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Krypton in PDB 5fsp: Structure of Thermolysin Prepared By the 'Soak-and-Freeze' Method Under 100 Bar of Krypton Pressure

Enzymatic activity of Structure of Thermolysin Prepared By the 'Soak-and-Freeze' Method Under 100 Bar of Krypton Pressure

All present enzymatic activity of Structure of Thermolysin Prepared By the 'Soak-and-Freeze' Method Under 100 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 100 Bar of Krypton Pressure, PDB code: 5fsp 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) 46.50 / 1.70
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 93.007, 93.007, 129.120, 90.00, 90.00, 120.00
R / Rfree (%) 15.5 / 17.8

Other elements in 5fsp:

The structure of Structure of Thermolysin Prepared By the 'Soak-and-Freeze' Method Under 100 Bar of Krypton Pressure also contains other interesting chemical elements:

Calcium (Ca) 4 atoms
Zinc (Zn) 1 atom

Krypton Binding Sites:

The binding sites of Krypton atom in the Structure of Thermolysin Prepared By the 'Soak-and-Freeze' Method Under 100 Bar of Krypton Pressure (pdb code 5fsp). This binding sites where shown within 5.0 Angstroms radius around Krypton atom.
In total 8 binding sites of Krypton where determined in the Structure of Thermolysin Prepared By the 'Soak-and-Freeze' Method Under 100 Bar of Krypton Pressure, PDB code: 5fsp:
Jump to Krypton binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Krypton binding site 1 out of 8 in 5fsp

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Krypton binding site 1 out of 8 in the Structure of Thermolysin Prepared By the 'Soak-and-Freeze' Method Under 100 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 100 Bar of Krypton Pressure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Kr1318

b:24.9
occ:1.00
 CD2 A:TYR84 3.6 11.4 1.0
C A:SER92 3.6 11.3 1.0
N A:TYR93 3.7 8.2 1.0
CD2 A:LEU144 3.7 23.4 1.0
CA A:SER92 3.8 9.1 1.0
CG A:LEU144 3.9 19.0 1.0
CA A:TYR93 4.0 13.1 1.0
O A:SER92 4.1 10.9 1.0
O A:HOH2108 4.1 10.1 1.0
CG A:TYR84 4.1 9.0 1.0
CB A:TYR84 4.2 8.1 1.0
CE2 A:TYR84 4.3 7.2 1.0
CG2 A:VAL148 4.3 10.7 1.0
CB A:TYR93 4.3 11.2 1.0
CA A:TYR81 4.5 8.7 1.0
O A:THR80 4.5 8.9 1.0
CD1 A:ILE100 4.5 12.1 1.0
CG2 A:THR80 4.6 7.8 1.0
CD1 A:LEU144 4.6 18.6 1.0
N A:SER92 4.7 10.4 1.0
OG A:SER92 4.7 10.3 1.0
N A:TYR81 4.8 7.7 1.0
C A:THR80 4.8 8.2 1.0
CB A:SER92 4.9 9.5 1.0

Krypton binding site 2 out of 8 in 5fsp

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Krypton binding site 2 out of 8 in the Structure of Thermolysin Prepared By the 'Soak-and-Freeze' Method Under 100 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 100 Bar of Krypton Pressure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Kr1319

b:27.3
occ:0.55
 O A:ALA98 3.2 11.3 1.0
O A:ARG35 3.3 14.0 1.0
O A:GLY38 3.4 10.4 1.0
CE2 A:TYR81 3.7 11.6 1.0
CD2 A:TYR81 3.8 9.1 1.0
OG A:SER92 3.8 10.3 1.0
CD1 A:ILE100 3.9 12.1 1.0
CG1 A:ILE100 4.0 9.0 1.0
C A:ARG35 4.0 10.8 1.0
N A:GLY38 4.0 9.5 1.0
N A:ASN37 4.0 11.9 1.0
C A:GLY38 4.0 9.0 1.0
CB A:SER92 4.0 9.5 1.0
CA A:GLY36 4.0 12.4 1.0
N A:ILE100 4.1 8.2 1.0
C A:ALA98 4.1 11.6 1.0
O A:ASN97 4.2 11.4 1.0
CA A:ALA99 4.3 9.6 1.0
CG1 A:ILE39 4.3 10.3 1.0
N A:GLY36 4.3 9.8 1.0
C A:GLY36 4.4 13.6 1.0
C A:ASN97 4.4 9.5 1.0
C A:ALA99 4.5 10.3 1.0
N A:ALA99 4.6 12.2 1.0
CA A:GLY38 4.6 6.9 1.0
CB A:ILE100 4.6 6.0 1.0
CB A:ARG35 4.8 8.0 1.0
C A:ASN37 4.8 11.8 1.0
CZ A:TYR81 4.8 13.0 1.0
N A:ILE39 4.8 7.4 1.0
CA A:ASN97 4.8 11.4 1.0
CG A:TYR81 4.8 6.5 1.0
CB A:ASN97 4.9 20.6 1.0
CA A:ASN37 4.9 12.4 1.0
CA A:ILE100 5.0 6.1 1.0

Krypton binding site 3 out of 8 in 5fsp

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Krypton binding site 3 out of 8 in the Structure of Thermolysin Prepared By the 'Soak-and-Freeze' Method Under 100 Bar of Krypton Pressure


Mono view


Stereo pair view

A full contact list of Krypton with other atoms in the Kr binding site number 3 of Structure of Thermolysin Prepared By the 'Soak-and-Freeze' Method Under 100 Bar of Krypton Pressure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Kr1320

b:20.6
occ:0.34
 O A:TYR193 3.3 12.5 1.0
CA A:PRO195 3.4 19.8 1.0
O A:ASP191 3.4 13.6 1.0
O A:HOH2201 3.5 19.3 1.0
C A:VAL192 3.5 12.1 1.0
N A:PRO195 3.6 14.4 1.0
N A:TYR193 3.7 11.2 1.0
CB A:PRO195 3.7 18.7 1.0
C A:TYR193 3.8 14.6 1.0
CA A:VAL192 3.8 10.7 1.0
O A:VAL192 3.8 13.1 1.0
CD1 A:ILE131 3.9 12.9 1.0
C A:ASP191 3.9 12.4 1.0
C A:THR194 4.0 13.7 1.0
CD A:PRO195 4.0 21.9 1.0
N A:VAL192 4.1 10.9 1.0
CG1 A:ILE131 4.1 8.6 1.0
O A:THR194 4.3 19.5 1.0
CA A:TYR193 4.3 9.7 1.0
N A:THR194 4.4 14.0 1.0
O A:GLU190 4.4 13.5 1.0
CG A:PRO195 4.4 20.1 1.0
CG2 A:ILE131 4.6 16.3 1.0
CA A:CA1326 4.7 13.9 1.0
C A:PRO195 4.7 22.1 1.0
CA A:THR194 4.8 15.3 1.0

Krypton binding site 4 out of 8 in 5fsp

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Krypton binding site 4 out of 8 in the Structure of Thermolysin Prepared By the 'Soak-and-Freeze' Method Under 100 Bar of Krypton Pressure


Mono view


Stereo pair view

A full contact list of Krypton with other atoms in the Kr binding site number 4 of Structure of Thermolysin Prepared By the 'Soak-and-Freeze' Method Under 100 Bar of Krypton Pressure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Kr1321

b:17.6
occ:0.20
 CE2 A:PHE281 3.3 13.6 1.0
O A:HOH2186 3.4 23.3 1.0
ND2 A:ASN233 3.6 14.4 1.0
CG A:GLU160 3.6 12.2 1.0
CZ A:PHE281 3.6 13.4 1.0
CG A:ASN233 3.6 13.6 1.0
CB A:ARG220 3.7 17.8 1.0
OE2 A:GLU160 3.7 17.1 1.0
CB A:ASN233 3.8 12.1 1.0
CD A:ARG220 3.8 16.7 1.0
CD A:GLU160 3.9 12.1 1.0
CE1 A:TYR217 3.9 17.7 1.0
CD2 A:PHE281 3.9 12.7 1.0
OD1 A:ASN233 4.2 12.8 1.0
CG A:ARG220 4.3 15.4 1.0
CE1 A:PHE281 4.4 10.9 1.0
CD1 A:ILE236 4.4 9.3 1.0
CD1 A:TYR217 4.4 14.2 1.0
O A:HOH2079 4.5 33.5 1.0
CG A:PHE281 4.7 13.0 1.0
CB A:GLU160 4.7 12.9 1.0
OE1 A:GLU160 4.8 13.6 1.0
CZ A:TYR217 4.8 15.5 1.0
O A:HOH2181 4.8 17.5 1.0
CD1 A:PHE281 4.9 12.0 1.0
CA A:ARG220 4.9 13.5 1.0
CA A:GLU160 5.0 9.9 1.0
OH A:TYR217 5.0 15.7 1.0
NE A:ARG220 5.0 20.6 1.0

Krypton binding site 5 out of 8 in 5fsp

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Krypton binding site 5 out of 8 in the Structure of Thermolysin Prepared By the 'Soak-and-Freeze' Method Under 100 Bar of Krypton Pressure


Mono view


Stereo pair view

A full contact list of Krypton with other atoms in the Kr binding site number 5 of Structure of Thermolysin Prepared By the 'Soak-and-Freeze' Method Under 100 Bar of Krypton Pressure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Kr1322

b:27.1
occ:0.28
 OE1 A:GLN119 3.4 10.3 1.0
O A:HOH2156 3.9 30.3 0.5
CD A:ARG101 3.9 16.2 1.0
CD A:GLN119 3.9 10.2 1.0
CB A:GLN119 4.1 5.7 1.0
CB A:PRO51 4.1 8.3 1.0
CG A:GLN119 4.1 6.7 1.0
CG A:PRO51 4.1 12.1 1.0
O A:HOH2153 4.2 31.7 1.0
CD A:PRO51 4.3 12.8 1.0
CB A:ARG101 4.5 8.3 1.0
O A:SER118 4.6 10.5 1.0
CB A:SER118 4.7 11.2 1.0
CG A:ARG101 4.7 12.1 1.0
NE A:ARG101 4.8 24.3 1.0
NE2 A:GLN119 4.8 13.5 1.0
N A:PRO51 4.9 11.0 1.0
C A:SER118 5.0 11.6 1.0

Krypton binding site 6 out of 8 in 5fsp

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Krypton binding site 6 out of 8 in the Structure of Thermolysin Prepared By the 'Soak-and-Freeze' Method Under 100 Bar of Krypton Pressure


Mono view


Stereo pair view

A full contact list of Krypton with other atoms in the Kr binding site number 6 of Structure of Thermolysin Prepared By the 'Soak-and-Freeze' Method Under 100 Bar of Krypton Pressure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Kr1323

b:23.6
occ:0.24
 O A:HOH2212 2.8 27.2 1.0
N A:PRO214 3.6 11.5 1.0
O A:GLY212 3.6 16.5 1.0
CA A:PRO214 3.7 14.0 1.0
C A:ASP213 3.9 11.9 1.0
CD A:PRO214 4.0 12.6 1.0
CB A:PRO214 4.1 12.8 1.0
O A:ASP213 4.1 13.7 1.0
O A:LYS219 4.3 16.0 1.0
C A:GLY212 4.3 17.5 1.0
CB A:LYS219 4.4 20.5 1.0
CA A:ASP213 4.5 11.8 1.0
CD A:LYS219 4.7 35.6 1.0
N A:ASP213 4.7 13.1 1.0
CG A:PRO214 4.7 10.7 1.0
O A:HOH2220 4.8 24.5 1.0

Krypton binding site 7 out of 8 in 5fsp

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Krypton binding site 7 out of 8 in the Structure of Thermolysin Prepared By the 'Soak-and-Freeze' Method Under 100 Bar of Krypton Pressure


Mono view


Stereo pair view

A full contact list of Krypton with other atoms in the Kr binding site number 7 of Structure of Thermolysin Prepared By the 'Soak-and-Freeze' Method Under 100 Bar of Krypton Pressure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Kr1324

b:22.5
occ:0.22
 O A:HOH2032 2.8 26.3 1.0
ND2 A:ASN21 3.3 10.2 1.0
CG A:ASN21 3.6 9.7 1.0
CG1 A:VAL7 3.6 9.9 1.0
OD1 A:ASN21 3.6 14.9 1.0
O A:HOH2039 3.6 22.0 1.0
O A:HOH2037 3.8 20.3 1.0
C A:ILE20 3.9 11.6 0.4
C A:ILE20 3.9 11.6 0.6
N A:ASN21 3.9 9.2 1.0
CB A:ASN19 4.0 12.5 1.0
C A:ASN19 4.1 10.5 1.0
CG2 A:VAL7 4.1 12.6 1.0
N A:ILE20 4.1 10.7 0.4
N A:ILE20 4.1 10.8 0.6
O A:ASN19 4.1 11.0 1.0
O A:ILE20 4.2 11.1 0.4
O A:ILE20 4.2 11.2 0.6
CA A:ILE20 4.2 10.5 0.4
CA A:ILE20 4.2 10.5 0.6
CA A:ASN21 4.3 8.3 1.0
CB A:VAL7 4.4 9.8 1.0
O A:HOH2038 4.5 18.7 1.0
CB A:ASN21 4.6 9.7 1.0
O A:HOH2015 4.6 33.8 1.0
CA A:ASN19 4.7 11.6 1.0
O A:HOH2036 5.0 12.4 1.0

Krypton binding site 8 out of 8 in 5fsp

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Krypton binding site 8 out of 8 in the Structure of Thermolysin Prepared By the 'Soak-and-Freeze' Method Under 100 Bar of Krypton Pressure


Mono view


Stereo pair view

A full contact list of Krypton with other atoms in the Kr binding site number 8 of Structure of Thermolysin Prepared By the 'Soak-and-Freeze' Method Under 100 Bar of Krypton Pressure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Kr1325

b:22.5
occ:0.23
 CG1 A:VAL2318 3.1 40.7 1.0
CA A:VAL2318 3.4 25.7 1.0
CG A:HIS142 3.4 9.9 1.0
NH2 A:ARG203 3.6 10.9 1.0
ND1 A:HIS142 3.6 8.3 1.0
CD2 A:HIS142 3.7 6.7 1.0
O A:VAL2318 3.7 23.6 1.0
CB A:VAL2318 3.8 32.4 1.0
CB A:HIS142 3.8 8.1 1.0
CG2 A:ILE188 3.8 13.0 1.0
C A:VAL2318 4.0 28.8 1.0
CE1 A:HIS142 4.0 10.3 1.0
NE2 A:HIS142 4.0 10.0 1.0
CA A:VAL139 4.1 6.7 1.0
CG1 A:VAL139 4.2 10.1 1.0
CG2 A:VAL139 4.3 10.4 1.0
OE2 A:GLU143 4.3 18.1 1.0
N A:VAL2318 4.4 24.1 1.0
CB A:VAL139 4.4 10.2 1.0
O A:VAL139 4.7 8.4 1.0
OD1 A:ASP170 4.7 11.2 1.0
CZ A:ARG203 4.8 13.8 1.0
O A:ASP138 4.9 10.9 1.0
O A:HOH2165 4.9 36.9 1.0
CD2 A:LEU202 5.0 23.3 1.0
C A:VAL139 5.0 9.6 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: Tue Aug 13 01:25:53 2024

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