Chlorine in PDB 4ma9: Wild Type Salmonella Alkyl Hydroperoxide Reductase C in Its Substrate- Ready Conformation
Enzymatic activity of Wild Type Salmonella Alkyl Hydroperoxide Reductase C in Its Substrate- Ready Conformation
All present enzymatic activity of Wild Type Salmonella Alkyl Hydroperoxide Reductase C in Its Substrate- Ready Conformation:
1.11.1.15;
Protein crystallography data
The structure of Wild Type Salmonella Alkyl Hydroperoxide Reductase C in Its Substrate- Ready Conformation, PDB code: 4ma9
was solved by
A.Perkins,
P.A.Karplus,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
36.76 /
1.82
|
Space group
|
C 2 2 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
126.840,
171.150,
135.320,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
20.4 /
24
|
Other elements in 4ma9:
The structure of Wild Type Salmonella Alkyl Hydroperoxide Reductase C in Its Substrate- Ready Conformation also contains other interesting chemical elements:
Chlorine Binding Sites:
The binding sites of Chlorine atom in the Wild Type Salmonella Alkyl Hydroperoxide Reductase C in Its Substrate- Ready Conformation
(pdb code 4ma9). This binding sites where shown within
5.0 Angstroms radius around Chlorine atom.
In total 5 binding sites of Chlorine where determined in the
Wild Type Salmonella Alkyl Hydroperoxide Reductase C in Its Substrate- Ready Conformation, PDB code: 4ma9:
Jump to Chlorine binding site number:
1;
2;
3;
4;
5;
Chlorine binding site 1 out
of 5 in 4ma9
Go back to
Chlorine Binding Sites List in 4ma9
Chlorine binding site 1 out
of 5 in the Wild Type Salmonella Alkyl Hydroperoxide Reductase C in Its Substrate- Ready Conformation
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 1 of Wild Type Salmonella Alkyl Hydroperoxide Reductase C in Its Substrate- Ready Conformation within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl201
b:37.4
occ:1.00
|
H
|
A:LEU2
|
2.3
|
26.7
|
1.0
|
HB2
|
A:SER1
|
2.8
|
29.3
|
1.0
|
O
|
A:HOH1089
|
2.9
|
37.4
|
1.0
|
O
|
A:HOH1011
|
2.9
|
30.1
|
1.0
|
O
|
A:HOH1006
|
2.9
|
28.2
|
1.0
|
HD13
|
A:ILE133
|
3.0
|
22.2
|
1.0
|
HA
|
A:SER1
|
3.0
|
26.6
|
1.0
|
HE2
|
A:PHE122
|
3.2
|
24.3
|
1.0
|
N
|
A:LEU2
|
3.3
|
27.0
|
1.0
|
HG21
|
A:ILE133
|
3.3
|
26.6
|
1.0
|
HG
|
A:LEU2
|
3.3
|
29.9
|
1.0
|
HD12
|
A:LEU2
|
3.3
|
30.7
|
1.0
|
HB2
|
A:LEU2
|
3.3
|
26.6
|
1.0
|
HD11
|
A:ILE133
|
3.6
|
23.4
|
1.0
|
CA
|
A:SER1
|
3.7
|
26.1
|
1.0
|
CB
|
A:SER1
|
3.7
|
30.8
|
1.0
|
H1
|
B:SER1
|
3.7
|
82.3
|
1.0
|
CD1
|
A:ILE133
|
3.8
|
24.5
|
1.0
|
HB3
|
B:SER1
|
3.8
|
29.6
|
1.0
|
C
|
A:SER1
|
3.9
|
30.4
|
1.0
|
HA
|
B:SER1
|
4.0
|
26.9
|
1.0
|
CB
|
A:LEU2
|
4.0
|
26.5
|
1.0
|
CG
|
A:LEU2
|
4.0
|
30.6
|
1.0
|
HZ
|
A:PHE122
|
4.0
|
25.9
|
1.0
|
CD1
|
A:LEU2
|
4.2
|
31.6
|
1.0
|
CE2
|
A:PHE122
|
4.2
|
27.4
|
1.0
|
CA
|
A:LEU2
|
4.2
|
26.5
|
1.0
|
HB2
|
A:ASP108
|
4.2
|
29.1
|
0.4
|
HB3
|
A:SER1
|
4.3
|
30.6
|
1.0
|
CG2
|
A:ILE133
|
4.4
|
26.7
|
1.0
|
HB3
|
A:ASP108
|
4.4
|
30.2
|
0.6
|
HD12
|
A:ILE133
|
4.5
|
24.6
|
1.0
|
CB
|
B:SER1
|
4.5
|
28.6
|
1.0
|
O
|
B:HOH1096
|
4.5
|
39.5
|
1.0
|
HB2
|
B:SER1
|
4.5
|
27.6
|
1.0
|
CZ
|
A:PHE122
|
4.6
|
25.1
|
1.0
|
CA
|
B:SER1
|
4.6
|
27.5
|
1.0
|
HG22
|
A:ILE133
|
4.7
|
26.1
|
1.0
|
OG
|
A:SER1
|
4.7
|
29.5
|
1.0
|
HD13
|
A:LEU2
|
4.7
|
31.6
|
1.0
|
HG12
|
A:ILE133
|
4.7
|
26.0
|
1.0
|
CL
|
B:CL201
|
4.7
|
41.8
|
1.0
|
CG1
|
A:ILE133
|
4.8
|
24.7
|
1.0
|
N
|
B:SER1
|
4.8
|
26.6
|
1.0
|
O
|
A:PHE107
|
4.8
|
28.0
|
1.0
|
HD11
|
A:LEU2
|
5.0
|
31.5
|
1.0
|
H
|
A:ILE3
|
5.0
|
20.0
|
1.0
|
HB3
|
A:LEU2
|
5.0
|
27.6
|
1.0
|
|
Chlorine binding site 2 out
of 5 in 4ma9
Go back to
Chlorine Binding Sites List in 4ma9
Chlorine binding site 2 out
of 5 in the Wild Type Salmonella Alkyl Hydroperoxide Reductase C in Its Substrate- Ready Conformation
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 2 of Wild Type Salmonella Alkyl Hydroperoxide Reductase C in Its Substrate- Ready Conformation within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Cl201
b:41.8
occ:1.00
|
H
|
B:LEU2
|
2.2
|
27.2
|
1.0
|
HB2
|
B:SER1
|
2.7
|
27.6
|
1.0
|
O
|
B:HOH1073
|
2.9
|
36.5
|
1.0
|
HA
|
B:SER1
|
2.9
|
26.9
|
1.0
|
O
|
A:HOH1011
|
2.9
|
30.1
|
1.0
|
HD13
|
B:ILE133
|
2.9
|
32.1
|
1.0
|
HE2
|
B:PHE122
|
3.0
|
26.5
|
1.0
|
O
|
B:HOH1096
|
3.0
|
39.5
|
1.0
|
N
|
B:LEU2
|
3.1
|
27.6
|
1.0
|
HG
|
B:LEU2
|
3.2
|
27.9
|
1.0
|
HB2
|
B:LEU2
|
3.3
|
26.0
|
1.0
|
HG21
|
B:ILE133
|
3.4
|
31.7
|
1.0
|
CB
|
B:SER1
|
3.6
|
28.6
|
1.0
|
CA
|
B:SER1
|
3.6
|
27.5
|
1.0
|
HD12
|
B:LEU2
|
3.6
|
30.6
|
1.0
|
H1
|
A:SER1
|
3.8
|
16.6
|
1.0
|
C
|
B:SER1
|
3.8
|
29.2
|
1.0
|
CD1
|
B:ILE133
|
3.9
|
32.6
|
1.0
|
CG
|
B:LEU2
|
3.9
|
29.6
|
1.0
|
HD12
|
B:ILE133
|
3.9
|
30.6
|
1.0
|
CB
|
B:LEU2
|
3.9
|
25.4
|
1.0
|
HZ
|
B:PHE122
|
3.9
|
22.4
|
1.0
|
CE2
|
B:PHE122
|
4.0
|
26.8
|
1.0
|
HB3
|
A:SER1
|
4.0
|
30.6
|
1.0
|
HA
|
A:SER1
|
4.0
|
26.6
|
1.0
|
HB3
|
B:SER1
|
4.1
|
29.6
|
1.0
|
CA
|
B:LEU2
|
4.1
|
26.1
|
1.0
|
CD1
|
B:LEU2
|
4.3
|
30.9
|
1.0
|
HB2
|
B:ASP108
|
4.4
|
29.9
|
0.4
|
HD11
|
B:ILE133
|
4.4
|
33.1
|
1.0
|
CZ
|
B:PHE122
|
4.4
|
25.4
|
1.0
|
HB2
|
A:SER1
|
4.4
|
29.3
|
1.0
|
CG2
|
B:ILE133
|
4.4
|
30.3
|
1.0
|
CB
|
A:SER1
|
4.6
|
30.8
|
1.0
|
HB3
|
B:ASP108
|
4.6
|
25.8
|
0.6
|
CA
|
A:SER1
|
4.7
|
26.1
|
1.0
|
OG
|
B:SER1
|
4.7
|
29.8
|
1.0
|
O
|
A:HOH1006
|
4.7
|
28.2
|
1.0
|
HD11
|
B:LEU2
|
4.7
|
31.1
|
1.0
|
CL
|
A:CL201
|
4.7
|
37.4
|
1.0
|
H
|
B:ILE3
|
4.8
|
26.4
|
1.0
|
O
|
B:PHE107
|
4.8
|
30.8
|
1.0
|
N
|
A:SER1
|
4.8
|
23.9
|
1.0
|
HG23
|
B:ILE133
|
4.9
|
30.4
|
1.0
|
HA
|
B:LEU2
|
4.9
|
27.3
|
1.0
|
HB3
|
B:LEU2
|
4.9
|
26.7
|
1.0
|
HG22
|
B:ILE133
|
4.9
|
30.4
|
1.0
|
N
|
B:SER1
|
4.9
|
26.6
|
1.0
|
CG1
|
B:ILE133
|
5.0
|
30.1
|
1.0
|
|
Chlorine binding site 3 out
of 5 in 4ma9
Go back to
Chlorine Binding Sites List in 4ma9
Chlorine binding site 3 out
of 5 in the Wild Type Salmonella Alkyl Hydroperoxide Reductase C in Its Substrate- Ready Conformation
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 3 of Wild Type Salmonella Alkyl Hydroperoxide Reductase C in Its Substrate- Ready Conformation within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Cl201
b:43.8
occ:1.00
|
H
|
C:LEU2
|
2.3
|
33.7
|
1.0
|
HB2
|
C:SER1
|
2.8
|
35.7
|
1.0
|
HD13
|
C:ILE133
|
2.8
|
34.8
|
1.0
|
HA
|
C:SER1
|
2.9
|
34.1
|
1.0
|
O
|
C:HOH1030
|
2.9
|
35.5
|
1.0
|
O
|
D:HOH1053
|
2.9
|
39.3
|
1.0
|
O
|
C:HOH1052
|
3.0
|
36.1
|
1.0
|
HE2
|
C:PHE122
|
3.2
|
35.5
|
1.0
|
HB2
|
C:LEU2
|
3.2
|
29.6
|
1.0
|
N
|
C:LEU2
|
3.2
|
32.5
|
1.0
|
HG
|
C:LEU2
|
3.3
|
33.2
|
1.0
|
HG21
|
C:ILE133
|
3.3
|
31.4
|
1.0
|
HD12
|
C:LEU2
|
3.4
|
35.5
|
1.0
|
CA
|
C:SER1
|
3.6
|
34.7
|
1.0
|
CB
|
C:SER1
|
3.6
|
35.4
|
1.0
|
CD1
|
C:ILE133
|
3.7
|
35.1
|
1.0
|
HD12
|
C:ILE133
|
3.7
|
35.4
|
1.0
|
HB3
|
D:SER1
|
3.8
|
36.3
|
1.0
|
CB
|
C:LEU2
|
3.9
|
31.0
|
1.0
|
C
|
C:SER1
|
3.9
|
37.5
|
1.0
|
HA
|
D:SER1
|
3.9
|
35.0
|
1.0
|
CG
|
C:LEU2
|
3.9
|
33.3
|
1.0
|
H1
|
D:SER1
|
4.1
|
10.8
|
1.0
|
CD1
|
C:LEU2
|
4.2
|
34.1
|
1.0
|
HB3
|
C:SER1
|
4.2
|
37.5
|
1.0
|
CA
|
C:LEU2
|
4.2
|
32.0
|
1.0
|
CE2
|
C:PHE122
|
4.2
|
34.9
|
1.0
|
HD11
|
C:ILE133
|
4.3
|
34.8
|
1.0
|
CG2
|
C:ILE133
|
4.4
|
31.4
|
1.0
|
HZ
|
C:PHE122
|
4.4
|
29.6
|
1.0
|
HB2
|
D:SER1
|
4.4
|
37.3
|
1.0
|
CB
|
D:SER1
|
4.4
|
36.8
|
1.0
|
CA
|
D:SER1
|
4.5
|
34.8
|
1.0
|
HB3
|
C:ASP108
|
4.5
|
37.4
|
1.0
|
HG22
|
C:ILE133
|
4.6
|
31.7
|
1.0
|
O
|
D:HOH1042
|
4.7
|
36.6
|
1.0
|
OG
|
C:SER1
|
4.7
|
43.0
|
1.0
|
N
|
D:SER1
|
4.7
|
35.6
|
1.0
|
O
|
C:PHE107
|
4.8
|
35.8
|
1.0
|
CZ
|
C:PHE122
|
4.8
|
31.5
|
1.0
|
HD11
|
C:LEU2
|
4.8
|
33.1
|
1.0
|
CG1
|
C:ILE133
|
4.8
|
32.9
|
1.0
|
CL
|
D:CL201
|
4.8
|
46.4
|
1.0
|
H
|
C:ILE3
|
4.8
|
33.9
|
1.0
|
HG12
|
C:ILE133
|
4.9
|
32.8
|
1.0
|
HB3
|
C:LEU2
|
4.9
|
30.3
|
1.0
|
N
|
C:SER1
|
4.9
|
37.0
|
1.0
|
HD13
|
C:LEU2
|
4.9
|
33.5
|
1.0
|
HA
|
C:LEU2
|
5.0
|
31.5
|
1.0
|
HG23
|
C:ILE133
|
5.0
|
30.1
|
1.0
|
|
Chlorine binding site 4 out
of 5 in 4ma9
Go back to
Chlorine Binding Sites List in 4ma9
Chlorine binding site 4 out
of 5 in the Wild Type Salmonella Alkyl Hydroperoxide Reductase C in Its Substrate- Ready Conformation
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 4 of Wild Type Salmonella Alkyl Hydroperoxide Reductase C in Its Substrate- Ready Conformation within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Cl201
b:46.4
occ:1.00
|
H
|
D:LEU2
|
2.1
|
32.8
|
1.0
|
HB2
|
D:SER1
|
2.7
|
37.3
|
1.0
|
HD13
|
D:ILE133
|
2.9
|
34.5
|
1.0
|
O
|
D:HOH1053
|
2.9
|
39.3
|
1.0
|
O
|
D:HOH1054
|
2.9
|
36.2
|
1.0
|
HA
|
D:SER1
|
3.0
|
35.0
|
1.0
|
HE2
|
D:PHE122
|
3.0
|
36.8
|
1.0
|
HB2
|
D:LEU2
|
3.1
|
30.9
|
1.0
|
N
|
D:LEU2
|
3.1
|
32.7
|
1.0
|
HG
|
D:LEU2
|
3.1
|
32.6
|
1.0
|
O
|
D:HOH1042
|
3.1
|
36.6
|
1.0
|
HG21
|
D:ILE133
|
3.2
|
32.1
|
1.0
|
HD12
|
D:LEU2
|
3.3
|
33.5
|
1.0
|
H1
|
C:SER1
|
3.3
|
21.8
|
1.0
|
CB
|
D:SER1
|
3.6
|
36.8
|
1.0
|
CA
|
D:SER1
|
3.6
|
34.8
|
1.0
|
HD12
|
D:ILE133
|
3.7
|
33.9
|
1.0
|
CB
|
D:LEU2
|
3.7
|
31.7
|
1.0
|
CD1
|
D:ILE133
|
3.7
|
34.8
|
1.0
|
CG
|
D:LEU2
|
3.8
|
33.3
|
1.0
|
C
|
D:SER1
|
3.8
|
37.1
|
1.0
|
HA
|
C:SER1
|
4.0
|
34.1
|
1.0
|
CA
|
D:LEU2
|
4.0
|
31.6
|
1.0
|
HB3
|
C:SER1
|
4.0
|
37.5
|
1.0
|
CE2
|
D:PHE122
|
4.0
|
36.2
|
1.0
|
CD1
|
D:LEU2
|
4.0
|
33.4
|
1.0
|
HZ
|
D:PHE122
|
4.1
|
32.2
|
1.0
|
HB3
|
D:SER1
|
4.2
|
36.3
|
1.0
|
CG2
|
D:ILE133
|
4.2
|
31.9
|
1.0
|
HD11
|
D:ILE133
|
4.3
|
34.4
|
1.0
|
HB2
|
D:ASP108
|
4.3
|
37.9
|
0.6
|
HG23
|
D:ILE133
|
4.5
|
32.3
|
1.0
|
CZ
|
D:PHE122
|
4.5
|
33.7
|
1.0
|
OG
|
D:SER1
|
4.6
|
36.8
|
1.0
|
HD11
|
D:LEU2
|
4.6
|
34.0
|
1.0
|
HB3
|
D:ASP108
|
4.6
|
32.0
|
0.4
|
CA
|
C:SER1
|
4.7
|
34.7
|
1.0
|
CB
|
C:SER1
|
4.7
|
35.4
|
1.0
|
HB2
|
C:SER1
|
4.7
|
35.7
|
1.0
|
HB3
|
D:LEU2
|
4.7
|
32.4
|
1.0
|
N
|
C:SER1
|
4.7
|
37.0
|
1.0
|
H
|
D:ILE3
|
4.7
|
29.4
|
1.0
|
O
|
D:PHE107
|
4.8
|
32.7
|
1.0
|
O
|
C:HOH1052
|
4.8
|
36.1
|
1.0
|
CL
|
C:CL201
|
4.8
|
43.8
|
1.0
|
HD13
|
D:LEU2
|
4.8
|
33.5
|
1.0
|
HA
|
D:LEU2
|
4.8
|
33.5
|
1.0
|
CG1
|
D:ILE133
|
4.8
|
33.8
|
1.0
|
HG22
|
D:ILE133
|
4.8
|
32.2
|
1.0
|
C
|
D:LEU2
|
5.0
|
34.2
|
1.0
|
N
|
D:SER1
|
5.0
|
35.6
|
1.0
|
HG12
|
D:ILE133
|
5.0
|
33.8
|
1.0
|
|
Chlorine binding site 5 out
of 5 in 4ma9
Go back to
Chlorine Binding Sites List in 4ma9
Chlorine binding site 5 out
of 5 in the Wild Type Salmonella Alkyl Hydroperoxide Reductase C in Its Substrate- Ready Conformation
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 5 of Wild Type Salmonella Alkyl Hydroperoxide Reductase C in Its Substrate- Ready Conformation within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Cl201
b:60.6
occ:1.00
|
H
|
E:LEU2
|
2.2
|
48.9
|
1.0
|
HA
|
E:SER1
|
2.9
|
45.6
|
1.0
|
HD13
|
E:ILE133
|
2.9
|
48.4
|
1.0
|
O
|
E:HOH1465
|
2.9
|
38.8
|
0.4
|
HB2
|
E:SER1
|
3.0
|
50.0
|
1.0
|
HE2
|
E:PHE122
|
3.1
|
47.7
|
1.0
|
N
|
E:LEU2
|
3.1
|
48.1
|
1.0
|
HG
|
E:LEU2
|
3.1
|
50.4
|
1.0
|
HD12
|
E:LEU2
|
3.2
|
51.4
|
1.0
|
HB2
|
E:LEU2
|
3.2
|
46.1
|
1.0
|
O
|
E:HOH1390
|
3.2
|
60.8
|
1.0
|
HG21
|
E:ILE133
|
3.2
|
46.7
|
1.0
|
HD12
|
E:ILE133
|
3.5
|
48.9
|
1.0
|
CA
|
E:SER1
|
3.6
|
45.9
|
1.0
|
CD1
|
E:ILE133
|
3.7
|
49.0
|
1.0
|
CB
|
E:SER1
|
3.7
|
49.6
|
1.0
|
CG
|
E:LEU2
|
3.8
|
50.0
|
1.0
|
CB
|
E:LEU2
|
3.8
|
46.6
|
1.0
|
C
|
E:SER1
|
3.8
|
51.7
|
1.0
|
CD1
|
E:LEU2
|
4.0
|
51.1
|
1.0
|
CE2
|
E:PHE122
|
4.1
|
48.5
|
1.0
|
CA
|
E:LEU2
|
4.1
|
47.5
|
1.0
|
HZ
|
E:PHE122
|
4.1
|
45.1
|
1.0
|
HD11
|
E:ILE133
|
4.2
|
49.1
|
1.0
|
CG2
|
E:ILE133
|
4.3
|
47.1
|
1.0
|
HG23
|
E:ILE133
|
4.5
|
47.4
|
1.0
|
HB3
|
E:ASP108
|
4.5
|
48.2
|
1.0
|
OG
|
E:SER1
|
4.5
|
50.6
|
1.0
|
HG
|
E:SER1
|
4.5
|
51.4
|
1.0
|
CZ
|
E:PHE122
|
4.6
|
45.6
|
1.0
|
HB3
|
E:SER1
|
4.6
|
49.5
|
1.0
|
HD11
|
E:LEU2
|
4.6
|
49.9
|
1.0
|
HD13
|
E:LEU2
|
4.7
|
51.2
|
1.0
|
O
|
E:PHE107
|
4.7
|
45.6
|
1.0
|
CG1
|
E:ILE133
|
4.8
|
47.5
|
1.0
|
HB3
|
E:LEU2
|
4.8
|
48.3
|
1.0
|
HA
|
E:LEU2
|
4.9
|
46.4
|
1.0
|
HG22
|
E:ILE133
|
4.9
|
46.7
|
1.0
|
H
|
E:ILE3
|
4.9
|
52.0
|
1.0
|
N
|
E:SER1
|
4.9
|
45.3
|
1.0
|
|
Reference:
A.Perkins,
K.J.Nelson,
J.R.Williams,
D.Parsonage,
L.B.Poole,
P.A.Karplus.
The Sensitive Balance Between the Fully Folded and Locally Unfolded Conformations of A Model Peroxiredoxin. Biochemistry V. 52 8708 2013.
ISSN: ISSN 0006-2960
PubMed: 24175952
DOI: 10.1021/BI4011573
Page generated: Sun Jul 21 19:38:42 2024
|