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

Enzymatic activity of 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;

Protein crystallography data

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

Other elements in 5fss:

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:

Calcium (Ca) 4 atoms
Zinc (Zn) 2 atoms

Krypton Binding Sites:

The binding sites of Krypton 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 Krypton atom.
In total 2 binding sites of Krypton 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 Krypton binding site number: 1; 2;

Krypton binding site 1 out of 2 in 5fss

Go back to Krypton Binding Sites List in 5fss
Krypton 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 Krypton with other atoms in the Kr 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:Kr407

b:22.1
occ:0.69
C A:SER92 3.6 10.1 1.0
CD2 A:TYR84 3.6 11.6 1.0
N A:TYR93 3.6 11.2 1.0
CD2 A:LEU144 3.8 19.7 1.0
CA A:SER92 3.8 9.1 1.0
CG A:LEU144 3.9 15.7 1.0
CA A:TYR93 4.0 12.0 1.0
O A:SER92 4.0 12.4 1.0
CG A:TYR84 4.1 9.1 1.0
O A:HOH2135 4.1 12.3 1.0
CB A:TYR84 4.2 10.5 1.0
CE2 A:TYR84 4.3 11.3 1.0
CG2 A:VAL148 4.3 13.1 1.0
CB A:TYR93 4.3 14.0 1.0
CD1 A:LEU144 4.3 20.6 1.0
O A:THR80 4.5 11.3 1.0
CA A:TYR81 4.5 11.6 1.0
CD1 A:ILE100 4.6 12.9 1.0
N A:SER92 4.7 11.4 1.0
CG2 A:THR80 4.7 12.2 1.0
OG A:SER92 4.8 12.7 1.0
N A:TYR81 4.8 10.8 1.0
C A:THR80 4.8 11.3 1.0
CB A:SER92 4.9 10.5 1.0

Krypton binding site 2 out of 2 in 5fss

Go back to Krypton Binding Sites List in 5fss
Krypton 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 Krypton with other atoms in the Kr 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:Kr408

b:25.0
occ:0.25
O A:ALA98 2.9 12.7 1.0
N A:ASN37 3.2 13.4 1.0
O A:ASN97 3.2 13.7 1.0
O A:ARG35 3.3 14.6 1.0
CA A:GLY36 3.5 16.5 1.0
C A:ASN97 3.7 11.2 1.0
O A:GLY38 3.7 12.6 1.0
C A:ALA98 3.7 11.3 1.0
N A:GLY38 3.7 12.4 1.0
C A:GLY36 3.8 15.4 1.0
CE2 A:TYR81 3.8 12.5 1.0
OG A:SER92 3.9 12.7 1.0
CB A:SER92 3.9 10.5 1.0
C A:ARG35 4.0 13.9 1.0
CA A:ASN97 4.1 13.2 1.0
CA A:ASN37 4.1 14.3 1.0
N A:GLY36 4.1 15.7 1.0
OD1 A:ASN97 4.2 19.1 1.0
CD2 A:TYR81 4.2 12.9 1.0
CA A:ALA99 4.2 10.6 1.0
C A:ASN37 4.2 12.4 1.0
N A:ALA99 4.2 12.7 1.0
C A:GLY38 4.3 9.9 1.0
N A:ALA98 4.4 11.3 1.0
CB A:ASN97 4.4 23.3 1.0
N A:ILE100 4.5 10.4 1.0
CA A:GLY38 4.6 11.1 1.0
CG1 A:ILE100 4.6 10.3 1.0
CG A:ASN97 4.6 18.8 1.0
CB A:ASN37 4.7 18.8 1.0
CD1 A:ILE100 4.7 12.9 1.0
CA A:ALA98 4.7 12.1 1.0
C A:ALA99 4.7 11.8 1.0
CZ A:TYR81 4.8 11.6 1.0
O A:GLY36 4.9 17.9 1.0

Reference:

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
Page generated: Mon Dec 14 02:53:04 2020

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