Calcium in PDB 6qf2: X-Ray Structure of Thermolysin Crystallized on A Silicon Chip

All present enzymatic activity of X-Ray Structure of Thermolysin Crystallized on A Silicon Chip:
3.4.24.27;

The structure of X-Ray Structure of Thermolysin Crystallized on A Silicon Chip, PDB code: 6qf2 was solved by J.Lieske, M.Cerv, S.Kreida, M.Barthelmess, P.Fischer, T.Pakendorf, O.Yefanov, V.Mariani, T.Seine, B.H.Ross, E.Crosas, O.Lorbeer, A.Burkhardt, T.J.Lane, S.Guenther, J.Bergtholdt, S.Schoen, S.Tornroth-Horsefield, H.N.Chapman, A.Meents, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.33 / 1.73
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	92.667, 92.667, 128.311, 90.00, 90.00, 120.00
R / Rfree (%)	12.8 / 16.1

The structure of X-Ray Structure of Thermolysin Crystallized on A Silicon Chip also contains other interesting chemical elements:

Zinc	(Zn)	2 atoms
Sodium	(Na)	1 atom

The binding sites of Calcium atom in the X-Ray Structure of Thermolysin Crystallized on A Silicon Chip (pdb code 6qf2). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the X-Ray Structure of Thermolysin Crystallized on A Silicon Chip, PDB code: 6qf2:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the X-Ray Structure of Thermolysin Crystallized on A Silicon Chip


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of X-Ray Structure of Thermolysin Crystallized on A Silicon Chip within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:10.4 occ:1.00 O A:GLU187 2.3 10.3 1.0 OD2 A:ASP138 2.4 13.6 1.0 OE1 A:GLU177 2.5 11.1 1.0 OD1 A:ASP185 2.5 11.7 1.0 O A:HOH618 2.5 12.5 1.0 OE1 A:GLU190 2.5 11.1 1.0 OE2 A:GLU190 2.5 12.4 1.0 OE2 A:GLU177 2.8 10.8 1.0 CD A:GLU190 2.8 12.6 1.0 CD A:GLU177 2.9 11.5 1.0 CG A:ASP138 3.4 15.0 1.0 C A:GLU187 3.4 10.7 1.0 CG A:ASP185 3.5 11.8 1.0 HB3 A:ASP138 3.6 10.2 1.0 HA A:ILE188 3.7 11.5 1.0 H A:GLY189 3.7 12.9 1.0 H A:GLU187 3.8 16.2 1.0 OD2 A:ASP185 3.8 12.8 1.0 CA A:CA403 3.8 13.7 1.0 CB A:ASP138 4.0 8.5 1.0 O A:ASP185 4.1 12.2 1.0 H A:ASP185 4.1 13.1 1.0 H A:GLU190 4.1 13.0 1.0 N A:GLU187 4.2 13.5 1.0 HD13 A:ILE188 4.2 20.2 1.0 HB2 A:ASP138 4.3 10.2 1.0 N A:ILE188 4.3 10.7 1.0 O A:HOH609 4.3 14.8 1.0 OD1 A:ASP138 4.3 13.9 1.0 HB2 A:GLU187 4.3 19.7 1.0 CG A:GLU190 4.3 12.9 1.0 CA A:GLU187 4.4 13.3 1.0 CA A:ILE188 4.4 9.6 1.0 CG A:GLU177 4.4 10.1 1.0 N A:GLY189 4.4 10.8 1.0 C A:ASP185 4.5 12.7 1.0 HG3 A:GLU190 4.6 15.5 1.0 HB2 A:GLU177 4.7 11.1 1.0 N A:ASP185 4.7 10.9 1.0 CB A:ASP185 4.7 15.4 1.0 HB3 A:GLU177 4.8 11.1 1.0 HG2 A:GLU190 4.8 15.5 1.0 HG2 A:GLU177 4.8 12.1 1.0 CB A:GLU187 4.8 16.4 1.0 C A:ILE188 4.9 11.8 1.0 HA A:THR174 4.9 10.6 1.0 CB A:GLU177 4.9 9.3 1.0 HG3 A:GLU177 4.9 12.1 1.0 CA A:ASP185 4.9 14.2 1.0 N A:GLU190 4.9 10.9 1.0 HB3 A:GLU190 5.0 15.0 1.0 O A:HOH549 5.0 15.9 1.0

Calcium binding site 2 out of 4 in the X-Ray Structure of Thermolysin Crystallized on A Silicon Chip


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of X-Ray Structure of Thermolysin Crystallized on A Silicon Chip within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca403 b:13.7 occ:1.00 O A:ASN183 2.2 13.9 1.0 OE2 A:GLU190 2.3 12.4 1.0 OD2 A:ASP185 2.3 12.8 1.0 O A:HOH549 2.4 15.9 1.0 O A:HOH639 2.4 17.2 1.0 OE2 A:GLU177 2.4 10.8 1.0 CG A:ASP185 3.2 11.8 1.0 CD A:GLU177 3.3 11.5 1.0 CD A:GLU190 3.3 12.6 1.0 C A:ASN183 3.4 11.9 1.0 HG3 A:GLU190 3.5 15.5 1.0 HA A:PRO184 3.5 15.4 1.0 HB2 A:ASN183 3.6 19.1 1.0 OD1 A:ASP185 3.6 11.7 1.0 HG2 A:GLU190 3.7 15.5 1.0 CG A:GLU190 3.8 12.9 1.0 OE1 A:GLU177 3.8 11.1 1.0 CA A:CA402 3.8 10.4 1.0 HB3 A:ASN183 3.8 19.1 1.0 H A:ASP185 4.0 13.1 1.0 CB A:ASN183 4.1 15.9 1.0 OD2 A:ASP191 4.1 19.4 1.0 CA A:PRO184 4.1 12.8 1.0 OD1 A:ASP191 4.1 18.8 1.0 O A:HOH698 4.2 24.4 1.0 N A:ASP185 4.2 10.9 1.0 N A:PRO184 4.2 13.0 1.0 HG2 A:GLU177 4.2 12.1 1.0 C A:PRO184 4.3 13.3 1.0 CG A:GLU177 4.3 10.1 1.0 OE1 A:GLU190 4.3 11.1 1.0 HG3 A:GLU177 4.3 12.1 1.0 O A:LYS182 4.3 19.3 1.0 HB3 A:ASP185 4.4 18.5 1.0 CB A:ASP185 4.4 15.4 1.0 CA A:ASN183 4.4 20.9 1.0 CG A:ASP191 4.4 17.4 1.0 H12 A:EDO411 4.5 24.2 0.7 O A:HOH893 4.5 29.8 1.0 CA A:ASP185 4.9 14.2 1.0 O A:PRO184 4.9 14.1 1.0 O A:HOH609 5.0 14.8 1.0

Calcium binding site 3 out of 4 in the X-Ray Structure of Thermolysin Crystallized on A Silicon Chip


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of X-Ray Structure of Thermolysin Crystallized on A Silicon Chip within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca404 b:10.3 occ:1.00 O A:GLN61 2.3 9.9 1.0 O A:HOH829 2.3 13.9 1.0 OD2 A:ASP57 2.4 10.7 1.0 OD1 A:ASP59 2.4 11.3 1.0 O A:HOH581 2.4 11.4 1.0 O A:HOH632 2.4 11.6 1.0 OD1 A:ASP57 2.5 11.9 1.0 CG A:ASP57 2.8 9.2 1.0 H A:GLN61 3.3 10.3 1.0 CG A:ASP59 3.4 11.0 1.0 C A:GLN61 3.4 10.0 1.0 H A:ASP59 3.5 12.3 1.0 HB2 A:GLN61 3.6 15.5 1.0 OD2 A:ASP59 3.8 13.4 1.0 N A:GLN61 3.9 8.6 1.0 O A:HOH728 4.0 15.3 1.0 HA A:PHE62 4.1 10.8 1.0 CA A:GLN61 4.1 9.1 1.0 H A:ALA58 4.2 12.2 1.0 CB A:ASP57 4.3 6.8 1.0 N A:ASP59 4.3 10.3 1.0 H A:ASN60 4.3 12.5 1.0 CB A:GLN61 4.3 12.9 1.0 O A:HOH914 4.4 35.9 1.0 O A:HOH904 4.5 28.2 1.0 N A:PHE62 4.5 8.0 1.0 O A:HOH530 4.6 10.4 1.0 CB A:ASP59 4.6 12.9 1.0 OD2 A:ASP67 4.6 11.2 1.0 N A:ASN60 4.6 10.4 1.0 HB2 A:ASP57 4.7 8.2 1.0 N A:ALA58 4.7 10.2 1.0 O A:HOH889 4.7 28.6 1.0 HB3 A:ASP57 4.7 8.2 1.0 CA A:ASP59 4.8 11.0 1.0 CA A:PHE62 4.8 9.0 1.0 HB3 A:GLN61 4.8 15.5 1.0 H A:PHE63 4.8 13.9 1.0 C A:ASP59 4.9 12.1 1.0 HA A:ASP57 4.9 12.4 1.0 HB3 A:ASP59 5.0 15.5 1.0

Calcium binding site 4 out of 4 in the X-Ray Structure of Thermolysin Crystallized on A Silicon Chip


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of X-Ray Structure of Thermolysin Crystallized on A Silicon Chip within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca405 b:14.2 occ:1.00 O A:ILE197 2.3 14.9 1.0 O A:THR194 2.4 17.9 1.0 OG1 A:THR194 2.4 16.7 1.0 OD1 A:ASP200 2.4 15.5 1.0 O A:TYR193 2.4 13.6 1.0 O A:HOH544 2.4 12.7 1.0 O A:HOH800 2.4 19.4 1.0 C A:THR194 3.2 17.0 1.0 C A:TYR193 3.3 13.8 1.0 HB A:ILE197 3.4 23.2 1.0 CB A:THR194 3.4 17.7 1.0 CG A:ASP200 3.4 16.6 1.0 C A:ILE197 3.5 22.5 1.0 H A:ILE197 3.6 23.4 1.0 CA A:THR194 3.6 16.1 1.0 HB A:THR194 3.7 21.2 1.0 H A:ASP200 3.8 18.3 1.0 OD2 A:ASP200 3.8 16.5 1.0 N A:THR194 3.8 15.4 1.0 HA A:SER198 4.0 25.2 0.8 HB3 A:TYR193 4.1 16.1 1.0 HD2 A:TYR193 4.1 15.9 1.0 HA A:SER198 4.1 25.3 0.2 CB A:ILE197 4.1 19.3 1.0 CA A:ILE197 4.2 19.4 1.0 O A:HOH729 4.2 46.5 1.0 HA A:PRO195 4.2 21.5 0.6 N A:PRO195 4.2 16.1 0.4 N A:ILE197 4.2 19.5 1.0 N A:PRO195 4.3 14.9 0.6 HG22 A:ILE197 4.3 22.7 1.0 HA A:PRO195 4.3 22.6 0.4 O A:ASP200 4.3 16.9 1.0 O A:HOH714 4.3 32.3 1.0 O A:HOH637 4.4 34.3 1.0 N A:SER198 4.5 21.4 1.0 CA A:TYR193 4.5 12.0 1.0 O A:GLU190 4.5 12.8 1.0 HA A:THR194 4.6 19.4 1.0 N A:ASP200 4.6 15.2 1.0 CA A:PRO195 4.6 17.9 0.6 CA A:SER198 4.6 21.0 0.8 H A:GLY199 4.7 21.6 1.0 CA A:SER198 4.7 21.1 0.2 H A:THR194 4.7 18.5 1.0 CB A:TYR193 4.7 13.4 1.0 O A:HOH832 4.7 31.0 1.0 CD2 A:TYR193 4.7 13.2 1.0 CG2 A:THR194 4.7 18.1 1.0 CA A:PRO195 4.7 18.8 0.4 CG2 A:ILE197 4.7 18.9 1.0 CB A:ASP200 4.8 18.4 1.0 C A:ASP200 4.8 19.9 1.0 HG23 A:THR194 4.8 21.7 1.0 H A:TYR193 4.8 17.4 1.0 C A:PRO195 4.9 15.9 0.6 N A:GLY199 5.0 17.9 1.0 C A:SER198 5.0 15.4 1.0 HG21 A:THR194 5.0 21.7 1.0 CA A:ASP200 5.0 18.0 1.0

J.Lieske, M.Cerv, S.Kreida, D.Komadina, J.Fischer, M.Barthelmess, P.Fischer, T.Pakendorf, O.Yefanov, V.Mariani, T.Seine, B.H.Ross, E.Crosas, O.Lorbeer, A.Burkhardt, T.J.Lane, S.Guenther, J.Bergtholdt, S.Schoen, S.Tornroth-Horsefield, H.N.Chapman, A.Meents. On-Chip Crystallization For Serial Crystallography Experiments and on-Chip Ligand-Binding Studies. Iucrj V. 6 714 2019.
ISSN: ESSN 2052-2525
PubMed: 31316815
DOI: 10.1107/S2052252519007395