Calcium in PDB 3t2i: Tetragonal Thermolysin in the Presence of Sarcosine

All present enzymatic activity of Tetragonal Thermolysin in the Presence of Sarcosine:
3.4.24.27;

The structure of Tetragonal Thermolysin in the Presence of Sarcosine, PDB code: 3t2i was solved by J.Cahn, N.S.Hti Lar Seng, D.Juers, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.22 / 2.10
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	96.346, 96.346, 105.875, 90.00, 90.00, 90.00
R / Rfree (%)	17.3 / 21.6

The structure of Tetragonal Thermolysin in the Presence of Sarcosine also contains other interesting chemical elements:

Zinc	(Zn)	2 atoms
Chlorine	(Cl)	3 atoms
Sodium	(Na)	1 atom

The binding sites of Calcium atom in the Tetragonal Thermolysin in the Presence of Sarcosine (pdb code 3t2i). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Tetragonal Thermolysin in the Presence of Sarcosine, PDB code: 3t2i:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Tetragonal Thermolysin in the Presence of Sarcosine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Tetragonal Thermolysin in the Presence of Sarcosine within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca317 b:15.3 occ:1.00 O E:GLU187 2.3 12.8 1.0 OD2 E:ASP138 2.4 14.1 1.0 OD1 E:ASP185 2.4 14.5 1.0 OE1 E:GLU177 2.4 14.4 1.0 O E:HOH414 2.5 15.6 1.0 OE1 E:GLU190 2.5 10.4 1.0 OE2 E:GLU190 2.6 7.2 1.0 OE2 E:GLU177 2.7 14.2 1.0 CD E:GLU190 2.9 11.4 1.0 CD E:GLU177 2.9 16.3 1.0 CG E:ASP138 3.3 14.7 1.0 C E:GLU187 3.4 13.3 1.0 CG E:ASP185 3.5 16.7 1.0 CA E:CA318 3.6 7.5 1.0 OD2 E:ASP185 3.8 11.9 1.0 CB E:ASP138 4.0 13.6 1.0 OD1 E:ASP138 4.2 13.7 1.0 O E:ASP185 4.2 13.0 1.0 N E:GLU187 4.2 15.3 1.0 N E:ILE188 4.3 12.4 1.0 CA E:GLU187 4.3 15.4 1.0 CA E:ILE188 4.3 11.2 1.0 CG E:GLU190 4.4 13.7 1.0 N E:GLY189 4.4 11.8 1.0 CG E:GLU177 4.4 13.5 1.0 O E:HOH421 4.5 12.8 1.0 O E:HOH418 4.5 12.6 1.0 CB E:GLU187 4.5 16.6 1.0 C E:ASP185 4.7 15.2 1.0 N E:ASP185 4.7 17.9 1.0 CB E:ASP185 4.8 15.6 1.0 C E:ILE188 4.8 11.5 1.0 CB E:GLU177 4.9 13.7 1.0 N E:GLU190 4.9 13.4 1.0

Calcium binding site 2 out of 4 in the Tetragonal Thermolysin in the Presence of Sarcosine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Tetragonal Thermolysin in the Presence of Sarcosine within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca318 b:7.5 occ:1.00 OE2 E:GLU190 1.9 7.2 1.0 O E:HOH421 2.0 12.8 1.0 OD2 E:ASP185 2.1 11.9 1.0 O E:HOH457 2.1 11.8 1.0 OE2 E:GLU177 2.3 14.2 1.0 O E:ASN183 2.3 18.8 1.0 CD E:GLU190 3.0 11.4 1.0 CD E:GLU177 3.0 16.3 1.0 CG E:ASP185 3.0 16.7 1.0 OD1 E:ASP185 3.4 14.5 1.0 OE1 E:GLU177 3.5 14.4 1.0 C E:ASN183 3.5 20.4 1.0 CA E:CA317 3.6 15.3 1.0 CG E:GLU190 3.6 13.7 1.0 OE1 E:GLU190 3.9 10.4 1.0 CA E:PRO184 4.0 19.2 1.0 CG E:GLU177 4.0 13.5 1.0 OD2 E:ASP191 4.0 18.7 1.0 N E:ASP185 4.1 17.9 1.0 ND2 E:ASN183 4.1 24.9 1.0 OD1 E:ASP191 4.2 17.3 1.0 C E:PRO184 4.2 18.5 1.0 CG E:ASN183 4.2 28.8 1.0 N E:PRO184 4.2 18.8 1.0 CB E:ASP185 4.3 15.6 1.0 CG E:ASP191 4.5 16.8 1.0 OD1 E:ASN183 4.5 36.7 1.0 CB E:ASN183 4.7 23.7 1.0 CA E:ASN183 4.7 22.5 1.0 CA E:ASP185 4.9 16.0 1.0 O E:PRO184 4.9 19.1 1.0

Calcium binding site 3 out of 4 in the Tetragonal Thermolysin in the Presence of Sarcosine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Tetragonal Thermolysin in the Presence of Sarcosine within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca319 b:22.6 occ:1.00 OD1 E:ASP59 2.3 24.6 1.0 O E:GLN61 2.3 20.4 1.0 O E:HOH467 2.3 24.0 1.0 O E:HOH447 2.3 15.6 1.0 OD1 E:ASP57 2.3 22.0 1.0 OD2 E:ASP57 2.5 16.5 1.0 O E:HOH463 2.6 18.1 1.0 CG E:ASP57 2.8 18.7 1.0 CG E:ASP59 3.3 23.7 1.0 C E:GLN61 3.5 20.1 1.0 OD2 E:ASP59 3.7 22.8 1.0 O E:HOH464 3.9 26.7 1.0 N E:GLN61 3.9 20.0 1.0 CA E:GLN61 4.1 21.7 1.0 N E:ASP59 4.2 19.6 1.0 O E:HOH469 4.2 22.2 1.0 CB E:GLN61 4.3 22.9 1.0 O E:HOH507 4.3 30.6 1.0 CB E:ASP57 4.3 16.6 1.0 O E:HOH491 4.4 26.6 1.0 N E:PHE62 4.5 18.3 1.0 CB E:ASP59 4.5 20.3 1.0 N E:ASN60 4.6 19.2 1.0 CA E:ASP59 4.7 20.1 1.0 N E:ALA58 4.7 19.2 1.0 OD2 E:ASP67 4.7 18.0 1.0 O E:HOH424 4.8 12.9 1.0 C E:ASP59 4.8 19.9 1.0 CA E:PHE62 4.8 17.9 1.0 CG E:GLN61 4.9 30.0 1.0

Calcium binding site 4 out of 4 in the Tetragonal Thermolysin in the Presence of Sarcosine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Tetragonal Thermolysin in the Presence of Sarcosine within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca320 b:17.5 occ:1.00 O E:HOH462 2.1 18.7 1.0 O E:ILE197 2.3 25.8 1.0 OD1 E:ASP200 2.3 18.9 1.0 OG1 E:THR194 2.4 15.0 1.0 O E:THR194 2.4 19.8 1.0 O E:HOH422 2.4 12.2 1.0 O E:TYR193 2.4 17.0 1.0 C E:THR194 3.3 18.6 1.0 CG E:ASP200 3.4 17.8 1.0 C E:TYR193 3.4 16.4 1.0 C E:ILE197 3.5 27.1 1.0 CB E:THR194 3.5 17.4 1.0 OD2 E:ASP200 3.8 17.4 1.0 CA E:THR194 3.8 17.3 1.0 N E:THR194 4.0 17.2 1.0 CB E:ILE197 4.3 26.2 1.0 CA E:ILE197 4.3 26.2 1.0 N E:PRO195 4.3 19.2 1.0 N E:ILE197 4.3 26.9 1.0 O E:HOH515 4.4 25.6 1.0 O E:ASP200 4.5 15.3 1.0 N E:SER198 4.5 27.3 1.0 CA E:TYR193 4.6 15.9 1.0 CA E:SER198 4.6 27.2 1.0 O E:GLU190 4.6 17.3 1.0 N E:ASP200 4.6 19.7 1.0 CA E:PRO195 4.7 21.2 1.0 O E:HOH458 4.7 25.4 1.0 CG2 E:THR194 4.7 14.0 1.0 CB E:TYR193 4.7 16.1 1.0 CB E:ASP200 4.7 15.6 1.0 O E:HOH594 4.8 29.4 1.0 CD2 E:TYR193 4.8 17.6 1.0 C E:ASP200 4.8 16.4 1.0 CG2 E:ILE197 4.9 27.1 1.0 C E:SER198 4.9 26.3 1.0 C E:PRO195 5.0 22.4 1.0

H.Marshall, M.Venkat, N.S.Hti Lar Seng, J.Cahn, D.H.Juers. The Use of Trimethylamine N-Oxide As A Primary Precipitating Agent and Related Methylamine Osmolytes As Cryoprotective Agents For Macromolecular Crystallography. Acta Crystallogr.,Sect.D V. 68 69 2012.
ISSN: ISSN 0907-4449
PubMed: 22194335
DOI: 10.1107/S0907444911050360