Calcium in PDB 8zm4: Crystal Structure of Thermolysin (Dose I)

All present enzymatic activity of Crystal Structure of Thermolysin (Dose I):
3.4.24.27;

The structure of Crystal Structure of Thermolysin (Dose I), PDB code: 8zm4 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)	34.09 / 1.40
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	92.919, 92.919, 128.378, 90, 90, 120
R / Rfree (%)	14.8 / 16.7

The structure of Crystal Structure of Thermolysin (Dose I) also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Calcium atom in the Crystal Structure of Thermolysin (Dose I) (pdb code 8zm4). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of Thermolysin (Dose I), PDB code: 8zm4:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of Thermolysin (Dose I)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Thermolysin (Dose I) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1402 b:8.6 occ:1.00 O A:GLU187 2.4 9.1 1.0 OD2 A:ASP138 2.4 8.8 1.0 OD1 A:ASP185 2.4 10.2 1.0 OE2 A:GLU190 2.4 10.5 1.0 O A:HOH1621 2.5 9.3 1.0 OE1 A:GLU177 2.5 8.6 1.0 OE1 A:GLU190 2.6 9.8 1.0 OE2 A:GLU177 2.6 9.7 1.0 CD A:GLU190 2.8 9.1 1.0 CD A:GLU177 2.9 9.4 1.0 CG A:ASP138 3.4 8.5 1.0 CG A:ASP185 3.4 10.5 1.0 C A:GLU187 3.4 9.5 1.0 CA A:CA1405 3.8 18.2 1.0 OD2 A:ASP185 3.8 12.4 1.0 CB A:ASP138 4.0 7.6 1.0 O A:ASP185 4.1 10.7 1.0 N A:GLU187 4.2 11.1 1.0 O A:HOH1613 4.3 9.7 1.0 CA A:GLU187 4.3 11.3 1.0 CG A:GLU190 4.3 9.9 1.0 OD1 A:ASP138 4.3 8.6 1.0 N A:ILE188 4.3 8.7 1.0 CG A:GLU177 4.4 9.3 1.0 O A:HOH1603 4.4 11.2 1.0 CA A:ILE188 4.4 8.7 1.0 N A:GLY189 4.4 8.6 1.0 C A:ASP185 4.5 11.2 1.0 CB A:GLU187 4.5 13.7 1.0 N A:ASP185 4.6 10.1 1.0 CB A:ASP185 4.7 9.8 1.0 C A:ILE188 4.8 9.4 1.0 CA A:ASP185 4.8 10.4 1.0 CB A:GLU177 4.9 8.6 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of Thermolysin (Dose I)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Thermolysin (Dose I) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1403 b:12.9 occ:1.00 O A:ILE197 2.2 18.6 1.0 O A:TYR193 2.3 12.7 1.0 OD1 A:ASP200 2.3 13.3 1.0 O A:THR194 2.4 14.4 1.0 O A:HOH1608 2.4 13.1 1.0 OG1 A:THR194 2.4 15.0 1.0 O A:HOH1784 2.5 19.4 1.0 C A:THR194 3.2 14.6 1.0 C A:TYR193 3.3 10.7 1.0 CG A:ASP200 3.4 11.9 1.0 C A:ILE197 3.4 21.2 1.0 CB A:THR194 3.5 13.5 1.0 CA A:THR194 3.6 13.1 1.0 OD2 A:ASP200 3.8 15.0 1.0 N A:THR194 3.9 12.1 1.0 CA A:ILE197 4.2 19.7 1.0 CB A:ILE197 4.2 19.8 1.0 N A:ILE197 4.2 22.6 1.0 N A:PRO195 4.3 15.0 1.0 O A:HOH1711 4.3 32.5 1.0 O A:ASP200 4.5 13.2 1.0 O A:HOH1698 4.5 34.9 1.0 N A:SER198 4.5 21.7 1.0 O A:GLU190 4.6 12.6 1.0 O A:HOH1646 4.6 34.3 1.0 CA A:TYR193 4.6 10.9 1.0 O A:HOH1796 4.6 23.8 1.0 N A:ASP200 4.6 15.4 1.0 CA A:PRO195 4.7 16.6 1.0 CB A:TYR193 4.7 11.9 1.0 CD2 A:TYR193 4.7 14.2 1.0 CB A:ASP200 4.7 13.1 1.0 CG2 A:THR194 4.8 15.5 1.0 CA A:SER198 4.8 22.9 1.0 CG2 A:ILE197 4.8 20.4 1.0 C A:ASP200 4.8 11.7 1.0 CA A:ASP200 5.0 13.5 1.0 N A:GLY199 5.0 19.0 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of Thermolysin (Dose I)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Thermolysin (Dose I) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1404 b:8.5 occ:1.00 O A:GLN61 2.3 7.6 1.0 O A:HOH1801 2.3 12.3 1.0 O A:HOH1623 2.4 10.8 1.0 OD2 A:ASP57 2.4 9.9 1.0 OD1 A:ASP59 2.4 9.7 1.0 O A:HOH1576 2.5 9.4 1.0 OD1 A:ASP57 2.6 8.6 1.0 CG A:ASP57 2.8 9.5 1.0 CG A:ASP59 3.4 10.5 1.0 C A:GLN61 3.5 7.7 1.0 OD2 A:ASP59 3.8 12.6 1.0 N A:GLN61 4.0 8.4 1.0 O A:HOH1729 4.0 13.7 1.0 CA A:GLN61 4.1 8.1 1.0 CB A:GLN61 4.3 10.0 1.0 N A:ASP59 4.3 9.2 1.0 CB A:ASP57 4.3 8.6 1.0 O A:HOH1877 4.5 20.1 1.0 O A:HOH1743 4.5 13.0 1.0 N A:PHE62 4.5 7.2 1.0 CB A:ASP59 4.6 10.0 1.0 OD2 A:ASP67 4.6 8.0 1.0 O A:HOH1537 4.6 9.2 1.0 O A:HOH1891 4.6 30.1 1.0 N A:ASN60 4.7 9.0 1.0 O A:HOH1858 4.7 26.1 1.0 N A:ALA58 4.8 9.1 1.0 CA A:PHE62 4.8 7.0 1.0 CA A:ASP59 4.8 9.2 1.0 C A:ASP59 4.9 9.2 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of Thermolysin (Dose I)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Thermolysin (Dose I) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1405 b:18.2 occ:1.00 O A:ASN183 2.3 11.6 1.0 OE2 A:GLU190 2.3 10.5 1.0 O A:HOH1603 2.3 11.2 1.0 O A:HOH1598 2.4 15.4 1.0 OD2 A:ASP185 2.4 12.4 1.0 OE2 A:GLU177 2.8 9.7 1.0 CG A:ASP185 3.2 10.5 1.0 CD A:GLU190 3.3 9.1 1.0 CD A:GLU177 3.4 9.4 1.0 C A:ASN183 3.5 11.3 1.0 OD1 A:ASP185 3.6 10.2 1.0 OE1 A:GLU177 3.7 8.6 1.0 CG A:GLU190 3.8 9.9 1.0 CA A:CA1402 3.8 8.6 1.0 O A:HOH1591 4.0 29.2 1.0 CA A:PRO184 4.1 11.6 1.0 N A:ASP185 4.1 10.1 1.0 C A:PRO184 4.2 12.1 1.0 OD1 A:ASP191 4.2 13.1 1.0 OD2 A:ASP191 4.2 11.2 1.0 O A:HOH1747 4.3 11.7 1.0 N A:PRO184 4.3 11.7 1.0 CB A:ASN183 4.3 14.2 1.0 OE1 A:GLU190 4.3 9.8 1.0 CB A:ASP185 4.3 9.8 1.0 CG A:GLU177 4.4 9.3 1.0 CA A:ASN183 4.5 12.9 1.0 CG A:ASP191 4.5 11.5 1.0 O A:HOH1613 4.8 9.7 1.0 CA A:ASP185 4.8 10.4 1.0 O A:PRO184 4.9 13.8 1.0 O A:HOH1761 5.0 35.0 1.0

K.H.Nam, K.H.Nam. N/A N/A.