Calcium in PDB 9f56: Identification of Calcium Ions in Thermolysin.

All present enzymatic activity of Identification of Calcium Ions in Thermolysin.:
3.4.24.27;

The structure of Identification of Calcium Ions in Thermolysin., PDB code: 9f56 was solved by K.El Omari, I.Forsyth, A.Wagner, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	80.67 / 2.10
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	93.151, 93.151, 128.981, 90, 90, 120
R / Rfree (%)	18.1 / 21.9

The structure of Identification of Calcium Ions in Thermolysin. also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Calcium atom in the Identification of Calcium Ions in Thermolysin. (pdb code 9f56). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Identification of Calcium Ions in Thermolysin., PDB code: 9f56:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Identification of Calcium Ions in Thermolysin.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Identification of Calcium Ions in Thermolysin. within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca400 b:23.7 occ:1.00 O A:GLU187 2.2 25.0 1.0 OD1 A:ASP185 2.4 30.4 1.0 O A:HOH550 2.4 24.4 1.0 OE2 A:GLU190 2.5 29.3 1.0 OD2 A:ASP138 2.5 25.5 1.0 OE1 A:GLU190 2.7 28.9 1.0 OE1 A:GLU177 2.7 23.3 1.0 OE2 A:GLU177 2.8 24.1 1.0 CD A:GLU190 2.9 28.4 1.0 CD A:GLU177 3.1 23.3 1.0 C A:GLU187 3.3 26.2 1.0 CG A:ASP185 3.4 29.8 1.0 CG A:ASP138 3.5 24.7 1.0 OD2 A:ASP185 3.9 31.5 1.0 O A:ASP185 3.9 24.8 1.0 N A:GLU187 4.1 26.4 1.0 CB A:ASP138 4.1 23.1 1.0 CA A:GLU187 4.2 27.7 1.0 N A:ILE188 4.2 26.0 1.0 CA A:ILE188 4.3 26.1 1.0 C A:ASP185 4.4 26.7 1.0 CG A:GLU190 4.4 29.0 1.0 N A:GLY189 4.4 27.3 1.0 OD1 A:ASP138 4.5 25.3 1.0 CB A:GLU187 4.5 30.7 1.0 CG A:GLU177 4.5 21.3 1.0 O A:HOH524 4.6 25.7 1.0 N A:ASP185 4.6 26.9 1.0 CB A:ASP185 4.7 28.7 1.0 C A:ILE188 4.8 27.6 1.0 CA A:ASP185 4.8 27.3 1.0

Calcium binding site 2 out of 3 in the Identification of Calcium Ions in Thermolysin.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Identification of Calcium Ions in Thermolysin. within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:22.6 occ:1.00 O A:GLN61 2.2 19.2 1.0 O A:HOH533 2.3 21.2 1.0 O A:HOH638 2.4 23.9 1.0 OD2 A:ASP57 2.4 25.0 1.0 O A:HOH564 2.4 21.8 1.0 OD1 A:ASP59 2.5 22.2 1.0 OD1 A:ASP57 2.8 21.2 1.0 CG A:ASP57 3.0 23.4 1.0 C A:GLN61 3.4 20.1 1.0 CG A:ASP59 3.5 21.9 1.0 O A:HOH568 3.8 23.9 1.0 OD2 A:ASP59 3.8 22.6 1.0 N A:GLN61 4.0 21.2 1.0 CA A:GLN61 4.1 22.8 1.0 CB A:GLN61 4.3 25.8 1.0 O A:HOH676 4.4 29.8 1.0 N A:PHE62 4.5 19.3 1.0 CB A:ASP57 4.5 22.1 1.0 OD2 A:ASP67 4.5 19.1 1.0 O A:HOH622 4.5 22.9 1.0 N A:ASP59 4.5 21.1 1.0 O A:HOH554 4.7 17.9 1.0 CA A:PHE62 4.7 20.1 1.0 CB A:ASP59 4.7 20.6 1.0 O A:HOH674 4.8 38.0 1.0 N A:ASN60 4.8 20.5 1.0 N A:ALA58 4.9 21.8 1.0 CA A:ASP59 5.0 20.7 1.0

Calcium binding site 3 out of 3 in the Identification of Calcium Ions in Thermolysin.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Identification of Calcium Ions in Thermolysin. within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:32.3 occ:1.00 O A:ILE197 2.2 37.0 1.0 O A:HOH616 2.3 31.9 1.0 O A:TYR193 2.4 26.2 1.0 OD1 A:ASP200 2.4 29.2 1.0 O A:THR194 2.4 31.7 1.0 O A:HOH513 2.4 32.3 1.0 OG1 A:THR194 2.6 29.7 1.0 C A:THR194 3.3 30.7 1.0 C A:TYR193 3.4 27.1 1.0 C A:ILE197 3.4 38.4 1.0 CG A:ASP200 3.5 29.0 1.0 CB A:THR194 3.7 30.0 1.0 CA A:THR194 3.8 30.0 1.0 N A:THR194 4.0 28.4 1.0 OD2 A:ASP200 4.0 29.2 1.0 CA A:ILE197 4.3 39.9 1.0 N A:ILE197 4.3 44.0 1.0 N A:PRO195 4.4 32.8 1.0 O A:ASP200 4.4 27.6 1.0 N A:SER198 4.4 36.1 1.0 CB A:ILE197 4.4 38.9 1.0 CA A:SER198 4.5 39.5 1.0 O A:HOH647 4.5 43.1 1.0 O A:GLU190 4.5 28.0 1.0 N A:ASP200 4.5 31.8 1.0 CA A:TYR193 4.6 26.9 1.0 CA A:PRO195 4.7 36.0 1.0 C A:SER198 4.8 38.5 1.0 CB A:ASP200 4.8 28.1 1.0 C A:ASP200 4.8 27.9 1.0 CD2 A:TYR193 4.8 30.4 1.0 N A:GLY199 4.8 38.2 1.0 CB A:TYR193 4.8 27.8 1.0 CA A:ASP200 4.9 28.8 1.0 CG2 A:THR194 5.0 31.4 1.0 C A:PRO195 5.0 40.1 1.0

K.El Omari, I.Forsyth, R.Duman, C.M.Orr, V.Mykhaylyk, E.J.Mancini, A.Wagner. Utilizing Anomalous Signals For Element Identification in Macromolecular Crystallography. Acta Crystallogr D Struct 2024BIOL.
ISSN: ISSN 2059-7983
PubMed: 39291627
DOI: 10.1107/S2059798324008659