Zinc in PDB 5wr3: Thermolysin, Sfx Liganded Form with Water-Based Carrier

All present enzymatic activity of Thermolysin, Sfx Liganded Form with Water-Based Carrier:
3.4.24.27;

The structure of Thermolysin, Sfx Liganded Form with Water-Based Carrier, PDB code: 5wr3 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)	44.10 / 2.10
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	93.590, 93.590, 131.220, 90.00, 90.00, 120.00
R / Rfree (%)	12.6 / 16

The structure of Thermolysin, Sfx Liganded Form with Water-Based Carrier also contains other interesting chemical elements:

Calcium

(Ca)

4 atoms

The binding sites of Zinc atom in the Thermolysin, Sfx Liganded Form with Water-Based Carrier (pdb code 5wr3). 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, Sfx Liganded Form with Water-Based Carrier, PDB code: 5wr3:

Zinc binding site 1 out of 1 in the Thermolysin, Sfx Liganded Form with Water-Based Carrier


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Thermolysin, Sfx Liganded Form with Water-Based Carrier within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:24.8 occ:1.00 O A:NX6401 2.0 23.7 1.0 OE2 A:GLU166 2.0 24.4 1.0 NE2 A:HIS146 2.0 20.2 1.0 NE2 A:HIS142 2.1 20.3 1.0 C A:NX6401 2.6 28.2 1.0 OXT A:NX6401 2.6 26.4 1.0 CD A:GLU166 2.8 25.4 1.0 CE1 A:HIS146 2.9 23.0 1.0 OE1 A:GLU166 3.0 24.3 1.0 CE1 A:HIS142 3.0 20.9 1.0 CD2 A:HIS142 3.1 20.4 1.0 CD2 A:HIS146 3.1 22.2 1.0 OH A:TYR157 3.7 31.1 1.0 ND1 A:HIS146 4.1 22.8 1.0 CA A:NX6401 4.1 26.8 1.0 ND1 A:HIS142 4.1 20.7 1.0 O A:HOH507 4.2 38.4 1.0 CG A:HIS142 4.2 22.4 1.0 CG A:HIS146 4.2 24.2 1.0 NE2 A:HIS231 4.2 24.8 1.0 CG A:GLU166 4.2 25.1 1.0 CB A:SER169 4.5 19.5 1.0 CD2 A:HIS231 4.7 28.8 1.0 OG A:SER169 4.7 21.6 1.0 CZ A:TYR157 4.7 33.9 1.0 CA A:GLU166 4.8 21.9 1.0 O A:HOH647 4.8 24.4 1.0 OE2 A:GLU143 4.9 24.0 1.0 CB A:NX6401 4.9 29.1 1.0 OD1 A:NX6401 4.9 36.9 0.6 N A:NX6401 4.9 35.3 1.0 CG A:NX6401 5.0 33.5 0.6

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