Chlorine in PDB 6ebc: Ohrb (Organic Hydroperoxide Resistance Protein) Wild Type From Chromobacterium Violaceum and Reduced By Dtt
Protein crystallography data
The structure of Ohrb (Organic Hydroperoxide Resistance Protein) Wild Type From Chromobacterium Violaceum and Reduced By Dtt, PDB code: 6ebc
was solved by
R.M.Domingos,
R.D.Teixeira,
T.G.P.Alegria,
P.S.Vieira,
M.T.Murakami,
L.E.S.Netto,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
35.00 /
1.87
|
Space group
|
P 61
|
Cell size a, b, c (Å), α, β, γ (°)
|
88.160,
88.160,
169.916,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
19.3 /
21.4
|
Chlorine Binding Sites:
The binding sites of Chlorine atom in the Ohrb (Organic Hydroperoxide Resistance Protein) Wild Type From Chromobacterium Violaceum and Reduced By Dtt
(pdb code 6ebc). This binding sites where shown within
5.0 Angstroms radius around Chlorine atom.
In total 7 binding sites of Chlorine where determined in the
Ohrb (Organic Hydroperoxide Resistance Protein) Wild Type From Chromobacterium Violaceum and Reduced By Dtt, PDB code: 6ebc:
Jump to Chlorine binding site number:
1;
2;
3;
4;
5;
6;
7;
Chlorine binding site 1 out
of 7 in 6ebc
Go back to
Chlorine Binding Sites List in 6ebc
Chlorine binding site 1 out
of 7 in the Ohrb (Organic Hydroperoxide Resistance Protein) Wild Type From Chromobacterium Violaceum and Reduced By Dtt
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 1 of Ohrb (Organic Hydroperoxide Resistance Protein) Wild Type From Chromobacterium Violaceum and Reduced By Dtt within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl201
b:39.8
occ:1.00
|
N
|
A:SER77
|
3.1
|
38.9
|
1.0
|
C
|
A:LEU105
|
3.3
|
42.4
|
1.0
|
N
|
A:GLY107
|
3.4
|
45.5
|
1.0
|
CB
|
A:SER77
|
3.4
|
38.6
|
1.0
|
CA
|
A:LEU105
|
3.4
|
40.7
|
1.0
|
OG
|
A:SER77
|
3.6
|
41.6
|
1.0
|
N
|
A:PRO106
|
3.6
|
43.4
|
1.0
|
CD
|
A:PRO106
|
3.7
|
41.1
|
1.0
|
CA
|
A:SER77
|
3.8
|
38.8
|
1.0
|
CB
|
A:LEU105
|
3.9
|
41.3
|
1.0
|
O
|
A:LEU105
|
3.9
|
43.8
|
1.0
|
CA
|
A:GLY107
|
4.0
|
47.6
|
1.0
|
C
|
A:LEU76
|
4.0
|
41.1
|
1.0
|
CA
|
A:LEU76
|
4.0
|
42.4
|
1.0
|
CG
|
A:LEU108
|
4.1
|
48.4
|
1.0
|
CB
|
A:ALA80
|
4.3
|
32.5
|
1.0
|
CD2
|
A:LEU105
|
4.3
|
39.3
|
1.0
|
N
|
A:LEU108
|
4.3
|
48.1
|
1.0
|
CB
|
A:LEU76
|
4.4
|
41.4
|
1.0
|
C
|
A:PRO106
|
4.4
|
47.6
|
1.0
|
C
|
A:GLY107
|
4.5
|
49.4
|
1.0
|
CD2
|
A:LEU76
|
4.5
|
45.5
|
1.0
|
CD1
|
A:LEU108
|
4.5
|
47.8
|
1.0
|
CG
|
A:PRO106
|
4.6
|
43.6
|
1.0
|
CA
|
A:PRO106
|
4.6
|
45.3
|
1.0
|
O
|
A:SER77
|
4.7
|
33.3
|
1.0
|
CG
|
A:LEU105
|
4.7
|
39.7
|
1.0
|
C
|
A:SER77
|
4.8
|
35.3
|
1.0
|
N
|
A:LEU105
|
4.8
|
38.1
|
1.0
|
CA
|
A:ALA80
|
4.9
|
33.1
|
1.0
|
CD2
|
A:LEU108
|
4.9
|
52.2
|
1.0
|
CB
|
A:LEU108
|
4.9
|
49.5
|
1.0
|
|
Chlorine binding site 2 out
of 7 in 6ebc
Go back to
Chlorine Binding Sites List in 6ebc
Chlorine binding site 2 out
of 7 in the Ohrb (Organic Hydroperoxide Resistance Protein) Wild Type From Chromobacterium Violaceum and Reduced By Dtt
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 2 of Ohrb (Organic Hydroperoxide Resistance Protein) Wild Type From Chromobacterium Violaceum and Reduced By Dtt within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl202
b:43.2
occ:1.00
|
OG
|
A:SER25
|
2.6
|
39.4
|
1.0
|
OG1
|
A:THR10
|
2.8
|
33.5
|
1.0
|
N
|
A:ASP26
|
3.3
|
31.1
|
1.0
|
O
|
A:HOH303
|
3.4
|
33.6
|
1.0
|
N
|
A:GLN11
|
3.5
|
32.5
|
1.0
|
N
|
A:SER25
|
3.6
|
30.8
|
1.0
|
CG
|
A:ASP26
|
3.6
|
31.1
|
1.0
|
CB
|
A:ASP26
|
3.7
|
32.0
|
1.0
|
O
|
A:GLN11
|
3.7
|
30.2
|
1.0
|
CB
|
A:THR10
|
3.7
|
32.4
|
1.0
|
CA
|
A:THR10
|
3.8
|
34.1
|
1.0
|
NE2
|
C:GLN51
|
3.8
|
27.1
|
1.0
|
CB
|
A:SER25
|
3.9
|
36.0
|
1.0
|
OD2
|
A:ASP26
|
3.9
|
31.3
|
1.0
|
OD1
|
A:ASP26
|
3.9
|
29.0
|
1.0
|
C
|
A:SER25
|
4.0
|
32.2
|
1.0
|
CA
|
A:SER25
|
4.0
|
33.5
|
1.0
|
CA
|
A:ASP26
|
4.1
|
32.4
|
1.0
|
C
|
A:THR10
|
4.2
|
33.2
|
1.0
|
CB
|
A:SER24
|
4.4
|
26.8
|
1.0
|
C
|
A:SER24
|
4.5
|
29.4
|
1.0
|
CA
|
A:GLN11
|
4.6
|
33.6
|
1.0
|
C
|
A:GLN11
|
4.6
|
31.1
|
1.0
|
CA
|
A:SER24
|
4.8
|
28.2
|
1.0
|
CD
|
C:GLN51
|
4.9
|
28.2
|
1.0
|
OG
|
A:SER24
|
4.9
|
26.2
|
1.0
|
CB
|
A:GLN11
|
4.9
|
36.0
|
1.0
|
O
|
A:ARG9
|
5.0
|
38.2
|
1.0
|
O
|
A:SER25
|
5.0
|
32.2
|
1.0
|
|
Chlorine binding site 3 out
of 7 in 6ebc
Go back to
Chlorine Binding Sites List in 6ebc
Chlorine binding site 3 out
of 7 in the Ohrb (Organic Hydroperoxide Resistance Protein) Wild Type From Chromobacterium Violaceum and Reduced By Dtt
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 3 of Ohrb (Organic Hydroperoxide Resistance Protein) Wild Type From Chromobacterium Violaceum and Reduced By Dtt within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Cl202
b:51.9
occ:1.00
|
N
|
B:SER77
|
3.1
|
64.2
|
1.0
|
N
|
B:GLY107
|
3.2
|
53.9
|
1.0
|
CA
|
B:LEU105
|
3.4
|
45.6
|
1.0
|
C
|
B:LEU105
|
3.4
|
47.4
|
1.0
|
CB
|
B:SER77
|
3.6
|
63.5
|
1.0
|
N
|
B:PRO106
|
3.6
|
49.1
|
1.0
|
CA
|
B:GLY107
|
3.7
|
56.2
|
1.0
|
CB
|
B:LEU105
|
3.8
|
46.2
|
1.0
|
CD
|
B:PRO106
|
3.8
|
48.1
|
1.0
|
CA
|
B:LEU76
|
3.8
|
66.0
|
1.0
|
O
|
B:LEU105
|
3.9
|
49.5
|
1.0
|
CA
|
B:SER77
|
3.9
|
62.9
|
1.0
|
C
|
B:LEU76
|
3.9
|
67.6
|
1.0
|
CD2
|
B:LEU105
|
3.9
|
44.0
|
1.0
|
CG
|
B:LEU108
|
4.0
|
48.2
|
1.0
|
N
|
B:LEU108
|
4.1
|
55.1
|
1.0
|
CD2
|
B:LEU76
|
4.2
|
62.7
|
1.0
|
CB
|
B:LEU76
|
4.2
|
62.9
|
1.0
|
C
|
B:GLY107
|
4.2
|
56.5
|
1.0
|
C
|
B:PRO106
|
4.3
|
54.6
|
1.0
|
CB
|
B:ALA80
|
4.4
|
45.9
|
1.0
|
CG
|
B:LEU105
|
4.5
|
44.1
|
1.0
|
CA
|
B:PRO106
|
4.6
|
52.6
|
1.0
|
OG
|
B:SER77
|
4.6
|
63.4
|
1.0
|
CD1
|
B:LEU108
|
4.6
|
46.0
|
1.0
|
CG
|
B:PRO106
|
4.6
|
50.0
|
1.0
|
O
|
B:SER77
|
4.7
|
55.4
|
1.0
|
N
|
B:LEU105
|
4.8
|
44.3
|
1.0
|
CB
|
B:LEU108
|
4.8
|
50.1
|
1.0
|
CD2
|
B:LEU108
|
4.8
|
51.2
|
1.0
|
C
|
B:SER77
|
4.8
|
59.0
|
1.0
|
CG
|
B:LEU76
|
4.8
|
62.5
|
1.0
|
CA
|
B:ALA80
|
4.9
|
47.0
|
1.0
|
O
|
B:THR75
|
4.9
|
76.2
|
1.0
|
|
Chlorine binding site 4 out
of 7 in 6ebc
Go back to
Chlorine Binding Sites List in 6ebc
Chlorine binding site 4 out
of 7 in the Ohrb (Organic Hydroperoxide Resistance Protein) Wild Type From Chromobacterium Violaceum and Reduced By Dtt
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 4 of Ohrb (Organic Hydroperoxide Resistance Protein) Wild Type From Chromobacterium Violaceum and Reduced By Dtt within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Cl203
b:55.1
occ:1.00
|
NE2
|
B:GLN11
|
2.8
|
53.7
|
1.0
|
OG1
|
B:THR13
|
2.9
|
40.6
|
1.0
|
N
|
B:THR13
|
3.5
|
35.6
|
1.0
|
CG
|
B:GLN11
|
3.5
|
50.2
|
1.0
|
C
|
B:ALA12
|
3.6
|
36.6
|
1.0
|
CB
|
B:SER25
|
3.6
|
49.6
|
1.0
|
CD
|
B:GLN11
|
3.6
|
54.7
|
1.0
|
N
|
B:SER25
|
3.6
|
42.6
|
1.0
|
O
|
B:GLN11
|
3.7
|
39.2
|
1.0
|
CA
|
B:SER25
|
3.7
|
46.3
|
1.0
|
C
|
B:GLN11
|
3.7
|
39.5
|
1.0
|
CB
|
B:THR13
|
3.7
|
38.0
|
1.0
|
CA
|
B:ALA12
|
3.7
|
35.9
|
1.0
|
N
|
B:ALA12
|
3.8
|
36.8
|
1.0
|
O
|
B:GLU23
|
3.8
|
37.9
|
1.0
|
CB
|
B:GLN11
|
4.0
|
46.3
|
1.0
|
CA
|
B:THR13
|
4.2
|
36.4
|
1.0
|
O
|
B:ALA12
|
4.2
|
37.0
|
1.0
|
C
|
B:SER24
|
4.2
|
39.8
|
1.0
|
OG
|
B:SER25
|
4.4
|
54.5
|
1.0
|
CA
|
B:GLN11
|
4.5
|
41.5
|
1.0
|
OG
|
D:SER83
|
4.8
|
41.0
|
1.0
|
OE1
|
B:GLN11
|
4.8
|
59.9
|
1.0
|
O
|
B:SER24
|
4.8
|
39.9
|
1.0
|
CA
|
B:SER24
|
4.8
|
37.0
|
1.0
|
C
|
B:GLU23
|
4.9
|
36.3
|
1.0
|
|
Chlorine binding site 5 out
of 7 in 6ebc
Go back to
Chlorine Binding Sites List in 6ebc
Chlorine binding site 5 out
of 7 in the Ohrb (Organic Hydroperoxide Resistance Protein) Wild Type From Chromobacterium Violaceum and Reduced By Dtt
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 5 of Ohrb (Organic Hydroperoxide Resistance Protein) Wild Type From Chromobacterium Violaceum and Reduced By Dtt within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Cl202
b:45.7
occ:1.00
|
N
|
C:GLY107
|
3.1
|
49.7
|
1.0
|
N
|
C:SER77
|
3.1
|
51.2
|
1.0
|
C
|
C:LEU105
|
3.3
|
43.9
|
1.0
|
CA
|
C:LEU105
|
3.4
|
42.8
|
1.0
|
N
|
C:PRO106
|
3.5
|
45.0
|
1.0
|
CB
|
C:SER77
|
3.5
|
53.2
|
1.0
|
CA
|
C:GLY107
|
3.6
|
52.8
|
1.0
|
CD
|
C:PRO106
|
3.8
|
44.2
|
1.0
|
O
|
C:LEU105
|
3.8
|
45.0
|
1.0
|
CB
|
C:LEU105
|
3.8
|
42.9
|
1.0
|
CA
|
C:SER77
|
3.9
|
52.6
|
1.0
|
CA
|
C:LEU76
|
4.0
|
56.3
|
1.0
|
N
|
C:LEU108
|
4.0
|
50.7
|
1.0
|
C
|
C:LEU76
|
4.0
|
54.9
|
1.0
|
CD2
|
C:LEU105
|
4.1
|
41.6
|
1.0
|
C
|
C:GLY107
|
4.1
|
52.3
|
1.0
|
C
|
C:PRO106
|
4.2
|
50.1
|
1.0
|
CG
|
C:LEU108
|
4.2
|
49.0
|
1.0
|
CB
|
C:ALA80
|
4.3
|
41.8
|
1.0
|
CB
|
C:LEU76
|
4.3
|
52.6
|
1.0
|
OG
|
C:SER77
|
4.4
|
52.3
|
1.0
|
CA
|
C:PRO106
|
4.4
|
48.2
|
1.0
|
CD2
|
C:LEU76
|
4.4
|
54.9
|
1.0
|
CG
|
C:PRO106
|
4.6
|
46.8
|
1.0
|
CG
|
C:LEU105
|
4.6
|
40.6
|
1.0
|
O
|
C:SER77
|
4.7
|
46.3
|
1.0
|
N
|
C:LEU105
|
4.7
|
41.5
|
1.0
|
CA
|
C:ALA80
|
4.8
|
41.3
|
1.0
|
CD1
|
C:LEU108
|
4.8
|
47.0
|
1.0
|
C
|
C:SER77
|
4.8
|
49.8
|
1.0
|
CB
|
C:LEU108
|
4.8
|
49.2
|
1.0
|
CG
|
C:LEU76
|
5.0
|
52.7
|
1.0
|
CD2
|
C:LEU108
|
5.0
|
52.8
|
1.0
|
N
|
C:ALA80
|
5.0
|
42.0
|
1.0
|
|
Chlorine binding site 6 out
of 7 in 6ebc
Go back to
Chlorine Binding Sites List in 6ebc
Chlorine binding site 6 out
of 7 in the Ohrb (Organic Hydroperoxide Resistance Protein) Wild Type From Chromobacterium Violaceum and Reduced By Dtt
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 6 of Ohrb (Organic Hydroperoxide Resistance Protein) Wild Type From Chromobacterium Violaceum and Reduced By Dtt within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Cl203
b:45.0
occ:1.00
|
OG1
|
C:THR13
|
2.8
|
29.5
|
1.0
|
O
|
B:HOH338
|
2.9
|
52.8
|
1.0
|
NE2
|
C:GLN11
|
2.9
|
41.9
|
1.0
|
CG
|
C:GLN11
|
3.4
|
39.1
|
1.0
|
N
|
C:THR13
|
3.5
|
28.8
|
1.0
|
CD
|
C:GLN11
|
3.6
|
40.3
|
1.0
|
C
|
C:ALA12
|
3.6
|
28.2
|
1.0
|
CB
|
C:SER25
|
3.6
|
30.0
|
1.0
|
N
|
C:SER25
|
3.6
|
26.7
|
1.0
|
CA
|
C:SER25
|
3.6
|
29.0
|
1.0
|
CB
|
C:THR13
|
3.7
|
29.9
|
1.0
|
CA
|
C:ALA12
|
3.8
|
28.3
|
1.0
|
O
|
C:GLU23
|
3.8
|
27.9
|
1.0
|
O
|
C:GLN11
|
3.9
|
28.6
|
1.0
|
C
|
C:GLN11
|
3.9
|
29.7
|
1.0
|
N
|
C:ALA12
|
3.9
|
28.7
|
1.0
|
CB
|
C:GLN11
|
4.1
|
33.8
|
1.0
|
O
|
C:ALA12
|
4.2
|
28.5
|
1.0
|
CA
|
C:THR13
|
4.2
|
29.2
|
1.0
|
C
|
C:SER24
|
4.2
|
26.7
|
1.0
|
OG
|
C:SER25
|
4.5
|
29.3
|
1.0
|
CA
|
C:GLN11
|
4.6
|
31.0
|
1.0
|
OE1
|
C:GLN11
|
4.7
|
45.3
|
1.0
|
O
|
C:SER24
|
4.7
|
28.4
|
1.0
|
OG
|
A:SER83
|
4.8
|
33.8
|
1.0
|
CA
|
C:SER24
|
4.8
|
26.0
|
1.0
|
C
|
C:GLU23
|
4.9
|
27.6
|
1.0
|
|
Chlorine binding site 7 out
of 7 in 6ebc
Go back to
Chlorine Binding Sites List in 6ebc
Chlorine binding site 7 out
of 7 in the Ohrb (Organic Hydroperoxide Resistance Protein) Wild Type From Chromobacterium Violaceum and Reduced By Dtt
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 7 of Ohrb (Organic Hydroperoxide Resistance Protein) Wild Type From Chromobacterium Violaceum and Reduced By Dtt within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Cl202
b:41.6
occ:1.00
|
OG
|
D:SER25
|
2.7
|
41.4
|
1.0
|
OG1
|
D:THR10
|
2.8
|
33.0
|
1.0
|
N
|
D:ASP26
|
3.3
|
32.3
|
1.0
|
N
|
D:GLN11
|
3.4
|
35.4
|
1.0
|
N
|
D:SER25
|
3.6
|
31.8
|
1.0
|
CG
|
D:ASP26
|
3.7
|
30.6
|
1.0
|
O
|
D:GLN11
|
3.7
|
31.4
|
1.0
|
CA
|
D:THR10
|
3.7
|
35.1
|
1.0
|
CB
|
D:THR10
|
3.7
|
32.6
|
1.0
|
CB
|
D:ASP26
|
3.7
|
32.4
|
1.0
|
O
|
D:HOH304
|
3.7
|
36.0
|
1.0
|
NE2
|
B:GLN51
|
3.8
|
31.9
|
1.0
|
OD1
|
D:ASP26
|
3.9
|
27.5
|
1.0
|
CB
|
D:SER25
|
3.9
|
37.4
|
1.0
|
OD2
|
D:ASP26
|
4.0
|
33.1
|
1.0
|
C
|
D:SER25
|
4.0
|
34.2
|
1.0
|
CA
|
D:SER25
|
4.0
|
35.1
|
1.0
|
C
|
D:THR10
|
4.1
|
36.8
|
1.0
|
CA
|
D:ASP26
|
4.1
|
33.3
|
1.0
|
CB
|
D:SER24
|
4.4
|
26.6
|
1.0
|
C
|
D:SER24
|
4.5
|
31.1
|
1.0
|
CA
|
D:GLN11
|
4.5
|
36.3
|
1.0
|
C
|
D:GLN11
|
4.5
|
34.1
|
1.0
|
CA
|
D:SER24
|
4.8
|
29.5
|
1.0
|
CB
|
D:GLN11
|
4.8
|
40.6
|
1.0
|
O
|
D:ARG9
|
4.9
|
35.3
|
1.0
|
CD
|
B:GLN51
|
4.9
|
31.3
|
1.0
|
OG
|
D:SER24
|
5.0
|
26.8
|
1.0
|
|
Reference:
R.M.Domingos,
R.D.Teixeira,
T.G.P.Alegria,
P.S.Vieira,
M.T.Murakami,
L.E.S.Netto.
Ohrb (Organic Hydroperoxide Resistance Protein) Wild Type From Chromobacterium Violaceum and Reduced By Dtt at 1.85 Angstroms Resolution To Be Published.
Page generated: Sat Jul 27 22:16:28 2024
|