Sodium 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
Calcium	(Ca)	4 atoms

The binding sites of Sodium 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 Sodium atom.
In total only one binding site of Sodium was determined in the X-Ray Structure of Thermolysin Crystallized on A Silicon Chip, PDB code: 6qf2:

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


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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:Na409 b:24.9 occ:1.00 O A:HOH523 2.1 11.9 1.0 O A:HOH923 2.2 41.6 1.0 O A:HOH629 2.3 45.7 1.0 O A:HOH805 2.4 35.0 1.0 O A:HOH562 2.5 17.5 1.0 O A:TYR211 2.6 19.5 1.0 O A:HOH697 3.0 23.5 1.0 HB3 A:TYR211 3.1 14.9 1.0 C A:TYR211 3.8 17.0 1.0 O A:HOH610 3.9 34.0 1.0 O A:HOH802 3.9 39.3 1.0 CB A:TYR211 3.9 12.4 1.0 HB2 A:TYR211 4.0 14.9 1.0 OD1 A:ASP213 4.1 15.8 1.0 O A:HOH835 4.3 33.3 1.0 O A:LEU202 4.4 13.6 1.0 CA A:TYR211 4.4 14.9 1.0 OD2 A:ASP213 4.4 14.5 1.0 CG A:ASP213 4.6 13.6 1.0 HA A:TYR211 4.6 17.9 1.0 HA3 A:GLY212 4.7 21.6 1.0 O A:HOH866 4.7 39.3 1.0 O A:HOH742 4.8 20.6 1.0 N A:GLY212 4.9 15.9 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