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Krypton in PDB 6sp8: Structure of Hyperstable Haloalkane Dehalogenase Variant DHAA115 Prepared By the 'Soak-and-Freeze' Method Under 150 Bar of Krypton Pressure

Enzymatic activity of Structure of Hyperstable Haloalkane Dehalogenase Variant DHAA115 Prepared By the 'Soak-and-Freeze' Method Under 150 Bar of Krypton Pressure

All present enzymatic activity of Structure of Hyperstable Haloalkane Dehalogenase Variant DHAA115 Prepared By the 'Soak-and-Freeze' Method Under 150 Bar of Krypton Pressure:
3.8.1.5;

Protein crystallography data

The structure of Structure of Hyperstable Haloalkane Dehalogenase Variant DHAA115 Prepared By the 'Soak-and-Freeze' Method Under 150 Bar of Krypton Pressure, PDB code: 6sp8 was solved by K.Chmelova, K.Markova, J.Damborsky, M.Marek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.20 / 1.55
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 67.978, 82.045, 144.176, 90.00, 90.00, 90.00
R / Rfree (%) 16 / 18.1

Krypton Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 21;

Binding sites:

The binding sites of Krypton atom in the Structure of Hyperstable Haloalkane Dehalogenase Variant DHAA115 Prepared By the 'Soak-and-Freeze' Method Under 150 Bar of Krypton Pressure (pdb code 6sp8). This binding sites where shown within 5.0 Angstroms radius around Krypton atom.
In total 21 binding sites of Krypton where determined in the Structure of Hyperstable Haloalkane Dehalogenase Variant DHAA115 Prepared By the 'Soak-and-Freeze' Method Under 150 Bar of Krypton Pressure, PDB code: 6sp8:
Jump to Krypton binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Krypton binding site 1 out of 21 in 6sp8

Go back to Krypton Binding Sites List in 6sp8
Krypton binding site 1 out of 21 in the Structure of Hyperstable Haloalkane Dehalogenase Variant DHAA115 Prepared By the 'Soak-and-Freeze' Method Under 150 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 Hyperstable Haloalkane Dehalogenase Variant DHAA115 Prepared By the 'Soak-and-Freeze' Method Under 150 Bar of Krypton Pressure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Kr301

b:18.6
occ:0.16
CE A:MET22 3.2 28.9 1.0
CD1 A:LEU88 3.2 16.6 1.0
CA A:LEU88 3.7 13.7 1.0
CB A:PRO64 3.8 13.5 1.0
CB A:LEU88 3.9 12.3 1.0
CB A:PHE91 3.9 15.3 1.0
CG A:PRO64 3.9 12.8 1.0
CG A:PHE91 4.0 12.8 1.0
CD2 A:LEU66 4.0 16.2 1.0
SD A:MET22 4.1 19.4 1.0
CG A:LEU88 4.2 15.8 1.0
O A:HOH562 4.3 15.6 1.0
N A:LEU88 4.3 13.7 1.0
CD2 A:PHE91 4.3 12.5 1.0
O A:ASP65 4.4 13.0 1.0
CA A:LEU66 4.4 12.1 1.0
CD1 A:PHE91 4.5 16.2 1.0
O A:TYR87 4.5 14.3 1.0
C A:TYR87 4.6 13.8 1.0
C A:ASP65 4.8 11.9 1.0
N A:LEU66 4.8 13.0 1.0
C A:LEU88 4.9 14.1 1.0
CE2 A:PHE91 5.0 13.0 1.0
O A:LEU88 5.0 14.1 1.0

Krypton binding site 2 out of 21 in 6sp8

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Krypton binding site 2 out of 21 in the Structure of Hyperstable Haloalkane Dehalogenase Variant DHAA115 Prepared By the 'Soak-and-Freeze' Method Under 150 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 Hyperstable Haloalkane Dehalogenase Variant DHAA115 Prepared By the 'Soak-and-Freeze' Method Under 150 Bar of Krypton Pressure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Kr302

b:17.0
occ:0.13
CB A:TRP115 3.4 14.3 1.0
CD2 A:LEU102 3.5 17.4 1.0
CD1 A:ILE92 3.5 16.9 1.0
CG A:TRP115 3.5 12.4 1.0
CD2 A:TRP115 3.6 15.5 1.0
CE3 A:TRP115 3.7 16.8 1.0
CD2 A:LEU36 3.8 14.9 1.0
CD1 A:LEU38 3.9 13.1 1.0
CA A:GLY112 4.0 12.6 1.0
CD2 A:LEU88 4.0 15.4 1.0
CD1 A:TRP115 4.3 15.8 1.0
CE2 A:TRP115 4.4 14.8 1.0
CD1 A:LEU102 4.4 14.0 1.0
O A:GLY112 4.4 13.4 1.0
O A:LEU111 4.5 13.7 1.0
CG A:LEU102 4.5 14.1 1.0
CZ3 A:TRP115 4.6 17.7 1.0
CG A:LEU88 4.7 15.8 1.0
C A:GLY112 4.7 12.2 1.0
NE1 A:TRP115 4.7 16.6 1.0
N A:GLY112 4.8 13.1 1.0
CG1 A:ILE92 4.8 16.1 1.0
CA A:TRP115 4.9 13.7 1.0
C A:LEU111 4.9 13.0 1.0

Krypton binding site 3 out of 21 in 6sp8

Go back to Krypton Binding Sites List in 6sp8
Krypton binding site 3 out of 21 in the Structure of Hyperstable Haloalkane Dehalogenase Variant DHAA115 Prepared By the 'Soak-and-Freeze' Method Under 150 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 Hyperstable Haloalkane Dehalogenase Variant DHAA115 Prepared By the 'Soak-and-Freeze' Method Under 150 Bar of Krypton Pressure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Kr303

b:22.6
occ:0.53
KR A:KR304 2.9 23.5 0.2
N A:SCN313 3.2 25.9 1.0
CE1 A:HIS272 3.8 14.5 1.0
ND1 A:HIS272 3.8 13.9 1.0
CD2 A:LEU246 3.8 20.4 1.0
CG A:LEU246 3.9 13.6 1.0
CE2 A:PHE176 3.9 17.4 1.0
NE2 A:HIS272 3.9 16.4 1.0
CG A:HIS272 4.0 12.9 1.0
C A:SCN313 4.0 20.3 1.0
CG1 A:VAL245 4.0 16.6 1.0
CD1 A:LEU246 4.0 14.8 1.0
CH2 A:TRP141 4.0 19.5 1.0
OD1 A:ASP106 4.1 19.0 1.0
CD2 A:HIS272 4.1 16.2 1.0
CZ2 A:TRP141 4.3 16.3 1.0
CD2 A:PHE176 4.3 17.5 1.0
CZ A:PHE149 4.4 15.8 1.0
CE2 A:PHE149 4.7 15.8 1.0
CB A:HIS272 4.7 15.3 1.0
CZ A:PHE176 4.9 19.1 1.0
CB A:VAL245 4.9 14.7 1.0

Krypton binding site 4 out of 21 in 6sp8

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Krypton binding site 4 out of 21 in the Structure of Hyperstable Haloalkane Dehalogenase Variant DHAA115 Prepared By the 'Soak-and-Freeze' Method Under 150 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 Hyperstable Haloalkane Dehalogenase Variant DHAA115 Prepared By the 'Soak-and-Freeze' Method Under 150 Bar of Krypton Pressure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Kr304

b:23.5
occ:0.16
KR A:KR303 2.9 22.6 0.5
N A:SCN313 3.1 25.9 1.0
OH A:TYR273 3.1 17.4 1.0
CD2 A:HIS272 3.5 16.2 1.0
CE2 A:PHE168 3.5 16.6 1.0
CZ A:PHE168 3.6 14.6 1.0
C A:SCN313 3.6 20.3 1.0
NE2 A:HIS272 3.7 16.4 1.0
O A:ASN41 3.8 14.2 1.0
CD2 A:PHE176 3.9 17.5 1.0
CZ A:TYR273 3.9 16.0 1.0
CE2 A:PHE176 4.0 17.4 1.0
CG2 A:ILE172 4.1 16.9 1.0
CG A:HIS272 4.2 12.9 1.0
O A:HOH459 4.2 17.5 1.0
OD1 A:ASP106 4.3 19.0 1.0
CZ A:PHE149 4.4 15.8 1.0
CE1 A:HIS272 4.5 14.5 1.0
CE2 A:TYR273 4.5 14.1 1.0
CE1 A:TYR273 4.7 15.7 1.0
ND1 A:HIS272 4.7 13.9 1.0
CD2 A:PHE168 4.8 17.0 1.0
CG A:ASP106 4.8 17.6 1.0
S A:SCN313 4.9 18.4 1.0
C A:ASN41 4.9 12.8 1.0
CE1 A:PHE168 5.0 14.8 1.0
CE2 A:PHE149 5.0 15.8 1.0
OD2 A:ASP106 5.0 16.1 1.0
CB A:HIS272 5.0 15.3 1.0

Krypton binding site 5 out of 21 in 6sp8

Go back to Krypton Binding Sites List in 6sp8
Krypton binding site 5 out of 21 in the Structure of Hyperstable Haloalkane Dehalogenase Variant DHAA115 Prepared By the 'Soak-and-Freeze' Method Under 150 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 Hyperstable Haloalkane Dehalogenase Variant DHAA115 Prepared By the 'Soak-and-Freeze' Method Under 150 Bar of Krypton Pressure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Kr305

b:35.6
occ:0.30
CD1 A:ILE172 3.7 20.0 1.0
CB A:LYS175 3.8 22.6 1.0
CD1 A:LEU148 3.8 48.0 1.0
CB A:ALA145 3.9 22.2 1.0
O A:HOH661 4.0 36.7 0.5
CE2 A:PHE144 4.0 39.1 1.0
CE1 A:PHE176 4.0 20.6 1.0
O A:PHE144 4.1 29.7 1.0
CG A:LYS175 4.1 37.0 1.0
CD2 A:PHE144 4.2 38.8 1.0
CA A:ALA145 4.2 22.1 1.0
CZ A:PHE176 4.6 19.1 1.0
CD1 A:PHE176 4.6 21.1 1.0
C A:PHE144 4.7 26.7 1.0
N A:ALA145 4.8 22.1 1.0
CZ A:PHE144 4.8 33.0 1.0
CA A:ILE172 4.9 19.0 1.0

Krypton binding site 6 out of 21 in 6sp8

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Krypton binding site 6 out of 21 in the Structure of Hyperstable Haloalkane Dehalogenase Variant DHAA115 Prepared By the 'Soak-and-Freeze' Method Under 150 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 Hyperstable Haloalkane Dehalogenase Variant DHAA115 Prepared By the 'Soak-and-Freeze' Method Under 150 Bar of Krypton Pressure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Kr306

b:19.9
occ:0.35
O A:ARG133 3.3 15.6 1.0
CG1 A:ILE135 3.4 25.3 1.0
CD A:PRO210 3.7 13.2 1.0
CD2 A:LEU209 3.8 17.9 1.0
CD1 A:ILE135 3.9 26.2 1.0
CD2 A:LEU246 4.0 20.4 1.0
CG A:PRO210 4.1 17.4 1.0
O A:PRO210 4.1 16.2 1.0
CG2 A:ILE132 4.1 14.8 0.4
N A:PRO210 4.3 14.4 1.0
N A:ARG133 4.3 15.2 1.0
CG2 A:ILE132 4.3 15.0 0.6
CG1 A:ILE132 4.3 14.5 0.6
CB A:LEU209 4.4 15.8 1.0
CD1 A:ILE132 4.4 17.3 0.4
C A:ARG133 4.5 14.4 1.0
CA A:ILE132 4.5 12.8 0.6
CZ3 A:TRP141 4.5 20.9 1.0
CA A:ILE132 4.6 12.9 0.4
CG A:LEU209 4.6 17.9 1.0
CB A:ILE132 4.6 14.2 0.6
CG1 A:ILE211 4.7 18.8 1.0
CB A:ILE135 4.7 17.6 1.0
C A:PRO210 4.7 15.2 1.0
CA A:LEU209 4.7 13.9 1.0
C A:LEU209 4.8 15.9 1.0
CB A:ILE132 4.8 14.1 0.4
CD1 A:LEU246 4.9 14.8 1.0
C A:ILE132 4.9 14.2 0.6
N A:ILE135 4.9 16.3 1.0
C A:ILE132 4.9 14.2 0.4
CA A:PRO210 5.0 15.5 1.0
CG A:LEU246 5.0 13.6 1.0

Krypton binding site 7 out of 21 in 6sp8

Go back to Krypton Binding Sites List in 6sp8
Krypton binding site 7 out of 21 in the Structure of Hyperstable Haloalkane Dehalogenase Variant DHAA115 Prepared By the 'Soak-and-Freeze' Method Under 150 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 Hyperstable Haloalkane Dehalogenase Variant DHAA115 Prepared By the 'Soak-and-Freeze' Method Under 150 Bar of Krypton Pressure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Kr307

b:30.4
occ:0.25
O A:GLU140 2.9 35.4 1.0
O A:VAL245 3.2 17.2 1.0
CD1 A:ILE135 3.4 26.2 1.0
C A:GLU140 3.5 32.6 1.0
NH2 A:ARG133 3.6 23.3 1.0
CA A:TRP141 3.8 28.2 1.0
CG2 A:ILE135 3.8 17.6 1.0
N A:TRP141 3.9 27.3 1.0
CE3 A:TRP141 3.9 25.9 1.0
O A:HOH487 4.0 27.6 1.0
O A:LEU246 4.1 17.6 1.0
CA A:LEU246 4.2 14.9 1.0
CD A:PRO142 4.2 23.7 1.0
C A:VAL245 4.3 15.6 1.0
CG1 A:ILE135 4.3 25.3 1.0
CB A:GLU140 4.4 31.8 1.0
C A:LEU246 4.4 14.8 1.0
CZ3 A:TRP141 4.6 20.9 1.0
CD2 A:TRP141 4.6 22.1 1.0
CA A:GLU140 4.6 28.1 1.0
CB A:TRP141 4.7 25.1 1.0
CZ A:ARG133 4.7 19.9 1.0
CB A:ILE135 4.7 17.6 1.0
N A:LEU246 4.7 13.0 1.0
C A:TRP141 4.8 30.2 1.0
CD2 A:LEU246 4.8 20.4 1.0
N A:PRO142 4.9 23.3 1.0
CG A:TRP141 4.9 22.9 1.0
CD A:PRO248 5.0 14.6 1.0

Krypton binding site 8 out of 21 in 6sp8

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Krypton binding site 8 out of 21 in the Structure of Hyperstable Haloalkane Dehalogenase Variant DHAA115 Prepared By the 'Soak-and-Freeze' Method Under 150 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 Hyperstable Haloalkane Dehalogenase Variant DHAA115 Prepared By the 'Soak-and-Freeze' Method Under 150 Bar of Krypton Pressure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Kr308

b:25.4
occ:0.12
CD1 A:PHE205 3.2 14.4 1.0
CG A:GLU208 3.4 21.5 1.0
N A:PHE81 3.4 16.3 1.0
OE1 A:GLU208 3.5 25.1 1.0
O A:TYR79 3.5 21.1 1.0
CE1 A:PHE205 3.5 16.4 1.0
O A:HOH548 3.6 15.2 1.0
C A:ARG80 3.7 19.6 0.5
C A:ARG80 3.8 19.7 0.5
CA A:PHE81 3.8 15.0 1.0
CA A:PHE205 3.8 13.7 1.0
CD A:GLU208 3.9 36.5 1.0
N A:PHE205 3.9 14.3 1.0
C A:ARG204 3.9 14.2 1.0
O A:ARG204 4.0 15.8 1.0
CG A:PHE205 4.0 14.7 1.0
CB A:GLU208 4.1 14.7 1.0
CA A:ARG80 4.1 19.1 0.5
CA A:ARG80 4.1 19.1 0.5
CB A:ARG204 4.1 14.2 1.0
CB A:PHE81 4.2 16.4 1.0
O A:ARG80 4.2 17.4 0.5
CD2 A:HIS84 4.4 14.3 1.0
C A:TYR79 4.5 17.4 1.0
O A:ARG80 4.5 16.4 0.5
CZ A:PHE205 4.6 15.7 1.0
CB A:PHE205 4.6 12.1 1.0
CA A:ARG204 4.7 12.9 1.0
N A:ARG80 4.8 17.5 0.5
N A:ARG80 4.8 17.5 0.5
C A:PHE205 4.9 14.9 1.0
NE2 A:HIS84 5.0 13.5 1.0
CD2 A:PHE205 5.0 15.8 1.0
O A:PHE205 5.0 15.1 1.0

Krypton binding site 9 out of 21 in 6sp8

Go back to Krypton Binding Sites List in 6sp8
Krypton binding site 9 out of 21 in the Structure of Hyperstable Haloalkane Dehalogenase Variant DHAA115 Prepared By the 'Soak-and-Freeze' Method Under 150 Bar of Krypton Pressure


Mono view


Stereo pair view

A full contact list of Krypton with other atoms in the Kr binding site number 9 of Structure of Hyperstable Haloalkane Dehalogenase Variant DHAA115 Prepared By the 'Soak-and-Freeze' Method Under 150 Bar of Krypton Pressure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Kr309

b:19.7
occ:0.79
NE1 A:TRP240 3.6 14.8 1.0
O A:ALA252 3.6 14.9 1.0
CE2 A:TRP240 3.7 14.3 1.0
C A:ALA252 3.8 13.0 1.0
CZ2 A:TRP240 3.8 15.2 1.0
OG1 A:THR264 3.8 18.2 1.0
N A:ALA253 3.9 14.1 1.0
O A:HOH495 4.0 16.5 1.0
CB A:ALA256 4.0 16.2 1.0
CB A:ALA252 4.0 16.5 1.0
CA A:ALA253 4.1 14.7 1.0
CB A:THR264 4.1 15.5 1.0
CG2 A:THR264 4.2 17.3 1.0
O A:HOH432 4.4 35.0 1.0
CD1 A:TRP240 4.4 14.4 1.0
CA A:ALA252 4.5 13.9 1.0
CD2 A:TRP240 4.6 14.1 1.0
CH2 A:TRP240 4.6 17.3 1.0
CB A:ALA253 4.9 14.1 1.0
CG A:TRP240 4.9 12.8 1.0

Krypton binding site 10 out of 21 in 6sp8

Go back to Krypton Binding Sites List in 6sp8
Krypton binding site 10 out of 21 in the Structure of Hyperstable Haloalkane Dehalogenase Variant DHAA115 Prepared By the 'Soak-and-Freeze' Method Under 150 Bar of Krypton Pressure


Mono view


Stereo pair view

A full contact list of Krypton with other atoms in the Kr binding site number 10 of Structure of Hyperstable Haloalkane Dehalogenase Variant DHAA115 Prepared By the 'Soak-and-Freeze' Method Under 150 Bar of Krypton Pressure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Kr310

b:21.9
occ:0.72
CB A:ALA253 3.8 14.1 1.0
CA A:ALA250 4.3 16.6 1.0
O A:ALA250 4.4 16.1 1.0
CB A:ALA250 4.4 16.1 1.0
C A:ALA250 4.8 17.3 1.0

Reference:

K.Markova, K.Chmelova, S.M.Marques, P.Carpentier, D.Bednar, J.Damborsky, M.Marek. Decoding the Intricate Network of Molecular Interactions of A Hyperstable Engineered Biocatalyst Chem Sci 2020.
ISSN: ESSN 2041-6539
DOI: 10.1039/D0SC03367G
Page generated: Mon Dec 14 02:56:51 2020

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