD A:GLU190 3.1 24.7 1.0
CD A:GLU177 3.2 24.5 1.0
CG A:ASP138 3.5 18.7 1.0
CG A:ASP185 3.7 30.9 1.0
C A:GLU187 3.7 22.4 1.0
CA A:CA403 3.8 24.7 1.0
OD2 A:ASP185 3.9 21.1 1.0
CB A:ASP138 4.1 16.7 1.0
N A:GLU187 4.2 20.5 1.0
O A:ASP185 4.2 21.4 1.0
OD1 A:ASP138 4.3 21.2 1.0
CA A:ILE188 4.4 16.9 1.0
O A:HOH1029 4.4 25.3 1.0
N A:ILE188 4.5 18.3 1.0
CA A:GLU187 4.5 19.5 1.0
N A:GLY189 4.5 22.5 1.0
CG A:GLU190 4.5 16.0 1.0
CG A:GLU177 4.6 15.9 1.0
CB A:GLU187 4.7 20.1 1.0
C A:ASP185 4.7 23.8 1.0
C A:ILE188 4.8 20.7 1.0
N A:ASP185 4.8 21.0 1.0
O A:HOH1030 4.9 30.1 1.0
CB A:GLU177 5.0 19.0 1.0
CB A:ASP185 5.0 18.9 1.0

Calcium binding site 2 out of 4 in 7tli

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Calcium binding site 2 out of 4 in the Thermolysin (90% 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 (90% Isopropanol Soaked Crystals) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca403

b:24.7
occ:1.00
O A:HOH1030 2.4 30.1 1.0
OD2 A:ASP185 2.5 21.1 1.0
OE2 A:GLU190 2.5 17.1 1.0
OE2 A:GLU177 2.5 16.1 1.0
O A:HOH1013 2.6 25.7 1.0
O A:ASN183 2.6 22.7 1.0
CG A:ASP185 3.3 30.9 1.0
CD A:GLU177 3.4 24.5 1.0
CD A:GLU190 3.5 24.7 1.0
OD1 A:ASP185 3.5 19.0 1.0
C A:ASN183 3.7 24.4 1.0
CA A:CA402 3.8 21.6 1.0
OE1 A:GLU177 3.8 19.0 1.0
O A:LYS182 3.9 25.8 1.0
CG A:GLU190 4.0 16.0 1.0
CA A:PRO184 4.2 24.4 1.0
N A:ASP185 4.2 21.0 1.0
CB A:ASN183 4.2 34.0 1.0
OD1 A:ASP191 4.3 21.3 1.0
C A:PRO184 4.3 25.5 1.0
OE1 A:GLU190 4.3 18.1 1.0
N A:PRO184 4.4 24.7 1.0
CG A:GLU177 4.4 15.9 1.0
OD2 A:ASP191 4.4 24.7 1.0
CB A:ASP185 4.5 18.9 1.0
CA A:ASN183 4.6 26.7 1.0
CG A:ASP191 4.7 25.3 1.0
C A:LYS182 4.9 27.1 1.0
CA A:ASP185 4.9 22.0 1.0
O A:PRO184 5.0 24.9 1.0

Calcium binding site 3 out of 4 in 7tli

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Calcium binding site 3 out of 4 in the Thermolysin (90% 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 (90% Isopropanol Soaked Crystals) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca404

b:24.2
occ:1.00
O A:HOH1027 2.4 23.5 1.0
O A:GLN61 2.5 17.8 1.0
OD1 A:ASP59 2.6 25.0 1.0
O A:HOH1016 2.6 29.5 1.0
OD1 A:ASP57 2.6 25.0 1.0
O A:HOH1047 2.6 34.4 1.0
OD2 A:ASP57 2.8 22.7 1.0
CG A:ASP57 3.1 25.6 1.0
CG A:ASP59 3.6 31.8 1.0
C A:GLN61 3.6 23.3 1.0
OD2 A:ASP59 3.8 28.8 1.0
N A:GLN61 3.9 20.6 1.0
O A:HOH1052 3.9 40.9 1.0
CA A:GLN61 4.2 22.1 1.0
N A:ASP59 4.3 23.0 1.0
CB A:GLN61 4.4 29.9 1.0
O A:HOH1009 4.6 20.8 1.0
CB A:ASP57 4.6 18.3 1.0
N A:ASN60 4.6 21.4 1.0
O A:HOH1044 4.6 31.0 1.0
N A:PHE62 4.6 19.8 1.0
O A:HOH1088 4.6 57.4 1.0
OD2 A:ASP67 4.7 20.8 1.0
CA A:PHE62 4.7 23.2 1.0
N A:ALA58 4.7 21.9 1.0
CB A:ASP59 4.8 24.9 1.0
CA A:ASP59 4.9 25.1 1.0
C A:ASP59 4.9 25.2 1.0

Calcium binding site 4 out of 4 in 7tli

Go back to Calcium Binding Sites List in 7tli
Calcium binding site 4 out of 4 in the Thermolysin (90% 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 (90% Isopropanol Soaked Crystals) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca405

b:27.2
occ:1.00
O A:ILE197 2.6 31.9 1.0
O A:TYR193 2.6 20.7 1.0
OD1 A:ASP200 2.6 23.8 1.0
O A:HOH1065 2.6 30.8 1.0
O A:HOH1038 2.6 41.3 1.0
O A:THR194 2.7 28.0 1.0
OG1 A:THR194 2.8 29.3 1.0
C A:THR194 3.4 27.6 1.0
C A:TYR193 3.5 25.3 1.0
CB A:THR194 3.7 26.7 1.0
CG A:ASP200 3.7 24.8 1.0
C A:ILE197 3.7 37.7 1.0
CA A:THR194 3.8 26.5 1.0
OD2 A:ASP200 3.8 22.4 1.0
N A:THR194 4.0 26.7 1.0
CB A:ILE197 4.3 40.0 1.0
CA A:ILE197 4.3 39.2 1.0
N A:ILE197 4.4 39.9 1.0
O A:ASP200 4.4 22.8 1.0
N A:ASP200 4.4 28.5 1.0
N A:PRO195 4.5 28.9 1.0
CA A:TYR193 4.7 21.7 1.0
O A:GLU190 4.7 20.3 1.0
N A:SER198 4.7 32.8 1.0
CD2 A:TYR193 4.7 26.2 1.0
CB A:TYR193 4.8 25.4 1.0
CA A:SER198 4.8 33.6 1.0
O A:HOH1107 4.8 65.5 1.0
C A:ASP200 4.8 24.5 1.0
CG2 A:ILE197 4.9 39.4 1.0
CA A:PRO195 4.9 30.4 1.0
CB A:ASP200 4.9 28.1 1.0
CG2 A:THR194 4.9 27.3 1.0
CA A:ASP200 4.9 23.6 1.0
C A:SER198 4.9 32.9 1.0
N A:TYR193 5.0 22.1 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 08:08:09 2020

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