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Calcium in PDB 5dpf: Thermolysin in Complex with Inhibitor.

Enzymatic activity of Thermolysin in Complex with Inhibitor.

All present enzymatic activity of Thermolysin in Complex with Inhibitor.:
3.4.24.27;

Protein crystallography data

The structure of Thermolysin in Complex with Inhibitor., PDB code: 5dpf was solved by S.G.Krimmer, A.Heine, G.Klebe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.16 / 1.47
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 92.747, 92.747, 130.222, 90.00, 90.00, 120.00
R / Rfree (%) 11.9 / 15.2

Other elements in 5dpf:

The structure of Thermolysin in Complex with Inhibitor. also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Thermolysin in Complex with Inhibitor. (pdb code 5dpf). 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 in Complex with Inhibitor., PDB code: 5dpf:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 5dpf

Go back to Calcium Binding Sites List in 5dpf
Calcium binding site 1 out of 4 in the Thermolysin in Complex with Inhibitor.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Thermolysin in Complex with Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca403

b:10.6
occ:1.00
O E:GLU187 2.3 10.3 1.0
OD2 E:ASP138 2.4 10.1 1.0
O E:HOH596 2.4 10.5 1.0
OE1 E:GLU177 2.5 11.2 1.0
OE2 E:GLU190 2.5 12.2 1.0
OD1 E:ASP185 2.5 11.2 1.0
OE1 E:GLU190 2.5 11.1 1.0
OE2 E:GLU177 2.7 12.2 1.0
CD E:GLU190 2.8 11.1 1.0
CD E:GLU177 2.9 11.6 1.0
CG E:ASP138 3.4 10.7 1.0
C E:GLU187 3.4 11.5 1.0
CG E:ASP185 3.5 11.4 1.0
HB3 E:ASP138 3.6 11.0 1.0
HA E:ILE188 3.7 12.2 1.0
H E:GLY189 3.8 13.2 1.0
H E:GLU187 3.8 13.8 1.0
CA E:CA406 3.8 13.6 1.0
OD2 E:ASP185 3.8 13.1 1.0
HB2 E:GLU187 3.9 16.9 1.0
CB E:ASP138 4.0 9.2 1.0
O E:ASP185 4.1 11.3 1.0
H E:ASP185 4.1 13.8 1.0
H E:GLU190 4.2 13.7 1.0
N E:GLU187 4.2 11.5 1.0
N E:ILE188 4.2 10.9 1.0
OD1 E:ASP138 4.3 12.0 1.0
HB2 E:ASP138 4.3 11.0 1.0
CA E:GLU187 4.3 12.1 1.0
CG E:GLU190 4.3 12.6 1.0
CA E:ILE188 4.3 10.2 1.0
O E:HOH594 4.4 17.0 1.0
HD13 E:ILE188 4.4 15.1 1.0
CG E:GLU177 4.4 10.4 1.0
N E:GLY189 4.4 11.0 1.0
HG3 E:GLU190 4.6 15.1 1.0
C E:ASP185 4.6 10.8 1.0
CB E:GLU187 4.6 14.1 1.0
HB2 E:GLU177 4.7 11.6 1.0
CB E:ASP185 4.7 11.2 1.0
N E:ASP185 4.8 11.5 1.0
HB3 E:GLU177 4.8 11.6 1.0
C E:ILE188 4.8 10.9 1.0
HG2 E:GLU190 4.8 15.1 1.0
HG2 E:GLU177 4.8 12.5 1.0
HA E:THR174 4.9 10.8 1.0
CB E:GLU177 4.9 9.7 1.0
O E:HOH548 4.9 16.9 1.0
HG3 E:GLU177 4.9 12.5 1.0
HB3 E:GLU190 5.0 14.5 1.0
N E:GLU190 5.0 11.4 1.0
CA E:ASP185 5.0 10.8 1.0

Calcium binding site 2 out of 4 in 5dpf

Go back to Calcium Binding Sites List in 5dpf
Calcium binding site 2 out of 4 in the Thermolysin in Complex with Inhibitor.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Thermolysin in Complex with Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca404

b:10.8
occ:1.00
O E:GLN61 2.3 11.2 1.0
O E:HOH771 2.3 12.9 1.0
O E:HOH561 2.4 14.1 1.0
OD1 E:ASP57 2.4 11.4 1.0
OD1 E:ASP59 2.4 11.0 1.0
O E:HOH617 2.4 12.8 1.0
OD2 E:ASP57 2.6 10.8 1.0
CG E:ASP57 2.8 11.0 1.0
H E:GLN61 3.3 12.4 0.5
H E:GLN61 3.3 12.4 0.5
CG E:ASP59 3.4 11.0 1.0
C E:GLN61 3.4 10.1 1.0
H E:ASP59 3.5 12.6 1.0
HB2 E:GLN61 3.6 16.0 0.5
HB2 E:GLN61 3.6 15.3 0.5
OD2 E:ASP59 3.8 13.8 1.0
N E:GLN61 3.9 10.4 1.0
O E:HOH698 3.9 16.0 1.0
HA E:PHE62 4.1 12.2 1.0
CA E:GLN61 4.1 10.9 0.5
CA E:GLN61 4.1 10.6 0.5
CB E:GLN61 4.3 13.3 0.5
CB E:GLN61 4.3 12.7 0.5
CB E:ASP57 4.3 10.3 1.0
H E:ALA58 4.3 12.4 1.0
H E:ASN60 4.3 12.4 1.0
N E:ASP59 4.3 10.5 1.0
O E:HOH738 4.4 14.1 1.0
O E:HOH837 4.5 21.9 1.0
N E:PHE62 4.5 9.6 1.0
O E:HOH522 4.6 11.5 1.0
CB E:ASP59 4.6 10.5 1.0
N E:ASN60 4.6 10.3 1.0
OD2 E:ASP67 4.6 10.5 1.0
HB2 E:ASP57 4.7 12.3 1.0
O E:HOH818 4.7 30.8 1.0
N E:ALA58 4.8 10.3 1.0
HB3 E:ASP57 4.8 12.3 1.0
CA E:PHE62 4.8 10.2 1.0
CA E:ASP59 4.8 10.6 1.0
O E:HOH859 4.8 32.9 1.0
HB3 E:GLN61 4.8 15.3 0.5
H E:PHE63 4.9 13.7 1.0
HA E:ASP57 4.9 12.1 1.0
HB3 E:GLN61 4.9 16.0 0.5
C E:ASP59 4.9 9.9 1.0
HB3 E:ASP59 5.0 12.6 1.0

Calcium binding site 3 out of 4 in 5dpf

Go back to Calcium Binding Sites List in 5dpf
Calcium binding site 3 out of 4 in the Thermolysin in Complex with Inhibitor.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Thermolysin in Complex with Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca405

b:13.6
occ:1.00
O E:ILE197 2.3 17.7 1.0
OG1 E:THR194 2.4 14.0 1.0
O E:TYR193 2.4 13.9 1.0
O E:THR194 2.4 14.4 1.0
OD1 E:ASP200 2.4 14.6 1.0
O E:HOH752 2.4 20.5 1.0
O E:HOH578 2.4 15.1 1.0
C E:THR194 3.2 14.2 1.0
C E:TYR193 3.4 13.4 1.0
CB E:THR194 3.4 14.2 1.0
CG E:ASP200 3.4 14.8 1.0
HB E:ILE197 3.5 24.3 1.0
C E:ILE197 3.5 18.6 1.0
CA E:THR194 3.6 14.1 1.0
H E:ILE197 3.6 25.2 1.0
HB E:THR194 3.7 17.1 1.0
OD2 E:ASP200 3.8 15.9 1.0
H E:ASP200 3.9 18.1 1.0
N E:THR194 3.9 13.9 1.0
HA E:SER198 4.0 24.9 1.0
HB3 E:TYR193 4.1 15.8 1.0
HD2 E:TYR193 4.2 19.3 1.0
CA E:ILE197 4.2 20.2 1.0
CB E:ILE197 4.3 20.2 1.0
O E:HOH765 4.3 41.4 1.0
N E:ILE197 4.3 21.0 1.0
N E:PRO195 4.3 15.3 1.0
HA E:PRO195 4.3 20.4 1.0
HG22 E:ILE197 4.5 24.1 1.0
N E:SER198 4.5 19.3 1.0
O E:ASP200 4.5 13.4 1.0
CA E:TYR193 4.5 11.8 1.0
HA E:THR194 4.6 16.9 1.0
O E:HOH680 4.6 35.9 1.0
O E:HOH775 4.6 31.7 1.0
O E:GLU190 4.6 12.9 1.0
CA E:SER198 4.6 20.8 1.0
N E:ASP200 4.7 15.1 1.0
CD2 E:TYR193 4.7 16.1 1.0
CB E:TYR193 4.7 13.2 1.0
CG2 E:THR194 4.7 14.2 1.0
CA E:PRO195 4.7 17.0 1.0
H E:GLY199 4.7 21.2 1.0
H E:THR194 4.7 16.7 1.0
CB E:ASP200 4.8 14.5 1.0
HG23 E:THR194 4.8 17.0 1.0
C E:ASP200 4.9 13.9 1.0
CG2 E:ILE197 4.9 20.1 1.0
H E:TYR193 4.9 13.2 1.0
C E:SER198 4.9 19.3 1.0
HG21 E:THR194 5.0 17.0 1.0
C E:PRO195 5.0 19.9 1.0
CA E:ASP200 5.0 14.0 1.0
CG E:TYR193 5.0 14.4 1.0
N E:GLY199 5.0 17.6 1.0

Calcium binding site 4 out of 4 in 5dpf

Go back to Calcium Binding Sites List in 5dpf
Calcium binding site 4 out of 4 in the Thermolysin in Complex with Inhibitor.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Thermolysin in Complex with Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca406

b:13.6
occ:1.00
O E:ASN183 2.2 14.7 1.0
O E:HOH609 2.3 15.1 1.0
OE2 E:GLU190 2.3 12.2 1.0
OD2 E:ASP185 2.3 13.1 1.0
O E:HOH548 2.4 16.9 1.0
OE2 E:GLU177 2.4 12.2 1.0
CG E:ASP185 3.2 11.4 1.0
CD E:GLU177 3.2 11.6 1.0
CD E:GLU190 3.3 11.1 1.0
C E:ASN183 3.4 14.9 1.0
HA E:PRO184 3.5 15.4 1.0
HG3 E:GLU190 3.6 15.1 1.0
OD1 E:ASP185 3.6 11.2 1.0
HB2 E:ASN183 3.8 22.3 1.0
HG2 E:GLU190 3.8 15.1 1.0
OE1 E:GLU177 3.8 11.2 1.0
HB3 E:ASN183 3.8 22.3 1.0
CA E:CA403 3.8 10.6 1.0
CG E:GLU190 3.8 12.6 1.0
H E:ASP185 3.9 13.8 1.0
O E:HOH623 4.1 39.5 1.0
CA E:PRO184 4.1 12.8 1.0
N E:ASP185 4.1 11.5 1.0
CB E:ASN183 4.1 18.6 1.0
OD2 E:ASP191 4.2 16.0 1.0
C E:PRO184 4.2 13.0 1.0
HG2 E:GLU177 4.2 12.5 1.0
N E:PRO184 4.3 13.3 1.0
CG E:GLU177 4.3 10.4 1.0
OD1 E:ASP191 4.3 15.8 1.0
OE1 E:GLU190 4.3 11.1 1.0
HG3 E:GLU177 4.4 12.5 1.0
CB E:ASP185 4.4 11.2 1.0
HB3 E:ASP185 4.4 13.4 1.0
O E:LYS182 4.4 17.6 1.0
CA E:ASN183 4.4 17.2 1.0
O E:HOH829 4.5 39.0 1.0
CG E:ASP191 4.6 14.5 1.0
CA E:ASP185 4.9 10.8 1.0
O E:PRO184 5.0 14.1 1.0

Reference:

S.G.Krimmer, G.Klebe. Thermodynamics of Protein-Ligand Interactions As A Reference For Computational Analysis: How to Assess Accuracy, Reliability and Relevance of Experimental Data. J. Comput. Aided Mol. Des. V. 29 867 2015.
ISSN: ISSN 1573-4951
PubMed: 26376645
DOI: 10.1007/S10822-015-9867-Y
Page generated: Wed Jul 9 05:12:27 2025

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