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Bromine in PDB 2fe8: Sars Coronavirus Papain-Like Protease: Structure of A Viral Deubiquitinating Enzyme

Protein crystallography data

The structure of Sars Coronavirus Papain-Like Protease: Structure of A Viral Deubiquitinating Enzyme, PDB code: 2fe8 was solved by K.Ratia, B.D.Santarsiero, A.D.Mesecar, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.85
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 142.872, 103.065, 91.728, 90.00, 111.15, 90.00
R / Rfree (%) 20.1 / 22.9

Other elements in 2fe8:

The structure of Sars Coronavirus Papain-Like Protease: Structure of A Viral Deubiquitinating Enzyme also contains other interesting chemical elements:

Zinc (Zn) 3 atoms

Bromine Binding Sites:

The binding sites of Bromine atom in the Sars Coronavirus Papain-Like Protease: Structure of A Viral Deubiquitinating Enzyme (pdb code 2fe8). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 9 binding sites of Bromine where determined in the Sars Coronavirus Papain-Like Protease: Structure of A Viral Deubiquitinating Enzyme, PDB code: 2fe8:
Jump to Bromine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Bromine binding site 1 out of 9 in 2fe8

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Bromine binding site 1 out of 9 in the Sars Coronavirus Papain-Like Protease: Structure of A Viral Deubiquitinating Enzyme


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Sars Coronavirus Papain-Like Protease: Structure of A Viral Deubiquitinating Enzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br317

b:36.5
occ:1.00
 N A:LYS307 3.3 20.1 1.0
O A:HOH468 3.3 39.8 1.0
C A:PHE259 3.6 22.6 1.0
N A:LEU260 3.6 19.7 1.0
CA A:PHE259 3.7 22.6 1.0
CA A:TYR306 3.8 18.4 1.0
C A:TYR306 4.1 18.8 1.0
O A:PHE259 4.2 21.8 1.0
CB A:TYR306 4.2 16.5 1.0
N A:PHE259 4.2 23.8 1.0
CB A:LEU260 4.2 21.4 1.0
CB A:LYS307 4.2 26.4 1.0
CA A:LEU260 4.3 19.5 1.0
CA A:LYS307 4.3 21.3 1.0
CD1 A:TYR306 4.4 17.1 1.0
O A:LYS307 4.5 21.5 1.0
C A:THR258 4.7 25.8 1.0
O A:THR258 4.7 25.6 1.0
CG A:TYR306 4.7 16.9 1.0
O A:PHE305 4.9 19.6 1.0
C A:LYS307 4.9 22.1 1.0

Bromine binding site 2 out of 9 in 2fe8

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Bromine binding site 2 out of 9 in the Sars Coronavirus Papain-Like Protease: Structure of A Viral Deubiquitinating Enzyme


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Sars Coronavirus Papain-Like Protease: Structure of A Viral Deubiquitinating Enzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br318

b:54.4
occ:1.00
 N A:PHE128 3.2 24.1 1.0
CA A:GLN134 3.4 28.7 1.0
CB A:GLN134 3.5 31.4 1.0
CA A:LYS127 3.6 28.6 1.0
CB A:LYS127 3.9 33.7 1.0
C A:LYS127 3.9 27.6 1.0
CG A:GLN134 4.1 37.4 1.0
O A:PHE128 4.1 24.8 1.0
CD2 A:PHE128 4.1 21.8 1.0
O A:GLN134 4.2 28.3 1.0
CA A:PHE128 4.2 23.9 1.0
C A:GLN134 4.3 26.7 1.0
CB A:PHE128 4.3 22.9 1.0
N A:GLN134 4.5 25.7 1.0
CD2 A:TYR137 4.5 30.2 1.0
C A:PHE128 4.6 23.8 1.0
CG A:PHE128 4.7 21.8 1.0
O A:VAL126 4.7 27.1 1.0
CD A:GLN134 4.9 39.5 1.0
N A:LYS127 4.9 25.2 1.0
CG A:LYS127 4.9 39.3 1.0
CB A:TYR137 5.0 25.5 1.0

Bromine binding site 3 out of 9 in 2fe8

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Bromine binding site 3 out of 9 in the Sars Coronavirus Papain-Like Protease: Structure of A Viral Deubiquitinating Enzyme


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of Sars Coronavirus Papain-Like Protease: Structure of A Viral Deubiquitinating Enzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br319

b:44.6
occ:1.00
 O A:HOH362 3.2 24.8 1.0
N A:VAL160 3.3 25.6 1.0
OG A:SER86 3.5 30.5 1.0
CA A:ALA87 3.7 22.0 1.0
N A:ALA87 3.8 23.4 1.0
CG2 A:VAL160 3.8 27.1 1.0
CB A:THR159 3.8 26.4 1.0
CA A:THR159 3.9 24.8 1.0
CB A:VAL160 3.9 26.1 1.0
C A:SER86 4.0 25.2 1.0
O A:SER86 4.0 22.8 1.0
CB A:ALA87 4.1 20.4 1.0
C A:THR159 4.1 24.3 1.0
CD2 A:HIS90 4.2 34.0 1.0
CA A:VAL160 4.3 25.9 1.0
CB A:SER86 4.3 26.7 1.0
CG2 A:THR159 4.3 26.5 1.0
O A:HOH413 4.4 32.4 1.0
NE2 A:HIS90 4.7 35.4 1.0
CA A:SER86 4.8 25.0 1.0
O A:ARG83 5.0 28.9 1.0
O A:VAL160 5.0 26.6 1.0

Bromine binding site 4 out of 9 in 2fe8

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Bromine binding site 4 out of 9 in the Sars Coronavirus Papain-Like Protease: Structure of A Viral Deubiquitinating Enzyme


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 4 of Sars Coronavirus Papain-Like Protease: Structure of A Viral Deubiquitinating Enzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br317

b:40.8
occ:1.00
 N B:LYS307 3.3 25.7 1.0
C B:PHE259 3.6 25.3 1.0
N B:LEU260 3.7 24.0 1.0
CA B:PHE259 3.7 24.6 1.0
CA B:TYR306 3.9 22.8 1.0
CB B:LYS307 4.0 32.8 1.0
C B:TYR306 4.1 24.3 1.0
N B:PHE259 4.1 27.9 1.0
O B:PHE259 4.1 24.8 1.0
CB B:TYR306 4.2 22.0 1.0
CA B:LYS307 4.2 28.5 1.0
CA B:LEU260 4.3 25.9 1.0
CD1 B:TYR306 4.4 22.4 1.0
CB B:LEU260 4.4 25.7 1.0
O B:LYS307 4.4 27.9 1.0
C B:THR258 4.4 29.6 1.0
O B:THR258 4.5 29.0 1.0
CG B:TYR306 4.7 22.2 1.0
C B:LYS307 4.8 28.3 1.0
O B:PHE305 4.9 23.6 1.0

Bromine binding site 5 out of 9 in 2fe8

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Bromine binding site 5 out of 9 in the Sars Coronavirus Papain-Like Protease: Structure of A Viral Deubiquitinating Enzyme


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 5 of Sars Coronavirus Papain-Like Protease: Structure of A Viral Deubiquitinating Enzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br318

b:41.8
occ:1.00
 O B:HOH373 3.0 28.9 1.0
N B:PHE128 3.3 25.1 1.0
CA B:LYS127 3.6 30.1 1.0
CA B:GLN134 3.8 22.9 1.0
CB B:LYS127 3.8 34.6 1.0
CB B:GLN134 4.0 25.5 1.0
C B:LYS127 4.0 28.8 1.0
CG B:GLN134 4.0 29.9 1.0
CD2 B:PHE128 4.2 21.2 1.0
O B:PHE128 4.3 27.8 1.0
CA B:PHE128 4.3 24.5 1.0
CB B:PHE128 4.3 22.8 1.0
CD2 B:TYR137 4.4 29.3 1.0
O B:GLN134 4.5 20.1 1.0
O B:VAL126 4.6 27.2 1.0
C B:GLN134 4.7 23.3 1.0
CG B:PHE128 4.7 20.9 1.0
N B:GLN134 4.7 20.8 1.0
C B:PHE128 4.8 24.3 1.0
N B:LYS127 4.9 28.5 1.0
O B:HOH486 4.9 48.4 1.0
CD B:GLN134 4.9 33.8 1.0
CB B:TYR137 4.9 22.4 1.0

Bromine binding site 6 out of 9 in 2fe8

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Bromine binding site 6 out of 9 in the Sars Coronavirus Papain-Like Protease: Structure of A Viral Deubiquitinating Enzyme


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 6 of Sars Coronavirus Papain-Like Protease: Structure of A Viral Deubiquitinating Enzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br319

b:54.3
occ:1.00
 O B:HOH395 3.0 30.4 1.0
N B:VAL160 3.4 25.5 1.0
OG B:SER86 3.6 32.0 1.0
CA B:ALA87 3.6 24.3 1.0
N B:ALA87 3.8 24.3 1.0
CG2 B:VAL160 3.8 26.4 1.0
CB B:THR159 3.8 28.5 1.0
CB B:VAL160 3.9 26.1 1.0
C B:SER86 3.9 26.6 1.0
O B:SER86 3.9 26.5 1.0
CA B:THR159 3.9 26.3 1.0
CB B:ALA87 4.1 23.7 1.0
O B:HOH438 4.2 38.2 1.0
C B:THR159 4.2 25.0 1.0
CG2 B:THR159 4.2 28.0 1.0
CB B:SER86 4.3 30.6 1.0
CA B:VAL160 4.3 26.1 1.0
CD2 B:HIS90 4.4 39.2 1.0
CA B:SER86 4.8 26.2 1.0
O B:ARG83 4.9 22.4 1.0
NE2 B:HIS90 5.0 39.3 1.0
C B:ALA87 5.0 23.1 1.0

Bromine binding site 7 out of 9 in 2fe8

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Bromine binding site 7 out of 9 in the Sars Coronavirus Papain-Like Protease: Structure of A Viral Deubiquitinating Enzyme


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 7 of Sars Coronavirus Papain-Like Protease: Structure of A Viral Deubiquitinating Enzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Br317

b:39.5
occ:1.00
 N C:LYS307 3.4 22.4 1.0
O C:HOH403 3.5 36.5 1.0
C C:PHE259 3.7 21.9 1.0
N C:LEU260 3.7 21.3 1.0
CA C:PHE259 3.7 22.9 1.0
CA C:TYR306 3.9 20.9 1.0
C C:TYR306 4.1 23.0 1.0
N C:PHE259 4.1 23.7 1.0
CB C:LYS307 4.2 28.5 1.0
CB C:TYR306 4.2 20.0 1.0
O C:PHE259 4.2 20.5 1.0
CA C:LYS307 4.3 24.4 1.0
O C:THR258 4.3 25.9 1.0
CD1 C:TYR306 4.4 20.5 1.0
CA C:LEU260 4.4 21.8 1.0
C C:THR258 4.4 24.9 1.0
CG C:LEU260 4.5 31.6 1.0
CB C:LEU260 4.5 25.0 1.0
O C:LYS307 4.7 24.2 1.0
CG C:LYS307 4.7 34.5 1.0
CG C:TYR306 4.7 20.7 1.0
O C:PHE305 4.9 19.8 1.0

Bromine binding site 8 out of 9 in 2fe8

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Bromine binding site 8 out of 9 in the Sars Coronavirus Papain-Like Protease: Structure of A Viral Deubiquitinating Enzyme


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 8 of Sars Coronavirus Papain-Like Protease: Structure of A Viral Deubiquitinating Enzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Br318

b:38.9
occ:1.00
 O C:HOH412 3.1 36.3 1.0
O C:HOH336 3.2 24.8 1.0
N C:PHE128 3.4 22.3 1.0
CG C:GLN134 3.7 27.8 1.0
CA C:LYS127 3.8 26.8 1.0
CA C:GLN134 3.9 22.6 1.0
CD C:LYS127 4.1 39.7 1.0
C C:LYS127 4.1 25.1 1.0
CD2 C:PHE128 4.1 21.3 1.0
CD2 C:TYR137 4.2 25.8 1.0
CB C:GLN134 4.2 24.5 1.0
CB C:LYS127 4.4 28.9 1.0
CB C:PHE128 4.4 19.2 1.0
CA C:PHE128 4.4 22.0 1.0
O C:VAL126 4.4 30.0 1.0
O C:PHE128 4.5 25.2 1.0
O C:GLN134 4.6 22.0 1.0
CG C:PHE128 4.7 20.2 1.0
C C:GLN134 4.8 22.8 1.0
N C:GLN134 4.8 21.3 1.0
CB C:TYR137 4.9 20.0 1.0
CG C:LYS127 4.9 36.0 1.0
N C:LYS127 4.9 26.3 1.0
CE2 C:TYR137 5.0 28.6 1.0
CD C:GLN134 5.0 30.1 1.0
C C:PHE128 5.0 23.0 1.0

Bromine binding site 9 out of 9 in 2fe8

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Bromine binding site 9 out of 9 in the Sars Coronavirus Papain-Like Protease: Structure of A Viral Deubiquitinating Enzyme


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 9 of Sars Coronavirus Papain-Like Protease: Structure of A Viral Deubiquitinating Enzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Br319

b:52.0
occ:1.00
 O C:HOH328 3.1 22.1 1.0
N C:VAL160 3.3 26.6 1.0
CA C:ALA87 3.6 21.2 1.0
N C:ALA87 3.7 23.1 1.0
CG2 C:VAL160 3.8 25.5 1.0
O C:HOH452 3.8 45.7 1.0
CB C:THR159 3.8 28.6 1.0
CB C:VAL160 3.8 26.7 1.0
CA C:THR159 3.9 26.6 1.0
CB C:ALA87 4.0 17.8 1.0
C C:SER86 4.0 24.3 1.0
C C:THR159 4.1 25.2 1.0
O C:SER86 4.1 24.8 1.0
CA C:VAL160 4.2 26.8 1.0
CG2 C:THR159 4.2 30.4 1.0
ND1 C:HIS90 4.3 36.8 1.0
CB C:SER86 4.3 24.5 1.0
O C:HOH383 4.4 32.3 1.0
CE1 C:HIS90 4.6 37.6 1.0
O C:VAL160 4.8 26.8 1.0
CA C:SER86 4.9 25.2 1.0
O C:ARG83 4.9 22.9 1.0
C C:ALA87 5.0 20.8 1.0

Reference:

K.Ratia, K.S.Saikatendu, B.D.Santarsiero, N.Barretto, S.C.Baker, R.C.Stevens, A.D.Mesecar. Severe Acute Respiratory Syndrome Coronavirus Papain-Like Protease: Structure of A Viral Deubiquitinating Enzyme Proc.Natl.Acad.Sci.Usa V. 103 5717 2006.
ISSN: ISSN 0027-8424
PubMed: 16581910
DOI: 10.1073/PNAS.0510851103
Page generated: Sat Dec 12 02:05:44 2020

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