Bromine in PDB 3il2: Crystal Structure of A Rex-Family Repressor R90D Mutant/Dna Complex From Thermus Aquaticus
Protein crystallography data
The structure of Crystal Structure of A Rex-Family Repressor R90D Mutant/Dna Complex From Thermus Aquaticus, PDB code: 3il2
was solved by
K.J.Mclaughlin,
C.L.Kielkopf,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
20.00 /
2.49
|
Space group
|
P 31 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
62.950,
62.950,
298.110,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
25.4 /
28.5
|
Bromine Binding Sites:
The binding sites of Bromine atom in the Crystal Structure of A Rex-Family Repressor R90D Mutant/Dna Complex From Thermus Aquaticus
(pdb code 3il2). This binding sites where shown within
5.0 Angstroms radius around Bromine atom.
In total 8 binding sites of Bromine where determined in the
Crystal Structure of A Rex-Family Repressor R90D Mutant/Dna Complex From Thermus Aquaticus, PDB code: 3il2:
Jump to Bromine binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Bromine binding site 1 out
of 8 in 3il2
Go back to
Bromine Binding Sites List in 3il2
Bromine binding site 1 out
of 8 in the Crystal Structure of A Rex-Family Repressor R90D Mutant/Dna Complex From Thermus Aquaticus
Mono view
Stereo pair view
|
A full contact list of Bromine with other atoms in the Br binding
site number 1 of Crystal Structure of A Rex-Family Repressor R90D Mutant/Dna Complex From Thermus Aquaticus within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Br4
b:80.9
occ:1.00
|
BR
|
C:BRU4
|
0.0
|
80.9
|
1.0
|
C5
|
C:BRU4
|
1.9
|
50.1
|
1.0
|
C6
|
C:BRU4
|
2.8
|
50.0
|
1.0
|
C4
|
C:BRU4
|
2.9
|
50.1
|
1.0
|
O4
|
C:BRU4
|
3.2
|
49.1
|
1.0
|
NH1
|
A:ARG46
|
3.2
|
47.2
|
1.0
|
CZ
|
A:ARG46
|
3.3
|
47.4
|
1.0
|
C2'
|
C:DC3
|
3.3
|
59.8
|
1.0
|
OP2
|
C:BRU4
|
3.5
|
55.9
|
1.0
|
NH2
|
A:ARG46
|
3.6
|
46.2
|
1.0
|
NE
|
A:ARG46
|
3.7
|
47.3
|
1.0
|
C6
|
C:DC3
|
3.8
|
54.0
|
1.0
|
N1
|
C:DC3
|
3.9
|
55.7
|
1.0
|
C1'
|
C:DC3
|
4.0
|
58.4
|
1.0
|
N1
|
C:BRU4
|
4.1
|
50.9
|
1.0
|
N3
|
C:BRU4
|
4.1
|
49.9
|
1.0
|
C5
|
C:DC3
|
4.2
|
51.9
|
1.0
|
C2
|
C:DC3
|
4.4
|
54.2
|
1.0
|
CD
|
A:ARG46
|
4.5
|
48.0
|
1.0
|
C3'
|
C:DC3
|
4.6
|
59.8
|
1.0
|
O6
|
C:DG5
|
4.6
|
49.3
|
1.0
|
P
|
C:BRU4
|
4.7
|
56.5
|
1.0
|
C2
|
C:BRU4
|
4.7
|
50.6
|
1.0
|
C4
|
C:DC3
|
4.7
|
51.6
|
1.0
|
N3
|
C:DC3
|
4.8
|
52.3
|
1.0
|
O3'
|
C:DC3
|
4.9
|
58.5
|
1.0
|
O5'
|
C:BRU4
|
4.9
|
55.1
|
1.0
|
|
Bromine binding site 2 out
of 8 in 3il2
Go back to
Bromine Binding Sites List in 3il2
Bromine binding site 2 out
of 8 in the Crystal Structure of A Rex-Family Repressor R90D Mutant/Dna Complex From Thermus Aquaticus
Mono view
Stereo pair view
|
A full contact list of Bromine with other atoms in the Br binding
site number 2 of Crystal Structure of A Rex-Family Repressor R90D Mutant/Dna Complex From Thermus Aquaticus within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Br6
b:72.8
occ:1.00
|
BR
|
C:BRU6
|
0.0
|
72.8
|
1.0
|
C5
|
C:BRU6
|
1.9
|
43.7
|
1.0
|
C6
|
C:BRU6
|
2.8
|
45.9
|
1.0
|
C4
|
C:BRU6
|
2.9
|
41.9
|
1.0
|
O4
|
C:BRU6
|
3.1
|
38.3
|
1.0
|
O
|
A:ARG46
|
3.5
|
49.4
|
1.0
|
C
|
A:ARG46
|
3.5
|
47.6
|
1.0
|
N
|
A:LYS47
|
3.6
|
47.3
|
1.0
|
C8
|
C:DG5
|
3.6
|
51.3
|
1.0
|
CB
|
A:ARG46
|
3.7
|
47.8
|
1.0
|
CA
|
A:LYS47
|
3.7
|
47.7
|
1.0
|
N7
|
C:DG5
|
3.8
|
50.8
|
1.0
|
OG
|
A:SER50
|
4.0
|
56.9
|
1.0
|
CB
|
A:SER50
|
4.0
|
55.7
|
1.0
|
N9
|
C:DG5
|
4.1
|
51.5
|
1.0
|
N3
|
C:BRU6
|
4.1
|
43.1
|
1.0
|
N1
|
C:BRU6
|
4.1
|
49.4
|
1.0
|
CA
|
A:ARG46
|
4.2
|
46.9
|
1.0
|
C5
|
C:DG5
|
4.3
|
50.8
|
1.0
|
C2'
|
C:DG5
|
4.3
|
54.0
|
1.0
|
CB
|
A:LYS47
|
4.4
|
47.6
|
1.0
|
CE
|
A:LYS47
|
4.4
|
51.3
|
1.0
|
C4
|
C:DG5
|
4.5
|
51.6
|
1.0
|
CD
|
A:LYS47
|
4.7
|
49.8
|
1.0
|
C2
|
C:BRU6
|
4.7
|
46.7
|
1.0
|
C1'
|
C:DG5
|
4.7
|
52.5
|
1.0
|
O
|
A:PHE43
|
4.8
|
52.3
|
1.0
|
NZ
|
A:LYS47
|
4.9
|
51.2
|
1.0
|
C
|
A:LYS47
|
4.9
|
48.4
|
1.0
|
|
Bromine binding site 3 out
of 8 in 3il2
Go back to
Bromine Binding Sites List in 3il2
Bromine binding site 3 out
of 8 in the Crystal Structure of A Rex-Family Repressor R90D Mutant/Dna Complex From Thermus Aquaticus
Mono view
Stereo pair view
|
A full contact list of Bromine with other atoms in the Br binding
site number 3 of Crystal Structure of A Rex-Family Repressor R90D Mutant/Dna Complex From Thermus Aquaticus within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Br14
b:62.7
occ:1.00
|
BR
|
C:BRU14
|
0.0
|
62.7
|
1.0
|
C5
|
C:BRU14
|
1.9
|
37.0
|
1.0
|
C6
|
C:BRU14
|
2.8
|
36.2
|
1.0
|
C4
|
C:BRU14
|
2.9
|
35.4
|
1.0
|
OH
|
B:TYR51
|
3.0
|
47.7
|
1.0
|
O4
|
C:BRU14
|
3.2
|
36.0
|
1.0
|
O
|
B:HOH225
|
3.3
|
42.5
|
1.0
|
C2'
|
C:DG13
|
3.8
|
34.5
|
1.0
|
C8
|
C:DG13
|
3.9
|
29.7
|
1.0
|
N9
|
C:DG13
|
4.0
|
33.3
|
1.0
|
N1
|
C:BRU14
|
4.1
|
36.5
|
1.0
|
N3
|
C:BRU14
|
4.1
|
35.0
|
1.0
|
CD
|
B:LYS47
|
4.2
|
47.8
|
1.0
|
CE
|
B:LYS47
|
4.2
|
50.0
|
1.0
|
N7
|
C:DG13
|
4.3
|
30.5
|
1.0
|
CZ
|
B:TYR51
|
4.3
|
46.1
|
1.0
|
CG
|
B:LYS47
|
4.3
|
45.0
|
1.0
|
C1'
|
C:DG13
|
4.4
|
34.2
|
1.0
|
O4
|
C:BRU15
|
4.4
|
36.3
|
1.0
|
C4
|
C:DG13
|
4.5
|
29.8
|
1.0
|
C5
|
C:DG13
|
4.6
|
31.2
|
1.0
|
C2
|
C:BRU14
|
4.7
|
35.5
|
1.0
|
OP2
|
C:BRU14
|
4.8
|
34.5
|
1.0
|
BR
|
C:BRU15
|
5.0
|
73.4
|
1.0
|
|
Bromine binding site 4 out
of 8 in 3il2
Go back to
Bromine Binding Sites List in 3il2
Bromine binding site 4 out
of 8 in the Crystal Structure of A Rex-Family Repressor R90D Mutant/Dna Complex From Thermus Aquaticus
Mono view
Stereo pair view
|
A full contact list of Bromine with other atoms in the Br binding
site number 4 of Crystal Structure of A Rex-Family Repressor R90D Mutant/Dna Complex From Thermus Aquaticus within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Br15
b:73.4
occ:1.00
|
BR
|
C:BRU15
|
0.0
|
73.4
|
1.0
|
C5
|
C:BRU15
|
1.9
|
40.6
|
1.0
|
C6
|
C:BRU15
|
2.8
|
41.5
|
1.0
|
C4
|
C:BRU15
|
2.9
|
39.7
|
1.0
|
O4
|
C:BRU15
|
3.2
|
36.3
|
1.0
|
C2'
|
C:BRU14
|
3.6
|
39.7
|
1.0
|
CG
|
B:LYS47
|
3.8
|
45.0
|
1.0
|
CB
|
B:LYS47
|
3.8
|
40.6
|
1.0
|
NE2
|
B:GLN44
|
3.8
|
53.0
|
1.0
|
C6
|
C:BRU14
|
3.9
|
36.2
|
1.0
|
N1
|
C:BRU14
|
4.0
|
36.5
|
1.0
|
N1
|
C:BRU15
|
4.1
|
41.3
|
1.0
|
O
|
B:HOH256
|
4.2
|
71.1
|
1.0
|
N3
|
C:BRU15
|
4.2
|
39.0
|
1.0
|
CA
|
B:GLN44
|
4.2
|
38.0
|
1.0
|
O
|
B:PHE43
|
4.3
|
35.6
|
1.0
|
C5
|
C:BRU14
|
4.3
|
37.0
|
1.0
|
C1'
|
C:BRU14
|
4.3
|
38.0
|
1.0
|
O
|
B:HOH210
|
4.4
|
63.7
|
1.0
|
CE
|
B:LYS47
|
4.4
|
50.0
|
1.0
|
N
|
B:GLN44
|
4.4
|
36.9
|
1.0
|
C
|
B:PHE43
|
4.4
|
38.0
|
1.0
|
CD
|
B:GLN44
|
4.6
|
51.1
|
1.0
|
C2
|
C:BRU14
|
4.6
|
35.5
|
1.0
|
CB
|
B:PHE43
|
4.6
|
44.2
|
1.0
|
C2
|
C:BRU15
|
4.7
|
40.0
|
1.0
|
CD
|
B:LYS47
|
4.7
|
47.8
|
1.0
|
N4
|
C:DC16
|
4.7
|
37.0
|
1.0
|
BR
|
C:BRU14
|
5.0
|
62.7
|
1.0
|
CB
|
B:GLN44
|
5.0
|
39.2
|
1.0
|
OP2
|
C:BRU15
|
5.0
|
47.8
|
1.0
|
C4
|
C:BRU14
|
5.0
|
35.4
|
1.0
|
C3'
|
C:BRU14
|
5.0
|
40.6
|
1.0
|
C5
|
C:DC16
|
5.0
|
38.7
|
1.0
|
|
Bromine binding site 5 out
of 8 in 3il2
Go back to
Bromine Binding Sites List in 3il2
Bromine binding site 5 out
of 8 in the Crystal Structure of A Rex-Family Repressor R90D Mutant/Dna Complex From Thermus Aquaticus
Mono view
Stereo pair view
|
A full contact list of Bromine with other atoms in the Br binding
site number 5 of Crystal Structure of A Rex-Family Repressor R90D Mutant/Dna Complex From Thermus Aquaticus within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Br4
b:76.2
occ:1.00
|
BR
|
D:BRU4
|
0.0
|
76.2
|
1.0
|
C5
|
D:BRU4
|
1.9
|
33.0
|
1.0
|
C6
|
D:BRU4
|
2.8
|
31.9
|
1.0
|
C4
|
D:BRU4
|
2.9
|
31.1
|
1.0
|
O4
|
D:BRU4
|
3.1
|
27.5
|
1.0
|
CZ
|
B:ARG46
|
3.4
|
41.1
|
1.0
|
C2'
|
D:DC3
|
3.4
|
36.4
|
1.0
|
NH2
|
B:ARG46
|
3.5
|
41.6
|
1.0
|
NE
|
B:ARG46
|
3.7
|
39.4
|
1.0
|
NH1
|
B:ARG46
|
3.7
|
39.2
|
1.0
|
OP2
|
D:BRU4
|
3.7
|
34.9
|
1.0
|
C6
|
D:DC3
|
3.9
|
34.6
|
1.0
|
N1
|
D:DC3
|
3.9
|
34.7
|
1.0
|
C1'
|
D:DC3
|
4.0
|
37.1
|
1.0
|
N1
|
D:BRU4
|
4.1
|
32.8
|
1.0
|
N3
|
D:BRU4
|
4.1
|
31.3
|
1.0
|
CD
|
B:ARG46
|
4.3
|
37.0
|
1.0
|
C5
|
D:DC3
|
4.5
|
32.4
|
1.0
|
O6
|
D:DG5
|
4.5
|
35.2
|
1.0
|
C2
|
D:DC3
|
4.6
|
34.4
|
1.0
|
C2
|
D:BRU4
|
4.7
|
31.8
|
1.0
|
C3'
|
D:DC3
|
4.7
|
36.6
|
1.0
|
P
|
D:BRU4
|
4.8
|
32.8
|
1.0
|
O5'
|
D:BRU4
|
5.0
|
32.7
|
1.0
|
|
Bromine binding site 6 out
of 8 in 3il2
Go back to
Bromine Binding Sites List in 3il2
Bromine binding site 6 out
of 8 in the Crystal Structure of A Rex-Family Repressor R90D Mutant/Dna Complex From Thermus Aquaticus
Mono view
Stereo pair view
|
A full contact list of Bromine with other atoms in the Br binding
site number 6 of Crystal Structure of A Rex-Family Repressor R90D Mutant/Dna Complex From Thermus Aquaticus within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Br6
b:67.5
occ:1.00
|
BR
|
D:BRU6
|
0.0
|
67.5
|
1.0
|
C5
|
D:BRU6
|
1.9
|
37.0
|
1.0
|
C6
|
D:BRU6
|
2.8
|
38.5
|
1.0
|
C4
|
D:BRU6
|
2.9
|
36.1
|
1.0
|
O4
|
D:BRU6
|
3.2
|
33.5
|
1.0
|
O
|
B:ARG46
|
3.4
|
33.5
|
1.0
|
C
|
B:ARG46
|
3.5
|
34.8
|
1.0
|
C8
|
D:DG5
|
3.6
|
33.5
|
1.0
|
N
|
B:LYS47
|
3.7
|
35.6
|
1.0
|
CA
|
B:LYS47
|
3.7
|
38.5
|
1.0
|
N7
|
D:DG5
|
3.8
|
33.0
|
1.0
|
O
|
B:HOH256
|
3.8
|
71.1
|
1.0
|
CB
|
B:SER50
|
3.9
|
43.7
|
1.0
|
CB
|
B:ARG46
|
3.9
|
35.9
|
1.0
|
N9
|
D:DG5
|
4.0
|
32.9
|
1.0
|
OG
|
B:SER50
|
4.0
|
48.5
|
1.0
|
N1
|
D:BRU6
|
4.1
|
39.6
|
1.0
|
N3
|
D:BRU6
|
4.1
|
36.6
|
1.0
|
C2'
|
D:DG5
|
4.2
|
33.0
|
1.0
|
C5
|
D:DG5
|
4.2
|
34.6
|
1.0
|
C4
|
D:DG5
|
4.3
|
33.9
|
1.0
|
CB
|
B:LYS47
|
4.4
|
40.6
|
1.0
|
CA
|
B:ARG46
|
4.4
|
34.3
|
1.0
|
C1'
|
D:DG5
|
4.6
|
32.6
|
1.0
|
C2
|
D:BRU6
|
4.7
|
39.2
|
1.0
|
C
|
B:LYS47
|
4.9
|
39.5
|
1.0
|
NZ
|
B:LYS47
|
4.9
|
50.0
|
1.0
|
CE
|
B:LYS47
|
5.0
|
50.0
|
1.0
|
|
Bromine binding site 7 out
of 8 in 3il2
Go back to
Bromine Binding Sites List in 3il2
Bromine binding site 7 out
of 8 in the Crystal Structure of A Rex-Family Repressor R90D Mutant/Dna Complex From Thermus Aquaticus
Mono view
Stereo pair view
|
A full contact list of Bromine with other atoms in the Br binding
site number 7 of Crystal Structure of A Rex-Family Repressor R90D Mutant/Dna Complex From Thermus Aquaticus within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Br14
b:63.5
occ:1.00
|
BR
|
D:BRU14
|
0.0
|
63.5
|
1.0
|
C5
|
D:BRU14
|
1.9
|
38.7
|
1.0
|
C6
|
D:BRU14
|
2.8
|
39.1
|
1.0
|
C4
|
D:BRU14
|
2.9
|
35.5
|
1.0
|
OH
|
A:TYR51
|
3.0
|
54.3
|
1.0
|
O4
|
D:BRU14
|
3.1
|
34.6
|
1.0
|
O
|
D:HOH80
|
3.6
|
51.3
|
1.0
|
C2'
|
D:DG13
|
3.8
|
42.0
|
1.0
|
N9
|
D:DG13
|
4.1
|
39.7
|
1.0
|
N1
|
D:BRU14
|
4.1
|
41.0
|
1.0
|
N3
|
D:BRU14
|
4.1
|
34.6
|
1.0
|
C8
|
D:DG13
|
4.1
|
38.5
|
1.0
|
C1'
|
D:DG13
|
4.3
|
41.7
|
1.0
|
CG
|
A:LYS47
|
4.3
|
48.7
|
1.0
|
CZ
|
A:TYR51
|
4.3
|
53.7
|
1.0
|
O4
|
D:BRU15
|
4.5
|
38.8
|
1.0
|
OP2
|
D:BRU14
|
4.5
|
49.0
|
1.0
|
C4
|
D:DG13
|
4.5
|
37.5
|
1.0
|
CD
|
A:LYS47
|
4.6
|
49.8
|
1.0
|
N7
|
D:DG13
|
4.6
|
38.6
|
1.0
|
C2
|
D:BRU14
|
4.7
|
38.4
|
1.0
|
C5
|
D:DG13
|
4.9
|
38.3
|
1.0
|
CE
|
A:LYS47
|
4.9
|
51.3
|
1.0
|
CE2
|
A:TYR51
|
4.9
|
53.7
|
1.0
|
|
Bromine binding site 8 out
of 8 in 3il2
Go back to
Bromine Binding Sites List in 3il2
Bromine binding site 8 out
of 8 in the Crystal Structure of A Rex-Family Repressor R90D Mutant/Dna Complex From Thermus Aquaticus
Mono view
Stereo pair view
|
A full contact list of Bromine with other atoms in the Br binding
site number 8 of Crystal Structure of A Rex-Family Repressor R90D Mutant/Dna Complex From Thermus Aquaticus within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Br15
b:76.9
occ:1.00
|
BR
|
D:BRU15
|
0.0
|
76.9
|
1.0
|
C5
|
D:BRU15
|
1.9
|
41.7
|
1.0
|
C6
|
D:BRU15
|
2.8
|
43.7
|
1.0
|
C4
|
D:BRU15
|
2.9
|
41.3
|
1.0
|
O4
|
D:BRU15
|
3.2
|
38.8
|
1.0
|
C2'
|
D:BRU14
|
3.6
|
46.0
|
1.0
|
CB
|
A:LYS47
|
3.9
|
47.6
|
1.0
|
C6
|
D:BRU14
|
3.9
|
39.1
|
1.0
|
CA
|
A:GLN44
|
4.0
|
51.3
|
1.0
|
CG
|
A:LYS47
|
4.0
|
48.7
|
1.0
|
N1
|
D:BRU14
|
4.1
|
41.0
|
1.0
|
N
|
A:GLN44
|
4.1
|
52.6
|
1.0
|
N1
|
D:BRU15
|
4.2
|
45.2
|
1.0
|
N3
|
D:BRU15
|
4.2
|
40.7
|
1.0
|
C
|
A:PHE43
|
4.3
|
53.3
|
1.0
|
C1'
|
D:BRU14
|
4.4
|
43.3
|
1.0
|
C5
|
D:BRU14
|
4.4
|
38.7
|
1.0
|
O
|
A:PHE43
|
4.4
|
52.3
|
1.0
|
CB
|
A:GLN44
|
4.4
|
52.7
|
1.0
|
CE
|
A:LYS47
|
4.5
|
51.3
|
1.0
|
CB
|
A:PHE43
|
4.5
|
57.2
|
1.0
|
C2
|
D:BRU14
|
4.7
|
38.4
|
1.0
|
N4
|
D:DC16
|
4.7
|
42.3
|
1.0
|
C2
|
D:BRU15
|
4.7
|
42.6
|
1.0
|
CG
|
A:GLN44
|
4.8
|
54.3
|
1.0
|
OP2
|
D:BRU15
|
4.9
|
56.9
|
1.0
|
CD
|
A:LYS47
|
4.9
|
49.8
|
1.0
|
|
Reference:
K.J.Mclaughlin,
C.M.Strain-Damerell,
K.Xie,
D.Brekasis,
A.S.Soares,
M.S.Paget,
C.L.Kielkopf.
Structural Basis For Nadh/Nad+ Redox Sensing By A Rex Family Repressor. Mol.Cell V. 38 563 2010.
ISSN: ISSN 1097-2765
PubMed: 20513431
DOI: 10.1016/J.MOLCEL.2010.05.006
Page generated: Wed Jul 10 19:42:13 2024
|