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Calcium in PDB 5m5f: Thermolysin in Complex with Inhibitor and Krypton

Enzymatic activity of Thermolysin in Complex with Inhibitor and Krypton

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

Protein crystallography data

The structure of Thermolysin in Complex with Inhibitor and Krypton, PDB code: 5m5f was solved by S.G.Krimmer, J.Cramer, A.Heine, G.Klebe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.55 / 1.33
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 92.428, 92.428, 130.192, 90.00, 90.00, 120.00
R / Rfree (%) 11.1 / 13.9

Other elements in 5m5f:

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

Zinc (Zn) 1 atom
Krypton (Kr) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Thermolysin in Complex with Inhibitor and Krypton (pdb code 5m5f). 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 and Krypton, PDB code: 5m5f:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 5m5f

Go back to Calcium Binding Sites List in 5m5f
Calcium binding site 1 out of 4 in the Thermolysin in Complex with Inhibitor and Krypton


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 and Krypton within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca402

b:8.8
occ:1.00
O E:GLU187 2.3 9.3 1.0
OD2 E:ASP138 2.4 8.7 1.0
O E:HOH559 2.4 9.1 1.0
OE1 E:GLU177 2.5 9.2 1.0
OD1 E:ASP185 2.5 9.6 1.0
OE1 E:GLU190 2.5 10.1 1.0
OE2 E:GLU190 2.5 10.1 1.0
OE2 E:GLU177 2.7 9.8 1.0
CD E:GLU190 2.8 9.6 1.0
CD E:GLU177 2.9 9.1 1.0
CG E:ASP138 3.4 8.4 1.0
C E:GLU187 3.4 9.8 1.0
CG E:ASP185 3.5 10.2 1.0
HB3 E:ASP138 3.6 8.8 1.0
HA E:ILE188 3.6 11.3 1.0
H E:GLY189 3.8 10.6 1.0
H E:GLU187 3.8 12.2 1.0
CA E:CA404 3.8 11.3 1.0
OD2 E:ASP185 3.8 11.6 1.0
HB2 E:GLU187 3.8 15.2 1.0
CB E:ASP138 4.0 7.3 1.0
O E:ASP185 4.1 9.1 1.0
H E:ASP185 4.1 12.4 1.0
H E:GLU190 4.2 11.5 1.0
N E:GLU187 4.2 10.1 1.0
HB2 E:ASP138 4.2 8.8 1.0
OD1 E:ASP138 4.3 9.8 1.0
N E:ILE188 4.3 9.5 1.0
CA E:GLU187 4.3 10.7 1.0
CA E:ILE188 4.3 9.4 1.0
HD13 E:ILE188 4.3 13.8 1.0
CG E:GLU190 4.4 10.7 1.0
CG E:GLU177 4.4 9.1 1.0
N E:GLY189 4.4 8.8 1.0
O E:HOH575 4.4 13.2 1.0
CB E:GLU187 4.6 12.6 1.0
C E:ASP185 4.6 9.5 1.0
HG3 E:GLU190 4.6 12.8 1.0
HB2 E:GLU177 4.7 9.8 1.0
HB3 E:GLU177 4.7 9.8 1.0
N E:ASP185 4.7 10.4 1.0
C E:ILE188 4.8 9.5 1.0
CB E:ASP185 4.8 10.1 1.0
HG2 E:GLU177 4.8 11.0 1.0
O E:HOH541 4.8 14.5 1.0
HG2 E:GLU190 4.8 12.8 1.0
CB E:GLU177 4.9 8.2 1.0
HA E:THR174 4.9 9.0 1.0
HG3 E:GLU177 4.9 11.0 1.0
CA E:ASP185 4.9 10.0 1.0
HB3 E:GLU190 5.0 12.8 1.0
N E:GLU190 5.0 9.6 1.0
HB3 E:GLU187 5.0 15.2 1.0

Calcium binding site 2 out of 4 in 5m5f

Go back to Calcium Binding Sites List in 5m5f
Calcium binding site 2 out of 4 in the Thermolysin in Complex with Inhibitor and Krypton


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 and Krypton within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca403

b:9.1
occ:1.00
O E:GLN61 2.3 9.4 1.0
O E:HOH768 2.3 11.5 1.0
OD1 E:ASP59 2.4 9.8 1.0
OD1 E:ASP57 2.4 9.7 1.0
O E:HOH547 2.4 11.4 1.0
O E:HOH577 2.4 10.8 1.0
OD2 E:ASP57 2.6 9.0 1.0
CG E:ASP57 2.8 9.3 1.0
H E:GLN61 3.3 11.1 1.0
CG E:ASP59 3.4 10.7 1.0
C E:GLN61 3.4 8.8 1.0
H E:ASP59 3.5 11.2 1.0
HB2 E:GLN61 3.6 14.2 1.0
OD2 E:ASP59 3.8 12.7 1.0
N E:GLN61 3.9 9.3 1.0
O E:HOH698 4.0 15.4 1.0
HA E:PHE62 4.0 9.9 1.0
CA E:GLN61 4.1 9.5 1.0
H E:ALA58 4.3 10.2 1.0
N E:ASP59 4.3 9.4 1.0
CB E:GLN61 4.3 11.8 1.0
CB E:ASP57 4.3 9.0 1.0
H E:ASN60 4.4 10.2 1.0
N E:PHE62 4.5 8.1 1.0
O E:HOH844 4.5 16.1 1.0
CB E:ASP59 4.6 9.6 1.0
O E:HOH521 4.6 9.0 1.0
OD2 E:ASP67 4.6 8.9 1.0
N E:ASN60 4.6 8.5 1.0
HB2 E:ASP57 4.7 10.8 1.0
O E:HOH867 4.7 26.6 1.0
O E:HOH835 4.7 26.1 1.0
N E:ALA58 4.7 8.5 1.0
CA E:PHE62 4.8 8.3 1.0
CA E:ASP59 4.8 9.4 1.0
HB3 E:ASP57 4.8 10.8 1.0
H E:PHE63 4.9 11.0 1.0
HA E:ASP57 4.9 10.3 1.0
C E:ASP59 4.9 8.8 1.0
HB3 E:GLN61 4.9 14.2 1.0
HB3 E:ASP59 5.0 11.6 1.0

Calcium binding site 3 out of 4 in 5m5f

Go back to Calcium Binding Sites List in 5m5f
Calcium binding site 3 out of 4 in the Thermolysin in Complex with Inhibitor and Krypton


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 and Krypton within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca404

b:11.3
occ:1.00
O E:ASN183 2.3 12.5 1.0
O E:HOH541 2.3 14.5 1.0
O E:HOH585 2.3 13.8 1.0
OE2 E:GLU190 2.3 10.1 1.0
OD2 E:ASP185 2.3 11.6 1.0
OE2 E:GLU177 2.4 9.8 1.0
CD E:GLU177 3.2 9.1 1.0
CG E:ASP185 3.2 10.2 1.0
CD E:GLU190 3.3 9.6 1.0
C E:ASN183 3.5 13.2 1.0
HA E:PRO184 3.6 13.1 1.0
OD1 E:ASP185 3.6 9.6 1.0
HG3 E:GLU190 3.6 12.8 1.0
HB2 E:ASN183 3.7 20.6 1.0
OE1 E:GLU177 3.7 9.2 1.0
HB3 E:ASN183 3.8 20.6 1.0
CA E:CA402 3.8 8.8 1.0
HG2 E:GLU190 3.9 12.8 1.0
CG E:GLU190 3.9 10.7 1.0
H E:ASP185 4.0 12.4 1.0
CB E:ASN183 4.1 17.2 1.0
N E:ASP185 4.1 10.4 1.0
CA E:PRO184 4.1 10.9 1.0
OD2 E:ASP191 4.2 13.4 1.0
HG2 E:GLU177 4.2 11.0 1.0
C E:PRO184 4.2 11.4 1.0
OD1 E:ASP191 4.2 13.5 1.0
CG E:GLU177 4.3 9.1 1.0
N E:PRO184 4.3 11.6 1.0
OE1 E:GLU190 4.3 10.1 1.0
HG3 E:GLU177 4.3 11.0 1.0
HB3 E:ASP185 4.4 12.2 1.0
CB E:ASP185 4.4 10.1 1.0
O E:LYS182 4.4 15.2 1.0
CA E:ASN183 4.5 15.1 1.0
O E:HOH837 4.6 38.6 1.0
CG E:ASP191 4.6 12.4 1.0
CA E:ASP185 4.9 10.0 1.0
O E:PRO184 4.9 12.4 1.0

Calcium binding site 4 out of 4 in 5m5f

Go back to Calcium Binding Sites List in 5m5f
Calcium binding site 4 out of 4 in the Thermolysin in Complex with Inhibitor and Krypton


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 and Krypton within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca405

b:11.8
occ:1.00
O E:ILE197 2.3 16.1 1.0
O E:TYR193 2.3 11.8 1.0
OG1 E:THR194 2.4 12.7 1.0
O E:HOH598 2.4 13.9 1.0
O E:HOH752 2.4 19.4 1.0
OD1 E:ASP200 2.4 12.5 1.0
O E:THR194 2.4 13.9 1.0
C E:THR194 3.2 13.4 1.0
C E:TYR193 3.3 11.7 1.0
CB E:THR194 3.5 13.4 1.0
CG E:ASP200 3.5 12.7 1.0
HB E:ILE197 3.5 23.6 1.0
C E:ILE197 3.5 16.9 1.0
H E:ILE197 3.6 22.3 1.0
CA E:THR194 3.6 12.7 1.0
HB E:THR194 3.7 16.1 1.0
OD2 E:ASP200 3.8 13.4 1.0
H E:ASP200 3.9 16.0 1.0
N E:THR194 3.9 11.7 1.0
HA E:SER198 4.0 23.1 1.0
HB3 E:TYR193 4.1 14.6 1.0
HD2 E:TYR193 4.1 17.2 1.0
CA E:ILE197 4.3 18.1 1.0
CB E:ILE197 4.3 19.6 1.0
N E:PRO195 4.3 14.5 1.0
N E:ILE197 4.3 18.6 1.0
HA E:PRO195 4.3 18.8 1.0
HG22 E:ILE197 4.3 24.0 1.0
O E:HOH734 4.5 40.8 1.0
O E:ASP200 4.5 12.5 1.0
N E:SER198 4.5 17.7 1.0
CA E:TYR193 4.5 11.5 1.0
O E:HOH773 4.6 28.0 1.0
HA E:THR194 4.6 15.2 1.0
O E:HOH683 4.6 34.7 1.0
CA E:SER198 4.6 19.3 1.0
CD2 E:TYR193 4.7 14.3 1.0
O E:GLU190 4.7 11.5 1.0
N E:ASP200 4.7 13.3 1.0
CB E:TYR193 4.7 12.1 1.0
H E:GLY199 4.7 20.2 1.0
CA E:PRO195 4.7 15.7 1.0
CG2 E:THR194 4.7 14.2 1.0
H E:THR194 4.7 14.0 1.0
CB E:ASP200 4.7 13.0 1.0
C E:ASP200 4.8 12.5 1.0
CG2 E:ILE197 4.8 20.0 1.0
HG23 E:THR194 4.8 17.1 1.0
H E:TYR193 4.9 12.5 1.0
C E:SER198 4.9 18.3 1.0
CA E:ASP200 5.0 13.2 1.0
C E:PRO195 5.0 17.5 1.0
N E:GLY199 5.0 16.9 1.0
HG21 E:THR194 5.0 17.1 1.0
CG E:TYR193 5.0 13.4 1.0

Reference:

S.G.Krimmer, J.Cramer, J.Schiebel, A.Heine, G.Klebe. How Nothing Boosts Affinity: Hydrophobic Ligand Binding to the Virtually Vacated S1' Pocket of Thermolysin. J. Am. Chem. Soc. V. 139 10419 2017.
ISSN: ESSN 1520-5126
PubMed: 28696673
DOI: 10.1021/JACS.7B05028
Page generated: Sat Dec 12 05:36:50 2020

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