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Bromine in PDB 4ifd: Crystal Structure of An 11-Subunit Eukaryotic Exosome Complex Bound to Rna

Protein crystallography data

The structure of Crystal Structure of An 11-Subunit Eukaryotic Exosome Complex Bound to Rna, PDB code: 4ifd was solved by D.L.Makino, E.Conti, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.64 / 2.81
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 154.090, 107.440, 150.460, 90.00, 110.63, 90.00
R / Rfree (%) 18.3 / 22.4

Other elements in 4ifd:

The structure of Crystal Structure of An 11-Subunit Eukaryotic Exosome Complex Bound to Rna also contains other interesting chemical elements:

Magnesium (Mg) 1 atom
Zinc (Zn) 1 atom

Bromine Binding Sites:

The binding sites of Bromine atom in the Crystal Structure of An 11-Subunit Eukaryotic Exosome Complex Bound to Rna (pdb code 4ifd). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 10 binding sites of Bromine where determined in the Crystal Structure of An 11-Subunit Eukaryotic Exosome Complex Bound to Rna, PDB code: 4ifd:
Jump to Bromine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Bromine binding site 1 out of 10 in 4ifd

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Bromine binding site 1 out of 10 in the Crystal Structure of An 11-Subunit Eukaryotic Exosome Complex Bound to Rna


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 An 11-Subunit Eukaryotic Exosome Complex Bound to Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br401

b:94.4
occ:1.00
 OG1 A:THR224 3.2 48.5 1.0
O A:HOH518 3.7 49.5 1.0
CB A:THR224 3.9 41.2 1.0
CG2 A:THR224 4.2 44.8 1.0
CD A:LYS226 4.2 40.1 1.0
CB A:LEU25 4.2 44.1 1.0
CB A:LYS226 4.3 48.9 1.0
CD2 A:LEU25 4.5 51.8 1.0
CG A:LYS226 4.6 45.8 1.0
N A:ASP26 4.9 44.5 1.0
OH G:TYR208 5.0 38.3 1.0

Bromine binding site 2 out of 10 in 4ifd

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Bromine binding site 2 out of 10 in the Crystal Structure of An 11-Subunit Eukaryotic Exosome Complex Bound to Rna


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Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Crystal Structure of An 11-Subunit Eukaryotic Exosome Complex Bound to Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br402

b:0.7
occ:1.00
 N A:PHE73 3.0 65.6 1.0
CB A:PHE73 3.1 60.7 1.0
CA A:PHE73 3.4 62.6 1.0
N A:GLU74 3.6 63.1 1.0
CA A:ARG71 3.6 83.8 1.0
CD2 A:PHE73 3.6 59.8 1.0
N A:PRO72 3.7 75.5 1.0
C A:ARG71 3.7 80.4 1.0
CD A:PRO72 3.7 68.6 1.0
CG A:GLU74 3.8 67.1 1.0
C A:PHE73 3.8 62.7 1.0
CD A:ARG71 3.9 95.7 1.0
CG A:PHE73 3.9 62.0 1.0
CB A:ARG71 3.9 86.4 1.0
C A:PRO72 4.2 68.1 1.0
O A:ARG71 4.3 80.8 1.0
CB A:GLU74 4.3 61.7 1.0
CG A:PRO72 4.4 62.8 1.0
CD A:GLU74 4.4 73.7 1.0
CA A:PRO72 4.5 69.2 1.0
CG A:ARG71 4.5 88.7 1.0
CA A:GLU74 4.6 62.4 1.0
O A:PHE73 4.7 61.5 1.0
OE1 A:GLU74 4.8 78.1 1.0
CE2 A:PHE73 4.9 63.2 1.0
O A:ASP70 4.9 94.4 1.0
OE2 A:GLU74 4.9 76.7 1.0
N A:ARG71 5.0 86.6 1.0

Bromine binding site 3 out of 10 in 4ifd

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Bromine binding site 3 out of 10 in the Crystal Structure of An 11-Subunit Eukaryotic Exosome Complex Bound to Rna


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 An 11-Subunit Eukaryotic Exosome Complex Bound to Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Br301

b:0.9
occ:1.00
 NE1 E:TRP217 3.7 51.0 1.0
CZ2 E:TRP217 3.7 60.6 1.0
CA E:PRO256 3.7 53.3 1.0
CB E:PRO256 3.9 51.6 1.0
CG E:PRO256 4.0 51.6 1.0
CA E:GLY220 4.0 63.8 1.0
CE2 E:TRP217 4.1 53.9 1.0
CG2 E:VAL259 4.2 54.1 1.0
CB E:VAL259 4.2 55.0 1.0
N E:PRO256 4.4 54.1 1.0
CG1 E:VAL259 4.4 55.9 1.0
N E:GLY220 4.5 60.9 1.0
CD E:PRO256 4.8 50.7 1.0
C E:PRO256 4.9 58.2 1.0
CH2 E:TRP217 4.9 61.4 1.0
O E:PRO256 5.0 63.8 1.0
CD1 E:TRP217 5.0 52.8 1.0
C E:ALA255 5.0 53.3 1.0

Bromine binding site 4 out of 10 in 4ifd

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Bromine binding site 4 out of 10 in the Crystal Structure of An 11-Subunit Eukaryotic Exosome Complex Bound to Rna


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 An 11-Subunit Eukaryotic Exosome Complex Bound to Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Br301

b:0.9
occ:1.00
 N F:GLY11 3.5 55.5 1.0
CA F:GLY11 3.9 57.2 1.0
CA F:LEU9 3.9 53.6 1.0
CE1 C:TYR131 3.9 63.2 1.0
N F:LEU10 3.9 51.5 1.0
CD1 C:TYR131 3.9 54.9 1.0
CB F:LEU9 4.1 47.6 1.0
O F:GLY11 4.1 54.9 1.0
C F:LEU9 4.1 56.4 1.0
C F:GLY11 4.3 58.6 1.0
CG F:LEU9 4.4 47.3 1.0
C F:LEU10 4.6 57.5 1.0
CD2 F:LEU9 4.7 49.5 1.0
CA F:LEU10 4.8 46.8 1.0
O F:ARG8 4.9 59.7 1.0
CZ C:TYR131 4.9 63.5 1.0
CG C:TYR131 5.0 47.1 1.0

Bromine binding site 5 out of 10 in 4ifd

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Bromine binding site 5 out of 10 in the Crystal Structure of An 11-Subunit Eukaryotic Exosome Complex Bound to Rna


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 An 11-Subunit Eukaryotic Exosome Complex Bound to Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Br401

b:75.3
occ:1.00
 O H:HOH523 3.3 62.2 1.0
N H:GLN132 3.3 37.5 1.0
N H:LYS131 3.5 49.4 1.0
O H:GLN132 3.8 54.6 1.0
CD H:PRO106 4.1 42.9 1.0
CG H:PRO106 4.1 41.0 1.0
CB H:GLN132 4.1 38.4 1.0
CA H:GLN132 4.1 36.4 1.0
CB H:LYS131 4.1 41.8 1.0
CA H:LYS131 4.1 39.6 1.0
C H:LYS131 4.2 38.2 1.0
C H:GLY130 4.2 49.6 1.0
CA H:GLY130 4.3 46.5 1.0
CA H:SER181 4.3 43.1 1.0
C H:GLN132 4.4 42.2 1.0
O H:GLY180 4.4 43.7 1.0
CG H:GLN132 4.5 48.0 1.0
CG H:LYS131 4.6 40.4 1.0
N H:SER181 4.7 41.9 1.0
C H:GLY180 4.8 42.3 1.0
OG H:SER181 4.9 61.0 1.0

Bromine binding site 6 out of 10 in 4ifd

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Bromine binding site 6 out of 10 in the Crystal Structure of An 11-Subunit Eukaryotic Exosome Complex Bound to Rna


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 An 11-Subunit Eukaryotic Exosome Complex Bound to Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Br301

b:90.8
occ:1.00
 C I:ALA248 3.6 82.7 1.0
N I:ARG249 3.7 83.3 1.0
N I:SER212 3.7 85.8 1.0
NZ I:LYS287 3.7 64.2 1.0
O I:ARG249 3.8 87.5 1.0
C I:ARG249 3.8 84.5 1.0
CA I:ARG249 3.9 85.3 1.0
O I:ALA248 3.9 88.3 1.0
CB I:SER212 4.0 94.7 1.0
CA I:ALA248 4.1 81.0 1.0
CE I:LYS287 4.1 78.8 1.0
CA I:ARG211 4.2 79.8 1.0
CB I:ARG211 4.3 73.2 1.0
N I:ASN250 4.4 82.4 1.0
C I:ARG211 4.4 81.5 1.0
CA I:SER212 4.5 91.7 1.0
O I:THR247 4.5 89.8 1.0
OD1 I:ASN250 4.6 0.8 1.0
CB I:ALA248 4.9 80.1 1.0
CA I:ASN250 5.0 85.0 1.0

Bromine binding site 7 out of 10 in 4ifd

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Bromine binding site 7 out of 10 in the Crystal Structure of An 11-Subunit Eukaryotic Exosome Complex Bound to Rna


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 An 11-Subunit Eukaryotic Exosome Complex Bound to Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Br1101

b:76.5
occ:1.00
 CG J:PRO293 3.2 71.6 1.0
CG J:ARG294 3.2 65.5 1.0
N J:ARG294 3.2 71.1 1.0
CD J:PRO293 3.2 70.1 1.0
CB J:ARG294 3.3 69.4 1.0
NH2 J:ARG294 3.7 57.1 1.0
CD J:ARG294 3.7 66.7 1.0
CD1 J:TYR274 3.7 70.2 1.0
N J:PRO293 3.8 73.7 1.0
CA J:ARG294 3.9 71.2 1.0
CB J:LEU292 4.0 67.4 1.0
CB J:TYR274 4.1 61.2 1.0
CG2 C:THR258 4.1 0.1 1.0
C J:PRO293 4.2 76.6 1.0
CG J:TYR274 4.3 67.5 1.0
CB J:PRO293 4.3 73.8 1.0
CA J:PRO293 4.3 74.3 1.0
C J:LEU292 4.4 78.2 1.0
NE J:ARG294 4.5 67.3 1.0
CZ J:ARG294 4.5 66.1 1.0
CA J:LEU292 4.5 74.0 1.0
CE1 J:TYR274 4.6 71.0 1.0
CD1 J:PHE295 4.7 65.8 1.0
CD2 J:LEU292 4.7 66.9 1.0
CE1 J:PHE295 4.7 63.8 1.0
CG J:LEU292 4.8 66.1 1.0
CD1 J:LEU292 4.9 66.1 1.0
C J:ARG294 4.9 71.1 1.0
CA J:TYR274 5.0 59.2 1.0

Bromine binding site 8 out of 10 in 4ifd

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Bromine binding site 8 out of 10 in the Crystal Structure of An 11-Subunit Eukaryotic Exosome Complex Bound to Rna


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 An 11-Subunit Eukaryotic Exosome Complex Bound to Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Br1102

b:0.9
occ:1.00
 N J:MET606 3.0 78.7 1.0
CG J:MET606 3.0 80.0 1.0
CB J:MET606 3.5 80.6 1.0
CA J:PRO605 3.7 72.9 1.0
CD2 J:PHE495 3.8 77.0 1.0
C J:PRO605 3.8 74.4 1.0
CA J:MET606 3.8 78.6 1.0
CE2 J:PHE495 3.9 75.6 1.0
CB J:PRO605 4.3 70.7 1.0
SD J:MET606 4.5 0.2 1.0
N J:PRO605 5.0 74.2 1.0

Bromine binding site 9 out of 10 in 4ifd

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Bromine binding site 9 out of 10 in the Crystal Structure of An 11-Subunit Eukaryotic Exosome Complex Bound to Rna


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 9 of Crystal Structure of An 11-Subunit Eukaryotic Exosome Complex Bound to Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Br1103

b:0.9
occ:1.00
 NE J:ARG137 3.4 69.2 1.0
CD J:ARG137 3.5 66.5 1.0
O J:HOH1226 3.6 57.0 1.0
CB J:ARG137 4.1 61.4 1.0
CG B:PRO9 4.1 50.1 1.0
CG J:ARG137 4.3 64.0 1.0
CD J:ARG133 4.6 47.8 1.0
CZ J:ARG137 4.6 75.0 1.0
O J:ARG133 4.8 68.5 1.0
CB J:ARG133 4.9 52.0 1.0

Bromine binding site 10 out of 10 in 4ifd

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Bromine binding site 10 out of 10 in the Crystal Structure of An 11-Subunit Eukaryotic Exosome Complex Bound to Rna


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 10 of Crystal Structure of An 11-Subunit Eukaryotic Exosome Complex Bound to Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Br1104

b:0.5
occ:1.00
 CA J:TYR618 3.7 83.3 1.0
CD1 J:TYR618 3.8 91.5 1.0
O J:SER648 3.8 90.8 1.0
CG J:ARG647 4.0 71.5 1.0
CD J:ARG647 4.0 75.9 1.0
NE J:ARG647 4.0 81.9 1.0
N J:TYR618 4.1 82.9 1.0
NE J:ARG649 4.2 85.5 1.0
CZ J:ARG649 4.2 84.9 1.0
NH1 J:ARG649 4.3 82.3 1.0
CA J:ARG649 4.3 93.8 1.0
O J:ARG649 4.4 0.8 1.0
CB J:TYR618 4.5 83.1 1.0
C J:SER648 4.6 89.8 1.0
C J:TYR618 4.6 81.2 1.0
CG J:TYR618 4.6 87.1 1.0
CE1 J:TYR618 4.6 96.3 1.0
NH2 J:ARG649 4.8 85.8 1.0
C J:ARG649 4.8 0.1 1.0
N J:ARG649 4.8 92.2 1.0
CD J:ARG649 4.8 86.8 1.0
O J:ARG647 5.0 81.1 1.0
O J:TYR618 5.0 88.0 1.0

Reference:

D.L.Makino, M.Baumgartner, E.Conti. Crystal Structure of An Rna-Bound 11-Subunit Eukaryotic Exosome Complex. Nature V. 495 70 2013.
ISSN: ISSN 0028-0836
PubMed: 23376952
DOI: 10.1038/NATURE11870
Page generated: Wed Jul 10 21:38:18 2024

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