Atomistry » Krypton » PDB 1c61-7r2s » 5fsp
Atomistry »
  Krypton »
    PDB 1c61-7r2s »
      5fsp »

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

Go back to Krypton Binding Sites List in 5fsp
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

Go back to Krypton Binding Sites List in 5fsp
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

Go back to Krypton Binding Sites List in 5fsp
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

Go back to Krypton Binding Sites List in 5fsp
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

Go back to Krypton Binding Sites List in 5fsp
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

Go back to Krypton Binding Sites List in 5fsp
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

Go back to Krypton Binding Sites List in 5fsp
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

Go back to Krypton Binding Sites List in 5fsp
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: Mon Dec 14 02:53:05 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy