Atomistry » Calcium » PDB 1qd6-1qlk » 1qf0
Atomistry »
  Calcium »
    PDB 1qd6-1qlk »
      1qf0 »

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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy