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
Go back to
Chlorine Binding Sites List in 3umg
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
Go back to
Chlorine Binding Sites List in 3umg
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
Go back to
Chlorine Binding Sites List in 3umg
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 Sites List in 3umg
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
Go back to
Chlorine Binding Sites List in 3umg
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
Go back to
Chlorine Binding Sites List in 3umg
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
Go back to
Chlorine Binding Sites List in 3umg
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: Sun Jul 21 06:14:16 2024
|