Zinc in PDB 5wr6: Thermolysin, Liganded Form with Cryo Condition 2

All present enzymatic activity of Thermolysin, Liganded Form with Cryo Condition 2:
3.4.24.27;

The structure of Thermolysin, Liganded Form with Cryo Condition 2, PDB code: 5wr6 was solved by N.Kunishima, H.Naitow, Y.Matsuura, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.20 / 2.30
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	92.929, 92.929, 129.140, 90.00, 90.00, 120.00
R / Rfree (%)	15.3 / 18.2

The structure of Thermolysin, Liganded Form with Cryo Condition 2 also contains other interesting chemical elements:

Calcium

(Ca)

4 atoms

The binding sites of Zinc atom in the Thermolysin, Liganded Form with Cryo Condition 2 (pdb code 5wr6). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total only one binding site of Zinc was determined in the Thermolysin, Liganded Form with Cryo Condition 2, PDB code: 5wr6:

Zinc binding site 1 out of 1 in the Thermolysin, Liganded Form with Cryo Condition 2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Thermolysin, Liganded Form with Cryo Condition 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:13.7 occ:1.00 OE2 A:GLU166 1.9 13.2 1.0 NE2 A:HIS142 2.0 15.7 1.0 O A:NX6401 2.0 15.5 1.0 NE2 A:HIS146 2.1 13.9 1.0 C A:NX6401 2.6 17.9 1.0 OXT A:NX6401 2.6 14.0 1.0 CD A:GLU166 2.7 18.6 1.0 OE1 A:GLU166 2.9 15.8 1.0 CD2 A:HIS142 3.0 14.2 1.0 CE1 A:HIS142 3.0 15.8 1.0 CE1 A:HIS146 3.1 13.9 1.0 CD2 A:HIS146 3.1 13.7 1.0 O A:HOH533 3.7 26.8 1.0 OH A:TYR157 3.8 26.2 1.0 ND1 A:HIS142 4.1 12.7 1.0 CG A:HIS142 4.1 16.6 1.0 CA A:NX6401 4.1 17.9 1.0 NE2 A:HIS231 4.1 23.3 1.0 CG A:GLU166 4.2 18.5 1.0 ND1 A:HIS146 4.2 16.8 1.0 CG A:HIS146 4.2 15.3 1.0 CB A:SER169 4.5 14.2 1.0 OD2 A:NX6401 4.6 31.3 1.0 O A:HOH576 4.6 13.2 1.0 CD2 A:HIS231 4.6 17.2 1.0 CG A:NX6401 4.7 27.0 1.0 OG A:SER169 4.7 13.5 1.0 CB A:NX6401 4.8 19.5 1.0 OE2 A:GLU143 4.8 14.0 1.0 OE1 A:GLU143 4.8 13.5 1.0 CA A:GLU166 4.9 14.7 1.0 CZ A:TYR157 4.9 31.3 1.0 N A:NX6401 5.0 18.4 1.0

H.Naitow, Y.Matsuura, K.Tono, Y.Joti, T.Kameshima, T.Hatsui, M.Yabashi, R.Tanaka, T.Tanaka, M.Sugahara, J.Kobayashi, E.Nango, S.Iwata, N.Kunishima. Protein-Ligand Complex Structure From Serial Femtosecond Crystallography Using Soaked Thermolysin Microcrystals and Comparison with Structures From Synchrotron Radiation Acta Crystallogr D Struct V. 73 702 2017BIOL.
ISSN: ISSN 2059-7983
PubMed: 28777085
DOI: 10.1107/S2059798317008919