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Calcium in PDB 5mnr: Thermolysin in Complex with Inhibitor JC256

Enzymatic activity of Thermolysin in Complex with Inhibitor JC256

All present enzymatic activity of Thermolysin in Complex with Inhibitor JC256:
3.4.24.27;

Protein crystallography data

The structure of Thermolysin in Complex with Inhibitor JC256, PDB code: 5mnr was solved by J.Cramer, 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 / 1.25
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 92.735, 92.735, 130.538, 90.00, 90.00, 120.00
R / Rfree (%) 10.3 / 12.7

Other elements in 5mnr:

The structure of Thermolysin in Complex with Inhibitor JC256 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 JC256 (pdb code 5mnr). 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 JC256, PDB code: 5mnr:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 5mnr

Go back to Calcium Binding Sites List in 5mnr
Calcium binding site 1 out of 4 in the Thermolysin in Complex with Inhibitor JC256


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 JC256 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca402

b:8.0
occ:1.00
 O E:GLU187 2.3 9.1 1.0
OD2 E:ASP138 2.4 8.1 1.0
O E:HOH570 2.4 8.6 1.0
OE1 E:GLU177 2.5 8.4 1.0
OD1 E:ASP185 2.5 9.0 1.0
OE1 E:GLU190 2.5 8.8 1.0
OE2 E:GLU190 2.5 9.3 1.0
OE2 E:GLU177 2.8 9.5 1.0
CD E:GLU190 2.8 8.9 1.0
CD E:GLU177 2.9 8.2 1.0
CG E:ASP138 3.4 8.1 1.0
C E:GLU187 3.4 9.2 1.0
CG E:ASP185 3.5 9.6 1.0
HB3 E:ASP138 3.6 8.3 1.0
HA E:ILE188 3.6 10.2 1.0
H E:GLU187 3.7 11.2 1.0
H E:GLY189 3.8 10.0 1.0
OD2 E:ASP185 3.8 11.0 1.0
CA E:CA404 3.8 10.4 1.0
HB2 E:GLU187 3.9 15.2 1.0
CB E:ASP138 4.0 7.0 1.0
O E:ASP185 4.1 9.3 1.0
H E:GLU190 4.2 10.8 1.0
H E:ASP185 4.2 11.5 1.0
N E:GLU187 4.2 9.3 1.0
N E:ILE188 4.2 8.6 1.0
OD1 E:ASP138 4.3 9.7 1.0
HB2 E:ASP138 4.3 8.3 1.0
CA E:GLU187 4.3 9.8 1.0
CA E:ILE188 4.3 8.5 1.0
CG E:GLU190 4.4 9.8 1.0
HD13 E:ILE188 4.4 12.8 1.0
CG E:GLU177 4.4 8.3 1.0
O E:HOH604 4.4 13.9 1.0
N E:GLY189 4.4 8.3 1.0
O E:HOH708 4.5 47.7 1.0
CB E:GLU187 4.6 12.6 1.0
C E:ASP185 4.6 9.3 1.0
HG3 E:GLU190 4.6 11.8 1.0
HB2 E:GLU177 4.7 9.3 1.0
HB3 E:GLU177 4.7 9.3 1.0
CB E:ASP185 4.8 9.6 1.0
C E:ILE188 4.8 8.6 1.0
N E:ASP185 4.8 9.6 1.0
HG2 E:GLU177 4.8 10.0 1.0
HG2 E:GLU190 4.8 11.8 1.0
HA E:THR174 4.9 8.5 1.0
CB E:GLU177 4.9 7.8 1.0
O E:HOH547 4.9 14.1 1.0
HG3 E:GLU177 4.9 10.0 1.0
N E:GLU190 5.0 9.0 1.0
HB3 E:GLU190 5.0 11.8 1.0
CA E:ASP185 5.0 9.5 1.0

Calcium binding site 2 out of 4 in 5mnr

Go back to Calcium Binding Sites List in 5mnr
Calcium binding site 2 out of 4 in the Thermolysin in Complex with Inhibitor JC256


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 JC256 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca403

b:8.3
occ:1.00
 O E:GLN61 2.3 8.6 1.0
O E:HOH789 2.3 11.0 1.0
OD1 E:ASP59 2.4 9.2 1.0
OD1 E:ASP57 2.4 9.0 1.0
O E:HOH577 2.4 10.5 1.0
O E:HOH613 2.4 9.8 1.0
OD2 E:ASP57 2.6 8.7 1.0
CG E:ASP57 2.8 8.4 1.0
H E:GLN61 3.3 10.4 1.0
CG E:ASP59 3.4 9.9 1.0
C E:GLN61 3.5 8.2 1.0
H E:ASP59 3.5 10.8 1.0
HB2 E:GLN61 3.7 14.1 1.0
OD2 E:ASP59 3.8 12.1 1.0
N E:GLN61 4.0 8.7 1.0
O E:HOH721 4.0 15.1 1.0
HA E:PHE62 4.0 9.5 1.0
CA E:GLN61 4.2 9.1 1.0
H E:ALA58 4.3 10.2 1.0
CB E:ASP57 4.3 8.6 1.0
N E:ASP59 4.3 9.0 1.0
H E:ASN60 4.4 9.5 1.0
CB E:GLN61 4.4 11.8 1.0
O E:HOH758 4.5 11.2 1.0
N E:PHE62 4.5 7.4 1.0
CB E:ASP59 4.6 9.3 1.0
O E:HOH523 4.6 8.2 1.0
N E:ASN60 4.6 7.9 1.0
OD2 E:ASP67 4.7 8.2 1.0
HB2 E:ASP57 4.7 10.3 1.0
O E:HOH878 4.7 22.4 1.0
O E:HOH847 4.7 26.1 1.0
N E:ALA58 4.7 8.5 1.0
CA E:PHE62 4.8 7.9 1.0
HB3 E:ASP57 4.8 10.3 1.0
CA E:ASP59 4.8 8.9 1.0
H E:PHE63 4.8 10.0 1.0
HA E:ASP57 4.9 9.9 1.0
C E:ASP59 4.9 8.3 1.0
HB3 E:ASP59 5.0 11.2 1.0

Calcium binding site 3 out of 4 in 5mnr

Go back to Calcium Binding Sites List in 5mnr
Calcium binding site 3 out of 4 in the Thermolysin in Complex with Inhibitor JC256


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 JC256 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca404

b:10.4
occ:1.00
 O E:ASN183 2.3 11.9 1.0
O E:HOH557 2.3 13.4 1.0
OE2 E:GLU190 2.3 9.3 1.0
OD2 E:ASP185 2.3 11.0 1.0
O E:HOH547 2.3 14.1 1.0
OE2 E:GLU177 2.4 9.5 1.0
CG E:ASP185 3.2 9.6 1.0
CD E:GLU177 3.2 8.2 1.0
CD E:GLU190 3.3 8.9 1.0
C E:ASN183 3.5 12.5 1.0
HA E:PRO184 3.6 13.0 1.0
HG3 E:GLU190 3.6 11.8 1.0
OD1 E:ASP185 3.6 9.0 1.0
OE1 E:GLU177 3.7 8.4 1.0
HB2 E:ASN183 3.7 21.2 1.0
HB3 E:ASN183 3.8 21.2 1.0
HG2 E:GLU190 3.8 11.8 1.0
CA E:CA402 3.8 8.0 1.0
CG E:GLU190 3.8 9.8 1.0
H E:ASP185 4.0 11.5 1.0
CB E:ASN183 4.1 17.7 1.0
CA E:PRO184 4.1 10.8 1.0
O E:HOH521 4.1 31.3 1.0
N E:ASP185 4.2 9.6 1.0
OD1 E:ASP191 4.2 12.5 1.0
OD2 E:ASP191 4.2 12.6 1.0
CG E:GLU177 4.2 8.3 1.0
HG2 E:GLU177 4.2 10.0 1.0
OE1 E:GLU190 4.3 8.8 1.0
C E:PRO184 4.3 10.9 1.0
N E:PRO184 4.3 11.3 1.0
HG3 E:GLU177 4.3 10.0 1.0
HB3 E:ASP185 4.3 11.6 1.0
CB E:ASP185 4.4 9.6 1.0
O E:LYS182 4.4 16.2 1.0
CA E:ASN183 4.5 15.2 1.0
CG E:ASP191 4.6 11.2 1.0
O E:HOH708 4.7 47.7 1.0
O E:HOH853 4.7 39.8 1.0
CA E:ASP185 4.9 9.5 1.0
O E:PRO184 5.0 12.3 1.0

Calcium binding site 4 out of 4 in 5mnr

Go back to Calcium Binding Sites List in 5mnr
Calcium binding site 4 out of 4 in the Thermolysin in Complex with Inhibitor JC256


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 JC256 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca405

b:12.4
occ:1.00
 O E:ILE197 2.3 18.2 1.0
OG1 E:THR194 2.4 13.2 1.0
OD1 E:ASP200 2.4 13.4 1.0
O E:TYR193 2.4 11.4 1.0
O E:HOH606 2.4 14.6 1.0
O E:THR194 2.4 13.8 1.0
O E:HOH774 2.4 18.1 1.0
C E:THR194 3.2 13.7 1.0
C E:TYR193 3.4 11.3 1.0
CG E:ASP200 3.4 13.5 1.0
CB E:THR194 3.4 13.4 1.0
HB E:ILE197 3.5 25.3 1.0
C E:ILE197 3.5 18.9 1.0
H E:ILE197 3.6 23.4 1.0
CA E:THR194 3.6 12.8 1.0
HB E:THR194 3.7 16.1 1.0
OD2 E:ASP200 3.8 14.6 1.0
H E:ASP200 3.9 18.2 1.0
N E:THR194 3.9 12.0 1.0
HD2 E:TYR193 4.0 15.3 1.0
HB3 E:TYR193 4.0 14.2 1.0
HA E:SER198 4.1 24.9 1.0
CB E:ILE197 4.2 21.1 1.0
CA E:ILE197 4.2 19.6 1.0
N E:PRO195 4.3 14.7 1.0
N E:ILE197 4.3 19.5 1.0
HA E:PRO195 4.3 19.9 1.0
HG22 E:ILE197 4.3 25.6 1.0
O E:HOH653 4.4 38.0 1.0
O E:HOH647 4.5 44.0 1.0
O E:ASP200 4.5 13.0 1.0
N E:SER198 4.5 19.5 1.0
CA E:TYR193 4.5 11.2 1.0
HA E:THR194 4.6 15.3 1.0
CD2 E:TYR193 4.6 12.8 1.0
N E:ASP200 4.6 15.2 1.0
CB E:TYR193 4.7 11.8 1.0
CA E:SER198 4.7 20.7 1.0
O E:GLU190 4.7 10.9 1.0
CA E:PRO195 4.7 16.6 1.0
H E:GLY199 4.7 21.9 1.0
CG2 E:THR194 4.7 13.7 1.0
H E:THR194 4.7 14.4 1.0
CB E:ASP200 4.7 14.2 1.0
O E:HOH794 4.8 26.4 1.0
O E:HOH634 4.8 36.0 1.0
C E:ASP200 4.8 13.1 1.0
CG2 E:ILE197 4.8 21.3 1.0
HG23 E:THR194 4.8 16.4 1.0
H E:TYR193 4.9 12.5 1.0
C E:SER198 4.9 20.1 1.0
C E:PRO195 5.0 18.3 1.0
CA E:ASP200 5.0 14.2 1.0
HG21 E:THR194 5.0 16.4 1.0
N E:GLY199 5.0 18.3 1.0

Reference:

J.Cramer, S.G.Krimmer, A.Heine, G.Klebe. Paying the Price of Desolvation in Solvent-Exposed Protein Pockets: Impact of Distal Solubilizing Groups on Affinity and Binding Thermodynamics in A Series of Thermolysin Inhibitors. J. Med. Chem. V. 60 5791 2017.
ISSN: ISSN 1520-4804
PubMed: 28590130
DOI: 10.1021/ACS.JMEDCHEM.7B00490
Page generated: Mon Jul 15 08:31:45 2024

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