Calcium in PDB 4mzn: Thermolysin in Complex with UBTLN59

All present enzymatic activity of Thermolysin in Complex with UBTLN59:
3.4.24.27;

The structure of Thermolysin in Complex with UBTLN59, PDB code: 4mzn was solved by 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)	20.71 / 1.17
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	92.493, 92.493, 131.183, 90.00, 90.00, 120.00
R / Rfree (%)	11.6 / 13.8

The structure of Thermolysin in Complex with UBTLN59 also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Calcium atom in the Thermolysin in Complex with UBTLN59 (pdb code 4mzn). 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 UBTLN59, PDB code: 4mzn:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Thermolysin in Complex with UBTLN59


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 UBTLN59 within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca402 b:8.4 occ:1.00 O E:GLU187 2.3 8.7 1.0 OD2 E:ASP138 2.4 8.9 1.0 O E:HOH501 2.4 8.9 1.0 OD1 E:ASP185 2.5 9.4 1.0 OE1 E:GLU177 2.5 9.0 1.0 OE1 E:GLU190 2.5 9.1 1.0 OE2 E:GLU190 2.5 9.7 1.0 OE2 E:GLU177 2.7 9.8 1.0 CD E:GLU190 2.8 9.2 1.0 CD E:GLU177 2.9 8.8 1.0 CG E:ASP138 3.4 8.4 1.0 C E:GLU187 3.4 9.1 1.0 CG E:ASP185 3.5 9.8 1.0 CA E:CA405 3.8 11.0 1.0 OD2 E:ASP185 3.8 11.2 1.0 CB E:ASP138 4.0 8.3 1.0 O E:ASP185 4.1 9.1 1.0 N E:GLU187 4.2 9.5 1.0 N E:ILE188 4.3 8.5 1.0 OD1 E:ASP138 4.3 9.9 1.0 CA E:GLU187 4.3 9.5 1.0 O E:HOH958 4.3 16.6 0.5 CA E:ILE188 4.3 8.5 1.0 CG E:GLU190 4.4 9.9 1.0 CG E:GLU177 4.4 9.2 1.0 O E:HOH564 4.4 14.3 1.0 N E:GLY189 4.4 8.7 1.0 CB E:GLU187 4.6 11.1 1.0 C E:ASP185 4.6 8.9 1.0 N E:ASP185 4.8 9.5 1.0 CB E:ASP185 4.8 10.3 1.0 C E:ILE188 4.8 8.4 1.0 CB E:GLU177 4.9 8.4 1.0 O E:HOH556 4.9 14.4 1.0 N E:GLU190 5.0 9.1 1.0 CA E:ASP185 5.0 9.1 1.0

Calcium binding site 2 out of 4 in the Thermolysin in Complex with UBTLN59


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 UBTLN59 within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca403 b:8.9 occ:1.00 O E:GLN61 2.3 9.3 0.5 O E:GLN61 2.3 9.4 0.5 O E:HOH525 2.4 11.5 1.0 OD1 E:ASP59 2.4 9.6 1.0 OD2 E:ASP57 2.4 9.7 1.0 O E:HOH547 2.4 11.8 1.0 O E:HOH516 2.4 10.6 1.0 OD1 E:ASP57 2.6 9.1 1.0 CG E:ASP57 2.8 9.0 1.0 CG E:ASP59 3.4 10.3 1.0 C E:GLN61 3.5 8.5 0.5 C E:GLN61 3.5 8.4 0.5 OD2 E:ASP59 3.8 12.2 1.0 N E:GLN61 3.9 8.9 0.5 N E:GLN61 3.9 8.8 0.5 O E:HOH585 4.0 16.1 1.0 CA E:GLN61 4.1 9.3 0.5 CA E:GLN61 4.1 9.1 0.5 CB E:GLN61 4.3 11.3 0.5 N E:ASP59 4.3 9.2 1.0 CB E:ASP57 4.3 8.8 1.0 CB E:GLN61 4.4 11.0 0.5 N E:PHE62 4.5 8.2 1.0 O E:HOH949 4.6 15.3 1.0 CB E:ASP59 4.6 10.2 1.0 O E:HOH503 4.6 8.4 1.0 OD2 E:ASP67 4.6 8.8 1.0 N E:ASN60 4.6 8.4 1.0 O E:HOH699 4.7 25.7 1.0 N E:ALA58 4.7 8.9 1.0 O E:HOH698 4.8 35.1 1.0 CA E:PHE62 4.8 8.6 1.0 CA E:ASP59 4.8 9.5 1.0 C E:ASP59 4.9 8.9 1.0

Calcium binding site 3 out of 4 in the Thermolysin in Complex with UBTLN59


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 UBTLN59 within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca404 b:11.3 occ:1.00 O E:ILE197 2.3 15.8 1.0 OD1 E:ASP200 2.4 12.3 1.0 O E:TYR193 2.4 11.2 1.0 O E:THR194 2.4 12.7 1.0 O E:HOH551 2.4 14.3 1.0 OG1 E:THR194 2.4 11.9 1.0 O E:HOH593 2.4 18.1 1.0 C E:THR194 3.2 12.1 1.0 C E:TYR193 3.4 10.8 1.0 CG E:ASP200 3.4 11.7 1.0 CB E:THR194 3.5 11.9 1.0 C E:ILE197 3.5 17.1 1.0 CA E:THR194 3.7 11.3 1.0 OD2 E:ASP200 3.8 12.6 1.0 N E:THR194 3.9 10.7 1.0 CA E:ILE197 4.2 17.5 1.0 CB E:ILE197 4.2 17.9 1.0 N E:PRO195 4.2 13.2 1.0 N E:ILE197 4.3 17.5 1.0 O E:HOH803 4.4 36.0 1.0 O E:ASP200 4.5 11.5 1.0 N E:SER198 4.5 18.1 0.4 N E:SER198 4.5 17.8 0.6 CA E:TYR193 4.6 10.2 1.0 O E:HOH850 4.6 45.2 1.0 N E:ASP200 4.6 13.3 1.0 CA E:PRO195 4.6 15.2 1.0 CD2 E:TYR193 4.6 12.3 1.0 O E:GLU190 4.7 10.7 1.0 CA E:SER198 4.7 19.2 0.4 CB E:TYR193 4.7 11.2 1.0 O E:HOH720 4.7 27.7 1.0 O E:HOH774 4.7 44.0 1.0 CA E:SER198 4.7 19.1 0.6 CB E:ASP200 4.7 12.5 1.0 CG2 E:THR194 4.7 12.6 1.0 C E:ASP200 4.8 11.5 1.0 CG2 E:ILE197 4.8 18.1 1.0 C E:SER198 4.9 19.0 0.6 CA E:ASP200 4.9 12.5 1.0 C E:PRO195 5.0 16.5 1.0

Calcium binding site 4 out of 4 in the Thermolysin in Complex with UBTLN59


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 UBTLN59 within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca405 b:11.0 occ:1.00 O E:ASN183 2.3 12.5 1.0 OE2 E:GLU190 2.3 9.7 1.0 O E:HOH867 2.3 14.5 1.0 OD2 E:ASP185 2.3 11.2 1.0 O E:HOH556 2.4 14.4 1.0 OE2 E:GLU177 2.4 9.8 1.0 CG E:ASP185 3.2 9.8 1.0 CD E:GLU177 3.2 8.8 1.0 CD E:GLU190 3.3 9.2 1.0 C E:ASN183 3.5 12.8 1.0 OD1 E:ASP185 3.6 9.4 1.0 OE1 E:GLU177 3.7 9.0 1.0 CA E:CA402 3.8 8.4 1.0 CG E:GLU190 3.9 9.9 1.0 CA E:PRO184 4.1 10.6 1.0 CB E:ASN183 4.1 17.2 1.0 N E:ASP185 4.2 9.5 1.0 O E:HOH843 4.2 40.4 1.0 OD2 E:ASP191 4.2 13.7 1.0 CG E:GLU177 4.2 9.2 1.0 C E:PRO184 4.3 10.5 1.0 OD1 E:ASP191 4.3 13.7 1.0 OE1 E:GLU190 4.3 9.1 1.0 N E:PRO184 4.3 11.6 1.0 CB E:ASP185 4.4 10.3 1.0 O E:LYS182 4.4 15.5 1.0 CA E:ASN183 4.5 14.8 1.0 O E:HOH958 4.5 16.6 0.5 CG E:ASP191 4.6 12.3 1.0 O E:HOH836 4.6 39.7 1.0 CA E:ASP185 4.9 9.1 1.0 O E:PRO184 4.9 11.9 1.0

S.G.Krimmer, M.Betz, A.Heine, G.Klebe. Methyl, Ethyl, Propyl, Butyl: Futile But Not For Water, As the Correlation of Structure and Thermodynamic Signature Shows in A Congeneric Series of Thermolysin Inhibitors. Chemmedchem V. 4 833 2014.
ISSN: ISSN 1860-7179
PubMed: 24623396
DOI: 10.1002/CMDC.201400013