Atomistry » Calcium » PDB 1qd6-1qlk » 1qf2
Atomistry »
  Calcium »
    PDB 1qd6-1qlk »
      1qf2 »

Calcium in PDB 1qf2: Thermolysin (E.C.3.4.24.27) Complexed with (2-Sulphanyl-3- Phenylpropanoyl)-Gly-(5-Phenylproline). Parameters For Zn- Monodentation of Mercaptoacyldipeptides in Metalloendopeptidase

Enzymatic activity of Thermolysin (E.C.3.4.24.27) Complexed with (2-Sulphanyl-3- Phenylpropanoyl)-Gly-(5-Phenylproline). Parameters For Zn- Monodentation of Mercaptoacyldipeptides in Metalloendopeptidase

All present enzymatic activity of Thermolysin (E.C.3.4.24.27) Complexed with (2-Sulphanyl-3- Phenylpropanoyl)-Gly-(5-Phenylproline). Parameters For Zn- Monodentation 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)-Gly-(5-Phenylproline). Parameters For Zn- Monodentation of Mercaptoacyldipeptides in Metalloendopeptidase, PDB code: 1qf2 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 / 2.06
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 93.500, 93.500, 131.300, 90.00, 90.00, 120.00
R / Rfree (%) 15.9 / 22.2

Other elements in 1qf2:

The structure of Thermolysin (E.C.3.4.24.27) Complexed with (2-Sulphanyl-3- Phenylpropanoyl)-Gly-(5-Phenylproline). Parameters For Zn- Monodentation 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)-Gly-(5-Phenylproline). Parameters For Zn- Monodentation of Mercaptoacyldipeptides in Metalloendopeptidase (pdb code 1qf2). 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)-Gly-(5-Phenylproline). Parameters For Zn- Monodentation of Mercaptoacyldipeptides in Metalloendopeptidase, PDB code: 1qf2:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 1qf2

Go back to Calcium Binding Sites List in 1qf2
Calcium binding site 1 out of 4 in the Thermolysin (E.C.3.4.24.27) Complexed with (2-Sulphanyl-3- Phenylpropanoyl)-Gly-(5-Phenylproline). Parameters For Zn- Monodentation 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)-Gly-(5-Phenylproline). Parameters For Zn- Monodentation of Mercaptoacyldipeptides in Metalloendopeptidase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca321

b:10.2
occ:1.00
 O A:GLU187 2.3 6.8 1.0
OD2 A:ASP138 2.4 6.9 1.0
O A:HOH331 2.4 6.3 1.0
OE1 A:GLU177 2.4 8.8 1.0
OE2 A:GLU190 2.5 7.1 1.0
OE1 A:GLU190 2.5 5.2 1.0
OD1 A:ASP185 2.5 9.7 1.0
CD A:GLU190 2.9 8.2 1.0
OE2 A:GLU177 2.9 8.2 1.0
CD A:GLU177 3.0 7.5 1.0
C A:GLU187 3.4 7.8 1.0
CG A:ASP138 3.4 6.6 1.0
CG A:ASP185 3.5 10.7 1.0
OD2 A:ASP185 3.8 9.7 1.0
CA A:CA322 3.9 6.8 1.0
CB A:ASP138 4.0 5.1 1.0
N A:GLU187 4.2 9.2 1.0
N A:ILE188 4.2 8.0 1.0
CA A:ILE188 4.3 8.3 1.0
CA A:GLU187 4.3 9.6 1.0
O A:ASP185 4.3 10.8 1.0
OD1 A:ASP138 4.3 7.7 1.0
CG A:GLU190 4.4 6.9 1.0
N A:GLY189 4.4 8.5 1.0
CG A:GLU177 4.5 5.7 1.0
O A:HOH485 4.5 39.6 1.0
CB A:GLU187 4.5 10.8 1.0
O A:HOH359 4.6 12.5 1.0
C A:ASP185 4.7 9.6 1.0
C A:ILE188 4.8 8.9 1.0
CB A:ASP185 4.8 11.5 1.0
N A:ASP185 4.9 11.3 1.0
O A:HOH341 4.9 9.2 1.0
CB A:GLU177 4.9 7.2 1.0
N A:GLU190 5.0 7.5 1.0

Calcium binding site 2 out of 4 in 1qf2

Go back to Calcium Binding Sites List in 1qf2
Calcium binding site 2 out of 4 in the Thermolysin (E.C.3.4.24.27) Complexed with (2-Sulphanyl-3- Phenylpropanoyl)-Gly-(5-Phenylproline). Parameters For Zn- Monodentation 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)-Gly-(5-Phenylproline). Parameters For Zn- Monodentation of Mercaptoacyldipeptides in Metalloendopeptidase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca322

b:6.8
occ:1.00
 O A:HOH351 2.3 11.1 1.0
OE2 A:GLU190 2.3 7.1 1.0
O A:HOH341 2.3 9.2 1.0
O A:ASN183 2.3 15.4 1.0
OE2 A:GLU177 2.4 8.2 1.0
OD2 A:ASP185 2.4 9.7 1.0
CD A:GLU177 3.2 7.5 1.0
CG A:ASP185 3.3 10.7 1.0
CD A:GLU190 3.3 8.2 1.0
C A:ASN183 3.5 14.1 1.0
OD1 A:ASP185 3.7 9.7 1.0
O A:LYS182 3.7 21.9 1.0
OE1 A:GLU177 3.8 8.8 1.0
CG A:GLU190 3.8 6.9 1.0
CA A:CA321 3.9 10.2 1.0
OD2 A:ASP191 4.2 9.7 1.0
OD1 A:ASP191 4.2 11.2 1.0
CB A:ASN183 4.2 17.1 1.0
CG A:GLU177 4.3 5.7 1.0
CA A:PRO184 4.3 11.6 1.0
OE1 A:GLU190 4.3 5.2 1.0
N A:ASP185 4.3 11.3 1.0
N A:PRO184 4.3 14.3 1.0
O A:HOH484 4.4 39.6 1.0
C A:PRO184 4.4 12.1 1.0
CB A:ASP185 4.5 11.5 1.0
CA A:ASN183 4.5 16.1 1.0
CG A:ASP191 4.5 9.9 1.0
O A:HOH532 4.6 46.6 1.0
O A:HOH485 4.6 39.6 1.0
C A:LYS182 4.8 20.3 1.0

Calcium binding site 3 out of 4 in 1qf2

Go back to Calcium Binding Sites List in 1qf2
Calcium binding site 3 out of 4 in the Thermolysin (E.C.3.4.24.27) Complexed with (2-Sulphanyl-3- Phenylpropanoyl)-Gly-(5-Phenylproline). Parameters For Zn- Monodentation 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)-Gly-(5-Phenylproline). Parameters For Zn- Monodentation of Mercaptoacyldipeptides in Metalloendopeptidase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca323

b:10.2
occ:1.00
 O A:GLN61 2.3 8.0 1.0
O A:HOH352 2.3 11.2 1.0
O A:HOH381 2.4 18.7 1.0
O A:HOH328 2.4 5.1 1.0
OD1 A:ASP59 2.4 10.9 1.0
OD1 A:ASP57 2.4 12.1 1.0
OD2 A:ASP57 2.6 8.7 1.0
CG A:ASP57 2.9 8.6 1.0
CG A:ASP59 3.4 8.9 1.0
C A:GLN61 3.4 10.3 1.0
OD2 A:ASP59 3.8 11.2 1.0
O A:HOH365 3.9 14.1 1.0
N A:GLN61 4.0 9.7 1.0
CA A:GLN61 4.2 11.3 1.0
O A:HOH446 4.3 34.8 1.0
N A:ASP59 4.3 7.5 1.0
CB A:ASP57 4.4 7.9 1.0
CB A:GLN61 4.4 12.1 1.0
O A:HOH363 4.4 13.7 1.0
N A:PHE62 4.5 8.6 1.0
OD2 A:ASP67 4.6 5.5 1.0
O A:HOH451 4.7 35.3 1.0
CB A:ASP59 4.7 7.7 1.0
O A:HOH329 4.7 5.4 1.0
CA A:PHE62 4.7 9.3 1.0
N A:ASN60 4.7 7.7 1.0
N A:ALA58 4.8 8.6 1.0
CA A:ASP59 4.8 9.9 1.0
O A:HOH454 4.9 35.5 1.0
C A:ASP59 4.9 8.4 1.0

Calcium binding site 4 out of 4 in 1qf2

Go back to Calcium Binding Sites List in 1qf2
Calcium binding site 4 out of 4 in the Thermolysin (E.C.3.4.24.27) Complexed with (2-Sulphanyl-3- Phenylpropanoyl)-Gly-(5-Phenylproline). Parameters For Zn- Monodentation 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)-Gly-(5-Phenylproline). Parameters For Zn- Monodentation of Mercaptoacyldipeptides in Metalloendopeptidase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca324

b:11.8
occ:1.00
 O A:ILE197 2.3 20.8 1.0
OG1 A:THR194 2.3 10.6 1.0
O A:TYR193 2.3 10.5 1.0
O A:HOH350 2.3 11.0 1.0
OD1 A:ASP200 2.4 11.1 1.0
O A:THR194 2.4 12.8 1.0
O A:HOH380 2.4 18.0 1.0
C A:THR194 3.2 14.9 1.0
C A:TYR193 3.3 10.5 1.0
CB A:THR194 3.4 11.9 1.0
CG A:ASP200 3.5 13.7 1.0
C A:ILE197 3.5 22.0 1.0
CA A:THR194 3.7 12.5 1.0
OD2 A:ASP200 3.9 11.0 1.0
N A:THR194 3.9 11.6 1.0
CA A:ILE197 4.2 19.5 1.0
N A:ILE197 4.3 22.1 1.0
CB A:ILE197 4.3 20.1 1.0
N A:PRO195 4.3 15.8 1.0
O A:ASP200 4.4 13.7 1.0
O A:HOH459 4.5 36.2 1.0
N A:SER198 4.5 22.0 1.0
O A:GLU190 4.5 8.6 1.0
CA A:TYR193 4.5 10.7 1.0
CD2 A:TYR193 4.6 14.1 1.0
CB A:TYR193 4.7 10.4 1.0
CG2 A:THR194 4.7 11.4 1.0
CA A:SER198 4.7 22.9 1.0
O A:HOH549 4.7 50.2 1.0
N A:ASP200 4.7 16.6 1.0
C A:ASP200 4.8 14.7 1.0
CA A:PRO195 4.8 18.6 1.0
CB A:ASP200 4.8 12.9 1.0
CG A:TYR193 4.9 13.2 1.0
CA A:ASP200 5.0 13.9 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 21:43:04 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy