Zinc in PDB 5uu8: Tetragonal Thermolysin Cryocooled to 100 K with 30% Xylose As Cryoprotectant

All present enzymatic activity of Tetragonal Thermolysin Cryocooled to 100 K with 30% Xylose As Cryoprotectant:
3.4.24.27;

The structure of Tetragonal Thermolysin Cryocooled to 100 K with 30% Xylose As Cryoprotectant, PDB code: 5uu8 was solved by D.H.Juers, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.30 / 2.50
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	97.500, 97.500, 107.920, 90.00, 90.00, 90.00
R / Rfree (%)	22.9 / 28.9

The structure of Tetragonal Thermolysin Cryocooled to 100 K with 30% Xylose As Cryoprotectant also contains other interesting chemical elements:

Calcium

(Ca)

3 atoms

The binding sites of Zinc atom in the Tetragonal Thermolysin Cryocooled to 100 K with 30% Xylose As Cryoprotectant (pdb code 5uu8). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Tetragonal Thermolysin Cryocooled to 100 K with 30% Xylose As Cryoprotectant, PDB code: 5uu8:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Tetragonal Thermolysin Cryocooled to 100 K with 30% Xylose As Cryoprotectant


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Tetragonal Thermolysin Cryocooled to 100 K with 30% Xylose As Cryoprotectant within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:26.8 occ:1.00 OD2 A:ASP185 2.0 23.1 1.0 OE2 A:GLU190 2.1 22.9 1.0 OE2 A:GLU177 2.1 22.0 1.0 O A:HOH505 2.1 19.1 1.0 O A:HOH509 2.4 22.1 1.0 O A:ASN183 2.5 29.8 1.0 CG A:ASP185 3.1 30.2 1.0 CD A:GLU177 3.1 18.0 1.0 CD A:GLU190 3.1 20.0 1.0 HG3 A:GLU190 3.5 19.0 1.0 C A:ASN183 3.7 27.4 1.0 OD1 A:ASP191 3.7 24.9 1.0 OD1 A:ASP185 3.7 39.2 1.0 HG2 A:GLU190 3.7 19.0 1.0 OE1 A:GLU177 3.7 20.7 1.0 CG A:GLU190 3.7 15.8 1.0 OD2 A:ASP191 3.7 16.1 1.0 HA A:PRO184 3.7 29.1 1.0 OD1 A:ASN183 3.7 45.4 1.0 CA A:CA401 3.8 22.9 1.0 CG A:ASP191 4.0 20.2 1.0 CG A:ASN183 4.1 46.1 1.0 HB2 A:ASN183 4.1 52.7 1.0 OE1 A:GLU190 4.1 20.6 1.0 H A:ASP185 4.1 22.7 1.0 CG A:GLU177 4.2 15.7 1.0 HG2 A:GLU177 4.2 18.9 1.0 HB3 A:ASP185 4.2 27.4 1.0 N A:ASP185 4.2 18.9 1.0 CB A:ASP185 4.2 22.8 1.0 CA A:PRO184 4.3 24.2 1.0 C A:PRO184 4.3 23.3 1.0 HG3 A:GLU177 4.3 18.9 1.0 N A:PRO184 4.4 19.2 1.0 CB A:ASN183 4.5 43.9 1.0 ND2 A:ASN183 4.7 41.4 1.0 CA A:ASN183 4.7 37.5 1.0 HD21 A:ASN183 4.8 49.7 1.0 O A:PRO184 4.8 25.1 1.0 CA A:ASP185 4.9 17.2 1.0 HB2 A:ASP185 5.0 27.4 1.0

Zinc binding site 2 out of 3 in the Tetragonal Thermolysin Cryocooled to 100 K with 30% Xylose As Cryoprotectant


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Tetragonal Thermolysin Cryocooled to 100 K with 30% Xylose As Cryoprotectant within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn405 b:19.6 occ:1.00 OE2 A:GLU166 1.9 20.8 1.0 NE2 A:HIS142 2.1 14.0 1.0 O A:HOH548 2.1 43.8 1.0 NE2 A:HIS146 2.1 12.5 1.0 CD A:GLU166 2.6 24.2 1.0 OE1 A:GLU166 2.8 30.9 1.0 CD2 A:HIS142 2.9 14.1 1.0 HD2 A:HIS142 3.0 16.9 1.0 CD2 A:HIS146 3.1 13.0 1.0 CE1 A:HIS146 3.1 18.4 1.0 CE1 A:HIS142 3.1 23.3 1.0 HH A:TYR157 3.2 78.8 1.0 HD2 A:HIS146 3.3 15.7 1.0 HE1 A:HIS146 3.3 22.0 1.0 ZN A:ZN406 3.4 30.1 0.6 HE1 A:HIS142 3.4 27.9 1.0 OE2 A:GLU143 3.8 32.1 1.0 HA A:GLU166 3.9 26.1 1.0 HE1 A:TYR157 3.9 70.9 1.0 OH A:TYR157 4.0 65.7 1.0 HB2 A:SER169 4.0 25.9 1.0 CG A:GLU166 4.1 14.8 1.0 CG A:HIS142 4.1 18.8 1.0 ND1 A:HIS142 4.2 24.3 1.0 ND1 A:HIS146 4.2 14.4 1.0 CG A:HIS146 4.2 16.8 1.0 HG2 A:GLU166 4.2 17.7 1.0 HB3 A:SER169 4.4 25.9 1.0 CD A:GLU143 4.4 26.0 1.0 NE2 A:HIS231 4.5 29.0 1.0 O A:HOH637 4.5 28.2 1.0 CB A:SER169 4.5 21.6 1.0 OE1 A:GLU143 4.6 29.6 1.0 CE1 A:TYR157 4.6 59.1 1.0 HG3 A:GLU166 4.6 17.7 1.0 OG A:SER169 4.7 23.2 1.0 HH22 A:ARG203 4.7 26.9 1.0 CZ A:TYR157 4.8 62.6 1.0 CA A:GLU166 4.8 21.8 1.0 HA A:GLU143 4.8 29.4 1.0 HD2 A:HIS231 4.8 30.7 1.0 CB A:GLU166 4.9 16.9 1.0 HB3 A:GLU166 5.0 20.2 1.0 CD2 A:HIS231 5.0 25.6 1.0 HD1 A:HIS146 5.0 17.2 1.0 HD1 A:HIS142 5.0 29.2 1.0

Zinc binding site 3 out of 3 in the Tetragonal Thermolysin Cryocooled to 100 K with 30% Xylose As Cryoprotectant


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Tetragonal Thermolysin Cryocooled to 100 K with 30% Xylose As Cryoprotectant within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn406 b:30.1 occ:0.63 O A:HOH548 2.0 43.8 1.0 O A:HOH636 2.1 39.5 1.0 NE2 A:HIS231 2.2 29.0 1.0 O A:HOH637 2.6 28.2 1.0 HH A:TYR157 3.1 78.8 1.0 CE1 A:HIS231 3.1 37.3 1.0 CD2 A:HIS231 3.2 25.6 1.0 HE1 A:HIS231 3.3 44.8 1.0 OH A:TYR157 3.3 65.7 1.0 HD2 A:HIS231 3.3 30.7 1.0 ZN A:ZN405 3.4 19.6 1.0 OE2 A:GLU166 3.5 20.8 1.0 OE1 A:GLU166 3.9 30.9 1.0 CD A:GLU166 4.0 24.2 1.0 OE2 A:GLU143 4.1 32.1 1.0 ND1 A:HIS231 4.2 40.4 1.0 CG A:HIS231 4.3 34.6 1.0 NE2 A:HIS142 4.5 14.0 1.0 CZ A:TYR157 4.6 62.6 1.0 HH22 A:ARG203 4.6 26.9 1.0

D.H.Juers, C.A.Farley, C.P.Saxby, R.A.Cotter, J.K.B.Cahn, R.C.Holton-Burke, K.Harrison, Z.Wu. The Impact of Cryosolution Thermal Contraction on Proteins and Protein Crystals: Volumes, Conformation and Order. Acta Crystallogr D Struct V. 74 922 2018BIOL.
ISSN: ISSN 2059-7983
PubMed: 30198901
DOI: 10.1107/S2059798318008793