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Calcium in PDB 1thl: Thermolysin Complexed with A Novel Glutaramide Derivative, N-(1-(2(R, S)-Carboxy-4-Phenylbutyl) Cyclopentylcarbonyl)-(S)-Tryptophan

Enzymatic activity of Thermolysin Complexed with A Novel Glutaramide Derivative, N-(1-(2(R, S)-Carboxy-4-Phenylbutyl) Cyclopentylcarbonyl)-(S)-Tryptophan

All present enzymatic activity of Thermolysin Complexed with A Novel Glutaramide Derivative, N-(1-(2(R, S)-Carboxy-4-Phenylbutyl) Cyclopentylcarbonyl)-(S)-Tryptophan:
3.4.24.27;

Protein crystallography data

The structure of Thermolysin Complexed with A Novel Glutaramide Derivative, N-(1-(2(R, S)-Carboxy-4-Phenylbutyl) Cyclopentylcarbonyl)-(S)-Tryptophan, PDB code: 1thl was solved by D.R.Holland, B.W.Matthews, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 1.70
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 94.100, 94.100, 131.400, 90.00, 90.00, 120.00
R / Rfree (%) 16.2 / n/a

Other elements in 1thl:

The structure of Thermolysin Complexed with A Novel Glutaramide Derivative, N-(1-(2(R, S)-Carboxy-4-Phenylbutyl) Cyclopentylcarbonyl)-(S)-Tryptophan also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Thermolysin Complexed with A Novel Glutaramide Derivative, N-(1-(2(R, S)-Carboxy-4-Phenylbutyl) Cyclopentylcarbonyl)-(S)-Tryptophan (pdb code 1thl). 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 Complexed with A Novel Glutaramide Derivative, N-(1-(2(R, S)-Carboxy-4-Phenylbutyl) Cyclopentylcarbonyl)-(S)-Tryptophan, PDB code: 1thl:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 1thl

Go back to Calcium Binding Sites List in 1thl
Calcium binding site 1 out of 4 in the Thermolysin Complexed with A Novel Glutaramide Derivative, N-(1-(2(R, S)-Carboxy-4-Phenylbutyl) Cyclopentylcarbonyl)-(S)-Tryptophan


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Thermolysin Complexed with A Novel Glutaramide Derivative, N-(1-(2(R, S)-Carboxy-4-Phenylbutyl) Cyclopentylcarbonyl)-(S)-Tryptophan within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca3231

b:9.5
occ:1.00
 O A:GLU187 2.2 10.2 1.0
OD2 A:ASP138 2.3 12.2 1.0
OE1 A:GLU190 2.4 10.4 1.0
OE2 A:GLU190 2.5 11.2 1.0
OD1 A:ASP185 2.5 9.2 1.0
OE1 A:GLU177 2.6 12.4 1.0
O A:HOH346 2.6 9.2 1.0
CD A:GLU190 2.7 10.2 1.0
OE2 A:GLU177 2.8 10.4 1.0
CD A:GLU177 3.1 12.9 1.0
CG A:ASP138 3.3 9.9 1.0
C A:GLU187 3.4 8.7 1.0
CG A:ASP185 3.5 14.6 1.0
OD2 A:ASP185 3.8 13.6 1.0
CA A:CA3232 3.8 12.9 1.0
CB A:ASP138 4.0 6.9 1.0
N A:ILE188 4.2 13.4 1.0
CG A:GLU190 4.2 10.8 1.0
O A:ASP185 4.2 17.1 1.0
O A:HOH469 4.2 29.0 1.0
N A:GLU187 4.3 15.6 1.0
OD1 A:ASP138 4.3 11.5 1.0
CA A:GLU187 4.3 11.2 1.0
CA A:ILE188 4.3 7.1 1.0
N A:GLY189 4.5 12.3 1.0
CG A:GLU177 4.5 5.8 1.0
CB A:GLU187 4.5 10.6 1.0
O A:HOH350 4.7 15.7 1.0
C A:ASP185 4.7 12.4 1.0
C A:ILE188 4.8 15.9 1.0
N A:ASP185 4.8 11.2 1.0
CB A:ASP185 4.8 11.7 1.0
N A:GLU190 4.9 8.2 1.0
O A:HOH353 4.9 13.0 1.0
CB A:GLU177 5.0 6.0 1.0

Calcium binding site 2 out of 4 in 1thl

Go back to Calcium Binding Sites List in 1thl
Calcium binding site 2 out of 4 in the Thermolysin Complexed with A Novel Glutaramide Derivative, N-(1-(2(R, S)-Carboxy-4-Phenylbutyl) Cyclopentylcarbonyl)-(S)-Tryptophan


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Thermolysin Complexed with A Novel Glutaramide Derivative, N-(1-(2(R, S)-Carboxy-4-Phenylbutyl) Cyclopentylcarbonyl)-(S)-Tryptophan within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca3232

b:12.9
occ:1.00
 OE2 A:GLU190 2.3 11.2 1.0
O A:HOH475 2.3 11.2 1.0
O A:HOH353 2.4 13.0 1.0
OD2 A:ASP185 2.4 13.6 1.0
OE2 A:GLU177 2.4 10.4 1.0
O A:ASN183 2.5 14.0 1.0
CD A:GLU177 3.3 12.9 1.0
CG A:ASP185 3.3 14.6 1.0
CD A:GLU190 3.4 10.2 1.0
C A:ASN183 3.7 9.5 1.0
OD1 A:ASP185 3.7 9.2 1.0
CG A:GLU190 3.8 10.8 1.0
CA A:CA3231 3.8 9.5 1.0
OE1 A:GLU177 3.8 12.4 1.0
O A:LYS182 4.0 25.5 1.0
OD2 A:ASP191 4.1 17.1 1.0
CB A:ASN183 4.2 18.3 1.0
N A:ASP185 4.2 11.2 1.0
CA A:PRO184 4.2 16.8 1.0
CG A:GLU177 4.3 5.8 1.0
OD1 A:ASP191 4.4 17.2 1.0
OE1 A:GLU190 4.4 10.4 1.0
C A:PRO184 4.4 19.9 1.0
N A:PRO184 4.4 19.6 1.0
O A:HOH512 4.5 36.0 1.0
O A:HOH469 4.5 29.0 1.0
CB A:ASP185 4.5 11.7 1.0
CG A:ASP191 4.6 18.7 1.0
CA A:ASN183 4.6 13.4 1.0
CA A:ASP185 5.0 6.2 1.0

Calcium binding site 3 out of 4 in 1thl

Go back to Calcium Binding Sites List in 1thl
Calcium binding site 3 out of 4 in the Thermolysin Complexed with A Novel Glutaramide Derivative, N-(1-(2(R, S)-Carboxy-4-Phenylbutyl) Cyclopentylcarbonyl)-(S)-Tryptophan


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Thermolysin Complexed with A Novel Glutaramide Derivative, N-(1-(2(R, S)-Carboxy-4-Phenylbutyl) Cyclopentylcarbonyl)-(S)-Tryptophan within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca3233

b:11.6
occ:1.00
 O A:GLN61 2.3 10.6 1.0
O A:HOH482 2.3 18.4 1.0
OD1 A:ASP59 2.4 13.4 1.0
OD1 A:ASP57 2.4 12.7 1.0
O A:HOH419 2.5 13.4 1.0
OD2 A:ASP57 2.7 11.8 1.0
CG A:ASP57 2.9 11.8 1.0
CG A:ASP59 3.4 17.5 1.0
C A:GLN61 3.4 13.3 1.0
OD2 A:ASP59 3.9 18.3 1.0
O A:HOH484 3.9 22.6 1.0
N A:GLN61 4.0 10.2 1.0
CA A:GLN61 4.2 11.0 1.0
N A:ASP59 4.4 10.3 1.0
CB A:GLN61 4.4 8.5 1.0
CB A:ASP57 4.4 5.7 1.0
N A:PHE62 4.4 12.6 1.0
O A:HOH356 4.5 12.5 1.0
OD2 A:ASP67 4.6 7.5 1.0
CB A:ASP59 4.6 10.5 1.0
N A:ASN60 4.7 10.5 1.0
CA A:PHE62 4.7 7.3 1.0
N A:ALA58 4.8 9.8 1.0
CA A:ASP59 4.8 9.4 1.0
C A:ASP59 4.9 15.5 1.0

Calcium binding site 4 out of 4 in 1thl

Go back to Calcium Binding Sites List in 1thl
Calcium binding site 4 out of 4 in the Thermolysin Complexed with A Novel Glutaramide Derivative, N-(1-(2(R, S)-Carboxy-4-Phenylbutyl) Cyclopentylcarbonyl)-(S)-Tryptophan


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Thermolysin Complexed with A Novel Glutaramide Derivative, N-(1-(2(R, S)-Carboxy-4-Phenylbutyl) Cyclopentylcarbonyl)-(S)-Tryptophan within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca3234

b:14.1
occ:1.00
 O A:HOH480 2.0 30.0 1.0
OD1 A:ASP200 2.2 16.0 1.0
O A:ILE197 2.3 27.5 1.0
OG1 A:THR194 2.4 16.7 1.0
O A:TYR193 2.4 13.6 1.0
O A:THR194 2.4 17.6 1.0
O A:HOH354 2.5 16.1 1.0
C A:THR194 3.3 18.9 1.0
CG A:ASP200 3.3 8.0 1.0
C A:TYR193 3.4 15.4 1.0
CB A:THR194 3.5 13.7 1.0
C A:ILE197 3.5 31.4 1.0
CA A:THR194 3.7 11.7 1.0
OD2 A:ASP200 3.8 16.1 1.0
N A:THR194 4.0 16.4 1.0
N A:PRO195 4.3 14.7 1.0
N A:ILE197 4.3 38.6 1.0
CA A:ILE197 4.3 20.4 1.0
O A:ASP200 4.3 14.2 1.0
N A:ASP200 4.5 14.6 1.0
N A:SER198 4.5 24.7 1.0
O A:GLU190 4.5 13.0 1.0
CA A:SER198 4.6 21.0 1.0
CB A:ASP200 4.6 12.9 1.0
CA A:TYR193 4.6 9.5 1.0
CG2 A:THR194 4.7 12.1 1.0
CA A:PRO195 4.7 12.9 1.0
O A:HOH476 4.7 35.8 1.0
C A:ASP200 4.7 5.1 1.0
CB A:TYR193 4.8 10.0 1.0
CG1 A:ILE197 4.8 36.2 1.0
CD2 A:TYR193 4.8 23.9 1.0
CA A:ASP200 4.8 11.9 1.0
C A:SER198 4.9 28.8 1.0
C A:PRO195 4.9 45.7 1.0
N A:GLY199 4.9 22.2 1.0
CB A:ILE197 4.9 31.4 1.0

Reference:

D.R.Holland, P.L.Barclay, J.C.Danilewicz, B.W.Matthews, K.James. Inhibition of Thermolysin and Neutral Endopeptidase 24.11 By A Novel Glutaramide Derivative; X-Ray Structure Determination of the Thermolysin-Inhibitor Complex Biochemistry V. 33 51 1994.
ISSN: ISSN 0006-2960
PubMed: 8286362
DOI: 10.1021/BI00167A007
Page generated: Thu Jul 11 23:03:10 2024

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