Zinc in PDB 5fss: Structure of Thermolysin Prepared By the 'Soak-and-Freeze' Method Under 40 Bar of Krypton Pressure

All present enzymatic activity of Structure of Thermolysin Prepared By the 'Soak-and-Freeze' Method Under 40 Bar of Krypton Pressure:
3.4.24.27;

The structure of Structure of Thermolysin Prepared By the 'Soak-and-Freeze' Method Under 40 Bar of Krypton Pressure, PDB code: 5fss was solved by B.Lafumat, C.Mueller-Dieckmann, N.Colloc'h, T.Prange, A.Royant, P.Van Derlinden, P.Carpentier, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.38 / 1.50
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	92.749, 92.749, 128.995, 90.00, 90.00, 120.00
R / Rfree (%)	16.2 / 18

The structure of Structure of Thermolysin Prepared By the 'Soak-and-Freeze' Method Under 40 Bar of Krypton Pressure also contains other interesting chemical elements:

Krypton	(Kr)	2 atoms
Calcium	(Ca)	4 atoms

The binding sites of Zinc atom in the Structure of Thermolysin Prepared By the 'Soak-and-Freeze' Method Under 40 Bar of Krypton Pressure (pdb code 5fss). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Structure of Thermolysin Prepared By the 'Soak-and-Freeze' Method Under 40 Bar of Krypton Pressure, PDB code: 5fss:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Structure of Thermolysin Prepared By the 'Soak-and-Freeze' Method Under 40 Bar of Krypton Pressure


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Thermolysin Prepared By the 'Soak-and-Freeze' Method Under 40 Bar of Krypton Pressure within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn405 b:10.8 occ:1.00 OE2 A:GLU166 2.0 12.2 1.0 NE2 A:HIS146 2.0 10.3 1.0 NE2 A:HIS142 2.0 10.2 1.0 ZN A:ZN406 2.2 20.0 0.5 CD A:GLU166 2.8 10.3 1.0 CE1 A:HIS146 2.9 10.8 1.0 CE1 A:HIS142 3.0 10.6 1.0 CD2 A:HIS142 3.0 8.0 1.0 OE1 A:GLU166 3.0 13.7 1.0 CD2 A:HIS146 3.1 10.7 1.0 OH A:TYR157 3.9 15.5 1.0 ND1 A:HIS146 4.1 12.3 1.0 ND1 A:HIS142 4.1 10.5 1.0 CG A:HIS142 4.2 7.9 1.0 CG A:HIS146 4.2 11.3 1.0 NE2 A:HIS231 4.2 11.2 1.0 CG A:GLU166 4.2 10.8 1.0 OE1 A:GLU143 4.4 14.6 1.0 CB A:SER169 4.4 9.7 1.0 O A:HOH2181 4.5 16.6 1.0 CA A:VAL1001 4.6 17.1 1.0 O A:VAL1001 4.6 17.0 1.0 OG A:SER169 4.6 11.8 1.0 CD2 A:HIS231 4.7 13.0 1.0 CZ A:TYR157 4.8 14.4 1.0 C A:VAL1001 4.9 21.0 1.0 N A:VAL1001 4.9 19.3 1.0 CA A:GLU166 4.9 9.1 1.0 CE1 A:TYR157 4.9 13.1 1.0

Zinc binding site 2 out of 2 in the Structure of Thermolysin Prepared By the 'Soak-and-Freeze' Method Under 40 Bar of Krypton Pressure


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Thermolysin Prepared By the 'Soak-and-Freeze' Method Under 40 Bar of Krypton Pressure within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn406 b:20.0 occ:0.49 ZN A:ZN405 2.2 10.8 1.0 OE2 A:GLU166 3.2 12.2 1.0 NE2 A:HIS231 3.2 11.2 1.0 N A:VAL1001 3.3 19.3 1.0 CA A:VAL1001 3.5 17.1 1.0 OH A:TYR157 3.5 15.5 1.0 C A:VAL1001 3.6 21.0 1.0 NE2 A:HIS142 3.6 10.2 1.0 NE2 A:HIS146 3.7 10.3 1.0 O A:VAL1001 3.8 17.0 1.0 O A:HOH2181 3.8 16.6 1.0 N A:LYS1002 4.0 17.5 0.5 CD A:GLU166 4.0 10.3 1.0 N A:LYS1002 4.0 17.5 0.5 CE1 A:HIS231 4.1 12.9 1.0 OE1 A:GLU166 4.1 13.7 1.0 CD2 A:HIS231 4.1 13.0 1.0 OE1 A:GLU143 4.2 14.6 1.0 CD2 A:HIS142 4.3 8.0 1.0 CD2 A:HIS146 4.4 10.7 1.0 OE2 A:GLU143 4.6 17.5 1.0 CE1 A:HIS142 4.6 10.6 1.0 CE1 A:HIS146 4.7 10.8 1.0 CZ A:TYR157 4.7 14.4 1.0 O A:LYS1002 4.8 20.5 0.5 O A:LYS1002 4.8 20.5 0.5 CA A:LYS1002 4.8 22.6 0.5 CA A:LYS1002 4.8 22.6 0.5 O A:ALA113 4.8 14.8 1.0 CD A:GLU143 4.9 13.6 1.0 CB A:VAL1001 4.9 15.8 1.0

B.Lafumat, C.Mueller-Dieckmann, N.Colloc'h, T.Prange, A.Royant, P.Van Der Linden, P.Carpentier. Gas-Sensitive Biological Crystals Processed in Pressurized Oxygen and Krypton Atmospheres: Deciphering Gas Channels in Proteins Using A Novel `Soak-and-Freeze' Methodology. J.Appl.Crystallogr. V. 49 1478 2016.
ISSN: ISSN 0021-8898
DOI: 10.1107/S1600576716010992