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Chlorine in PDB 3umg: Crystal Structure of the Defluorinating L-2-Haloacid Dehalogenase RHA0230

Enzymatic activity of Crystal Structure of the Defluorinating L-2-Haloacid Dehalogenase RHA0230

All present enzymatic activity of Crystal Structure of the Defluorinating L-2-Haloacid Dehalogenase RHA0230:
3.8.1.2;

Protein crystallography data

The structure of Crystal Structure of the Defluorinating L-2-Haloacid Dehalogenase RHA0230, PDB code: 3umg was solved by P.W.Y.Chan, A.Savchenko, A.F.Yakunin, E.A.Edwards, E.F.Pai, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.49 / 2.25
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 102.180, 148.650, 152.550, 90.00, 90.00, 90.00
R / Rfree (%) 21.2 / 27.2

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of the Defluorinating L-2-Haloacid Dehalogenase RHA0230 (pdb code 3umg). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 7 binding sites of Chlorine where determined in the Crystal Structure of the Defluorinating L-2-Haloacid Dehalogenase RHA0230, PDB code: 3umg:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7;

Chlorine binding site 1 out of 7 in 3umg

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Chlorine binding site 1 out of 7 in the Crystal Structure of the Defluorinating L-2-Haloacid Dehalogenase RHA0230


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of the Defluorinating L-2-Haloacid Dehalogenase RHA0230 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl255

b:51.4
occ:1.00
OD1 A:ASP21 2.9 25.0 1.0
OG A:SER138 3.0 20.3 1.0
N A:ASN139 3.4 22.6 1.0
CB A:SER138 3.6 21.8 1.0
CA A:SER138 3.6 21.8 1.0
CD2 A:PHE23 3.7 22.3 1.0
N A:THR22 3.7 22.9 1.0
OH A:TYR61 3.8 39.8 1.0
N A:PHE23 3.8 22.9 1.0
O A:HOH604 3.9 41.8 1.0
NZ A:LYS169 3.9 36.7 1.0
CG A:ASP21 4.0 25.9 1.0
C A:SER138 4.0 21.2 1.0
CE A:LYS169 4.2 35.9 1.0
CB A:PHE23 4.4 23.0 1.0
CG A:PHE23 4.4 19.8 1.0
CE2 A:PHE23 4.5 22.3 1.0
CA A:THR22 4.5 22.4 1.0
CA A:ASN139 4.5 24.1 1.0
CB A:ASN139 4.5 24.2 1.0
CB A:THR22 4.6 21.8 1.0
CA A:ASP21 4.6 23.5 1.0
OD2 A:ASP21 4.6 25.5 1.0
C A:ASP21 4.7 23.8 1.0
C A:THR22 4.7 22.9 1.0
CA A:PHE23 4.7 22.9 1.0
ND2 A:ASN139 4.8 24.0 1.0
N A:GLY140 4.8 25.9 1.0
O A:PHE23 4.8 25.6 1.0
CG A:ASN139 4.8 24.8 1.0
O A:LEU137 4.8 21.4 1.0
CB A:ASP21 4.9 24.2 1.0
N A:SER138 5.0 21.6 1.0

Chlorine binding site 2 out of 7 in 3umg

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Chlorine binding site 2 out of 7 in the Crystal Structure of the Defluorinating L-2-Haloacid Dehalogenase RHA0230


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of the Defluorinating L-2-Haloacid Dehalogenase RHA0230 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl255

b:47.5
occ:1.00
OD1 C:ASP21 2.8 23.0 1.0
OG C:SER138 3.3 20.9 1.0
N C:ASN139 3.4 18.4 1.0
OH C:TYR61 3.5 44.0 1.0
CB C:SER138 3.6 18.8 1.0
CA C:SER138 3.6 18.6 1.0
CD2 C:PHE23 3.9 29.5 1.0
CG C:ASP21 3.9 25.0 1.0
N C:THR22 3.9 23.3 1.0
C C:SER138 4.0 18.5 1.0
N C:PHE23 4.1 24.0 1.0
CE C:LYS169 4.2 24.4 1.0
NZ C:LYS169 4.2 24.6 1.0
CB C:PHE23 4.3 25.1 1.0
CB C:ASN139 4.5 19.0 1.0
CA C:ASN139 4.5 17.5 1.0
CG C:PHE23 4.5 26.9 1.0
CA C:ASP21 4.6 23.3 1.0
OD2 C:ASP21 4.7 25.0 1.0
CA C:THR22 4.8 23.6 1.0
CE2 C:PHE23 4.8 33.0 1.0
CB C:THR22 4.8 23.2 1.0
CA C:PHE23 4.8 25.2 1.0
C C:ASP21 4.8 23.5 1.0
CB C:ASP21 4.8 23.4 1.0
N C:GLY140 4.8 16.7 1.0
CZ C:TYR61 4.8 46.8 1.0
ND2 C:ASN139 4.9 19.6 1.0
C C:THR22 4.9 23.5 1.0
N C:SER138 4.9 19.1 1.0
O C:PHE23 4.9 24.6 1.0
O C:LEU137 5.0 21.1 1.0

Chlorine binding site 3 out of 7 in 3umg

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Chlorine binding site 3 out of 7 in the Crystal Structure of the Defluorinating L-2-Haloacid Dehalogenase RHA0230


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of the Defluorinating L-2-Haloacid Dehalogenase RHA0230 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl255

b:44.1
occ:1.00
OD1 D:ASP21 2.9 22.9 1.0
OG D:SER138 3.1 14.3 1.0
N D:ASN139 3.4 14.0 1.0
CA D:SER138 3.7 13.8 1.0
OH D:TYR61 3.7 30.1 1.0
O D:HOH286 3.7 19.6 1.0
CB D:SER138 3.7 13.0 1.0
CD2 D:PHE23 3.9 17.8 1.0
NZ D:LYS169 4.0 16.2 1.0
N D:THR22 4.0 17.2 1.0
CG D:ASP21 4.0 19.1 1.0
C D:SER138 4.1 14.3 1.0
N D:PHE23 4.1 15.2 1.0
CE D:LYS169 4.3 16.4 1.0
CB D:ASN139 4.3 14.6 1.0
CB D:PHE23 4.4 16.5 1.0
CA D:ASN139 4.4 15.3 1.0
ND2 D:ASN139 4.4 14.7 1.0
CG D:PHE23 4.5 13.9 1.0
CG D:ASN139 4.6 14.7 1.0
CA D:ASP21 4.7 17.0 1.0
CE2 D:PHE23 4.7 19.2 1.0
CA D:THR22 4.8 15.8 1.0
N D:GLY140 4.8 15.1 1.0
OD2 D:ASP21 4.8 20.8 1.0
CA D:PHE23 4.8 15.5 1.0
C D:ASP21 4.8 16.9 1.0
CB D:ASP21 4.9 16.7 1.0
O D:PHE23 4.9 18.0 1.0
O D:LEU137 4.9 14.8 1.0
C D:THR22 4.9 15.7 1.0
CB D:THR22 5.0 15.8 1.0
CZ D:TYR61 5.0 26.9 1.0
N D:SER138 5.0 14.3 1.0

Chlorine binding site 4 out of 7 in 3umg

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Chlorine binding site 4 out of 7 in the Crystal Structure of the Defluorinating L-2-Haloacid Dehalogenase RHA0230


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of the Defluorinating L-2-Haloacid Dehalogenase RHA0230 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl255

b:43.0
occ:1.00
OD1 E:ASP21 2.9 21.1 1.0
OG E:SER138 3.2 12.1 1.0
N E:ASN139 3.3 12.8 1.0
OH E:TYR61 3.4 33.7 1.0
O E:HOH311 3.6 31.8 1.0
CD2 E:PHE23 3.8 15.9 1.0
CA E:SER138 3.8 13.2 1.0
CB E:SER138 3.9 13.8 1.0
CG E:ASP21 4.0 20.4 1.0
C E:SER138 4.0 13.5 1.0
NZ E:LYS169 4.1 18.7 1.0
N E:PHE23 4.1 16.8 1.0
N E:THR22 4.1 18.0 1.0
CB E:ASN139 4.2 12.0 1.0
CA E:ASN139 4.3 12.8 1.0
CB E:PHE23 4.4 16.7 1.0
CG E:PHE23 4.5 14.4 1.0
ND2 E:ASN139 4.5 21.6 1.0
CG E:ASN139 4.5 15.7 1.0
CE E:LYS169 4.5 20.2 1.0
CE2 E:PHE23 4.6 18.7 1.0
OD2 E:ASP21 4.6 25.6 1.0
CZ E:TYR61 4.7 33.7 1.0
N E:GLY140 4.7 11.6 1.0
CA E:PHE23 4.8 16.6 1.0
CA E:ASP21 4.9 17.6 1.0
O E:PHE23 4.9 19.7 1.0
CA E:THR22 4.9 17.4 1.0
C E:ASP21 5.0 18.0 1.0
CB E:ASP21 5.0 17.4 1.0
C E:THR22 5.0 17.7 1.0

Chlorine binding site 5 out of 7 in 3umg

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Chlorine binding site 5 out of 7 in the Crystal Structure of the Defluorinating L-2-Haloacid Dehalogenase RHA0230


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Crystal Structure of the Defluorinating L-2-Haloacid Dehalogenase RHA0230 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cl255

b:42.6
occ:1.00
O F:HOH353 2.7 35.1 1.0
OG F:SER138 2.8 26.9 1.0
OD1 F:ASP21 3.0 30.5 1.0
N F:ASN139 3.5 26.5 1.0
CB F:SER138 3.7 23.9 1.0
CA F:SER138 3.7 24.1 1.0
NZ F:LYS169 3.8 28.2 1.0
N F:THR22 3.8 23.2 1.0
N F:PHE23 3.9 25.8 1.0
CG F:ASP21 3.9 25.4 1.0
CD2 F:PHE23 4.0 27.0 1.0
OH F:TYR61 4.2 49.9 1.0
C F:SER138 4.2 25.9 1.0
OD2 F:ASP21 4.4 24.4 1.0
CB F:PHE23 4.4 25.8 1.0
CE F:LYS169 4.5 27.6 1.0
CA F:THR22 4.5 23.9 1.0
CB F:ASN139 4.5 26.5 1.0
CA F:ASN139 4.6 26.6 1.0
ND2 F:ASN139 4.6 24.7 1.0
CB F:THR22 4.6 24.4 1.0
CG F:PHE23 4.6 26.1 1.0
CA F:ASP21 4.7 23.1 1.0
C F:THR22 4.7 24.8 1.0
C F:ASP21 4.7 23.6 1.0
CA F:PHE23 4.7 25.7 1.0
N F:GLY140 4.8 25.5 1.0
O F:PHE23 4.8 26.5 1.0
CE2 F:PHE23 4.8 29.1 1.0
CB F:ASP21 4.8 24.5 1.0
CG F:ASN139 4.8 27.0 1.0
O F:LEU137 4.9 23.0 1.0

Chlorine binding site 6 out of 7 in 3umg

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Chlorine binding site 6 out of 7 in the Crystal Structure of the Defluorinating L-2-Haloacid Dehalogenase RHA0230


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Crystal Structure of the Defluorinating L-2-Haloacid Dehalogenase RHA0230 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Cl255

b:50.5
occ:1.00
OD1 G:ASP21 2.7 23.0 1.0
OG G:SER138 3.0 21.2 1.0
O G:HOH277 3.3 33.5 1.0
N G:ASN139 3.6 21.6 1.0
CB G:SER138 3.6 21.8 1.0
OH G:TYR61 3.7 41.6 1.0
CD2 G:PHE23 3.7 24.0 1.0
N G:THR22 3.7 21.8 1.0
CG G:ASP21 3.8 26.6 1.0
CA G:SER138 3.8 21.7 1.0
N G:PHE23 3.9 20.7 1.0
C G:SER138 4.2 22.1 1.0
CB G:PHE23 4.3 20.4 1.0
NZ G:LYS169 4.4 26.2 1.0
CG G:PHE23 4.4 22.4 1.0
OD2 G:ASP21 4.4 28.8 1.0
CE G:LYS169 4.5 28.5 1.0
CA G:THR22 4.5 21.1 1.0
CA G:ASP21 4.6 22.3 1.0
CA G:ASN139 4.6 21.9 1.0
CE2 G:PHE23 4.6 23.0 1.0
CB G:ASN139 4.6 21.7 1.0
CA G:PHE23 4.6 20.6 1.0
C G:ASP21 4.6 21.8 1.0
C G:THR22 4.7 20.9 1.0
CB G:THR22 4.7 21.3 1.0
O G:PHE23 4.7 20.6 1.0
ND2 G:ASN139 4.8 26.1 1.0
CB G:ASP21 4.8 23.3 1.0
N G:GLY140 4.8 21.5 1.0
CZ G:TYR61 5.0 39.1 1.0
O G:LEU137 5.0 20.4 1.0

Chlorine binding site 7 out of 7 in 3umg

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Chlorine binding site 7 out of 7 in the Crystal Structure of the Defluorinating L-2-Haloacid Dehalogenase RHA0230


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Crystal Structure of the Defluorinating L-2-Haloacid Dehalogenase RHA0230 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Cl255

b:54.9
occ:1.00
OD1 H:ASP21 2.8 41.0 1.0
OG H:SER138 3.1 29.4 1.0
OH H:TYR61 3.3 54.5 1.0
N H:ASN139 3.5 29.1 1.0
CA H:SER138 3.7 28.6 1.0
NZ H:LYS169 3.7 34.5 1.0
CD2 H:PHE23 3.7 35.1 1.0
CB H:SER138 3.8 28.3 1.0
CG H:ASP21 4.0 38.9 1.0
N H:THR22 4.0 33.9 1.0
N H:PHE23 4.0 34.8 1.0
C H:SER138 4.1 28.9 1.0
CB H:PHE23 4.2 34.7 1.0
CE H:LYS169 4.3 34.6 1.0
CG H:PHE23 4.4 34.6 1.0
ND2 H:ASN139 4.4 35.0 1.0
CB H:ASN139 4.5 28.3 1.0
CA H:ASP21 4.5 34.4 1.0
CA H:ASN139 4.5 29.0 1.0
CZ H:TYR61 4.6 52.2 1.0
CE2 H:PHE23 4.6 34.2 1.0
C H:ASP21 4.7 34.0 1.0
CA H:PHE23 4.7 34.8 1.0
CG H:ASN139 4.7 29.8 1.0
CB H:ASP21 4.7 35.5 1.0
O H:LEU137 4.7 29.8 1.0
OD2 H:ASP21 4.8 41.9 1.0
O H:PHE23 4.9 34.1 1.0
N H:GLY140 4.9 28.1 1.0
CA H:THR22 4.9 33.1 1.0
N H:SER138 4.9 28.6 1.0
C H:THR22 5.0 34.6 1.0

Reference:

P.W.Y.Chan, T.K.W.To, P.Petit, C.Tran, M.Waelti, A.Savchenko, A.F.Yakunin, E.A.Edwards, E.F.Pai. Structural Adaptations of L-2-Haloacid Dehalogenases That Enable Hydrolytic Defluorination To Be Published.
Page generated: Fri Jul 11 11:19:01 2025

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