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Calcium in PDB 5jxn: Thermolysin in Complex with JC240.

Enzymatic activity of Thermolysin in Complex with JC240.

All present enzymatic activity of Thermolysin in Complex with JC240.:
3.4.24.27;

Protein crystallography data

The structure of Thermolysin in Complex with JC240., PDB code: 5jxn 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) 46.51 / 1.38
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 93.014, 93.014, 131.203, 90.00, 90.00, 120.00
R / Rfree (%) 11 / 13.5

Other elements in 5jxn:

The structure of Thermolysin in Complex with JC240. 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 JC240. (pdb code 5jxn). 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 JC240., PDB code: 5jxn:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 5jxn

Go back to Calcium Binding Sites List in 5jxn
Calcium binding site 1 out of 4 in the Thermolysin in Complex with JC240.


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 JC240. within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca402

b:10.4
occ:1.00
O E:GLU187 2.3 10.9 1.0
OD2 E:ASP138 2.4 10.4 1.0
O E:HOH610 2.4 10.3 1.0
OE1 E:GLU190 2.5 10.8 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 10.7 1.0
OE2 E:GLU177 2.7 12.0 1.0
CD E:GLU190 2.8 11.1 1.0
CD E:GLU177 2.9 10.6 1.0
CG E:ASP138 3.4 10.3 1.0
C E:GLU187 3.4 11.2 1.0
CG E:ASP185 3.5 11.8 1.0
HB3 E:ASP138 3.6 11.1 1.0
HA E:ILE188 3.7 11.9 1.0
H E:GLU187 3.8 13.1 1.0
H E:GLY189 3.8 12.8 1.0
CA E:CA404 3.8 14.1 1.0
OD2 E:ASP185 3.8 14.1 1.0
HB2 E:GLU187 3.9 15.9 1.0
CB E:ASP138 4.0 9.2 1.0
O E:ASP185 4.2 11.3 1.0
H E:ASP185 4.2 14.5 1.0
H E:GLU190 4.2 13.2 1.0
N E:GLU187 4.2 10.9 1.0
N E:ILE188 4.2 10.2 1.0
HB2 E:ASP138 4.3 11.1 1.0
CA E:GLU187 4.3 11.5 1.0
OD1 E:ASP138 4.3 11.2 1.0
CA E:ILE188 4.3 9.9 1.0
CG E:GLU190 4.4 12.1 1.0
HD13 E:ILE188 4.4 16.0 1.0
CG E:GLU177 4.4 10.6 1.0
N E:GLY189 4.4 10.7 1.0
O E:HOH563 4.5 16.2 1.0
CB E:GLU187 4.6 13.3 1.0
C E:ASP185 4.6 11.6 1.0
HG3 E:GLU190 4.6 14.6 1.0
HB2 E:GLU177 4.7 12.4 1.0
HB3 E:GLU177 4.7 12.4 1.0
C E:ILE188 4.8 10.4 1.0
N E:ASP185 4.8 12.1 1.0
CB E:ASP185 4.8 11.6 1.0
HG2 E:GLU190 4.8 14.6 1.0
HG2 E:GLU177 4.8 12.7 1.0
O E:HOH580 4.9 17.3 1.0
CB E:GLU177 4.9 10.3 1.0
HA E:THR174 4.9 11.4 1.0
HG3 E:GLU177 4.9 12.7 1.0
N E:GLU190 5.0 11.0 1.0
HB3 E:GLU190 5.0 14.5 1.0
CA E:ASP185 5.0 11.8 1.0

Calcium binding site 2 out of 4 in 5jxn

Go back to Calcium Binding Sites List in 5jxn
Calcium binding site 2 out of 4 in the Thermolysin in Complex with JC240.


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 JC240. within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca403

b:11.1
occ:1.00
O E:GLN61 2.2 11.0 1.0
O E:HOH783 2.3 13.1 1.0
OD1 E:ASP57 2.4 11.4 1.0
OD1 E:ASP59 2.4 11.3 1.0
O E:HOH605 2.4 13.6 1.0
O E:HOH582 2.4 12.8 1.0
OD2 E:ASP57 2.6 11.4 1.0
CG E:ASP57 2.8 10.5 1.0
H E:GLN61 3.3 12.9 1.0
CG E:ASP59 3.4 12.4 1.0
C E:GLN61 3.4 10.2 1.0
H E:ASP59 3.5 13.3 1.0
HB2 E:GLN61 3.6 17.1 1.0
OD2 E:ASP59 3.8 14.9 1.0
N E:GLN61 4.0 10.8 1.0
O E:HOH707 4.0 18.7 1.0
HA E:PHE62 4.0 12.1 1.0
CA E:GLN61 4.1 11.8 1.0
H E:ALA58 4.3 12.8 1.0
CB E:GLN61 4.3 14.2 1.0
N E:ASP59 4.3 11.1 1.0
CB E:ASP57 4.3 10.6 1.0
H E:ASN60 4.4 12.4 1.0
N E:PHE62 4.5 9.8 1.0
CB E:ASP59 4.6 11.7 1.0
OD2 E:ASP67 4.7 10.7 1.0
O E:HOH531 4.7 10.8 1.0
N E:ASN60 4.7 10.3 1.0
O E:HOH891 4.7 30.0 1.0
HB2 E:ASP57 4.7 12.8 1.0
N E:ALA58 4.7 10.7 1.0
CA E:PHE62 4.8 10.1 1.0
HB3 E:ASP57 4.8 12.8 1.0
CA E:ASP59 4.8 11.0 1.0
HA E:ASP57 4.9 12.2 1.0
H E:PHE63 4.9 13.6 1.0
C E:ASP59 4.9 10.9 1.0
HB3 E:GLN61 4.9 17.1 1.0
HB3 E:ASP59 5.0 14.0 1.0

Calcium binding site 3 out of 4 in 5jxn

Go back to Calcium Binding Sites List in 5jxn
Calcium binding site 3 out of 4 in the Thermolysin in Complex with JC240.


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 JC240. within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca404

b:14.1
occ:1.00
OE2 E:GLU190 2.3 12.2 1.0
O E:ASN183 2.3 15.9 1.0
OD2 E:ASP185 2.3 14.1 1.0
O E:HOH580 2.3 17.3 1.0
O E:HOH591 2.3 17.6 1.0
OE2 E:GLU177 2.4 12.0 1.0
CG E:ASP185 3.2 11.8 1.0
CD E:GLU177 3.2 10.6 1.0
CD E:GLU190 3.3 11.1 1.0
C E:ASN183 3.5 15.8 1.0
HA E:PRO184 3.5 15.9 1.0
HG3 E:GLU190 3.6 14.6 1.0
OD1 E:ASP185 3.6 10.7 1.0
OE1 E:GLU177 3.7 11.2 1.0
CA E:CA402 3.8 10.4 1.0
HB3 E:ASN183 3.8 24.7 1.0
HG2 E:GLU190 3.8 14.6 1.0
HB2 E:ASN183 3.8 24.7 1.0
CG E:GLU190 3.8 12.1 1.0
H E:ASP185 4.0 14.5 1.0
CA E:PRO184 4.1 13.2 1.0
N E:ASP185 4.2 12.1 1.0
CB E:ASN183 4.2 20.6 1.0
OD1 E:ASP191 4.3 16.1 1.0
OD2 E:ASP191 4.3 15.2 1.0
CG E:GLU177 4.3 10.6 1.0
HG2 E:GLU177 4.3 12.7 1.0
OE1 E:GLU190 4.3 10.8 1.0
C E:PRO184 4.3 13.7 1.0
N E:PRO184 4.3 14.1 1.0
HB3 E:ASP185 4.3 13.9 1.0
HG3 E:GLU177 4.4 12.7 1.0
CB E:ASP185 4.4 11.6 1.0
O E:LYS182 4.4 19.2 1.0
O E:HOH540 4.4 42.0 1.0
CA E:ASN183 4.5 17.8 1.0
CG E:ASP191 4.6 14.8 1.0
O E:HOH861 4.7 41.4 1.0
CA E:ASP185 4.9 11.8 1.0
O E:PRO184 5.0 15.6 1.0

Calcium binding site 4 out of 4 in 5jxn

Go back to Calcium Binding Sites List in 5jxn
Calcium binding site 4 out of 4 in the Thermolysin in Complex with JC240.


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 JC240. within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca405

b:14.2
occ:1.00
O E:ILE197 2.3 20.0 1.0
OG1 E:THR194 2.4 14.7 1.0
O E:THR194 2.4 15.7 1.0
OD1 E:ASP200 2.4 14.9 1.0
O E:TYR193 2.4 13.6 1.0
O E:HOH554 2.4 16.4 1.0
O E:HOH774 2.4 22.1 1.0
C E:THR194 3.2 15.2 1.0
C E:TYR193 3.4 13.7 1.0
CG E:ASP200 3.4 14.6 1.0
CB E:THR194 3.4 14.6 1.0
C E:ILE197 3.5 21.1 1.0
HB E:ILE197 3.5 27.5 1.0
CA E:THR194 3.6 14.1 1.0
H E:ILE197 3.6 26.2 1.0
HB E:THR194 3.7 17.6 1.0
OD2 E:ASP200 3.8 16.2 1.0
N E:THR194 3.9 13.6 1.0
H E:ASP200 3.9 20.5 1.0
HD2 E:TYR193 4.0 17.6 1.0
HB3 E:TYR193 4.0 15.9 1.0
HA E:SER198 4.2 29.3 1.0
CA E:ILE197 4.2 22.1 1.0
N E:PRO195 4.3 15.9 1.0
CB E:ILE197 4.3 22.9 1.0
HA E:PRO195 4.3 20.8 1.0
N E:ILE197 4.3 21.8 1.0
HG22 E:ILE197 4.4 26.8 1.0
O E:ASP200 4.5 15.1 1.0
N E:SER198 4.5 22.9 1.0
HA E:THR194 4.6 16.9 1.0
O E:HOH761 4.6 46.0 1.0
CA E:TYR193 4.6 12.8 1.0
O E:HOH753 4.6 38.6 1.0
CD2 E:TYR193 4.6 14.7 1.0
O E:HOH787 4.6 27.6 1.0
CA E:PRO195 4.7 17.4 1.0
O E:GLU190 4.7 13.1 1.0
CB E:TYR193 4.7 13.2 1.0
N E:ASP200 4.7 17.1 1.0
CA E:SER198 4.7 24.4 1.0
H E:THR194 4.7 16.4 1.0
CB E:ASP200 4.7 15.6 1.0
CG2 E:THR194 4.7 15.2 1.0
H E:GLY199 4.8 24.9 1.0
C E:ASP200 4.8 15.3 1.0
CG2 E:ILE197 4.9 22.4 1.0
HG23 E:THR194 4.9 18.3 1.0
H E:TYR193 4.9 14.4 1.0
C E:PRO195 4.9 20.1 1.0
C E:SER198 5.0 23.4 1.0
CA E:ASP200 5.0 15.8 1.0
HG21 E:THR194 5.0 18.3 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 07:15:08 2025

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