Chlorine in PDB 8oe2: Structure of Hyperstable Haloalkane Dehalogenase Variant DHAA223

Enzymatic activity of Structure of Hyperstable Haloalkane Dehalogenase Variant DHAA223

All present enzymatic activity of Structure of Hyperstable Haloalkane Dehalogenase Variant DHAA223:
3.8.1.5;

Protein crystallography data

The structure of Structure of Hyperstable Haloalkane Dehalogenase Variant DHAA223, PDB code: 8oe2 was solved by M.Marek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.72 / 1.51
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 67.35, 143.144, 106.676, 90, 108.38, 90
R / Rfree (%) 16.8 / 19.5

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Structure of Hyperstable Haloalkane Dehalogenase Variant DHAA223 (pdb code 8oe2). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the Structure of Hyperstable Haloalkane Dehalogenase Variant DHAA223, PDB code: 8oe2:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 8oe2

Go back to Chlorine Binding Sites List in 8oe2
Chlorine binding site 1 out of 6 in the Structure of Hyperstable Haloalkane Dehalogenase Variant DHAA223


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Structure of Hyperstable Haloalkane Dehalogenase Variant DHAA223 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl301

b:15.9
occ:1.00
 O A:HOH468 3.1 34.6 1.0
NE1 A:TRP107 3.2 12.8 1.0
N A:PRO206 3.4 13.2 1.0
ND2 A:ASN41 3.5 13.7 1.0
CA A:PRO206 3.5 13.0 1.0
C A:PHE205 3.7 12.3 1.0
CD A:PRO206 3.7 11.7 1.0
CZ A:PHE168 3.7 29.2 1.0
CB A:PHE205 3.8 12.2 1.0
CD1 A:TRP107 3.8 11.6 1.0
CB A:PRO206 3.8 12.5 1.0
O A:PHE205 4.0 13.3 1.0
CD1 A:LEU209 4.1 16.8 1.0
CB A:ASN41 4.1 9.9 1.0
CE2 A:PHE168 4.1 34.8 1.0
CG A:LEU209 4.2 16.0 1.0
CG A:ASN41 4.3 12.3 1.0
CG A:PRO206 4.3 12.0 1.0
CD2 A:LEU209 4.4 14.6 1.0
CA A:PHE205 4.4 13.4 1.0
CE2 A:PHE149 4.4 14.5 1.0
CE2 A:TRP107 4.4 12.3 1.0
CE1 A:PHE168 4.6 28.8 1.0
CG A:PHE205 4.8 13.8 1.0
OD2 A:ASP106 4.9 15.6 1.0
OD1 A:ASP106 5.0 20.2 1.0
C A:PRO206 5.0 13.0 1.0

Chlorine binding site 2 out of 6 in 8oe2

Go back to Chlorine Binding Sites List in 8oe2
Chlorine binding site 2 out of 6 in the Structure of Hyperstable Haloalkane Dehalogenase Variant DHAA223


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Structure of Hyperstable Haloalkane Dehalogenase Variant DHAA223 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl301

b:15.3
occ:1.00
 O B:HOH428 3.0 28.4 1.0
NE1 B:TRP107 3.2 12.4 1.0
ND2 B:ASN41 3.4 10.9 1.0
N B:PRO206 3.4 13.4 1.0
CA B:PRO206 3.5 11.9 1.0
CD B:PRO206 3.6 12.5 1.0
C B:PHE205 3.6 13.7 1.0
CD1 B:TRP107 3.7 11.0 1.0
CZ B:PHE168 3.8 12.4 1.0
CB B:PHE205 3.8 11.9 1.0
CB B:PRO206 3.8 12.2 1.0
O B:PHE205 4.0 13.0 1.0
CE2 B:PHE168 4.0 14.8 1.0
CD1 B:LEU209 4.0 15.1 1.0
CB B:ASN41 4.1 11.4 1.0
CG B:LEU209 4.2 14.4 1.0
CG B:ASN41 4.2 11.9 1.0
CG B:PRO206 4.3 13.0 1.0
CD2 B:LEU209 4.3 15.5 1.0
CA B:PHE205 4.4 12.5 1.0
CE2 B:TRP107 4.4 13.5 1.0
CE2 B:PHE149 4.4 15.6 1.0
CE1 B:PHE168 4.8 16.3 1.0
CG B:PHE205 4.9 12.3 1.0
C B:PRO206 4.9 12.6 1.0
OD2 B:ASP106 4.9 13.5 1.0
OD1 B:ASP106 5.0 22.1 1.0

Chlorine binding site 3 out of 6 in 8oe2

Go back to Chlorine Binding Sites List in 8oe2
Chlorine binding site 3 out of 6 in the Structure of Hyperstable Haloalkane Dehalogenase Variant DHAA223


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Structure of Hyperstable Haloalkane Dehalogenase Variant DHAA223 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl301

b:16.0
occ:1.00
 O C:HOH417 3.0 27.5 1.0
NE1 C:TRP107 3.2 14.7 1.0
N C:PRO206 3.4 14.5 1.0
ND2 C:ASN41 3.4 12.5 1.0
CA C:PRO206 3.5 14.9 1.0
CD C:PRO206 3.5 14.8 1.0
C C:PHE205 3.7 14.8 1.0
CZ C:PHE168 3.7 15.5 1.0
CB C:PHE205 3.8 13.9 1.0
CD1 C:TRP107 3.8 12.8 1.0
CB C:PRO206 3.8 15.4 1.0
CE2 C:PHE168 3.8 17.8 1.0
O C:PHE205 4.0 14.6 1.0
CD1 C:LEU209 4.0 19.7 1.0
CB C:ASN41 4.1 12.1 1.0
CG C:LEU209 4.2 17.5 1.0
CG C:ASN41 4.3 13.0 1.0
CD2 C:LEU209 4.3 17.0 1.0
CG C:PRO206 4.3 15.4 1.0
CE2 C:PHE149 4.3 14.7 1.0
CA C:PHE205 4.4 13.2 1.0
CE2 C:TRP107 4.4 14.2 1.0
CG C:PHE205 4.8 12.8 1.0
CE1 C:PHE168 4.9 17.2 1.0
C C:PRO206 4.9 14.2 1.0
OD2 C:ASP106 4.9 15.2 1.0

Chlorine binding site 4 out of 6 in 8oe2

Go back to Chlorine Binding Sites List in 8oe2
Chlorine binding site 4 out of 6 in the Structure of Hyperstable Haloalkane Dehalogenase Variant DHAA223


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Structure of Hyperstable Haloalkane Dehalogenase Variant DHAA223 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl301

b:16.8
occ:1.00
 O D:HOH451 3.1 27.2 1.0
NE1 D:TRP107 3.3 13.7 1.0
N D:PRO206 3.4 13.9 1.0
ND2 D:ASN41 3.4 12.7 1.0
CA D:PRO206 3.5 14.8 1.0
C D:PHE205 3.7 15.0 1.0
CD D:PRO206 3.7 14.3 1.0
CB D:PHE205 3.8 12.8 1.0
CD1 D:TRP107 3.8 12.6 1.0
CB D:PRO206 3.8 15.1 1.0
CZ D:PHE168 3.9 17.5 1.0
CE2 D:PHE168 4.0 20.1 1.0
O D:PHE205 4.0 14.5 1.0
CD1 D:LEU209 4.1 18.3 1.0
CB D:ASN41 4.1 11.8 1.0
CG D:LEU209 4.2 16.2 1.0
CD2 D:LEU209 4.2 16.4 1.0
CG D:ASN41 4.3 12.3 1.0
CE2 D:PHE149 4.3 15.6 1.0
CG D:PRO206 4.3 13.3 1.0
CA D:PHE205 4.4 13.3 1.0
CE2 D:TRP107 4.5 14.7 1.0
CG D:PHE205 4.9 12.7 1.0
OD2 D:ASP106 4.9 15.6 1.0
C D:PRO206 4.9 14.1 1.0
OD1 D:ASP106 4.9 19.8 1.0

Chlorine binding site 5 out of 6 in 8oe2

Go back to Chlorine Binding Sites List in 8oe2
Chlorine binding site 5 out of 6 in the Structure of Hyperstable Haloalkane Dehalogenase Variant DHAA223


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Structure of Hyperstable Haloalkane Dehalogenase Variant DHAA223 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl301

b:17.6
occ:1.00
 O E:HOH407 3.0 32.1 1.0
NE1 E:TRP107 3.2 15.9 1.0
ND2 E:ASN41 3.4 12.7 1.0
N E:PRO206 3.4 14.5 1.0
CA E:PRO206 3.5 14.7 1.0
CD E:PRO206 3.6 14.3 1.0
C E:PHE205 3.7 14.5 1.0
CZ E:PHE168 3.7 16.8 1.0
CB E:PHE205 3.8 13.3 1.0
CD1 E:TRP107 3.8 14.0 1.0
CB E:PRO206 3.9 13.4 1.0
CE2 E:PHE168 3.9 18.3 1.0
CD1 E:LEU209 3.9 16.7 1.0
O E:PHE205 4.0 14.6 1.0
CB E:ASN41 4.1 11.7 1.0
CG E:LEU209 4.2 17.0 1.0
CG E:ASN41 4.3 13.0 1.0
CD2 E:LEU209 4.3 19.1 1.0
CE2 E:PHE149 4.3 16.6 1.0
CG E:PRO206 4.3 12.6 1.0
CA E:PHE205 4.4 14.0 1.0
CE2 E:TRP107 4.5 15.0 1.0
CE1 E:PHE168 4.8 18.3 1.0
CG E:PHE205 4.9 12.8 1.0
C E:PRO206 5.0 16.0 1.0
OD2 E:ASP106 5.0 14.6 1.0
O E:HOH623 5.0 23.7 1.0
OD1 E:ASP106 5.0 21.2 1.0

Chlorine binding site 6 out of 6 in 8oe2

Go back to Chlorine Binding Sites List in 8oe2
Chlorine binding site 6 out of 6 in the Structure of Hyperstable Haloalkane Dehalogenase Variant DHAA223


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Structure of Hyperstable Haloalkane Dehalogenase Variant DHAA223 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cl301

b:14.7
occ:1.00
 NE1 F:TRP107 3.2 11.9 1.0
O F:HOH415 3.3 31.1 1.0
N F:PRO206 3.4 10.4 1.0
ND2 F:ASN41 3.5 11.1 1.0
CA F:PRO206 3.5 12.3 1.0
CD F:PRO206 3.6 12.1 1.0
C F:PHE205 3.7 10.7 1.0
CZ F:PHE168 3.7 12.4 1.0
CD1 F:TRP107 3.8 11.2 1.0
CB F:PHE205 3.8 11.5 1.0
CB F:PRO206 3.8 12.5 1.0
O F:PHE205 4.0 12.2 1.0
CE2 F:PHE168 4.0 14.8 1.0
CD1 F:LEU209 4.1 15.0 1.0
CB F:ASN41 4.2 11.8 1.0
CG F:LEU209 4.2 14.8 1.0
CD2 F:LEU209 4.3 15.5 1.0
CG F:PRO206 4.3 11.3 1.0
CG F:ASN41 4.3 10.7 1.0
CE2 F:PHE149 4.4 13.9 1.0
CA F:PHE205 4.4 10.7 1.0
CE2 F:TRP107 4.4 12.4 1.0
CE1 F:PHE168 4.8 14.5 1.0
CG F:PHE205 4.9 10.2 1.0
C F:PRO206 4.9 13.6 1.0
OD2 F:ASP106 5.0 13.5 1.0
OD1 F:ASP106 5.0 16.9 1.0

Reference:

A.Kunka, S.M.Marques, M.Havlasek, M.Vasina, N.Velatova, L.Cengelova, D.Kovar, J.Damborsky, M.Marek, D.Bednar, Z.Prokop. Advancing Enzyme'S Stability and Catalytic Efficiency Through Synergy of Force-Field Calculations, Evolutionary Analysis, and Machine Learning. Acs Catalysis V. 13 12506 2023.
ISSN: ESSN 2155-5435
PubMed: 37822856
DOI: 10.1021/ACSCATAL.3C02575
Page generated: Tue Jul 30 11:05:43 2024

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