Calcium in PDB 2g4z: Anomalous Substructure of Thermolysin

All present enzymatic activity of Anomalous Substructure of Thermolysin:
3.4.24.27;

The structure of Anomalous Substructure of Thermolysin, PDB code: 2g4z was solved by C.Mueller-Dieckmann, M.S.Weiss, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 1.98
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	92.487, 92.487, 127.529, 90.00, 90.00, 120.00
R / Rfree (%)	19 / 23.7

The structure of Anomalous Substructure of Thermolysin also contains other interesting chemical elements:

Chlorine	(Cl)	8 atoms
Zinc	(Zn)	1 atom

The binding sites of Calcium atom in the Anomalous Substructure of Thermolysin (pdb code 2g4z). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Anomalous Substructure of Thermolysin, PDB code: 2g4z:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Anomalous Substructure of Thermolysin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Anomalous Substructure of Thermolysin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca322 b:35.5 occ:1.00 O A:GLN61 2.3 35.4 1.0 OD1 A:ASP57 2.3 34.6 1.0 OD1 A:ASP59 2.4 37.6 1.0 O A:HOH367 2.4 35.2 1.0 O A:HOH395 2.4 32.6 1.0 O A:HOH382 2.4 34.2 1.0 OD2 A:ASP57 2.6 32.2 1.0 CG A:ASP57 2.8 38.5 1.0 CG A:ASP59 3.4 32.6 1.0 C A:GLN61 3.4 34.4 1.0 OD2 A:ASP59 3.8 36.2 1.0 N A:GLN61 3.9 36.1 1.0 O A:HOH365 4.0 36.4 1.0 CA A:GLN61 4.1 37.5 1.0 CB A:ASP57 4.3 36.2 1.0 N A:ASP59 4.4 35.6 1.0 CB A:GLN61 4.4 38.3 1.0 N A:PHE62 4.5 34.9 1.0 O A:HOH346 4.5 33.5 1.0 OD2 A:ASP67 4.6 35.3 1.0 CB A:ASP59 4.6 36.9 1.0 CA A:PHE62 4.7 33.7 1.0 N A:ASN60 4.7 35.7 1.0 N A:ALA58 4.8 33.4 1.0 CA A:ASP59 4.9 36.4 1.0 C A:ASP59 4.9 36.6 1.0

Calcium binding site 2 out of 3 in the Anomalous Substructure of Thermolysin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Anomalous Substructure of Thermolysin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca323 b:36.0 occ:1.00 O A:GLU187 2.3 34.4 1.0 OE2 A:GLU190 2.4 35.4 1.0 OD2 A:ASP138 2.4 37.3 1.0 O A:HOH358 2.4 33.5 1.0 OD1 A:ASP185 2.5 35.3 1.0 OE1 A:GLU177 2.5 32.7 1.0 OE1 A:GLU190 2.6 39.7 1.0 OE2 A:GLU177 2.8 36.5 1.0 CD A:GLU190 2.8 35.2 1.0 CD A:GLU177 3.0 38.3 1.0 CG A:ASP138 3.4 37.5 1.0 C A:GLU187 3.4 35.5 1.0 CG A:ASP185 3.5 42.9 1.0 OD2 A:ASP185 3.8 40.3 1.0 CB A:ASP138 3.9 33.7 1.0 O A:ASP185 4.1 37.0 1.0 N A:GLU187 4.2 36.7 1.0 O A:HOH402 4.3 36.1 1.0 OD1 A:ASP138 4.3 34.4 1.0 N A:ILE188 4.3 37.0 1.0 CA A:GLU187 4.3 37.3 1.0 CA A:ILE188 4.3 35.8 1.0 CG A:GLU190 4.4 38.5 1.0 CG A:GLU177 4.4 35.7 1.0 N A:GLY189 4.5 36.9 1.0 C A:ASP185 4.5 37.9 1.0 CB A:GLU187 4.5 37.9 1.0 N A:ASP185 4.6 38.0 1.0 CB A:ASP185 4.8 38.4 1.0 C A:ILE188 4.8 37.6 1.0 CA A:ASP185 4.8 37.8 1.0 CB A:GLU177 4.9 34.0 1.0

Calcium binding site 3 out of 3 in the Anomalous Substructure of Thermolysin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Anomalous Substructure of Thermolysin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca324 b:40.9 occ:1.00 O A:HOH356 2.1 48.0 1.0 OG1 A:THR194 2.2 42.8 1.0 OD1 A:ASP200 2.3 38.7 1.0 O A:ILE197 2.3 47.7 1.0 O A:THR194 2.4 45.4 1.0 O A:HOH339 2.4 38.7 1.0 O A:TYR193 2.4 35.8 1.0 C A:THR194 3.2 43.9 1.0 CB A:THR194 3.3 43.5 1.0 C A:TYR193 3.4 39.3 1.0 CG A:ASP200 3.4 37.6 1.0 C A:ILE197 3.5 50.5 1.0 CA A:THR194 3.6 43.0 1.0 OD2 A:ASP200 3.8 37.3 1.0 N A:THR194 3.9 41.1 1.0 N A:PRO195 4.2 45.2 1.0 CA A:ILE197 4.2 51.1 1.0 N A:ILE197 4.3 52.6 1.0 CB A:ILE197 4.3 51.6 1.0 O A:ASP200 4.4 40.6 1.0 CA A:TYR193 4.5 38.9 1.0 CG2 A:THR194 4.5 44.6 1.0 N A:SER198 4.5 47.9 1.0 O A:GLU190 4.6 38.0 1.0 N A:ASP200 4.6 42.7 1.0 CB A:TYR193 4.6 40.0 1.0 CA A:PRO195 4.6 47.3 1.0 O A:HOH418 4.7 48.5 1.0 CA A:SER198 4.7 49.8 1.0 CB A:ASP200 4.7 42.2 1.0 CD2 A:TYR193 4.7 45.5 1.0 C A:ASP200 4.8 41.4 1.0 C A:PRO195 4.9 48.6 1.0 C A:SER198 4.9 49.1 1.0 CA A:ASP200 4.9 41.3 1.0 N A:TYR193 4.9 37.2 1.0 N A:GLY199 5.0 48.7 1.0 CG A:TYR193 5.0 42.9 1.0

C.Mueller-Dieckmann, S.Panjikar, A.Schmidt, S.Mueller, J.Kuper, A.Geerlof, M.Wilmanns, R.K.Singh, P.A.Tucker, M.S.Weiss. On the Routine Use of Soft X-Rays in Macromolecular Crystallography. Part IV. Efficient Determination of Anomalous Substructures in Biomacromolecules Using Longer X-Ray Wavelengths. Acta Crystallogr.,Sect.D V. 63 366 2007.
ISSN: ISSN 0907-4449
PubMed: 17327674
DOI: 10.1107/S0907444906055624