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Calcium in PDB 1qf1: Thermolysin (E.C.3.4.24.27) Complexed with (2-Sulphanylheptanoyl)-Phe- Ala. Parameters For Zn-Bidentation of Mercaptoacyldipeptides in Metalloendopeptidase

Enzymatic activity of Thermolysin (E.C.3.4.24.27) Complexed with (2-Sulphanylheptanoyl)-Phe- Ala. Parameters For Zn-Bidentation of Mercaptoacyldipeptides in Metalloendopeptidase

All present enzymatic activity of Thermolysin (E.C.3.4.24.27) Complexed with (2-Sulphanylheptanoyl)-Phe- Ala. 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-Sulphanylheptanoyl)-Phe- Ala. Parameters For Zn-Bidentation of Mercaptoacyldipeptides in Metalloendopeptidase, PDB code: 1qf1 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 / 2.00
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 93.310, 93.310, 131.820, 90.00, 90.00, 120.00
R / Rfree (%) 16.5 / 22.4

Other elements in 1qf1:

The structure of Thermolysin (E.C.3.4.24.27) Complexed with (2-Sulphanylheptanoyl)-Phe- Ala. 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-Sulphanylheptanoyl)-Phe- Ala. Parameters For Zn-Bidentation of Mercaptoacyldipeptides in Metalloendopeptidase (pdb code 1qf1). 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-Sulphanylheptanoyl)-Phe- Ala. Parameters For Zn-Bidentation of Mercaptoacyldipeptides in Metalloendopeptidase, PDB code: 1qf1:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 1qf1

Go back to Calcium Binding Sites List in 1qf1
Calcium binding site 1 out of 4 in the Thermolysin (E.C.3.4.24.27) Complexed with (2-Sulphanylheptanoyl)-Phe- Ala. 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-Sulphanylheptanoyl)-Phe- Ala. Parameters For Zn-Bidentation of Mercaptoacyldipeptides in Metalloendopeptidase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca321

b:6.4
occ:1.00
 O A:GLU187 2.3 8.0 1.0
OD2 A:ASP138 2.4 6.9 1.0
OE1 A:GLU177 2.4 9.1 1.0
O A:HOH329 2.4 6.2 1.0
OE2 A:GLU190 2.5 6.2 1.0
OE1 A:GLU190 2.5 8.3 1.0
OD1 A:ASP185 2.6 9.9 1.0
OE2 A:GLU177 2.8 6.6 1.0
CD A:GLU190 2.9 7.2 1.0
CD A:GLU177 3.0 9.5 1.0
C A:GLU187 3.4 8.6 1.0
CG A:ASP138 3.4 6.9 1.0
CG A:ASP185 3.6 7.3 1.0
CA A:CA322 3.9 8.2 1.0
OD2 A:ASP185 3.9 10.6 1.0
CB A:ASP138 4.0 5.2 1.0
N A:GLU187 4.2 10.0 1.0
O A:ASP185 4.2 10.6 1.0
N A:ILE188 4.2 8.9 1.0
CA A:GLU187 4.3 11.5 1.0
CA A:ILE188 4.3 9.5 1.0
O A:HOH376 4.3 16.3 1.0
CG A:GLU190 4.4 5.4 1.0
OD1 A:ASP138 4.4 8.7 1.0
CG A:GLU177 4.4 7.0 1.0
N A:GLY189 4.5 8.9 1.0
CB A:GLU187 4.5 12.6 1.0
O A:HOH364 4.6 13.6 1.0
C A:ASP185 4.7 8.0 1.0
C A:ILE188 4.8 10.2 1.0
O A:HOH337 4.9 7.3 1.0
CB A:ASP185 4.9 7.8 1.0
N A:ASP185 4.9 9.9 1.0
CB A:GLU177 4.9 6.6 1.0
N A:GLU190 5.0 5.9 1.0

Calcium binding site 2 out of 4 in 1qf1

Go back to Calcium Binding Sites List in 1qf1
Calcium binding site 2 out of 4 in the Thermolysin (E.C.3.4.24.27) Complexed with (2-Sulphanylheptanoyl)-Phe- Ala. 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-Sulphanylheptanoyl)-Phe- Ala. Parameters For Zn-Bidentation of Mercaptoacyldipeptides in Metalloendopeptidase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca322

b:8.2
occ:1.00
 OE2 A:GLU190 2.3 6.2 1.0
OE2 A:GLU177 2.3 6.6 1.0
O A:HOH378 2.4 16.6 1.0
O A:ASN183 2.4 16.3 1.0
O A:HOH337 2.4 7.3 1.0
OD2 A:ASP185 2.4 10.6 1.0
CD A:GLU177 3.3 9.5 1.0
CD A:GLU190 3.3 7.2 1.0
CG A:ASP185 3.3 7.3 1.0
C A:ASN183 3.6 14.7 1.0
OD1 A:ASP185 3.7 9.9 1.0
CG A:GLU190 3.7 5.4 1.0
O A:LYS182 3.8 22.0 1.0
OE1 A:GLU177 3.8 9.1 1.0
CA A:CA321 3.9 6.4 1.0
OD1 A:ASP191 4.1 8.9 1.0
OD2 A:ASP191 4.2 9.7 1.0
CB A:ASN183 4.2 19.0 1.0
OE1 A:GLU190 4.2 8.3 1.0
CG A:GLU177 4.3 7.0 1.0
CA A:PRO184 4.3 11.1 1.0
N A:ASP185 4.3 9.9 1.0
N A:PRO184 4.4 13.2 1.0
C A:PRO184 4.4 10.5 1.0
O A:HOH501 4.4 40.3 1.0
CB A:ASP185 4.5 7.8 1.0
CG A:ASP191 4.5 9.9 1.0
O A:HOH376 4.5 16.3 1.0
CA A:ASN183 4.6 17.6 1.0
O A:HOH494 4.7 38.8 1.0
C A:LYS182 4.9 21.1 1.0
O A:HOH474 4.9 34.4 1.0

Calcium binding site 3 out of 4 in 1qf1

Go back to Calcium Binding Sites List in 1qf1
Calcium binding site 3 out of 4 in the Thermolysin (E.C.3.4.24.27) Complexed with (2-Sulphanylheptanoyl)-Phe- Ala. 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-Sulphanylheptanoyl)-Phe- Ala. Parameters For Zn-Bidentation of Mercaptoacyldipeptides in Metalloendopeptidase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca323

b:8.9
occ:1.00
 O A:GLN61 2.3 6.4 1.0
OD1 A:ASP57 2.4 10.3 1.0
O A:HOH333 2.4 7.0 1.0
O A:HOH327 2.4 5.0 1.0
OD1 A:ASP59 2.4 13.4 1.0
O A:HOH356 2.4 12.3 1.0
OD2 A:ASP57 2.6 9.1 1.0
CG A:ASP57 2.8 8.4 1.0
CG A:ASP59 3.4 10.2 1.0
C A:GLN61 3.5 8.2 1.0
OD2 A:ASP59 3.8 11.8 1.0
O A:HOH401 4.0 21.5 1.0
N A:GLN61 4.0 8.7 1.0
CA A:GLN61 4.2 10.5 1.0
CB A:ASP57 4.3 5.8 1.0
N A:ASP59 4.4 7.6 1.0
O A:HOH432 4.4 29.2 1.0
CB A:GLN61 4.4 11.5 1.0
N A:PHE62 4.5 8.0 1.0
OD2 A:ASP67 4.6 6.8 1.0
O A:HOH332 4.6 6.4 1.0
O A:HOH507 4.6 42.0 1.0
CA A:PHE62 4.7 8.7 1.0
CB A:ASP59 4.7 8.8 1.0
N A:ASN60 4.7 8.8 1.0
N A:ALA58 4.8 7.8 1.0
CA A:ASP59 4.9 8.9 1.0
O A:HOH443 5.0 31.6 1.0
C A:ASP59 5.0 8.8 1.0

Calcium binding site 4 out of 4 in 1qf1

Go back to Calcium Binding Sites List in 1qf1
Calcium binding site 4 out of 4 in the Thermolysin (E.C.3.4.24.27) Complexed with (2-Sulphanylheptanoyl)-Phe- Ala. 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-Sulphanylheptanoyl)-Phe- Ala. Parameters For Zn-Bidentation 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 19.6 1.0
OG1 A:THR194 2.3 10.0 1.0
O A:TYR193 2.3 9.6 1.0
OD1 A:ASP200 2.3 11.8 1.0
O A:THR194 2.4 16.1 1.0
O A:HOH343 2.4 10.1 1.0
O A:HOH384 2.4 18.1 1.0
C A:THR194 3.2 15.1 1.0
C A:TYR193 3.3 10.9 1.0
CG A:ASP200 3.4 11.8 1.0
C A:ILE197 3.5 20.5 1.0
CB A:THR194 3.5 12.6 1.0
CA A:THR194 3.7 12.8 1.0
OD2 A:ASP200 3.8 11.7 1.0
N A:THR194 3.9 10.5 1.0
CA A:ILE197 4.2 19.2 1.0
CB A:ILE197 4.2 19.3 1.0
N A:ILE197 4.2 22.0 1.0
N A:PRO195 4.3 16.5 1.0
N A:SER198 4.5 21.1 1.0
O A:ASP200 4.5 11.1 1.0
CA A:TYR193 4.5 10.0 1.0
O A:GLU190 4.6 8.2 1.0
CD2 A:TYR193 4.6 12.4 1.0
CA A:SER198 4.7 23.3 1.0
N A:ASP200 4.7 16.7 1.0
CG2 A:THR194 4.7 13.2 1.0
CB A:TYR193 4.7 9.4 1.0
CB A:ASP200 4.7 13.5 1.0
C A:ASP200 4.8 11.9 1.0
CA A:PRO195 4.8 18.5 1.0
CA A:ASP200 4.9 13.6 1.0
CG2 A:ILE197 5.0 17.9 1.0
CG A:TYR193 5.0 10.6 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 21:42:23 2024

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