Bromine in PDB 3dlu: Structures of SRP54 and SRP19, the Two Proteins Assembling the Ribonucleic Core of the Signal Recognition Particle From the Archaeon Pyrococcus Furiosus.
Protein crystallography data
The structure of Structures of SRP54 and SRP19, the Two Proteins Assembling the Ribonucleic Core of the Signal Recognition Particle From the Archaeon Pyrococcus Furiosus., PDB code: 3dlu
was solved by
P.F.Egea,
J.Napetschnig,
P.Walter,
R.M.Stroud,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
42.00 /
1.80
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
44.074,
79.699,
60.548,
90.00,
107.65,
90.00
|
R / Rfree (%)
|
19.1 /
22.5
|
Bromine Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
20;
Page 3, Binding sites: 21 -
30;
Page 4, Binding sites: 31 -
39;
Binding sites:
The binding sites of Bromine atom in the Structures of SRP54 and SRP19, the Two Proteins Assembling the Ribonucleic Core of the Signal Recognition Particle From the Archaeon Pyrococcus Furiosus.
(pdb code 3dlu). This binding sites where shown within
5.0 Angstroms radius around Bromine atom.
In total 39 binding sites of Bromine where determined in the
Structures of SRP54 and SRP19, the Two Proteins Assembling the Ribonucleic Core of the Signal Recognition Particle From the Archaeon Pyrococcus Furiosus., PDB code: 3dlu:
Jump to Bromine binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Bromine binding site 1 out
of 39 in 3dlu
Go back to
Bromine Binding Sites List in 3dlu
Bromine binding site 1 out
of 39 in the Structures of SRP54 and SRP19, the Two Proteins Assembling the Ribonucleic Core of the Signal Recognition Particle From the Archaeon Pyrococcus Furiosus.
Mono view
Stereo pair view
|
A full contact list of Bromine with other atoms in the Br binding
site number 1 of Structures of SRP54 and SRP19, the Two Proteins Assembling the Ribonucleic Core of the Signal Recognition Particle From the Archaeon Pyrococcus Furiosus. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Br107
b:21.8
occ:0.58
|
NE1
|
A:TRP7
|
3.1
|
17.1
|
1.0
|
O
|
A:HOH195
|
3.1
|
32.2
|
1.0
|
BR
|
B:BR110
|
3.4
|
38.6
|
0.6
|
N
|
A:GLY71
|
3.7
|
18.6
|
1.0
|
CB
|
A:PHE70
|
3.8
|
14.7
|
1.0
|
CA
|
A:PHE70
|
3.8
|
21.1
|
1.0
|
CD
|
B:ARG50
|
3.8
|
24.6
|
1.0
|
O
|
A:HOH157
|
3.9
|
38.0
|
1.0
|
CD1
|
A:TRP7
|
3.9
|
17.7
|
1.0
|
CD2
|
A:PHE70
|
4.0
|
23.5
|
1.0
|
NH1
|
B:ARG50
|
4.0
|
24.5
|
1.0
|
O
|
A:GLY71
|
4.2
|
14.9
|
1.0
|
CE2
|
A:TRP7
|
4.2
|
13.6
|
1.0
|
C
|
A:PHE70
|
4.2
|
26.1
|
1.0
|
NE
|
B:ARG50
|
4.4
|
17.3
|
1.0
|
CG
|
A:PHE70
|
4.4
|
21.4
|
1.0
|
CE
|
B:MET72
|
4.4
|
19.6
|
1.0
|
CZ
|
B:ARG50
|
4.4
|
19.4
|
1.0
|
CG2
|
B:VAL74
|
4.5
|
17.3
|
1.0
|
CZ2
|
A:TRP7
|
4.7
|
15.5
|
1.0
|
CA
|
A:GLY71
|
4.9
|
20.8
|
1.0
|
C
|
A:GLY71
|
4.9
|
17.3
|
1.0
|
|
Bromine binding site 2 out
of 39 in 3dlu
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Bromine Binding Sites List in 3dlu
Bromine binding site 2 out
of 39 in the Structures of SRP54 and SRP19, the Two Proteins Assembling the Ribonucleic Core of the Signal Recognition Particle From the Archaeon Pyrococcus Furiosus.
Mono view
Stereo pair view
|
A full contact list of Bromine with other atoms in the Br binding
site number 2 of Structures of SRP54 and SRP19, the Two Proteins Assembling the Ribonucleic Core of the Signal Recognition Particle From the Archaeon Pyrococcus Furiosus. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Br108
b:25.5
occ:0.43
|
BR
|
A:BR125
|
2.8
|
51.6
|
0.4
|
O
|
A:HOH192
|
3.1
|
25.6
|
1.0
|
N
|
A:GLU30
|
3.2
|
14.3
|
1.0
|
O
|
A:HOH149
|
3.6
|
33.7
|
1.0
|
NH1
|
A:ARG96
|
3.7
|
20.7
|
1.0
|
CB
|
A:GLU30
|
3.8
|
16.1
|
1.0
|
CA
|
A:VAL29
|
3.9
|
12.7
|
1.0
|
CB
|
A:VAL29
|
4.0
|
14.0
|
1.0
|
C
|
A:VAL29
|
4.0
|
15.6
|
1.0
|
CA
|
A:GLU30
|
4.1
|
17.5
|
1.0
|
BR
|
A:BR114
|
4.5
|
75.0
|
0.6
|
CG1
|
A:VAL29
|
4.5
|
15.9
|
1.0
|
NH2
|
A:ARG93
|
4.6
|
16.0
|
1.0
|
OG
|
A:SER13
|
4.8
|
18.3
|
1.0
|
O
|
A:GLU30
|
4.9
|
18.5
|
1.0
|
|
Bromine binding site 3 out
of 39 in 3dlu
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Bromine Binding Sites List in 3dlu
Bromine binding site 3 out
of 39 in the Structures of SRP54 and SRP19, the Two Proteins Assembling the Ribonucleic Core of the Signal Recognition Particle From the Archaeon Pyrococcus Furiosus.
Mono view
Stereo pair view
|
A full contact list of Bromine with other atoms in the Br binding
site number 3 of Structures of SRP54 and SRP19, the Two Proteins Assembling the Ribonucleic Core of the Signal Recognition Particle From the Archaeon Pyrococcus Furiosus. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Br109
b:30.4
occ:0.43
|
NH1
|
A:ARG25
|
3.4
|
27.9
|
1.0
|
CZ
|
A:ARG25
|
4.5
|
28.0
|
1.0
|
NH2
|
A:ARG25
|
4.8
|
20.8
|
1.0
|
|
Bromine binding site 4 out
of 39 in 3dlu
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Bromine Binding Sites List in 3dlu
Bromine binding site 4 out
of 39 in the Structures of SRP54 and SRP19, the Two Proteins Assembling the Ribonucleic Core of the Signal Recognition Particle From the Archaeon Pyrococcus Furiosus.
Mono view
Stereo pair view
|
A full contact list of Bromine with other atoms in the Br binding
site number 4 of Structures of SRP54 and SRP19, the Two Proteins Assembling the Ribonucleic Core of the Signal Recognition Particle From the Archaeon Pyrococcus Furiosus. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Br110
b:25.2
occ:0.25
|
O
|
A:HOH192
|
2.8
|
25.6
|
1.0
|
O
|
A:ARG25
|
2.9
|
18.7
|
1.0
|
O
|
A:ALA28
|
3.1
|
16.9
|
1.0
|
NH2
|
A:ARG93
|
3.2
|
16.0
|
1.0
|
O
|
A:SER26
|
3.4
|
16.9
|
1.0
|
CA
|
A:SER26
|
3.5
|
22.0
|
1.0
|
C
|
A:SER26
|
3.6
|
18.6
|
1.0
|
C
|
A:ARG25
|
3.8
|
16.2
|
1.0
|
CB
|
A:SER13
|
4.1
|
15.1
|
1.0
|
N
|
A:SER26
|
4.1
|
16.8
|
1.0
|
C
|
A:ALA28
|
4.2
|
18.0
|
1.0
|
OG
|
A:SER13
|
4.3
|
18.3
|
1.0
|
CZ
|
A:ARG93
|
4.4
|
13.7
|
1.0
|
CB
|
A:SER26
|
4.6
|
23.6
|
1.0
|
N
|
A:ILE27
|
4.6
|
18.0
|
1.0
|
O
|
A:HOH149
|
4.7
|
33.7
|
1.0
|
N
|
A:ALA28
|
5.0
|
14.7
|
1.0
|
|
Bromine binding site 5 out
of 39 in 3dlu
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Bromine Binding Sites List in 3dlu
Bromine binding site 5 out
of 39 in the Structures of SRP54 and SRP19, the Two Proteins Assembling the Ribonucleic Core of the Signal Recognition Particle From the Archaeon Pyrococcus Furiosus.
Mono view
Stereo pair view
|
A full contact list of Bromine with other atoms in the Br binding
site number 5 of Structures of SRP54 and SRP19, the Two Proteins Assembling the Ribonucleic Core of the Signal Recognition Particle From the Archaeon Pyrococcus Furiosus. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Br111
b:40.0
occ:0.39
|
O
|
A:THR102
|
3.0
|
43.3
|
1.0
|
CB
|
A:THR102
|
3.7
|
27.3
|
1.0
|
C
|
A:THR102
|
3.7
|
39.1
|
1.0
|
CA
|
A:THR102
|
3.9
|
22.2
|
1.0
|
CG
|
A:LEU103
|
4.1
|
60.8
|
1.0
|
CD1
|
A:LEU103
|
4.3
|
63.7
|
1.0
|
OG1
|
A:THR102
|
4.4
|
29.9
|
1.0
|
CB
|
A:LEU103
|
4.5
|
61.6
|
1.0
|
CG2
|
A:THR102
|
4.7
|
28.7
|
1.0
|
N
|
A:LEU103
|
4.7
|
46.6
|
1.0
|
|
Bromine binding site 6 out
of 39 in 3dlu
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Bromine Binding Sites List in 3dlu
Bromine binding site 6 out
of 39 in the Structures of SRP54 and SRP19, the Two Proteins Assembling the Ribonucleic Core of the Signal Recognition Particle From the Archaeon Pyrococcus Furiosus.
Mono view
Stereo pair view
|
A full contact list of Bromine with other atoms in the Br binding
site number 6 of Structures of SRP54 and SRP19, the Two Proteins Assembling the Ribonucleic Core of the Signal Recognition Particle From the Archaeon Pyrococcus Furiosus. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Br112
b:32.9
occ:0.42
|
O
|
A:HOH155
|
2.9
|
32.2
|
1.0
|
BR
|
B:BR108
|
3.2
|
20.9
|
0.6
|
O
|
A:HOH197
|
3.6
|
43.1
|
1.0
|
CB
|
A:ARG50
|
4.0
|
16.5
|
1.0
|
CG2
|
A:ILE49
|
4.0
|
21.1
|
1.0
|
CG2
|
A:VAL74
|
4.1
|
16.9
|
1.0
|
CD2
|
B:PHE70
|
4.1
|
25.6
|
1.0
|
CZ2
|
B:TRP7
|
4.2
|
13.8
|
1.0
|
O
|
B:HOH221
|
4.3
|
32.5
|
1.0
|
CD
|
A:ARG50
|
4.3
|
25.1
|
1.0
|
O
|
B:HOH248
|
4.4
|
47.9
|
1.0
|
CG1
|
A:VAL74
|
4.4
|
13.6
|
1.0
|
CE2
|
B:PHE70
|
4.4
|
31.2
|
1.0
|
CB
|
A:VAL74
|
4.4
|
14.8
|
1.0
|
NE1
|
B:TRP7
|
4.6
|
18.6
|
1.0
|
CE2
|
B:TRP7
|
4.8
|
13.0
|
1.0
|
CG
|
A:ARG50
|
4.8
|
25.0
|
1.0
|
|
Bromine binding site 7 out
of 39 in 3dlu
Go back to
Bromine Binding Sites List in 3dlu
Bromine binding site 7 out
of 39 in the Structures of SRP54 and SRP19, the Two Proteins Assembling the Ribonucleic Core of the Signal Recognition Particle From the Archaeon Pyrococcus Furiosus.
Mono view
Stereo pair view
|
A full contact list of Bromine with other atoms in the Br binding
site number 7 of Structures of SRP54 and SRP19, the Two Proteins Assembling the Ribonucleic Core of the Signal Recognition Particle From the Archaeon Pyrococcus Furiosus. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Br113
b:27.7
occ:0.29
|
O
|
A:GLY20
|
2.7
|
13.6
|
1.0
|
BR
|
B:BR107
|
2.8
|
24.3
|
0.3
|
O
|
B:ARG3
|
2.9
|
17.2
|
1.0
|
CD1
|
A:ILE22
|
3.4
|
19.6
|
0.5
|
CA
|
B:PHE4
|
3.4
|
15.8
|
1.0
|
CB
|
B:PHE4
|
3.5
|
15.4
|
1.0
|
C
|
A:GLY20
|
3.5
|
15.1
|
1.0
|
CG1
|
A:ILE22
|
3.5
|
27.2
|
0.5
|
CA
|
A:GLY20
|
3.5
|
18.8
|
1.0
|
CZ3
|
A:TRP7
|
3.8
|
14.0
|
1.0
|
C
|
B:ARG3
|
3.8
|
17.7
|
1.0
|
CE3
|
A:TRP7
|
4.1
|
15.2
|
1.0
|
CG
|
A:GLU10
|
4.1
|
15.1
|
1.0
|
N
|
B:PHE4
|
4.1
|
17.7
|
1.0
|
CG1
|
A:ILE22
|
4.1
|
15.6
|
0.5
|
O
|
A:HOH137
|
4.4
|
26.6
|
1.0
|
CD1
|
A:ILE22
|
4.6
|
8.7
|
0.5
|
C
|
B:PHE4
|
4.6
|
14.0
|
1.0
|
N
|
B:VAL5
|
4.7
|
14.4
|
1.0
|
OE2
|
A:GLU10
|
4.7
|
21.8
|
1.0
|
N
|
A:ARG21
|
4.7
|
14.3
|
1.0
|
N
|
A:GLY20
|
4.8
|
16.2
|
1.0
|
CG
|
B:PHE4
|
4.9
|
19.3
|
1.0
|
CD
|
A:GLU10
|
5.0
|
19.2
|
1.0
|
CB
|
A:ILE22
|
5.0
|
21.2
|
0.5
|
|
Bromine binding site 8 out
of 39 in 3dlu
Go back to
Bromine Binding Sites List in 3dlu
Bromine binding site 8 out
of 39 in the Structures of SRP54 and SRP19, the Two Proteins Assembling the Ribonucleic Core of the Signal Recognition Particle From the Archaeon Pyrococcus Furiosus.
Mono view
Stereo pair view
|
A full contact list of Bromine with other atoms in the Br binding
site number 8 of Structures of SRP54 and SRP19, the Two Proteins Assembling the Ribonucleic Core of the Signal Recognition Particle From the Archaeon Pyrococcus Furiosus. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Br114
b:75.0
occ:0.61
|
CB
|
A:GLU30
|
3.2
|
16.1
|
1.0
|
O
|
A:HOH139
|
4.3
|
29.9
|
1.0
|
NH1
|
A:ARG96
|
4.5
|
20.7
|
1.0
|
BR
|
A:BR108
|
4.5
|
25.5
|
0.4
|
CA
|
A:GLU30
|
4.5
|
17.5
|
1.0
|
O
|
A:GLU30
|
4.5
|
18.5
|
1.0
|
C
|
A:GLU30
|
4.7
|
16.5
|
1.0
|
O
|
A:HOH170
|
4.8
|
48.4
|
1.0
|
|
Bromine binding site 9 out
of 39 in 3dlu
Go back to
Bromine Binding Sites List in 3dlu
Bromine binding site 9 out
of 39 in the Structures of SRP54 and SRP19, the Two Proteins Assembling the Ribonucleic Core of the Signal Recognition Particle From the Archaeon Pyrococcus Furiosus.
Mono view
Stereo pair view
|
A full contact list of Bromine with other atoms in the Br binding
site number 9 of Structures of SRP54 and SRP19, the Two Proteins Assembling the Ribonucleic Core of the Signal Recognition Particle From the Archaeon Pyrococcus Furiosus. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Br115
b:38.8
occ:0.45
|
NZ
|
A:LYS45
|
3.1
|
41.4
|
1.0
|
CE
|
A:LYS45
|
4.1
|
30.8
|
1.0
|
|
Bromine binding site 10 out
of 39 in 3dlu
Go back to
Bromine Binding Sites List in 3dlu
Bromine binding site 10 out
of 39 in the Structures of SRP54 and SRP19, the Two Proteins Assembling the Ribonucleic Core of the Signal Recognition Particle From the Archaeon Pyrococcus Furiosus.
Mono view
Stereo pair view
|
A full contact list of Bromine with other atoms in the Br binding
site number 10 of Structures of SRP54 and SRP19, the Two Proteins Assembling the Ribonucleic Core of the Signal Recognition Particle From the Archaeon Pyrococcus Furiosus. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Br116
b:33.0
occ:0.33
|
O
|
A:HOH201
|
2.8
|
33.1
|
1.0
|
CD1
|
A:ILE22
|
3.9
|
8.7
|
0.5
|
CG
|
A:LYS81
|
3.9
|
17.8
|
1.0
|
N
|
A:SER82
|
4.0
|
15.6
|
1.0
|
CG2
|
A:ILE22
|
4.0
|
26.7
|
0.5
|
CB
|
A:SER82
|
4.1
|
26.5
|
1.0
|
CD
|
A:LYS81
|
4.1
|
22.1
|
1.0
|
CA
|
A:SER82
|
4.1
|
23.2
|
1.0
|
CB
|
A:LYS81
|
4.2
|
20.4
|
1.0
|
CG2
|
A:ILE22
|
4.2
|
30.3
|
0.5
|
O
|
A:HOH200
|
4.3
|
42.6
|
1.0
|
O
|
A:HOH144
|
4.4
|
35.1
|
1.0
|
CE
|
A:LYS81
|
4.4
|
13.0
|
1.0
|
O
|
A:HOH145
|
4.4
|
33.6
|
1.0
|
C
|
A:LYS81
|
4.5
|
21.0
|
1.0
|
CD1
|
A:LEU85
|
4.8
|
15.0
|
1.0
|
OG
|
A:SER82
|
4.8
|
49.4
|
1.0
|
CA
|
A:LYS81
|
5.0
|
22.9
|
1.0
|
|
Reference:
P.F.Egea,
J.Napetschnig,
P.Walter,
R.M.Stroud.
Structures of SRP54 and SRP19, the Two Proteins That Organize the Ribonucleic Core of the Signal Recognition Particle From Pyrococcus Furiosus. Plos One V. 3 E3528 2008.
ISSN: ESSN 1932-6203
PubMed: 18953414
DOI: 10.1371/JOURNAL.PONE.0003528
Page generated: Wed Jul 10 19:17:45 2024
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