Calcium in PDB 8zm5: Crystal Structure of Thermolysin (Dose II)

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

The structure of Crystal Structure of Thermolysin (Dose II), PDB code: 8zm5 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)	34.16 / 1.40
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	93.081, 93.081, 128.694, 90, 90, 120
R / Rfree (%)	14.9 / 16.8

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

Zinc

(Zn)

1 atom

The binding sites of Calcium atom in the Crystal Structure of Thermolysin (Dose II) (pdb code 8zm5). 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 II), PDB code: 8zm5:
Jump to Calcium binding site number: 1; 2; 3; 4;

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


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 II) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca404 b:9.2 occ:1.00 O A:GLU187 2.4 10.3 1.0 OD2 A:ASP138 2.4 9.7 1.0 OD1 A:ASP185 2.4 10.9 1.0 O A:HOH635 2.5 10.2 1.0 OE2 A:GLU190 2.5 11.3 1.0 OE1 A:GLU177 2.5 9.2 1.0 OE1 A:GLU190 2.6 11.1 1.0 OE2 A:GLU177 2.6 10.7 1.0 CD A:GLU190 2.8 10.0 1.0 CD A:GLU177 2.9 9.7 1.0 CG A:ASP138 3.4 9.3 1.0 CG A:ASP185 3.4 11.2 1.0 C A:GLU187 3.4 10.3 1.0 OD2 A:ASP185 3.8 13.7 1.0 CA A:CA407 3.8 19.6 1.0 CB A:ASP138 4.0 7.8 1.0 O A:ASP185 4.1 11.3 1.0 N A:GLU187 4.2 11.9 1.0 O A:HOH618 4.3 11.1 1.0 CA A:GLU187 4.3 11.7 1.0 N A:ILE188 4.3 9.4 1.0 OD1 A:ASP138 4.3 9.6 1.0 CG A:GLU190 4.3 10.9 1.0 CA A:ILE188 4.4 8.7 1.0 N A:GLY189 4.4 8.9 1.0 CG A:GLU177 4.4 9.7 1.0 O A:HOH588 4.4 12.9 1.0 C A:ASP185 4.5 11.9 1.0 CB A:GLU187 4.6 14.8 1.0 N A:ASP185 4.6 10.6 1.0 CB A:ASP185 4.7 10.4 1.0 C A:ILE188 4.8 9.7 1.0 CA A:ASP185 4.9 10.5 1.0 CB A:GLU177 5.0 8.7 1.0

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


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 II) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca405 b:13.4 occ:1.00 O A:ILE197 2.2 19.5 1.0 O A:TYR193 2.3 13.5 1.0 OD1 A:ASP200 2.4 13.8 1.0 O A:HOH607 2.4 14.0 1.0 O A:THR194 2.4 14.9 1.0 OG1 A:THR194 2.4 15.2 1.0 O A:HOH768 2.4 19.5 1.0 C A:THR194 3.2 14.9 1.0 C A:TYR193 3.3 11.3 1.0 CG A:ASP200 3.4 12.6 1.0 C A:ILE197 3.4 22.0 1.0 CB A:THR194 3.5 14.2 1.0 CA A:THR194 3.7 13.5 1.0 OD2 A:ASP200 3.8 15.2 1.0 N A:THR194 3.9 12.5 1.0 CA A:ILE197 4.2 20.8 1.0 CB A:ILE197 4.2 21.7 1.0 N A:ILE197 4.2 23.6 1.0 N A:PRO195 4.3 15.8 1.0 O A:HOH653 4.3 35.5 1.0 O A:HOH658 4.4 34.6 1.0 O A:ASP200 4.5 14.0 1.0 N A:SER198 4.5 22.4 1.0 O A:GLU190 4.6 13.1 1.0 CA A:TYR193 4.6 11.5 1.0 N A:ASP200 4.6 15.5 1.0 O A:HOH791 4.7 26.1 1.0 CA A:PRO195 4.7 17.1 1.0 CB A:TYR193 4.7 12.8 1.0 CB A:ASP200 4.7 13.5 1.0 CD2 A:TYR193 4.7 14.6 1.0 CA A:SER198 4.8 23.9 1.0 CG2 A:THR194 4.8 16.2 1.0 C A:ASP200 4.9 12.7 1.0 CG2 A:ILE197 4.9 23.0 1.0 CA A:ASP200 5.0 13.8 1.0

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


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 II) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca406 b:9.0 occ:1.00 O A:GLN61 2.3 7.8 1.0 O A:HOH785 2.3 12.6 1.0 O A:HOH608 2.4 11.8 1.0 OD1 A:ASP59 2.4 10.5 1.0 OD2 A:ASP57 2.4 10.2 1.0 O A:HOH585 2.5 10.4 1.0 OD1 A:ASP57 2.6 9.0 1.0 CG A:ASP57 2.8 10.0 1.0 CG A:ASP59 3.4 10.7 1.0 C A:GLN61 3.4 7.8 1.0 OD2 A:ASP59 3.8 13.5 1.0 O A:HOH712 4.0 15.0 1.0 N A:GLN61 4.0 8.6 1.0 CA A:GLN61 4.1 8.2 1.0 CB A:GLN61 4.3 9.7 1.0 CB A:ASP57 4.3 8.7 1.0 N A:ASP59 4.3 9.4 1.0 O A:HOH852 4.4 21.8 1.0 O A:HOH754 4.5 13.2 1.0 N A:PHE62 4.5 7.5 1.0 CB A:ASP59 4.6 10.4 1.0 OD2 A:ASP67 4.6 8.8 1.0 O A:HOH539 4.6 9.2 1.0 O A:HOH865 4.7 32.0 1.0 N A:ASN60 4.7 9.4 1.0 O A:HOH834 4.7 24.8 1.0 N A:ALA58 4.8 9.4 1.0 CA A:PHE62 4.8 7.1 1.0 CA A:ASP59 4.8 9.3 1.0 C A:ASP59 4.9 9.4 1.0

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


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 II) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca407 b:19.6 occ:1.00 O A:ASN183 2.3 11.6 1.0 O A:HOH588 2.3 12.9 1.0 O A:HOH597 2.3 18.0 1.0 OE2 A:GLU190 2.4 11.3 1.0 OD2 A:ASP185 2.4 13.7 1.0 OE2 A:GLU177 2.8 10.7 1.0 CG A:ASP185 3.2 11.2 1.0 CD A:GLU190 3.3 10.0 1.0 CD A:GLU177 3.4 9.7 1.0 C A:ASN183 3.5 11.6 1.0 OD1 A:ASP185 3.7 10.9 1.0 OE1 A:GLU177 3.7 9.2 1.0 CG A:GLU190 3.8 10.9 1.0 CA A:CA404 3.8 9.2 1.0 CA A:PRO184 4.1 11.5 1.0 N A:ASP185 4.1 10.6 1.0 OD1 A:ASP191 4.2 15.1 1.0 C A:PRO184 4.2 12.1 1.0 O A:HOH739 4.2 12.6 1.0 CB A:ASN183 4.2 14.5 1.0 OD2 A:ASP191 4.2 12.7 1.0 N A:PRO184 4.3 11.7 1.0 CB A:ASP185 4.3 10.4 1.0 OE1 A:GLU190 4.3 11.1 1.0 CG A:GLU177 4.5 9.7 1.0 CA A:ASN183 4.5 12.7 1.0 CG A:ASP191 4.5 13.1 1.0 O A:HOH618 4.8 11.1 1.0 CA A:ASP185 4.9 10.5 1.0 O A:PRO184 4.9 14.9 1.0 O A:HOH748 5.0 37.4 1.0

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