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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

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