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

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

All present enzymatic activity of Structure of Lysozyme Prepared By the 'Soak-and-Freeze' Method Under 100 Bar of Krypton Pressure:
3.2.1.17;

Protein crystallography data

The structure of Structure of Lysozyme Prepared By the 'Soak-and-Freeze' Method Under 100 Bar of Krypton Pressure, PDB code: 5fst 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) 55.86 / 1.20
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 79.001, 79.001, 37.053, 90.00, 90.00, 90.00
R / Rfree (%) 10.9 / 13.4

Other elements in 5fst:

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

Chlorine (Cl) 8 atoms
Sodium (Na) 1 atom

Krypton Binding Sites:

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

Krypton binding site 1 out of 5 in 5fst

Go back to Krypton Binding Sites List in 5fst
Krypton binding site 1 out of 5 in the Structure of Lysozyme 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 Lysozyme 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:Kr1130

b:37.4
occ:0.33
 HA A:HIS15 3.0 14.4 1.0
CD2 A:HIS15 3.4 21.0 1.0
HG2 A:ARG14 3.4 26.1 1.0
HH12 A:ARG14 3.4 47.2 1.0
NH1 A:ARG14 3.4 58.5 1.0
HD2 A:HIS15 3.5 21.0 1.0
O A:HOH2027 3.5 38.3 1.0
NE2 A:HIS15 3.6 24.8 1.0
HH11 A:ARG14 3.6 47.2 1.0
O A:ARG14 3.6 17.2 1.0
CG A:HIS15 3.7 14.5 1.0
HE2 A:HIS15 3.8 24.8 1.0
CZ A:ARG14 3.8 45.8 1.0
CA A:HIS15 3.9 14.4 1.0
CE1 A:HIS15 4.1 17.9 1.0
HH22 A:ARG14 4.1 58.5 1.0
ND1 A:HIS15 4.1 17.5 1.0
NH2 A:ARG14 4.1 47.2 1.0
C A:ARG14 4.1 14.5 1.0
O A:HOH2024 4.2 33.5 1.0
N A:HIS15 4.3 13.2 1.0
CG A:ARG14 4.3 26.1 1.0
CB A:HIS15 4.3 14.5 1.0
O A:HOH2151 4.4 60.1 1.0
NE A:ARG14 4.4 41.1 1.0
HE1 A:HIS15 4.6 17.9 1.0
HH21 A:ARG14 4.6 58.5 1.0
HD1 A:HIS15 4.7 17.5 1.0
HB3 A:HIS15 4.7 14.5 1.0
O A:HOH2155 4.7 29.0 1.0
HG3 A:ARG14 4.8 26.1 1.0
CD A:ARG14 4.9 32.8 1.0
HB3 A:ARG14 4.9 20.4 1.0
HE A:ARG14 4.9 41.1 1.0

Krypton binding site 2 out of 5 in 5fst

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Krypton binding site 2 out of 5 in the Structure of Lysozyme 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 Lysozyme 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:Kr1131

b:17.5
occ:0.50
 HD12 A:ILE55 1.5 14.5 0.5
CD1 A:ILE55 2.4 14.5 0.5
HD13 A:ILE55 2.5 14.5 0.5
HG22 A:ILE55 2.9 19.8 0.5
HD11 A:ILE55 3.0 14.5 0.5
HG23 A:VAL92 3.1 11.9 1.0
HG21 A:VAL92 3.2 11.9 1.0
HG13 A:ILE55 3.2 8.8 0.5
HG21 A:ILE55 3.2 19.8 0.5
HD13 A:LEU56 3.2 11.9 1.0
HE3 A:MET12 3.2 11.9 1.0
HB3 A:SER91 3.3 9.5 1.0
HD13 A:ILE88 3.3 13.6 1.0
CG1 A:ILE55 3.4 8.8 0.5
CG2 A:ILE55 3.4 19.8 0.5
HG23 A:ILE55 3.4 19.8 0.5
HB A:ILE88 3.4 11.0 1.0
HD12 A:LEU56 3.4 11.9 1.0
HE1 A:MET12 3.5 11.9 1.0
CG2 A:VAL92 3.6 11.9 1.0
HB2 A:SER91 3.6 9.5 1.0
HG12 A:ILE55 3.6 8.8 0.5
HG A:LEU56 3.6 9.6 1.0
CD1 A:LEU56 3.7 11.9 1.0
HG2 A:MET12 3.8 9.3 1.0
CE A:MET12 3.8 11.9 1.0
HA A:VAL92 3.8 10.1 1.0
CB A:SER91 3.9 9.5 1.0
HD12 A:LEU17 4.0 14.1 1.0
N A:VAL92 4.1 9.7 1.0
H A:VAL92 4.2 9.7 1.0
CD1 A:ILE88 4.2 13.6 1.0
HG22 A:VAL92 4.2 11.9 1.0
CG A:LEU56 4.2 9.6 1.0
HD12 A:LEU8 4.3 11.1 1.0
C A:SER91 4.3 8.9 1.0
CB A:ILE88 4.3 11.0 1.0
CA A:VAL92 4.3 10.1 1.0
HD13 A:LEU17 4.4 14.1 1.0
HD11 A:ILE88 4.4 13.6 1.0
HE2 A:MET12 4.4 11.9 1.0
HG22 A:ILE88 4.5 12.2 1.0
O A:ILE88 4.6 10.2 1.0
CG A:MET12 4.6 9.3 1.0
HD11 A:LEU56 4.6 11.9 1.0
CB A:VAL92 4.6 12.0 1.0
CD1 A:LEU17 4.6 14.1 1.0
O A:SER91 4.7 9.6 1.0
CG1 A:ILE88 4.7 11.8 1.0
CB A:ILE55 4.7 11.0 0.5
HG3 A:MET12 4.7 9.3 1.0
HG23 A:ILE88 4.8 12.2 1.0
CA A:SER91 4.8 9.2 1.0
CG2 A:ILE88 4.8 12.2 1.0
HG13 A:ILE88 4.8 11.8 1.0
HG22 A:ILE55 4.8 11.3 0.5
HG A:SER91 4.8 9.6 0.0
CB A:ILE55 4.8 14.4 0.5
HD11 A:ILE55 4.8 12.9 0.5
HB2 A:LEU56 4.9 9.2 1.0
HB A:ILE55 4.9 11.0 0.5
HD12 A:ILE88 4.9 13.6 1.0
HD11 A:LEU17 5.0 14.1 1.0
OG A:SER91 5.0 9.6 1.0

Krypton binding site 3 out of 5 in 5fst

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Krypton binding site 3 out of 5 in the Structure of Lysozyme 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 Lysozyme 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:Kr1132

b:24.8
occ:0.25
 O A:HOH2096 2.3 15.7 0.5
HG1 A:THR43 2.9 13.0 0.0
OG1 A:THR43 3.1 13.0 1.0
HB A:THR43 3.2 11.1 1.0
CB A:THR43 3.7 11.1 1.0
HB2 A:ARG45 3.7 8.2 0.2
HE A:ARG45 3.8 20.0 0.2
HG21 A:THR51 3.8 8.8 1.0
H A:ARG45 3.9 11.9 0.5
HH22 A:ARG68 3.9 11.9 0.5
HB2 A:ARG45 3.9 14.5 0.2
HA A:ASN44 4.0 10.3 1.0
H A:ARG45 4.0 11.2 0.5
HB2 A:ARG45 4.0 18.6 0.5
HG22 A:THR51 4.1 8.8 1.0
O A:HOH2092 4.2 24.0 1.0
NH2 A:ARG45 4.2 37.0 0.5
HH21 A:ARG45 4.2 19.2 0.2
CZ A:ARG45 4.2 15.5 0.5
C A:THR43 4.2 11.0 1.0
N A:ASN44 4.2 9.3 1.0
N A:ARG45 4.2 11.9 0.5
HH22 A:ARG45 4.2 37.0 0.5
N A:ARG45 4.3 11.2 0.5
O A:THR43 4.3 14.7 1.0
CA A:ASN44 4.4 10.3 1.0
HH21 A:ARG45 4.4 37.0 0.5
CG2 A:THR51 4.4 8.8 1.0
C A:ASN44 4.4 9.4 1.0
H A:ASN44 4.5 9.3 1.0
NH2 A:ARG68 4.6 11.9 0.5
NE A:ARG45 4.6 14.0 0.5
HD3 A:ARG45 4.6 8.7 0.5
HH21 A:ARG68 4.6 11.9 0.5
CB A:ARG45 4.6 8.2 0.2
CA A:THR43 4.6 9.9 1.0
NH1 A:ARG45 4.7 22.7 0.5
HG22 A:THR43 4.7 11.0 1.0
NE A:ARG45 4.7 20.0 0.2
HH12 A:ARG45 4.7 22.7 0.5
CB A:ARG45 4.8 14.5 0.2
CG2 A:THR43 4.8 11.0 1.0
HE A:ARG45 4.9 14.0 0.5
CB A:ARG45 4.9 18.6 0.5
HG23 A:THR51 4.9 8.8 1.0
CA A:ARG45 4.9 13.0 0.5
HA A:ARG45 4.9 10.1 0.2
CA A:ARG45 4.9 10.1 0.2
NH2 A:ARG45 4.9 19.2 0.2
CA A:ARG45 5.0 12.0 0.2
HB3 A:ARG45 5.0 8.2 0.2
HD3 A:ARG45 5.0 12.2 0.2

Krypton binding site 4 out of 5 in 5fst

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Krypton binding site 4 out of 5 in the Structure of Lysozyme 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 Lysozyme 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:Kr1133

b:19.1
occ:0.20
 HD11 A:LEU84 2.4 15.6 1.0
HB3 A:GLN41 2.9 8.3 1.0
CD1 A:LEU84 3.2 15.6 1.0
OE1 A:GLN41 3.3 11.3 1.0
HD13 A:LEU84 3.4 15.6 1.0
HB3 A:LEU84 3.6 9.5 1.0
CB A:GLN41 3.6 8.3 1.0
HA A:GLN41 3.6 7.9 1.0
HG2 A:GLN41 3.7 9.0 1.0
O A:GLN41 3.7 10.6 1.0
HD12 A:LEU84 3.7 15.6 1.0
CG A:GLN41 4.0 9.0 1.0
CD A:GLN41 4.0 8.6 1.0
CA A:GLN41 4.1 7.9 1.0
HD23 A:LEU84 4.1 9.7 1.0
CG A:LEU84 4.3 10.4 1.0
CB A:LEU84 4.3 9.5 1.0
HG21 A:THR43 4.3 11.0 1.0
C A:GLN41 4.4 8.7 1.0
HB2 A:GLN41 4.4 8.3 1.0
HB2 A:LEU84 4.5 9.5 1.0
O A:HOH2089 4.6 9.9 1.0
CD2 A:LEU84 4.7 9.7 1.0
HG22 A:THR43 4.7 11.0 1.0
HG3 A:GLN41 4.9 9.0 1.0
CG2 A:THR43 5.0 11.0 1.0

Krypton binding site 5 out of 5 in 5fst

Go back to Krypton Binding Sites List in 5fst
Krypton binding site 5 out of 5 in the Structure of Lysozyme 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 Lysozyme 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:Kr1134

b:27.9
occ:0.25
 HG2 A:LYS13 3.2 18.1 1.0
HB2 A:ARG14 3.3 20.4 1.0
HB3 A:LYS13 3.3 14.2 1.0
HD3 A:LYS13 3.4 20.4 1.0
HA A:ARG14 3.4 15.1 1.0
N A:ARG14 3.7 13.6 1.0
H A:ARG14 3.7 13.6 1.0
CG A:LYS13 3.8 18.1 1.0
O A:ALA10 3.9 13.1 1.0
CA A:ARG14 3.9 15.1 1.0
CB A:LYS13 4.0 14.2 1.0
CB A:ARG14 4.0 20.4 1.0
CD A:LYS13 4.0 20.4 1.0
C A:LYS13 4.1 12.8 1.0
OXT A:LEU129 4.2 24.8 1.0
HE2 A:LYS13 4.4 27.0 1.0
HG3 A:ARG14 4.4 26.1 1.0
HA A:ALA10 4.4 12.8 1.0
HB2 A:ALA10 4.6 14.0 1.0
O A:LYS13 4.7 15.2 1.0
CA A:LYS13 4.7 13.2 1.0
HG3 A:LYS13 4.7 18.1 1.0
HB3 A:ARG14 4.7 20.4 1.0
HB2 A:LYS13 4.8 14.2 1.0
CE A:LYS13 4.8 27.0 1.0
CG A:ARG14 4.8 26.1 1.0
HD2 A:LYS13 4.8 20.4 1.0
C A:ALA10 4.8 12.4 1.0
HA A:LEU129 5.0 21.9 1.0
HZ1 A:LYS13 5.0 32.6 1.0
HD3 A:ARG14 5.0 32.8 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 01:26:32 2024

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