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Calcium in PDB 5jss: Thermolysin in Complex with JC149.

Enzymatic activity of Thermolysin in Complex with JC149.

All present enzymatic activity of Thermolysin in Complex with JC149.:
3.4.24.27;

Protein crystallography data

The structure of Thermolysin in Complex with JC149., PDB code: 5jss 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) 40.07 / 1.19
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 92.528, 92.528, 131.314, 90.00, 90.00, 120.00
R / Rfree (%) 10.3 / 12.1

Other elements in 5jss:

The structure of Thermolysin in Complex with JC149. 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 JC149. (pdb code 5jss). 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 JC149., PDB code: 5jss:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 5jss

Go back to Calcium Binding Sites List in 5jss
Calcium binding site 1 out of 4 in the Thermolysin in Complex with JC149.


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 JC149. within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca402

b:7.2
occ:1.00
O E:GLU187 2.3 7.9 1.0
OD2 E:ASP138 2.4 7.5 1.0
O E:HOH591 2.4 7.4 1.0
OE1 E:GLU177 2.5 7.6 1.0
OD1 E:ASP185 2.5 7.8 1.0
OE1 E:GLU190 2.5 8.1 1.0
OE2 E:GLU190 2.5 8.6 1.0
OE2 E:GLU177 2.7 8.7 1.0
CD E:GLU190 2.8 8.1 1.0
CD E:GLU177 2.9 7.5 1.0
CG E:ASP138 3.4 7.1 1.0
C E:GLU187 3.4 7.8 1.0
CG E:ASP185 3.5 8.7 1.0
HB3 E:ASP138 3.6 7.8 1.0
HA E:ILE188 3.7 8.6 1.0
H E:GLU187 3.7 9.7 1.0
CA E:CA404 3.8 10.2 1.0
OD2 E:ASP185 3.8 10.0 1.0
H E:GLY189 3.8 9.1 1.0
HB2 E:GLU187 3.9 11.6 1.0
CB E:ASP138 4.0 6.5 1.0
O E:ASP185 4.1 8.0 1.0
H E:ASP185 4.2 10.5 1.0
H E:GLU190 4.2 9.0 1.0
N E:GLU187 4.2 8.1 1.0
N E:ILE188 4.2 7.4 1.0
OD1 E:ASP138 4.3 8.6 1.0
HB2 E:ASP138 4.3 7.8 1.0
O E:HOH618 4.3 12.9 0.5
CA E:GLU187 4.3 8.0 1.0
CA E:ILE188 4.3 7.2 1.0
CG E:GLU190 4.4 8.7 1.0
CG E:GLU177 4.4 7.4 1.0
HD13 E:ILE188 4.4 12.0 1.0
O E:HOH608 4.4 12.4 1.0
N E:GLY189 4.4 7.5 1.0
CB E:GLU187 4.6 9.7 1.0
C E:ASP185 4.6 7.7 1.0
HG3 E:GLU190 4.6 10.4 1.0
HB2 E:GLU177 4.7 8.4 1.0
HB3 E:GLU177 4.7 8.4 1.0
N E:ASP185 4.8 8.8 1.0
CB E:ASP185 4.8 8.4 1.0
C E:ILE188 4.8 7.4 1.0
HG2 E:GLU177 4.8 8.9 1.0
HG2 E:GLU190 4.8 10.4 1.0
O E:HOH561 4.8 13.8 1.0
HA E:THR174 4.9 7.3 1.0
CB E:GLU177 4.9 7.0 1.0
HG3 E:GLU177 4.9 8.9 1.0
HB3 E:GLU190 4.9 10.3 1.0
CA E:ASP185 5.0 8.3 1.0
N E:GLU190 5.0 7.5 1.0

Calcium binding site 2 out of 4 in 5jss

Go back to Calcium Binding Sites List in 5jss
Calcium binding site 2 out of 4 in the Thermolysin in Complex with JC149.


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 JC149. within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca403

b:7.7
occ:1.00
O E:GLN61 2.3 8.0 1.0
O E:HOH803 2.3 10.1 1.0
OD1 E:ASP59 2.4 8.4 1.0
OD1 E:ASP57 2.4 8.4 1.0
O E:HOH575 2.4 10.2 1.0
O E:HOH606 2.4 9.4 1.0
OD2 E:ASP57 2.6 8.0 1.0
CG E:ASP57 2.8 8.0 1.0
H E:GLN61 3.3 9.1 1.0
CG E:ASP59 3.4 9.0 1.0
C E:GLN61 3.5 7.7 1.0
H E:ASP59 3.5 9.6 1.0
HB2 E:GLN61 3.6 12.5 1.0
OD2 E:ASP59 3.8 11.0 1.0
N E:GLN61 4.0 7.6 1.0
O E:HOH697 4.0 15.3 1.0
HA E:PHE62 4.1 8.7 1.0
CA E:GLN61 4.2 8.1 1.0
H E:ALA58 4.3 9.4 1.0
CB E:GLN61 4.3 10.4 1.0
N E:ASP59 4.3 8.0 1.0
CB E:ASP57 4.3 7.6 1.0
H E:ASN60 4.4 8.9 1.0
N E:PHE62 4.5 7.3 1.0
O E:HOH881 4.5 14.3 1.0
CB E:ASP59 4.6 8.8 1.0
O E:HOH533 4.6 7.3 1.0
OD2 E:ASP67 4.6 7.7 1.0
N E:ASN60 4.6 7.5 1.0
O E:HOH902 4.7 24.5 1.0
O E:HOH873 4.7 27.6 1.0
HB2 E:ASP57 4.7 9.2 1.0
N E:ALA58 4.7 7.8 1.0
CA E:ASP59 4.8 8.2 1.0
CA E:PHE62 4.8 7.3 1.0
HB3 E:ASP57 4.8 9.2 1.0
H E:PHE63 4.9 10.1 1.0
HA E:ASP57 4.9 9.2 1.0
C E:ASP59 4.9 7.8 1.0
HB3 E:GLN61 5.0 12.5 1.0
HB3 E:ASP59 5.0 10.6 1.0
HG2 E:GLN61 5.0 19.7 1.0

Calcium binding site 3 out of 4 in 5jss

Go back to Calcium Binding Sites List in 5jss
Calcium binding site 3 out of 4 in the Thermolysin in Complex with JC149.


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 JC149. within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca404

b:10.2
occ:1.00
OE2 E:GLU190 2.3 8.6 1.0
O E:ASN183 2.3 11.9 1.0
O E:HOH615 2.3 13.1 1.0
O E:HOH561 2.3 13.8 1.0
OD2 E:ASP185 2.3 10.0 1.0
OE2 E:GLU177 2.5 8.7 1.0
CG E:ASP185 3.2 8.7 1.0
CD E:GLU177 3.2 7.5 1.0
CD E:GLU190 3.3 8.1 1.0
C E:ASN183 3.5 12.1 1.0
HA E:PRO184 3.5 11.5 1.0
HG3 E:GLU190 3.6 10.4 1.0
OD1 E:ASP185 3.6 7.8 1.0
OE1 E:GLU177 3.7 7.6 1.0
HB2 E:ASN183 3.8 20.5 1.0
CA E:CA402 3.8 7.2 1.0
HB3 E:ASN183 3.8 20.5 1.0
HG2 E:GLU190 3.8 10.4 1.0
CG E:GLU190 3.8 8.7 1.0
H E:ASP185 4.0 10.5 1.0
CA E:PRO184 4.1 9.6 1.0
N E:ASP185 4.2 8.8 1.0
CB E:ASN183 4.2 17.1 1.0
OD2 E:ASP191 4.2 11.9 1.0
C E:PRO184 4.3 9.5 1.0
OE1 E:GLU190 4.3 8.1 1.0
CG E:GLU177 4.3 7.4 1.0
OD1 E:ASP191 4.3 11.9 1.0
HG2 E:GLU177 4.3 8.9 1.0
N E:PRO184 4.3 10.6 1.0
HB3 E:ASP185 4.3 10.1 1.0
CB E:ASP185 4.4 8.4 1.0
HG3 E:GLU177 4.4 8.9 1.0
O E:LYS182 4.4 15.2 1.0
CA E:ASN183 4.5 14.6 1.0
O E:HOH618 4.5 12.9 0.5
CG E:ASP191 4.6 10.4 1.0
O E:HOH883 4.6 42.5 1.0
CA E:ASP185 4.9 8.3 1.0
O E:PRO184 5.0 11.0 1.0

Calcium binding site 4 out of 4 in 5jss

Go back to Calcium Binding Sites List in 5jss
Calcium binding site 4 out of 4 in the Thermolysin in Complex with JC149.


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 JC149. within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca405

b:10.2
occ:1.00
O E:ILE197 2.3 14.6 1.0
OD1 E:ASP200 2.4 10.7 1.0
O E:TYR193 2.4 9.8 1.0
O E:HOH779 2.4 16.6 1.0
OG1 E:THR194 2.4 10.6 1.0
O E:THR194 2.4 11.4 1.0
O E:HOH610 2.4 13.1 1.0
C E:THR194 3.2 10.9 1.0
C E:TYR193 3.3 9.6 1.0
CG E:ASP200 3.4 10.5 1.0
CB E:THR194 3.5 10.6 1.0
HB E:ILE197 3.5 20.6 1.0
C E:ILE197 3.5 15.6 1.0
H E:ILE197 3.6 18.8 1.0
CA E:THR194 3.7 10.2 1.0
HB E:THR194 3.7 12.8 1.0
OD2 E:ASP200 3.8 11.4 1.0
H E:ASP200 3.9 15.1 1.0
N E:THR194 3.9 9.7 1.0
HD2 E:TYR193 4.0 13.2 1.0
HB3 E:TYR193 4.1 11.4 1.0
HA E:SER198 4.1 22.5 1.0
HA E:PRO195 4.2 16.5 1.0
CA E:ILE197 4.2 15.9 1.0
CB E:ILE197 4.3 17.1 1.0
N E:PRO195 4.3 12.2 1.0
N E:ILE197 4.3 15.7 1.0
HG22 E:ILE197 4.4 20.9 1.0
O E:HOH699 4.5 37.9 1.0
O E:ASP200 4.5 11.0 1.0
N E:SER198 4.5 16.9 1.0
O E:HOH710 4.5 36.2 1.0
CA E:TYR193 4.6 9.2 1.0
HA E:THR194 4.6 12.2 1.0
CA E:PRO195 4.6 13.8 1.0
CD2 E:TYR193 4.6 11.0 1.0
N E:ASP200 4.6 12.6 1.0
O E:HOH804 4.7 25.6 1.0
O E:GLU190 4.7 9.6 1.0
CA E:SER198 4.7 18.7 1.0
CB E:TYR193 4.7 9.5 1.0
H E:GLY199 4.7 19.6 1.0
CB E:ASP200 4.7 11.4 1.0
CG2 E:THR194 4.7 10.9 1.0
H E:THR194 4.7 11.7 1.0
C E:ASP200 4.8 10.9 1.0
HG23 E:THR194 4.9 13.1 1.0
CG2 E:ILE197 4.9 17.4 1.0
H E:TYR193 4.9 10.5 1.0
C E:PRO195 4.9 15.0 1.0
CA E:ASP200 4.9 11.7 1.0
C E:SER198 5.0 18.1 1.0
N E:GLY199 5.0 16.3 1.0
HG21 E:THR194 5.0 13.1 1.0

Reference:

S.G.Krimmer, J.Cramer, M.Betz, V.Fridh, R.Karlsson, A.Heine, G.Klebe. Rational Design of Thermodynamic and Kinetic Binding Profiles By Optimizing Surface Water Networks Coating Protein-Bound Ligands. J. Med. Chem. V. 59 10530 2016.
ISSN: ISSN 1520-4804
PubMed: 27933956
DOI: 10.1021/ACS.JMEDCHEM.6B00998
Page generated: Wed Jul 9 07:11:44 2025

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