Zinc 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:

Calcium	(Ca)	4 atoms
Sodium	(Na)	1 atom

The binding sites of Zinc 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 Zinc atom.
In total 2 binding sites of Zinc where determined in the X-Ray Structure of Thermolysin Crystallized on A Silicon Chip, PDB code: 6qf2:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the X-Ray Structure of Thermolysin Crystallized on A Silicon Chip


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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:Zn401 b:11.4 occ:1.00 OE2 A:GLU166 1.9 10.8 0.6 NE2 A:HIS142 2.0 9.3 1.0 OE1 A:GLU166 2.1 11.6 0.4 NE2 A:HIS146 2.1 9.6 1.0 O A:HOH531 2.1 18.7 1.0 CD A:GLU166 2.7 10.0 0.6 CD A:GLU166 2.9 12.3 0.4 OE1 A:GLU166 2.9 11.8 0.6 CE1 A:HIS142 3.0 12.5 1.0 OE2 A:GLU166 3.0 10.9 0.4 CE1 A:HIS146 3.0 11.9 1.0 CD2 A:HIS142 3.0 9.1 1.0 CD2 A:HIS146 3.1 12.0 1.0 HE1 A:HIS142 3.1 15.0 1.0 HE1 A:HIS146 3.2 14.3 1.0 ZN A:ZN408 3.2 18.1 0.5 HD2 A:HIS142 3.2 10.9 1.0 HD2 A:HIS146 3.3 14.4 1.0 HA A:LEU406 3.5 30.9 1.0 OH A:TYR157 3.9 14.3 0.5 HA A:GLU166 3.9 9.9 0.6 HA A:GLU166 3.9 11.2 0.4 HB2 A:SER169 4.0 11.1 1.0 ND1 A:HIS142 4.1 9.0 1.0 CG A:GLU166 4.1 12.0 0.6 CG A:HIS142 4.1 8.9 1.0 ND1 A:HIS146 4.1 10.8 1.0 NE2 A:HIS231 4.2 15.2 1.0 CG A:HIS146 4.2 9.4 1.0 CA A:LEU406 4.2 25.7 1.0 N A:LEU406 4.2 26.3 1.0 HB3 A:SER169 4.3 11.1 1.0 HG2 A:GLU166 4.3 14.4 0.6 CG A:GLU166 4.3 9.6 0.4 HD2 A:HIS231 4.4 22.0 1.0 O A:HOH796 4.4 22.3 1.0 HE1 A:TYR157 4.4 14.3 0.5 OE1 A:GLU143 4.4 17.0 1.0 O A:HOH635 4.5 38.8 1.0 O A:LEU406 4.5 26.3 1.0 CB A:SER169 4.5 9.2 1.0 HB3 A:GLU166 4.6 12.6 0.4 C A:LEU406 4.6 26.1 1.0 CD2 A:HIS231 4.6 18.3 1.0 OG A:SER169 4.6 11.2 1.0 HG3 A:GLU166 4.7 14.4 0.6 O A:HOH842 4.7 44.6 1.0 CA A:GLU166 4.7 9.3 0.4 HG2 A:GLU166 4.8 11.5 0.4 CB A:GLU166 4.8 10.5 0.4 CA A:GLU166 4.8 8.2 0.6 OE2 A:GLU143 4.8 19.6 1.0 HG3 A:GLU166 4.8 11.5 0.4 HH22 A:ARG203 4.8 11.7 1.0 HD1 A:HIS142 4.9 10.8 1.0 CZ A:TYR157 4.9 16.6 0.5 HE2 A:TYR157 4.9 25.1 0.5 HD12 A:LEU406 4.9 29.4 1.0 HD1 A:HIS146 4.9 12.9 1.0 CD A:GLU143 4.9 14.7 1.0 CE1 A:TYR157 5.0 11.9 0.5 CB A:GLU166 5.0 10.4 0.6

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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:Zn408 b:18.1 occ:0.47 OH A:TYR157 1.8 14.3 0.5 O A:HOH531 2.1 18.7 1.0 OE2 A:GLU166 2.2 10.9 0.4 NE2 A:HIS231 2.3 15.2 1.0 O A:HOH635 2.3 38.8 1.0 HE1 A:HIS231 2.6 17.8 1.0 OE2 A:GLU166 2.7 10.8 0.6 CE1 A:HIS231 2.7 14.8 1.0 CZ A:TYR157 3.0 16.6 0.5 CD A:GLU166 3.1 12.3 0.4 O A:HOH842 3.1 44.6 1.0 ZN A:ZN401 3.2 11.4 1.0 OE1 A:GLU166 3.4 11.6 0.4 CD2 A:HIS231 3.5 18.3 1.0 CD A:GLU166 3.5 10.0 0.6 HE2 A:TYR157 3.6 13.6 0.5 CE2 A:TYR157 3.7 11.3 0.5 HD2 A:HIS231 3.9 22.0 1.0 CE1 A:TYR157 4.0 11.9 0.5 ND1 A:HIS231 4.0 13.9 1.0 HE1 A:TYR157 4.0 14.3 0.5 N A:LEU406 4.1 26.3 1.0 OE1 A:GLU166 4.2 11.8 0.6 HG2 A:GLU166 4.2 14.4 0.6 CG A:GLU166 4.3 12.0 0.6 HG3 A:GLU166 4.3 11.5 0.4 HG3 A:GLU166 4.3 14.4 0.6 CG A:GLU166 4.3 9.6 0.4 NE2 A:HIS146 4.4 9.6 1.0 CG A:HIS231 4.4 12.6 1.0 O A:HOH796 4.4 22.3 1.0 C A:LEU406 4.5 26.1 1.0 OXT A:LYS407 4.5 27.6 1.0 HG23 A:VAL230 4.6 12.9 1.0 HD1 A:HIS231 4.7 16.6 1.0 N A:LYS407 4.7 26.4 1.0 HA A:LEU406 4.7 30.9 1.0 HG2 A:GLU166 4.7 11.5 0.4 HG21 A:VAL230 4.7 12.9 1.0 CA A:LEU406 4.7 25.7 1.0 HA A:LYS407 4.8 33.6 1.0 O A:LEU406 4.8 26.3 1.0 HE1 A:HIS146 4.9 14.3 1.0 C A:LYS407 4.9 27.5 1.0 H A:LYS407 4.9 31.7 1.0 HE2 A:TYR157 4.9 25.1 0.5 CE1 A:HIS146 4.9 11.9 1.0 HD2 A:TYR157 4.9 15.7 0.5 NE2 A:HIS142 5.0 9.3 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