Calcium in PDB 6lzn: Thermolysin

All present enzymatic activity of Thermolysin:
3.4.24.27;

The structure of Thermolysin, PDB code: 6lzn was solved by K.H.Nam, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.83 / 1.50
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	92.663, 92.663, 128.591, 90, 90, 120
R / Rfree (%)	15.7 / 18

The structure of Thermolysin also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Calcium atom in the Thermolysin (pdb code 6lzn). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Thermolysin, PDB code: 6lzn:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Thermolysin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Thermolysin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1402 b:18.1 occ:1.00 O A:ILE197 2.2 21.8 1.0 O A:HOH1683 2.3 23.6 1.0 O A:TYR193 2.4 17.2 1.0 OD1 A:ASP200 2.4 18.1 1.0 O A:THR194 2.4 23.0 1.0 OG1 A:THR194 2.4 20.6 1.0 O A:HOH1543 2.4 18.5 1.0 C A:THR194 3.2 19.9 1.0 C A:TYR193 3.4 17.1 1.0 C A:ILE197 3.4 28.1 1.0 CG A:ASP200 3.4 17.5 1.0 CB A:THR194 3.5 20.0 1.0 CA A:THR194 3.7 19.0 1.0 OD2 A:ASP200 3.8 20.4 1.0 N A:THR194 3.9 17.1 1.0 CA A:ILE197 4.1 25.3 1.0 N A:ILE197 4.2 29.6 1.0 N A:PRO195 4.3 21.1 1.0 CB A:ILE197 4.3 24.5 1.0 O A:ASP200 4.4 17.0 1.0 N A:SER198 4.5 26.2 1.0 O A:HOH1701 4.5 29.5 1.0 N A:ASP200 4.6 20.0 1.0 CA A:TYR193 4.6 16.4 1.0 O A:GLU190 4.6 15.8 1.0 CA A:PRO195 4.7 23.0 1.0 CD2 A:TYR193 4.7 20.1 1.0 CB A:TYR193 4.7 16.1 1.0 CB A:ASP200 4.7 18.7 1.0 CG2 A:THR194 4.7 21.6 1.0 C A:ASP200 4.8 15.0 1.0 CG2 A:ILE197 4.9 26.5 1.0 CA A:SER198 4.9 28.3 1.0 N A:GLY199 4.9 25.2 1.0 C A:SER198 4.9 24.4 1.0 C A:PRO195 5.0 24.6 1.0 CA A:ASP200 5.0 18.2 1.0

Calcium binding site 2 out of 3 in the Thermolysin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Thermolysin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1403 b:13.0 occ:1.00 O A:GLU187 2.3 14.9 1.0 OD2 A:ASP138 2.4 13.3 1.0 OD1 A:ASP185 2.4 14.1 1.0 OE2 A:GLU190 2.4 17.9 1.0 O A:HOH1592 2.5 14.9 1.0 OE1 A:GLU177 2.5 13.5 1.0 OE2 A:GLU177 2.6 15.1 1.0 OE1 A:GLU190 2.6 15.3 1.0 CD A:GLU190 2.8 15.7 1.0 CD A:GLU177 2.9 14.9 1.0 CG A:ASP138 3.4 14.6 1.0 C A:GLU187 3.4 15.0 1.0 CG A:ASP185 3.5 18.3 1.0 OD2 A:ASP185 3.9 19.0 1.0 CB A:ASP138 4.0 11.4 1.0 O A:ASP185 4.0 15.3 1.0 N A:GLU187 4.2 14.9 1.0 O A:HOH1520 4.2 29.1 1.0 O A:HOH1585 4.3 15.5 1.0 CA A:GLU187 4.3 15.6 1.0 N A:ILE188 4.3 14.8 1.0 OD1 A:ASP138 4.3 13.4 1.0 CG A:GLU190 4.3 16.2 1.0 CG A:GLU177 4.4 14.1 1.0 N A:GLY189 4.4 12.6 1.0 CA A:ILE188 4.4 13.8 1.0 O A:HOH1528 4.4 30.5 1.0 C A:ASP185 4.4 16.4 1.0 N A:ASP185 4.6 14.5 1.0 CB A:GLU187 4.7 18.7 1.0 CB A:ASP185 4.7 15.3 1.0 CA A:ASP185 4.8 17.0 1.0 C A:ILE188 4.8 13.1 1.0 CB A:GLU177 4.9 13.0 1.0

Calcium binding site 3 out of 3 in the Thermolysin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Thermolysin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1404 b:12.6 occ:1.00 O A:GLN61 2.3 11.7 1.0 OD1 A:ASP59 2.4 12.7 1.0 O A:HOH1721 2.4 16.4 1.0 OD1 A:ASP57 2.4 13.8 1.0 O A:HOH1602 2.4 14.4 1.0 O A:HOH1582 2.5 12.5 1.0 OD2 A:ASP57 2.6 12.8 1.0 CG A:ASP57 2.8 13.2 1.0 CG A:ASP59 3.4 14.1 1.0 C A:GLN61 3.5 11.2 1.0 OD2 A:ASP59 3.8 16.0 1.0 N A:GLN61 4.0 11.3 1.0 O A:HOH1669 4.0 16.9 1.0 CA A:GLN61 4.2 11.1 1.0 CB A:ASP57 4.3 11.4 1.0 N A:ASP59 4.3 11.9 1.0 CB A:GLN61 4.4 14.6 1.0 O A:HOH1684 4.5 15.8 1.0 O A:HOH1756 4.5 24.2 1.0 N A:PHE62 4.5 11.0 1.0 O A:HOH1763 4.6 37.0 1.0 CB A:ASP59 4.6 13.1 1.0 O A:HOH1527 4.6 12.2 1.0 OD2 A:ASP67 4.6 12.3 1.0 N A:ASN60 4.6 12.6 1.0 O A:HOH1751 4.7 36.0 1.0 N A:ALA58 4.8 12.4 1.0 CA A:ASP59 4.8 12.0 1.0 CA A:PHE62 4.8 10.8 1.0 C A:ASP59 4.9 12.0 1.0

K.H.Nam, K.H.Nam. N/A N/A.
ISSN: ISSN 0162-0134
PubMed: 33310458
DOI: 10.1016/J.JINORGBIO.2020.111319