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Calcium in PDB 5dpe: 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: 5dpe 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) 34.17 / 1.34
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 92.690, 92.690, 130.261, 90.00, 90.00, 120.00
R / Rfree (%) 12.7 / 15.6

Other elements in 5dpe:

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 5dpe). 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: 5dpe:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 5dpe

Go back to Calcium Binding Sites List in 5dpe
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:10.4
occ:1.00
O E:GLU187 2.4 10.3 1.0
OD2 E:ASP138 2.4 11.0 1.0
O E:HOH602 2.4 10.7 1.0
OE1 E:GLU177 2.5 10.6 1.0
OD1 E:ASP185 2.5 11.0 1.0
OE1 E:GLU190 2.5 11.1 1.0
OE2 E:GLU190 2.5 11.3 1.0
OE2 E:GLU177 2.7 11.5 1.0
CD E:GLU190 2.8 10.5 1.0
CD E:GLU177 2.9 10.3 1.0
CG E:ASP138 3.4 11.6 1.0
C E:GLU187 3.4 11.0 1.0
CG E:ASP185 3.5 11.6 1.0
HB3 E:ASP138 3.6 12.0 1.0
HA E:ILE188 3.6 12.5 1.0
H E:GLY189 3.8 13.4 1.0
CA E:CA405 3.8 12.8 1.0
OD2 E:ASP185 3.8 12.8 1.0
H E:GLU187 3.8 13.9 1.0
HB2 E:GLU187 4.0 16.9 1.0
CB E:ASP138 4.0 10.0 1.0
O E:ASP185 4.1 11.5 1.0
H E:ASP185 4.2 13.8 1.0
H E:GLU190 4.2 12.8 1.0
N E:GLU187 4.3 11.6 1.0
N E:ILE188 4.3 10.1 1.0
HB2 E:ASP138 4.3 12.0 1.0
OD1 E:ASP138 4.3 12.2 1.0
CA E:ILE188 4.3 10.4 1.0
CA E:GLU187 4.3 11.8 1.0
CG E:GLU190 4.3 12.2 1.0
HD13 E:ILE188 4.4 15.9 1.0
O E:HOH580 4.4 16.3 1.0
CG E:GLU177 4.4 10.3 1.0
N E:GLY189 4.4 11.2 1.0
C E:ASP185 4.6 10.6 1.0
HG3 E:GLU190 4.6 14.6 1.0
CB E:GLU187 4.6 14.1 1.0
HB2 E:GLU177 4.7 11.8 1.0
HB3 E:GLU177 4.7 11.8 1.0
C E:ILE188 4.8 10.7 1.0
CB E:ASP185 4.8 11.5 1.0
N E:ASP185 4.8 11.5 1.0
HG2 E:GLU190 4.8 14.6 1.0
HG2 E:GLU177 4.8 12.4 1.0
HA E:THR174 4.9 11.1 1.0
CB E:GLU177 4.9 9.8 1.0
HG3 E:GLU177 4.9 12.4 1.0
O E:HOH560 4.9 15.2 1.0
HB3 E:GLU190 5.0 15.0 1.0
N E:GLU190 5.0 10.7 1.0
CA E:ASP185 5.0 11.1 1.0

Calcium binding site 2 out of 4 in 5dpe

Go back to Calcium Binding Sites List in 5dpe
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:10.9
occ:1.00
O E:GLN61 2.3 10.7 1.0
O E:HOH780 2.3 13.3 1.0
OD1 E:ASP57 2.4 11.2 1.0
OD1 E:ASP59 2.4 11.1 1.0
O E:HOH556 2.4 13.8 1.0
O E:HOH605 2.4 12.6 1.0
OD2 E:ASP57 2.6 10.6 1.0
CG E:ASP57 2.8 10.5 1.0
H E:GLN61 3.3 12.5 0.6
H E:GLN61 3.3 12.5 0.4
CG E:ASP59 3.4 11.5 1.0
C E:GLN61 3.4 10.0 1.0
HB2 E:GLN61 3.5 15.3 0.4
H E:ASP59 3.5 12.8 1.0
HB2 E:GLN61 3.6 15.0 0.6
OD2 E:ASP59 3.8 13.8 1.0
N E:GLN61 3.9 10.4 1.0
O E:HOH699 4.0 16.9 1.0
HA E:PHE62 4.1 11.6 1.0
CA E:GLN61 4.1 10.9 0.4
CA E:GLN61 4.1 10.8 0.6
CB E:GLN61 4.3 12.8 0.4
H E:ALA58 4.3 12.3 1.0
CB E:GLN61 4.3 12.5 0.6
CB E:ASP57 4.3 10.6 1.0
N E:ASP59 4.3 10.7 1.0
H E:ASN60 4.3 11.9 1.0
O E:HOH728 4.4 14.3 1.0
N E:PHE62 4.5 9.4 1.0
O E:HOH853 4.5 21.6 1.0
CB E:ASP59 4.6 10.6 1.0
O E:HOH524 4.6 10.8 1.0
N E:ASN60 4.6 9.9 1.0
OD2 E:ASP67 4.6 10.5 1.0
O E:HOH839 4.7 30.3 1.0
HB2 E:ASP57 4.7 12.7 1.0
N E:ALA58 4.7 10.3 1.0
HB3 E:ASP57 4.8 12.7 1.0
O E:HOH872 4.8 31.0 1.0
CA E:PHE62 4.8 9.7 1.0
CA E:ASP59 4.8 10.2 1.0
HB3 E:GLN61 4.8 15.0 0.6
H E:PHE63 4.9 12.8 1.0
HB3 E:GLN61 4.9 15.3 0.4
HA E:ASP57 4.9 12.3 1.0
C E:ASP59 4.9 9.7 1.0
HB3 E:ASP59 5.0 12.7 1.0
HB3 E:ALA58 5.0 14.0 1.0

Calcium binding site 3 out of 4 in 5dpe

Go back to Calcium Binding Sites List in 5dpe
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:12.8
occ:1.00
O E:ASN183 2.3 14.5 1.0
OE2 E:GLU190 2.3 11.3 1.0
OD2 E:ASP185 2.3 12.8 1.0
O E:HOH560 2.3 15.2 1.0
O E:HOH631 2.3 15.0 1.0
OE2 E:GLU177 2.4 11.5 1.0
CG E:ASP185 3.2 11.6 1.0
CD E:GLU177 3.2 10.3 1.0
CD E:GLU190 3.3 10.5 1.0
C E:ASN183 3.5 14.7 1.0
HA E:PRO184 3.6 15.1 1.0
HG3 E:GLU190 3.6 14.6 1.0
OD1 E:ASP185 3.6 11.0 1.0
HB2 E:ASN183 3.7 22.9 1.0
OE1 E:GLU177 3.8 10.6 1.0
HG2 E:GLU190 3.8 14.6 1.0
HB3 E:ASN183 3.8 22.9 1.0
CA E:CA403 3.8 10.4 1.0
CG E:GLU190 3.8 12.2 1.0
H E:ASP185 3.9 13.8 1.0
N E:ASP185 4.1 11.5 1.0
CA E:PRO184 4.1 12.6 1.0
CB E:ASN183 4.1 19.1 1.0
HG2 E:GLU177 4.2 12.4 1.0
O E:HOH740 4.2 41.0 1.0
C E:PRO184 4.2 12.6 1.0
CG E:GLU177 4.2 10.3 1.0
OD2 E:ASP191 4.3 16.6 1.0
OD1 E:ASP191 4.3 16.2 1.0
N E:PRO184 4.3 12.8 1.0
OE1 E:GLU190 4.3 11.1 1.0
HG3 E:GLU177 4.3 12.4 1.0
HB3 E:ASP185 4.4 13.8 1.0
CB E:ASP185 4.4 11.5 1.0
O E:LYS182 4.4 17.3 1.0
CA E:ASN183 4.5 17.1 1.0
CG E:ASP191 4.6 14.7 1.0
O E:HOH855 4.6 31.8 1.0
CA E:ASP185 4.9 11.1 1.0
O E:PRO184 4.9 14.2 1.0

Calcium binding site 4 out of 4 in 5dpe

Go back to Calcium Binding Sites List in 5dpe
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:13.1
occ:1.00
O E:ILE197 2.3 17.3 1.0
O E:TYR193 2.4 13.3 1.0
OG1 E:THR194 2.4 14.7 1.0
OD1 E:ASP200 2.4 13.9 1.0
O E:HOH615 2.4 16.1 1.0
O E:THR194 2.4 14.5 1.0
O E:HOH751 2.4 18.9 1.0
C E:THR194 3.2 14.4 1.0
C E:TYR193 3.4 13.0 1.0
CB E:THR194 3.4 14.4 1.0
CG E:ASP200 3.4 14.3 1.0
HB E:ILE197 3.5 23.8 1.0
C E:ILE197 3.5 17.8 1.0
CA E:THR194 3.6 14.0 1.0
H E:ILE197 3.7 23.9 1.0
HB E:THR194 3.7 17.3 1.0
OD2 E:ASP200 3.8 14.7 1.0
H E:ASP200 3.9 17.2 1.0
N E:THR194 3.9 13.2 1.0
HA E:SER198 4.0 23.9 1.0
HB3 E:TYR193 4.1 16.1 1.0
HD2 E:TYR193 4.1 18.6 1.0
CA E:ILE197 4.3 18.7 1.0
CB E:ILE197 4.3 19.8 1.0
N E:PRO195 4.3 15.7 1.0
N E:ILE197 4.3 19.9 1.0
HA E:PRO195 4.4 20.3 1.0
O E:HOH764 4.4 45.4 1.0
HG22 E:ILE197 4.5 23.6 1.0
O E:ASP200 4.5 13.1 1.0
N E:SER198 4.5 18.8 1.0
CA E:TYR193 4.6 13.0 1.0
HA E:THR194 4.6 16.8 1.0
O E:HOH707 4.6 32.3 1.0
O E:HOH784 4.6 27.6 1.0
O E:GLU190 4.6 12.7 1.0
CD2 E:TYR193 4.6 15.5 1.0
CA E:SER198 4.7 19.9 1.0
N E:ASP200 4.7 14.3 1.0
CB E:TYR193 4.7 13.4 1.0
H E:GLY199 4.7 20.3 1.0
CG2 E:THR194 4.7 14.4 1.0
CA E:PRO195 4.7 16.9 1.0
CB E:ASP200 4.7 14.1 1.0
H E:THR194 4.8 15.8 1.0
HG23 E:THR194 4.8 17.2 1.0
C E:ASP200 4.8 13.5 1.0
CG2 E:ILE197 4.9 19.7 1.0
H E:TYR193 4.9 14.1 1.0
HG21 E:THR194 5.0 17.2 1.0
C E:SER198 5.0 18.7 1.0
CG E:TYR193 5.0 14.5 1.0
CA E:ASP200 5.0 14.1 1.0
N E:GLY199 5.0 16.9 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: Sat Dec 12 05:22:10 2020

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