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Calcium in PDB 1qf0: Thermolysin (E.C.3.4.24.27) Complexed with (2-Sulphanyl-3- Phenylpropanoyl)-Phe-Tyr. Parameters For Zn-Bidentation of Mercaptoacyldipeptides in Metalloendopeptidase

Enzymatic activity of Thermolysin (E.C.3.4.24.27) Complexed with (2-Sulphanyl-3- Phenylpropanoyl)-Phe-Tyr. Parameters For Zn-Bidentation of Mercaptoacyldipeptides in Metalloendopeptidase

All present enzymatic activity of Thermolysin (E.C.3.4.24.27) Complexed with (2-Sulphanyl-3- Phenylpropanoyl)-Phe-Tyr. Parameters For Zn-Bidentation of Mercaptoacyldipeptides in Metalloendopeptidase:
3.4.24.27;

Protein crystallography data

The structure of Thermolysin (E.C.3.4.24.27) Complexed with (2-Sulphanyl-3- Phenylpropanoyl)-Phe-Tyr. Parameters For Zn-Bidentation of Mercaptoacyldipeptides in Metalloendopeptidase, PDB code: 1qf0 was solved by J.-F.Gaucher, M.Selkti, G.Tiraboschi, T.Prange, B.P.Roques, A.Tomas, M.C.Fournie-Zaluski, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 2.20
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 93.370, 93.370, 131.790, 90.00, 90.00, 120.00
R / Rfree (%) 16.1 / 21.6

Other elements in 1qf0:

The structure of Thermolysin (E.C.3.4.24.27) Complexed with (2-Sulphanyl-3- Phenylpropanoyl)-Phe-Tyr. Parameters For Zn-Bidentation of Mercaptoacyldipeptides in Metalloendopeptidase also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Thermolysin (E.C.3.4.24.27) Complexed with (2-Sulphanyl-3- Phenylpropanoyl)-Phe-Tyr. Parameters For Zn-Bidentation of Mercaptoacyldipeptides in Metalloendopeptidase (pdb code 1qf0). 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 (E.C.3.4.24.27) Complexed with (2-Sulphanyl-3- Phenylpropanoyl)-Phe-Tyr. Parameters For Zn-Bidentation of Mercaptoacyldipeptides in Metalloendopeptidase, PDB code: 1qf0:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 1qf0

Go back to Calcium Binding Sites List in 1qf0
Calcium binding site 1 out of 4 in the Thermolysin (E.C.3.4.24.27) Complexed with (2-Sulphanyl-3- Phenylpropanoyl)-Phe-Tyr. Parameters For Zn-Bidentation of Mercaptoacyldipeptides in Metalloendopeptidase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Thermolysin (E.C.3.4.24.27) Complexed with (2-Sulphanyl-3- Phenylpropanoyl)-Phe-Tyr. Parameters For Zn-Bidentation of Mercaptoacyldipeptides in Metalloendopeptidase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca321

b:5.0
occ:1.00
 O A:GLU187 2.3 5.0 1.0
O A:HOH327 2.4 5.0 1.0
OE1 A:GLU177 2.4 7.9 1.0
OD2 A:ASP138 2.4 5.0 1.0
OE2 A:GLU190 2.5 6.3 1.0
OE1 A:GLU190 2.5 6.1 1.0
OD1 A:ASP185 2.5 7.8 1.0
CD A:GLU190 2.8 7.2 1.0
OE2 A:GLU177 2.8 7.3 1.0
CD A:GLU177 3.0 7.2 1.0
C A:GLU187 3.4 6.1 1.0
CG A:ASP138 3.5 5.0 1.0
CG A:ASP185 3.6 7.0 1.0
CA A:CA322 3.9 5.8 1.0
OD2 A:ASP185 3.9 6.4 1.0
CB A:ASP138 4.0 5.0 1.0
N A:GLU187 4.2 7.0 1.0
N A:ILE188 4.2 5.0 1.0
CA A:ILE188 4.3 5.8 1.0
CA A:GLU187 4.3 8.2 1.0
O A:ASP185 4.3 10.4 1.0
CG A:GLU190 4.3 5.4 1.0
N A:GLY189 4.4 8.2 1.0
O A:HOH377 4.4 15.4 1.0
OD1 A:ASP138 4.4 5.0 1.0
CG A:GLU177 4.4 5.0 1.0
CB A:GLU187 4.6 10.1 1.0
C A:ASP185 4.7 7.3 1.0
O A:HOH356 4.7 11.3 1.0
C A:ILE188 4.8 6.7 1.0
CB A:ASP185 4.9 5.0 1.0
O A:HOH348 4.9 9.8 1.0
N A:ASP185 4.9 6.8 1.0
N A:GLU190 4.9 5.7 1.0
CB A:GLU177 4.9 5.7 1.0
OG1 A:THR174 5.0 6.8 1.0

Calcium binding site 2 out of 4 in 1qf0

Go back to Calcium Binding Sites List in 1qf0
Calcium binding site 2 out of 4 in the Thermolysin (E.C.3.4.24.27) Complexed with (2-Sulphanyl-3- Phenylpropanoyl)-Phe-Tyr. Parameters For Zn-Bidentation of Mercaptoacyldipeptides in Metalloendopeptidase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Thermolysin (E.C.3.4.24.27) Complexed with (2-Sulphanyl-3- Phenylpropanoyl)-Phe-Tyr. Parameters For Zn-Bidentation of Mercaptoacyldipeptides in Metalloendopeptidase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca322

b:5.8
occ:1.00
 O A:HOH348 2.3 9.8 1.0
OE2 A:GLU190 2.4 6.3 1.0
OE2 A:GLU177 2.4 7.3 1.0
OD2 A:ASP185 2.4 6.4 1.0
O A:HOH351 2.4 10.5 1.0
O A:ASN183 2.4 11.3 1.0
CG A:ASP185 3.3 7.0 1.0
CD A:GLU177 3.3 7.2 1.0
CD A:GLU190 3.3 7.2 1.0
C A:ASN183 3.6 9.6 1.0
OD1 A:ASP185 3.7 7.8 1.0
O A:LYS182 3.7 20.7 1.0
CG A:GLU190 3.7 5.4 1.0
CA A:CA321 3.9 5.0 1.0
OE1 A:GLU177 3.9 7.9 1.0
CB A:ASN183 4.2 13.5 1.0
OD2 A:ASP191 4.2 9.3 1.0
OD1 A:ASP191 4.2 8.8 1.0
CG A:GLU177 4.3 5.0 1.0
OE1 A:GLU190 4.3 6.1 1.0
CA A:PRO184 4.3 6.3 1.0
N A:ASP185 4.4 6.8 1.0
N A:PRO184 4.4 8.0 1.0
C A:PRO184 4.4 6.8 1.0
O A:HOH492 4.4 49.8 1.0
CB A:ASP185 4.5 5.0 1.0
CG A:ASP191 4.5 9.9 1.0
CA A:ASN183 4.5 13.1 1.0
O A:HOH377 4.6 15.4 1.0
C A:LYS182 4.8 20.6 1.0
O A:PRO184 4.9 9.4 1.0
O A:HOH438 5.0 29.2 1.0

Calcium binding site 3 out of 4 in 1qf0

Go back to Calcium Binding Sites List in 1qf0
Calcium binding site 3 out of 4 in the Thermolysin (E.C.3.4.24.27) Complexed with (2-Sulphanyl-3- Phenylpropanoyl)-Phe-Tyr. Parameters For Zn-Bidentation of Mercaptoacyldipeptides in Metalloendopeptidase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Thermolysin (E.C.3.4.24.27) Complexed with (2-Sulphanyl-3- Phenylpropanoyl)-Phe-Tyr. Parameters For Zn-Bidentation of Mercaptoacyldipeptides in Metalloendopeptidase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca323

b:8.4
occ:1.00
 O A:GLN61 2.2 7.1 1.0
OD1 A:ASP59 2.4 11.0 1.0
OD1 A:ASP57 2.4 8.9 1.0
O A:HOH343 2.4 8.9 1.0
O A:HOH379 2.4 15.8 1.0
O A:HOH329 2.4 5.0 1.0
OD2 A:ASP57 2.5 8.3 1.0
CG A:ASP57 2.8 7.9 1.0
CG A:ASP59 3.4 8.0 1.0
C A:GLN61 3.4 7.0 1.0
OD2 A:ASP59 3.8 10.9 1.0
O A:HOH402 3.9 20.5 1.0
N A:GLN61 3.9 8.3 1.0
CA A:GLN61 4.2 9.7 1.0
CB A:ASP57 4.3 5.0 1.0
N A:ASP59 4.3 6.8 1.0
CB A:GLN61 4.4 11.4 1.0
N A:PHE62 4.5 6.6 1.0
OD2 A:ASP67 4.6 8.4 1.0
CB A:ASP59 4.7 7.0 1.0
CA A:PHE62 4.7 5.6 1.0
N A:ASN60 4.7 7.2 1.0
O A:HOH382 4.7 16.6 1.0
N A:ALA58 4.7 8.9 1.0
O A:HOH435 4.8 29.0 1.0
CA A:ASP59 4.8 7.3 1.0
C A:ASP59 4.9 6.5 1.0
CA A:ASP57 5.0 6.4 1.0

Calcium binding site 4 out of 4 in 1qf0

Go back to Calcium Binding Sites List in 1qf0
Calcium binding site 4 out of 4 in the Thermolysin (E.C.3.4.24.27) Complexed with (2-Sulphanyl-3- Phenylpropanoyl)-Phe-Tyr. Parameters For Zn-Bidentation of Mercaptoacyldipeptides in Metalloendopeptidase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Thermolysin (E.C.3.4.24.27) Complexed with (2-Sulphanyl-3- Phenylpropanoyl)-Phe-Tyr. Parameters For Zn-Bidentation of Mercaptoacyldipeptides in Metalloendopeptidase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca324

b:11.2
occ:1.00
 O A:ILE197 2.3 22.0 1.0
OD1 A:ASP200 2.3 9.4 1.0
O A:TYR193 2.3 7.2 1.0
O A:THR194 2.3 9.7 1.0
OG1 A:THR194 2.4 8.0 1.0
O A:HOH335 2.4 6.4 1.0
O A:HOH384 2.4 17.1 1.0
C A:THR194 3.2 11.1 1.0
C A:TYR193 3.3 7.5 1.0
CG A:ASP200 3.4 12.3 1.0
C A:ILE197 3.5 20.5 1.0
CB A:THR194 3.5 9.2 1.0
CA A:THR194 3.7 9.5 1.0
OD2 A:ASP200 3.8 10.7 1.0
N A:THR194 3.9 7.6 1.0
CA A:ILE197 4.3 17.4 1.0
N A:PRO195 4.3 12.4 1.0
CB A:ILE197 4.3 17.9 1.0
N A:ILE197 4.3 19.9 1.0
O A:ASP200 4.3 11.6 1.0
N A:SER198 4.5 22.1 1.0
CA A:TYR193 4.5 7.5 1.0
O A:GLU190 4.6 7.6 1.0
CA A:SER198 4.6 24.1 1.0
CD2 A:TYR193 4.7 12.1 1.0
CB A:TYR193 4.7 8.1 1.0
N A:ASP200 4.7 13.9 1.0
CB A:ASP200 4.7 11.5 1.0
C A:ASP200 4.7 11.2 1.0
CG2 A:THR194 4.7 6.9 1.0
CA A:PRO195 4.7 15.5 1.0
CA A:ASP200 4.9 12.0 1.0

Reference:

J.F.Gaucher, M.Selkti, G.Tiraboschi, T.Prange, B.P.Roques, A.Tomas, M.C.Fournie-Zaluski. Crystal Structures of Alpha-Mercaptoacyldipeptides in the Thermolysin Active Site: Structural Parameters For A Zn Monodentation or Bidentation in Metalloendopeptidases. Biochemistry V. 38 12569 1999.
ISSN: ISSN 0006-2960
PubMed: 10504225
DOI: 10.1021/BI991043Z
Page generated: Thu Jul 11 21:42:24 2024

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