Zinc in PDB 5fsj: Structure of Thermolysin Prepared By the 'Soak-and-Freeze' Method Under 45 Bar of Oxygen Pressure

All present enzymatic activity of Structure of Thermolysin Prepared By the 'Soak-and-Freeze' Method Under 45 Bar of Oxygen Pressure:
3.4.24.27;

The structure of Structure of Thermolysin Prepared By the 'Soak-and-Freeze' Method Under 45 Bar of Oxygen Pressure, PDB code: 5fsj 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)	46.46 / 1.20
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	92.922, 92.922, 130.252, 90.00, 90.00, 120.00
R / Rfree (%)	10.4 / 12.2

The structure of Structure of Thermolysin Prepared By the 'Soak-and-Freeze' Method Under 45 Bar of Oxygen Pressure also contains other interesting chemical elements:

Calcium

(Ca)

5 atoms

The binding sites of Zinc atom in the Structure of Thermolysin Prepared By the 'Soak-and-Freeze' Method Under 45 Bar of Oxygen Pressure (pdb code 5fsj). 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 45 Bar of Oxygen Pressure, PDB code: 5fsj:
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 45 Bar of Oxygen 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 45 Bar of Oxygen Pressure within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1006 b:14.5 occ:0.41 ZN A:ZN1007 2.2 10.1 1.0 HE2 A:HIS231 2.4 14.7 1.0 H1 A:VAL1001 2.7 19.0 1.0 HE2 A:HIS142 2.9 11.1 1.0 HE2 A:HIS146 2.9 11.8 1.0 H3 A:VAL1001 3.2 19.0 1.0 NE2 A:HIS231 3.2 12.3 1.0 OE2 A:GLU166 3.2 12.3 1.0 N A:VAL1001 3.2 15.8 1.0 HA A:VAL1001 3.3 15.9 1.0 HH A:TYR157 3.3 16.4 0.0 O A:HOH2330 3.5 37.5 1.0 O A:HOH2547 3.5 31.4 1.0 CA A:VAL1001 3.6 13.3 1.0 OH A:TYR157 3.6 13.6 1.0 NE2 A:HIS142 3.6 9.2 1.0 O A:HOH2291 3.6 42.9 1.0 C A:VAL1001 3.6 13.2 1.0 NE2 A:HIS146 3.7 9.8 1.0 O A:HOH2293 3.7 16.5 1.0 CD A:GLU166 4.0 11.3 1.0 O A:VAL1001 4.0 14.0 1.0 N A:LYS1002 4.0 14.1 1.0 H2 A:VAL1001 4.1 19.0 1.0 CE1 A:HIS231 4.1 12.1 1.0 HE1 A:HIS231 4.1 14.5 1.0 OE1 A:GLU166 4.2 12.2 1.0 OE1 A:GLU143 4.2 13.6 1.0 CD2 A:HIS231 4.2 11.2 1.0 H A:LYS1002 4.2 16.9 1.0 HD2 A:HIS142 4.3 10.3 1.0 HD2 A:HIS231 4.3 13.4 1.0 HD2 A:HIS146 4.3 11.4 1.0 CD2 A:HIS142 4.3 8.6 1.0 CD2 A:HIS146 4.4 9.5 1.0 HA A:LYS1002 4.5 20.4 1.0 CE1 A:HIS142 4.6 8.6 1.0 OE2 A:GLU143 4.6 15.3 1.0 CE1 A:HIS146 4.7 10.2 1.0 O A:LYS1002 4.7 20.1 1.0 CA A:LYS1002 4.7 17.0 1.0 CZ A:TYR157 4.8 12.7 1.0 HE1 A:HIS142 4.8 10.3 1.0 HA A:PHE114 4.8 12.1 1.0 HE1 A:HIS146 4.8 12.2 1.0 CD A:GLU143 4.9 12.2 1.0 O A:ALA113 4.9 11.6 1.0 C A:LYS1002 5.0 17.9 1.0

Zinc binding site 2 out of 2 in the Structure of Thermolysin Prepared By the 'Soak-and-Freeze' Method Under 45 Bar of Oxygen 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 45 Bar of Oxygen Pressure within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1007 b:10.1 occ:1.00 HE2 A:HIS142 1.2 11.1 1.0 HE2 A:HIS146 1.2 11.8 1.0 OE2 A:GLU166 2.0 12.3 1.0 NE2 A:HIS142 2.0 9.2 1.0 NE2 A:HIS146 2.1 9.8 1.0 ZN A:ZN1006 2.2 14.5 0.4 CD A:GLU166 2.8 11.3 1.0 CE1 A:HIS146 3.0 10.2 1.0 CE1 A:HIS142 3.0 8.6 1.0 CD2 A:HIS142 3.0 8.6 1.0 OE1 A:GLU166 3.0 12.2 1.0 HE1 A:HIS146 3.1 12.2 1.0 CD2 A:HIS146 3.1 9.5 1.0 HE1 A:HIS142 3.2 10.3 1.0 HD2 A:HIS142 3.2 10.3 1.0 HH A:TYR157 3.2 16.4 0.0 HD2 A:HIS146 3.4 11.4 1.0 HE2 A:HIS231 3.5 14.7 1.0 HA A:VAL1001 3.9 15.9 1.0 OH A:TYR157 3.9 13.6 1.0 HA A:GLU166 3.9 10.2 1.0 HB2 A:SER169 4.0 11.0 1.0 HG A:SER169 4.1 11.0 0.0 ND1 A:HIS142 4.1 8.4 1.0 ND1 A:HIS146 4.1 9.6 1.0 NE2 A:HIS231 4.1 12.3 1.0 CG A:HIS142 4.2 8.5 1.0 CG A:HIS146 4.2 9.3 1.0 CG A:GLU166 4.2 10.2 1.0 HB3 A:SER169 4.2 11.0 1.0 OE1 A:GLU143 4.3 13.6 1.0 HG2 A:GLU166 4.3 12.2 1.0 HE1 A:TYR157 4.4 15.6 1.0 O A:HOH2293 4.4 16.5 1.0 HD2 A:HIS231 4.4 13.4 1.0 H3 A:VAL1001 4.5 19.0 1.0 CB A:SER169 4.5 9.1 1.0 H1 A:VAL1001 4.5 19.0 1.0 CA A:VAL1001 4.6 13.3 1.0 CD2 A:HIS231 4.7 11.2 1.0 O A:VAL1001 4.7 14.0 1.0 OG A:SER169 4.7 9.2 1.0 N A:VAL1001 4.8 15.8 1.0 HG3 A:GLU166 4.8 12.2 1.0 C A:VAL1001 4.8 13.2 1.0 CA A:GLU166 4.8 8.5 1.0 HD1 A:HIS146 4.9 11.5 1.0 CZ A:TYR157 4.9 12.7 1.0 HH22 A:ARG203 4.9 12.1 1.0 HD1 A:HIS142 4.9 10.1 1.0 CE1 A:TYR157 5.0 13.0 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