Calcium in PDB 5l41: Thermolysin in Complex with JC148 (Mpd Cryo Protectant)

All present enzymatic activity of Thermolysin in Complex with JC148 (Mpd Cryo Protectant):
3.4.24.27;

The structure of Thermolysin in Complex with JC148 (Mpd Cryo Protectant), PDB code: 5l41 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)	43.65 / 1.25
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	92.598, 92.598, 130.822, 90.00, 90.00, 120.00
R / Rfree (%)	10.7 / 13

The structure of Thermolysin in Complex with JC148 (Mpd Cryo Protectant) also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Calcium atom in the Thermolysin in Complex with JC148 (Mpd Cryo Protectant) (pdb code 5l41). 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 JC148 (Mpd Cryo Protectant), PDB code: 5l41:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Thermolysin in Complex with JC148 (Mpd Cryo Protectant)


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 JC148 (Mpd Cryo Protectant) within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca402 b:7.9 occ:1.00 O E:GLU187 2.3 8.5 1.0 OD2 E:ASP138 2.4 8.0 1.0 O E:HOH602 2.4 8.2 1.0 OE1 E:GLU177 2.4 8.4 1.0 OD1 E:ASP185 2.5 8.5 1.0 OE1 E:GLU190 2.5 8.7 1.0 OE2 E:GLU190 2.5 9.0 1.0 OE2 E:GLU177 2.7 8.9 1.0 CD E:GLU190 2.9 8.9 1.0 CD E:GLU177 2.9 7.8 1.0 CG E:ASP138 3.4 8.0 1.0 C E:GLU187 3.4 8.4 1.0 CG E:ASP185 3.5 9.2 1.0 HB3 E:ASP138 3.6 8.7 1.0 HA E:ILE188 3.6 10.1 1.0 H E:GLU187 3.7 10.3 1.0 OD2 E:ASP185 3.8 10.6 1.0 CA E:CA404 3.8 10.3 1.0 H E:GLY189 3.8 9.9 1.0 HB2 E:GLU187 3.9 13.1 1.0 CB E:ASP138 4.0 7.2 1.0 O E:ASP185 4.1 8.6 1.0 H E:GLU190 4.2 10.6 1.0 H E:ASP185 4.2 11.2 1.0 N E:GLU187 4.2 8.6 1.0 N E:ILE188 4.2 7.9 1.0 O E:HOH622 4.3 14.9 0.5 OD1 E:ASP138 4.3 9.4 1.0 HB2 E:ASP138 4.3 8.7 1.0 CA E:GLU187 4.3 9.1 1.0 CA E:ILE188 4.3 8.4 1.0 CG E:GLU190 4.4 9.5 1.0 CG E:GLU177 4.4 8.0 1.0 HD13 E:ILE188 4.4 12.3 1.0 O E:HOH577 4.4 13.1 1.0 N E:GLY189 4.4 8.3 1.0 CB E:GLU187 4.6 10.9 1.0 C E:ASP185 4.6 8.8 1.0 HG3 E:GLU190 4.6 11.4 1.0 HB2 E:GLU177 4.6 9.4 1.0 HB3 E:GLU177 4.7 9.4 1.0 N E:ASP185 4.8 9.4 1.0 CB E:ASP185 4.8 9.3 1.0 C E:ILE188 4.8 8.3 1.0 HG2 E:GLU177 4.8 9.6 1.0 HG2 E:GLU190 4.8 11.4 1.0 CB E:GLU177 4.9 7.8 1.0 HA E:THR174 4.9 8.3 1.0 HG3 E:GLU177 4.9 9.6 1.0 O E:HOH560 4.9 12.8 1.0 HB3 E:GLU190 4.9 11.3 1.0 N E:GLU190 5.0 8.8 1.0 CA E:ASP185 5.0 9.3 1.0

Calcium binding site 2 out of 4 in the Thermolysin in Complex with JC148 (Mpd Cryo Protectant)


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 JC148 (Mpd Cryo Protectant) within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca403 b:8.2 occ:1.00 O E:GLN61 2.3 8.7 1.0 O E:HOH796 2.3 10.8 1.0 OD1 E:ASP57 2.4 8.9 1.0 OD1 E:ASP59 2.4 9.2 1.0 O E:HOH578 2.4 10.2 1.0 O E:HOH624 2.4 9.4 1.0 OD2 E:ASP57 2.6 8.6 1.0 CG E:ASP57 2.8 8.6 1.0 H E:GLN61 3.3 10.1 1.0 CG E:ASP59 3.4 9.9 1.0 C E:GLN61 3.4 8.3 1.0 H E:ASP59 3.5 10.4 1.0 HB2 E:GLN61 3.6 13.9 1.0 OD2 E:ASP59 3.8 11.9 1.0 N E:GLN61 4.0 8.4 1.0 O E:HOH700 4.0 16.0 1.0 HA E:PHE62 4.0 9.4 1.0 CA E:GLN61 4.2 9.1 1.0 H E:ALA58 4.3 10.0 1.0 N E:ASP59 4.3 8.7 1.0 CB E:ASP57 4.3 7.9 1.0 H E:ASN60 4.3 9.6 1.0 CB E:GLN61 4.4 11.6 1.0 N E:PHE62 4.5 7.7 1.0 CB E:ASP59 4.6 9.8 1.0 N E:ASN60 4.6 8.0 1.0 O E:HOH543 4.7 7.9 1.0 OD2 E:ASP67 4.7 8.2 1.0 O E:HOH899 4.7 24.4 1.0 HB2 E:ASP57 4.7 9.4 1.0 N E:ALA58 4.7 8.3 1.0 CA E:PHE62 4.8 7.8 1.0 CA E:ASP59 4.8 9.2 1.0 HB3 E:ASP57 4.8 9.4 1.0 H E:PHE63 4.8 10.1 1.0 O E:HOH884 4.8 25.9 1.0 HA E:ASP57 4.9 9.8 1.0 C E:ASP59 4.9 9.0 1.0 HB3 E:GLN61 5.0 13.9 1.0 HB3 E:ASP59 5.0 11.8 1.0 HB3 E:ALA58 5.0 11.8 1.0

Calcium binding site 3 out of 4 in the Thermolysin in Complex with JC148 (Mpd Cryo Protectant)


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 JC148 (Mpd Cryo Protectant) within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca404 b:10.3 occ:1.00 O E:ASN183 2.3 12.0 1.0 OE2 E:GLU190 2.3 9.0 1.0 O E:HOH571 2.3 12.9 1.0 OD2 E:ASP185 2.3 10.6 1.0 O E:HOH560 2.3 12.8 1.0 OE2 E:GLU177 2.4 8.9 1.0 CD E:GLU177 3.2 7.8 1.0 CG E:ASP185 3.2 9.2 1.0 CD E:GLU190 3.3 8.9 1.0 C E:ASN183 3.5 12.1 1.0 HA E:PRO184 3.6 12.2 1.0 HG3 E:GLU190 3.6 11.4 1.0 OD1 E:ASP185 3.6 8.5 1.0 HB2 E:ASN183 3.7 20.9 1.0 OE1 E:GLU177 3.7 8.4 1.0 CA E:CA402 3.8 7.9 1.0 HB3 E:ASN183 3.8 20.9 1.0 CG E:GLU190 3.9 9.5 1.0 HG2 E:GLU190 3.9 11.4 1.0 H E:ASP185 4.0 11.2 1.0 CB E:ASN183 4.1 17.4 1.0 CA E:PRO184 4.1 10.1 1.0 N E:ASP185 4.2 9.4 1.0 OD2 E:ASP191 4.2 12.9 1.0 OD1 E:ASP191 4.2 12.7 1.0 HG2 E:GLU177 4.2 9.6 1.0 CG E:GLU177 4.2 8.0 1.0 OE1 E:GLU190 4.3 8.7 1.0 C E:PRO184 4.3 10.1 1.0 N E:PRO184 4.3 10.8 1.0 HG3 E:GLU177 4.3 9.6 1.0 HB3 E:ASP185 4.3 11.2 1.0 CB E:ASP185 4.4 9.3 1.0 O E:LYS182 4.4 14.7 1.0 CA E:ASN183 4.5 14.6 1.0 O E:HOH622 4.5 14.9 0.5 CG E:ASP191 4.6 11.6 1.0 O E:HOH887 4.8 38.5 1.0 CA E:ASP185 4.9 9.3 1.0 O E:PRO184 5.0 11.6 1.0

Calcium binding site 4 out of 4 in the Thermolysin in Complex with JC148 (Mpd Cryo Protectant)


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 JC148 (Mpd Cryo Protectant) within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca405 b:12.1 occ:1.00 O E:ILE197 2.3 16.7 1.0 OD1 E:ASP200 2.4 12.8 1.0 O E:TYR193 2.4 11.4 1.0 OG1 E:THR194 2.4 12.7 1.0 O E:HOH775 2.4 18.5 1.0 O E:THR194 2.4 13.3 1.0 O E:HOH605 2.4 13.9 1.0 C E:THR194 3.2 12.6 1.0 C E:TYR193 3.4 11.0 1.0 CG E:ASP200 3.4 12.7 1.0 CB E:THR194 3.4 12.7 1.0 HB E:ILE197 3.5 24.0 1.0 C E:ILE197 3.5 17.7 1.0 H E:ILE197 3.6 21.9 1.0 CA E:THR194 3.6 12.0 1.0 HB E:THR194 3.7 15.2 1.0 OD2 E:ASP200 3.8 13.7 1.0 H E:ASP200 3.9 17.4 1.0 N E:THR194 3.9 11.4 1.0 HD2 E:TYR193 4.0 15.9 1.0 HB3 E:TYR193 4.0 13.2 1.0 HA E:SER198 4.1 23.8 1.0 CA E:ILE197 4.2 18.4 1.0 CB E:ILE197 4.2 20.0 1.0 HA E:PRO195 4.2 18.9 1.0 N E:PRO195 4.3 13.6 1.0 N E:ILE197 4.3 18.2 1.0 HG22 E:ILE197 4.4 24.8 1.0 O E:ASP200 4.5 12.6 1.0 O E:HOH607 4.5 38.9 1.0 N E:SER198 4.5 18.7 1.0 CA E:TYR193 4.6 10.8 1.0 HA E:THR194 4.6 14.4 1.0 O E:HOH730 4.6 39.0 1.0 CD2 E:TYR193 4.6 13.2 1.0 O E:HOH802 4.6 28.5 1.0 CA E:PRO195 4.7 15.8 1.0 CB E:TYR193 4.7 11.0 1.0 N E:ASP200 4.7 14.5 1.0 CA E:SER198 4.7 19.9 1.0 O E:GLU190 4.7 10.7 1.0 CB E:ASP200 4.7 13.3 1.0 CG2 E:THR194 4.7 13.2 1.0 H E:GLY199 4.7 21.5 1.0 H E:THR194 4.7 13.7 1.0 C E:ASP200 4.8 12.5 1.0 CG2 E:ILE197 4.8 20.7 1.0 HG23 E:THR194 4.9 15.8 1.0 H E:TYR193 4.9 11.9 1.0 C E:SER198 4.9 19.5 1.0 CA E:ASP200 5.0 13.5 1.0 C E:PRO195 5.0 17.3 1.0 HG21 E:THR194 5.0 15.8 1.0 N E:GLY199 5.0 17.9 1.0

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