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Calcium in PDB 1tmn: Binding of N-Carboxymethyl Dipeptide Inhibitors to Thermolysin Determined By X-Ray Crystallography. A Novel Class of Transition- State Analogues For Zinc Peptidases

Enzymatic activity of Binding of N-Carboxymethyl Dipeptide Inhibitors to Thermolysin Determined By X-Ray Crystallography. A Novel Class of Transition- State Analogues For Zinc Peptidases

All present enzymatic activity of Binding of N-Carboxymethyl Dipeptide Inhibitors to Thermolysin Determined By X-Ray Crystallography. A Novel Class of Transition- State Analogues For Zinc Peptidases:
3.4.24.27;

Protein crystallography data

The structure of Binding of N-Carboxymethyl Dipeptide Inhibitors to Thermolysin Determined By X-Ray Crystallography. A Novel Class of Transition- State Analogues For Zinc Peptidases, PDB code: 1tmn was solved by A.F.Monzingo, B.W.Matthews, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 14.90 / 1.90
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 94.200, 94.200, 131.400, 90.00, 90.00, 120.00
R / Rfree (%) 17.1 / n/a

Other elements in 1tmn:

The structure of Binding of N-Carboxymethyl Dipeptide Inhibitors to Thermolysin Determined By X-Ray Crystallography. A Novel Class of Transition- State Analogues For Zinc Peptidases also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Binding of N-Carboxymethyl Dipeptide Inhibitors to Thermolysin Determined By X-Ray Crystallography. A Novel Class of Transition- State Analogues For Zinc Peptidases (pdb code 1tmn). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Binding of N-Carboxymethyl Dipeptide Inhibitors to Thermolysin Determined By X-Ray Crystallography. A Novel Class of Transition- State Analogues For Zinc Peptidases, PDB code: 1tmn:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 1tmn

Go back to Calcium Binding Sites List in 1tmn
Calcium binding site 1 out of 4 in the Binding of N-Carboxymethyl Dipeptide Inhibitors to Thermolysin Determined By X-Ray Crystallography. A Novel Class of Transition- State Analogues For Zinc Peptidases


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Binding of N-Carboxymethyl Dipeptide Inhibitors to Thermolysin Determined By X-Ray Crystallography. A Novel Class of Transition- State Analogues For Zinc Peptidases within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca318

b:13.4
occ:1.00
O E:GLU187 2.3 10.1 1.0
OD1 E:ASP138 2.4 16.4 1.0
OE2 E:GLU190 2.5 10.7 1.0
OE1 E:GLU190 2.5 9.0 1.0
OD2 E:ASP185 2.6 12.1 1.0
O E:HOH346 2.6 11.2 1.0
OE1 E:GLU177 2.7 15.9 1.0
CD E:GLU190 2.8 14.6 1.0
OE2 E:GLU177 3.0 12.1 1.0
CD E:GLU177 3.2 18.9 1.0
C E:GLU187 3.3 12.6 1.0
CG E:ASP185 3.5 14.2 1.0
CG E:ASP138 3.5 18.7 1.0
OD1 E:ASP185 3.7 13.5 1.0
CA E:CA319 3.9 14.5 1.0
CB E:ASP138 4.1 3.0 1.0
N E:ILE188 4.1 13.2 1.0
CA E:GLU187 4.2 17.9 1.0
CA E:ILE188 4.3 13.8 1.0
N E:GLU187 4.3 14.1 1.0
OD2 E:ASP138 4.3 14.7 1.0
CG E:GLU190 4.3 7.1 1.0
O E:ASP185 4.4 13.9 1.0
O E:HOH469 4.4 37.4 1.0
CB E:GLU187 4.4 14.9 1.0
N E:GLY189 4.5 16.9 1.0
O E:HOH350 4.6 12.0 1.0
CG E:GLU177 4.7 6.3 1.0
C E:ASP185 4.7 16.2 1.0
C E:ILE188 4.8 23.5 1.0
CB E:ASP185 4.8 13.9 1.0
N E:ASP185 4.8 10.6 1.0
O E:HOH353 4.9 12.2 1.0
N E:GLU190 5.0 5.8 1.0

Calcium binding site 2 out of 4 in 1tmn

Go back to Calcium Binding Sites List in 1tmn
Calcium binding site 2 out of 4 in the Binding of N-Carboxymethyl Dipeptide Inhibitors to Thermolysin Determined By X-Ray Crystallography. A Novel Class of Transition- State Analogues For Zinc Peptidases


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Binding of N-Carboxymethyl Dipeptide Inhibitors to Thermolysin Determined By X-Ray Crystallography. A Novel Class of Transition- State Analogues For Zinc Peptidases within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca319

b:14.5
occ:1.00
O E:HOH475 2.2 34.6 1.0
O E:HOH353 2.2 12.2 1.0
OE2 E:GLU177 2.3 12.1 1.0
O E:ASN183 2.3 17.7 1.0
OD1 E:ASP185 2.4 13.5 1.0
OE2 E:GLU190 2.5 10.7 1.0
CD E:GLU177 3.3 18.9 1.0
CG E:ASP185 3.3 14.2 1.0
CD E:GLU190 3.5 14.6 1.0
C E:ASN183 3.5 20.8 1.0
OD2 E:ASP185 3.8 12.1 1.0
OE1 E:GLU177 3.8 15.9 1.0
CA E:CA318 3.9 13.4 1.0
O E:LYS182 3.9 26.6 1.0
CG E:GLU190 4.0 7.1 1.0
CB E:ASN183 4.0 16.9 1.0
CA E:PRO184 4.1 10.3 1.0
OD2 E:ASP191 4.2 19.5 1.0
N E:ASP185 4.2 10.6 1.0
N E:PRO184 4.2 15.1 1.0
C E:PRO184 4.3 15.3 1.0
OD1 E:ASP191 4.3 13.8 1.0
CG E:GLU177 4.3 6.3 1.0
OE1 E:GLU190 4.5 9.0 1.0
CA E:ASN183 4.5 20.5 1.0
O E:HOH469 4.5 37.4 1.0
CB E:ASP185 4.5 13.9 1.0
CG E:ASP191 4.6 23.0 1.0
O E:PRO184 4.9 19.0 1.0
C E:LYS182 5.0 25.8 1.0
CA E:ASP185 5.0 8.1 1.0

Calcium binding site 3 out of 4 in 1tmn

Go back to Calcium Binding Sites List in 1tmn
Calcium binding site 3 out of 4 in the Binding of N-Carboxymethyl Dipeptide Inhibitors to Thermolysin Determined By X-Ray Crystallography. A Novel Class of Transition- State Analogues For Zinc Peptidases


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Binding of N-Carboxymethyl Dipeptide Inhibitors to Thermolysin Determined By X-Ray Crystallography. A Novel Class of Transition- State Analogues For Zinc Peptidases within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca320

b:12.8
occ:1.00
O E:GLN61 2.2 13.8 1.0
OD1 E:ASP57 2.2 12.6 1.0
O E:HOH482 2.2 21.7 1.0
OD1 E:ASP59 2.4 16.0 1.0
O E:HOH419 2.5 16.4 1.0
OD2 E:ASP57 2.5 11.4 1.0
CG E:ASP57 2.7 11.2 1.0
C E:GLN61 3.4 20.0 1.0
CG E:ASP59 3.5 19.3 1.0
OD2 E:ASP59 3.9 12.3 1.0
N E:GLN61 4.0 13.8 1.0
CA E:GLN61 4.1 19.0 1.0
O E:HOH484 4.1 25.8 1.0
CB E:ASP57 4.2 3.7 1.0
N E:ASP59 4.3 13.6 1.0
N E:PHE62 4.5 13.7 1.0
CB E:GLN61 4.5 17.9 1.0
OD2 E:ASP67 4.5 11.0 1.0
N E:ALA58 4.6 10.4 1.0
O E:HOH356 4.7 7.8 1.0
CB E:ASP59 4.7 13.7 1.0
CA E:PHE62 4.7 7.8 1.0
N E:ASN60 4.7 7.9 1.0
CA E:ASP59 4.8 11.5 1.0
C E:ASP59 4.9 19.6 1.0
CA E:ASP57 5.0 3.4 1.0

Calcium binding site 4 out of 4 in 1tmn

Go back to Calcium Binding Sites List in 1tmn
Calcium binding site 4 out of 4 in the Binding of N-Carboxymethyl Dipeptide Inhibitors to Thermolysin Determined By X-Ray Crystallography. A Novel Class of Transition- State Analogues For Zinc Peptidases


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Binding of N-Carboxymethyl Dipeptide Inhibitors to Thermolysin Determined By X-Ray Crystallography. A Novel Class of Transition- State Analogues For Zinc Peptidases within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca321

b:16.8
occ:1.00
O E:HOH480 1.8 26.6 1.0
OD1 E:ASP200 2.3 15.4 1.0
O E:ILE197 2.4 23.1 1.0
OG1 E:THR194 2.4 17.6 1.0
O E:HOH354 2.4 12.6 1.0
O E:TYR193 2.5 17.4 1.0
O E:THR194 2.5 15.8 1.0
C E:THR194 3.3 13.0 1.0
CG E:ASP200 3.3 14.8 1.0
C E:TYR193 3.5 23.3 1.0
CB E:THR194 3.6 16.4 1.0
C E:ILE197 3.6 25.7 1.0
OD2 E:ASP200 3.7 12.5 1.0
CA E:THR194 3.8 11.5 1.0
N E:THR194 4.0 14.5 1.0
O E:ASP200 4.3 16.6 1.0
N E:PRO195 4.3 18.4 1.0
CA E:ILE197 4.4 18.9 1.0
N E:ILE197 4.4 22.8 1.0
N E:ASP200 4.5 17.1 1.0
N E:SER198 4.5 25.4 1.0
O E:GLU190 4.6 15.0 1.0
CA E:SER198 4.6 24.2 1.0
CB E:ASP200 4.7 15.3 1.0
CA E:TYR193 4.7 15.2 1.0
CA E:PRO195 4.8 19.9 1.0
CG2 E:THR194 4.8 12.1 1.0
C E:ASP200 4.8 12.0 1.0
O E:HOH476 4.8 29.0 1.0
CB E:TYR193 4.8 17.5 1.0
CD2 E:TYR193 4.9 16.3 1.0
CA E:ASP200 4.9 6.8 1.0
C E:SER198 4.9 27.2 1.0
CB E:ILE197 4.9 27.1 1.0
CG2 E:ILE197 4.9 29.1 1.0

Reference:

A.F.Monzingo, B.W.Matthews. Binding of N-Carboxymethyl Dipeptide Inhibitors to Thermolysin Determined By X-Ray Crystallography: A Novel Class of Transition-State Analogues For Zinc Peptidases Biochemistry V. 23 5724 1984.
ISSN: ISSN 0006-2960
PubMed: 6395881
DOI: 10.1021/BI00319A010
Page generated: Sat Dec 12 03:21:41 2020

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