Calcium in PDB 5dlh: Sfx Structure of Thermolysin

All present enzymatic activity of Sfx Structure of Thermolysin:
3.4.24.27;

The structure of Sfx Structure of Thermolysin, PDB code: 5dlh was solved by H.D.Demirci, N.K.Sauter, A.S.Brewster, J.Kern, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.20 / 2.25
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	93.794, 93.794, 132.243, 90.00, 90.00, 120.00
R / Rfree (%)	17.9 / 22.7

The structure of Sfx Structure of Thermolysin also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Calcium atom in the Sfx Structure of Thermolysin (pdb code 5dlh). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Sfx Structure of Thermolysin, PDB code: 5dlh:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Sfx Structure of Thermolysin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Sfx Structure of Thermolysin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:38.6 occ:1.00 O A:GLU187 2.3 38.0 1.0 OE2 A:GLU190 2.5 34.7 1.0 OE1 A:GLU190 2.5 36.6 1.0 OE1 A:GLU177 2.5 37.6 1.0 OD1 A:ASP185 2.6 35.5 1.0 OD2 A:ASP138 2.6 35.6 1.0 O A:HOH518 2.7 36.2 1.0 CD A:GLU190 2.8 35.5 1.0 OE2 A:GLU177 3.0 37.3 1.0 CD A:GLU177 3.1 38.0 1.0 C A:GLU187 3.3 38.2 1.0 HA A:ILE188 3.5 45.0 1.0 CG A:ASP185 3.5 38.8 1.0 CG A:ASP138 3.6 37.5 1.0 H A:GLY189 3.7 42.5 1.0 HB3 A:ASP138 3.7 45.2 1.0 OD2 A:ASP185 3.7 39.2 1.0 CA A:CA403 3.8 35.0 1.0 HB2 A:GLU187 3.8 51.6 1.0 H A:GLU190 4.0 44.3 1.0 O A:ASP185 4.1 42.4 1.0 N A:ILE188 4.1 37.4 1.0 CB A:ASP138 4.1 37.7 1.0 HD13 A:ILE188 4.2 53.6 1.0 CA A:ILE188 4.2 37.5 1.0 H A:GLU187 4.2 50.3 1.0 H A:ASP185 4.2 47.5 1.0 CA A:GLU187 4.2 41.0 1.0 CG A:GLU190 4.3 35.7 1.0 N A:GLY189 4.3 35.4 1.0 N A:GLU187 4.3 41.9 1.0 HB2 A:ASP138 4.4 45.2 1.0 OD1 A:ASP138 4.5 38.8 1.0 CB A:GLU187 4.5 43.0 1.0 O A:HOH538 4.5 43.4 1.0 CG A:GLU177 4.5 38.6 1.0 HG3 A:GLU190 4.6 42.8 1.0 C A:ASP185 4.6 41.7 1.0 C A:ILE188 4.7 36.0 1.0 HB2 A:GLU177 4.7 44.1 1.0 HG2 A:GLU190 4.8 42.8 1.0 CB A:ASP185 4.8 41.4 1.0 N A:ASP185 4.8 39.5 1.0 HA A:THR174 4.8 46.4 1.0 HB3 A:GLU190 4.8 42.4 1.0 HB3 A:GLU177 4.9 44.1 1.0 N A:GLU190 4.9 37.0 1.0 O A:HOH512 4.9 38.8 1.0 H A:ILE188 4.9 44.9 1.0 HB3 A:GLU187 4.9 51.6 1.0 CA A:ASP185 5.0 41.4 1.0 CB A:GLU177 5.0 36.7 1.0

Calcium binding site 2 out of 4 in the Sfx Structure of Thermolysin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Sfx Structure of Thermolysin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca403 b:35.0 occ:1.00 OE2 A:GLU190 2.2 34.7 1.0 OD2 A:ASP185 2.2 39.2 1.0 O A:ASN183 2.3 39.2 1.0 O A:HOH524 2.3 27.6 1.0 O A:HOH512 2.3 38.8 1.0 OE2 A:GLU177 2.3 37.3 1.0 CD A:GLU177 3.2 38.0 1.0 CD A:GLU190 3.2 35.5 1.0 CG A:ASP185 3.2 38.8 1.0 C A:ASN183 3.4 41.0 1.0 HG3 A:GLU190 3.4 42.8 1.0 HA A:PRO184 3.6 48.2 1.0 OE1 A:GLU177 3.7 37.6 1.0 HG2 A:GLU190 3.7 42.8 1.0 CG A:GLU190 3.7 35.7 1.0 HB3 A:ASN183 3.7 61.3 1.0 HB2 A:ASN183 3.8 61.3 1.0 OD1 A:ASP185 3.8 35.5 1.0 CA A:CA402 3.8 38.6 1.0 H A:ASP185 4.0 47.5 1.0 O A:LYS182 4.0 48.1 1.0 OD1 A:ASP191 4.1 41.7 1.0 CB A:ASN183 4.1 51.1 1.0 N A:ASP185 4.1 39.5 1.0 CA A:PRO184 4.2 40.2 1.0 OD2 A:ASP191 4.2 42.2 1.0 C A:PRO184 4.2 39.9 1.0 OE1 A:GLU190 4.2 36.6 1.0 HG2 A:GLU177 4.2 46.4 1.0 CG A:GLU177 4.2 38.6 1.0 N A:PRO184 4.3 41.4 1.0 HB3 A:ASP185 4.3 49.7 1.0 CB A:ASP185 4.3 41.4 1.0 CA A:ASN183 4.4 46.0 1.0 HG3 A:GLU177 4.4 46.4 1.0 CG A:ASP191 4.5 41.0 1.0 O A:PRO184 4.8 40.8 1.0 CA A:ASP185 4.9 41.4 1.0 C A:LYS182 5.0 48.3 1.0

Calcium binding site 3 out of 4 in the Sfx Structure of Thermolysin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Sfx Structure of Thermolysin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca404 b:40.3 occ:1.00 O A:TYR193 2.3 39.1 1.0 O A:ILE197 2.3 46.8 1.0 OG1 A:THR194 2.3 42.3 1.0 O A:HOH510 2.4 40.0 1.0 OD1 A:ASP200 2.4 43.8 1.0 O A:THR194 2.5 42.2 1.0 C A:THR194 3.2 43.5 1.0 C A:TYR193 3.4 39.5 1.0 CG A:ASP200 3.4 43.4 1.0 HB A:ILE197 3.5 61.8 1.0 C A:ILE197 3.5 51.2 1.0 CB A:THR194 3.5 42.7 1.0 CA A:THR194 3.7 42.3 1.0 H A:ILE197 3.8 79.2 1.0 OD2 A:ASP200 3.8 42.8 1.0 HB A:THR194 3.9 51.2 1.0 H A:ASP200 3.9 57.6 1.0 N A:THR194 4.0 40.5 1.0 HB3 A:TYR193 4.1 49.9 1.0 HD2 A:TYR193 4.2 56.0 1.0 HA A:SER198 4.2 67.8 1.0 CB A:ILE197 4.2 51.5 1.0 CA A:ILE197 4.2 56.2 1.0 HA A:PRO195 4.2 61.4 1.0 N A:PRO195 4.3 46.5 1.0 N A:ILE197 4.3 66.0 1.0 HG22 A:ILE197 4.4 60.8 1.0 O A:ASP200 4.4 40.5 1.0 O A:GLU190 4.5 38.8 1.0 N A:SER198 4.5 53.4 1.0 CA A:TYR193 4.6 39.6 1.0 CA A:PRO195 4.7 51.2 1.0 HA A:THR194 4.7 50.8 1.0 CG2 A:THR194 4.7 42.2 1.0 N A:ASP200 4.7 48.0 1.0 CB A:TYR193 4.7 41.6 1.0 HG23 A:THR194 4.7 50.6 1.0 CA A:SER198 4.8 56.5 1.0 CB A:ASP200 4.8 44.0 1.0 CD2 A:TYR193 4.8 46.6 1.0 H A:THR194 4.8 48.6 1.0 C A:ASP200 4.8 41.8 1.0 CG2 A:ILE197 4.8 50.7 1.0 H A:GLY199 4.8 65.3 1.0 H A:TYR193 4.9 46.6 1.0 HG21 A:THR194 5.0 50.6 1.0

Calcium binding site 4 out of 4 in the Sfx Structure of Thermolysin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Sfx Structure of Thermolysin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca405 b:40.0 occ:1.00 OD1 A:ASP59 2.3 34.6 1.0 O A:HOH540 2.3 40.1 1.0 OD1 A:ASP57 2.3 32.6 1.0 O A:GLN61 2.3 40.1 1.0 O A:HOH521 2.4 42.0 1.0 OD2 A:ASP57 2.5 35.3 1.0 O A:HOH503 2.5 33.2 1.0 CG A:ASP57 2.7 33.6 1.0 H A:GLN61 3.2 45.0 1.0 CG A:ASP59 3.2 36.0 1.0 H A:ASP59 3.5 48.3 1.0 C A:GLN61 3.5 39.5 1.0 OD2 A:ASP59 3.6 36.9 1.0 HA A:PHE62 3.7 46.1 1.0 O A:HOH537 3.8 37.5 1.0 HB2 A:GLN61 3.9 54.6 1.0 N A:GLN61 3.9 37.5 1.0 H A:ALA58 4.1 42.5 1.0 CA A:GLN61 4.2 40.4 1.0 CB A:ASP57 4.2 33.4 1.0 N A:ASP59 4.3 40.2 1.0 H A:ASN60 4.3 47.8 1.0 O A:HOH554 4.4 38.5 1.0 N A:PHE62 4.4 38.9 1.0 CA A:PHE62 4.5 38.4 1.0 CB A:ASP59 4.6 38.5 1.0 O A:HOH513 4.6 35.3 1.0 CB A:GLN61 4.6 45.5 1.0 HB2 A:ASP57 4.6 40.1 1.0 N A:ASN60 4.6 39.9 1.0 N A:ALA58 4.7 35.4 1.0 HB3 A:ASP57 4.7 40.1 1.0 OD2 A:ASP67 4.7 45.1 1.0 CA A:ASP59 4.8 40.0 1.0 H A:PHE63 4.8 49.9 1.0 HA A:ASP57 4.8 41.6 1.0 HB3 A:ALA58 4.9 44.9 1.0 C A:ASP59 4.9 40.6 1.0

H.D.Demirci, H.D.Demirci, N.K.Sauter, A.S.Brewster, J.Kern. N/A N/A.