Calcium in PDB 6lzo: Thermolysin with 1,10-Phenanthroline

All present enzymatic activity of Thermolysin with 1,10-Phenanthroline:
3.4.24.27;

The structure of Thermolysin with 1,10-Phenanthroline, PDB code: 6lzo 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)	19.85 / 1.80
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	92.772, 92.772, 129.103, 90, 90, 120
R / Rfree (%)	17.2 / 21.1

The binding sites of Calcium atom in the Thermolysin with 1,10-Phenanthroline (pdb code 6lzo). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Thermolysin with 1,10-Phenanthroline, PDB code: 6lzo:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Thermolysin with 1,10-Phenanthroline


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Thermolysin with 1,10-Phenanthroline within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:55.5 occ:1.00 O A:THR194 2.1 49.0 1.0 O A:TYR193 2.4 32.3 1.0 O A:HOH511 2.4 44.5 1.0 O A:ILE197 2.5 49.2 1.0 OG1 A:THR194 2.7 33.4 1.0 OD1 A:ASP200 2.9 58.0 1.0 C A:THR194 2.9 48.0 1.0 C A:TYR193 3.4 34.8 1.0 CA A:THR194 3.6 38.9 1.0 CB A:THR194 3.6 38.6 1.0 C A:ILE197 3.7 57.2 1.0 N A:THR194 3.9 34.0 1.0 N A:PRO195 3.9 57.9 1.0 CG A:ASP200 4.0 56.3 1.0 O A:ASP200 4.1 40.6 1.0 N A:ILE197 4.1 59.4 1.0 CA A:PRO195 4.3 61.5 1.0 C A:PRO195 4.3 68.3 1.0 CA A:ILE197 4.3 59.3 1.0 O A:PRO195 4.3 74.2 1.0 CB A:ILE197 4.5 60.0 1.0 O A:GLU190 4.5 29.4 1.0 OD2 A:ASP200 4.6 63.2 1.0 CA A:TYR193 4.7 30.6 1.0 N A:SER198 4.8 61.2 1.0 N A:ASP200 4.8 42.4 1.0 C A:ASP200 4.8 45.5 1.0 N A:GLY196 4.9 65.5 1.0 CB A:TYR193 4.9 33.4 1.0 CG2 A:THR194 5.0 39.4 1.0

Calcium binding site 2 out of 2 in the Thermolysin with 1,10-Phenanthroline


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Thermolysin with 1,10-Phenanthroline within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:28.3 occ:1.00 O A:GLU187 2.4 27.1 1.0 OD1 A:ASP185 2.4 30.0 1.0 OD2 A:ASP138 2.4 24.3 1.0 OE1 A:GLU177 2.4 23.5 1.0 OE2 A:GLU190 2.5 36.7 1.0 OE1 A:GLU190 2.6 29.6 1.0 OE2 A:GLU177 2.6 26.3 1.0 O A:HOH554 2.7 28.7 1.0 CD A:GLU190 2.8 29.9 1.0 CD A:GLU177 2.8 24.9 1.0 CG A:ASP138 3.4 26.2 1.0 CG A:ASP185 3.5 36.2 1.0 C A:GLU187 3.5 29.2 1.0 O A:ASP185 3.9 29.0 1.0 OD2 A:ASP185 4.0 33.6 1.0 CB A:ASP138 4.1 23.2 1.0 N A:GLU187 4.2 29.8 1.0 OD1 A:ASP138 4.3 23.5 1.0 CG A:GLU190 4.3 31.5 1.0 CG A:GLU177 4.3 24.3 1.0 N A:ILE188 4.3 27.2 1.0 CA A:GLU187 4.3 29.4 1.0 O A:HOH535 4.4 27.9 1.0 C A:ASP185 4.4 31.0 1.0 CA A:ILE188 4.4 28.8 1.0 N A:GLY189 4.5 26.7 1.0 O A:HOH547 4.5 41.7 1.0 CB A:GLU187 4.6 33.7 1.0 N A:ASP185 4.6 28.7 1.0 O A:HOH504 4.6 38.3 1.0 CB A:ASP185 4.7 32.4 1.0 CA A:ASP185 4.8 34.8 1.0 C A:ILE188 4.9 27.5 1.0 CB A:GLU177 4.9 23.9 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