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Bromine in PDB 4g86: Crystal Structure of the Redox-Active Cofactor Dbmib Bound to the Full Length Circadian Clock Protein Kaia From Synechococcus Elongatus

Protein crystallography data

The structure of Crystal Structure of the Redox-Active Cofactor Dbmib Bound to the Full Length Circadian Clock Protein Kaia From Synechococcus Elongatus, PDB code: 4g86 was solved by R.Pattanayek, M.Egli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.58 / 2.39
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 47.247, 126.354, 56.383, 90.00, 114.36, 90.00
R / Rfree (%) 21.9 / 26.5

Bromine Binding Sites:

The binding sites of Bromine atom in the Crystal Structure of the Redox-Active Cofactor Dbmib Bound to the Full Length Circadian Clock Protein Kaia From Synechococcus Elongatus (pdb code 4g86). 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 the Redox-Active Cofactor Dbmib Bound to the Full Length Circadian Clock Protein Kaia From Synechococcus Elongatus, PDB code: 4g86:
Jump to Bromine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Bromine binding site 1 out of 8 in 4g86

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Bromine binding site 1 out of 8 in the Crystal Structure of the Redox-Active Cofactor Dbmib Bound to the Full Length Circadian Clock Protein Kaia From Synechococcus Elongatus


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 the Redox-Active Cofactor Dbmib Bound to the Full Length Circadian Clock Protein Kaia From Synechococcus Elongatus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br301

b:64.2
occ:0.70
 BRAH A:BNT301 0.0 64.2 0.7
CAG A:BNT301 1.9 65.9 0.7
CAL A:BNT301 2.9 62.5 0.7
CAF A:BNT301 3.0 63.8 0.7
OAB A:BNT301 3.1 69.5 0.7
CAM A:BNT301 3.1 64.9 0.7
OG A:SER87 3.3 44.4 1.0
NH2 A:ARG85 3.6 43.9 1.0
CB A:SER87 4.0 42.1 1.0
CAK A:BNT301 4.3 53.2 0.7
CAE A:BNT301 4.4 61.7 0.7
CZ A:ARG85 4.6 49.8 1.0
CAJ A:BNT301 4.9 58.2 0.7
NH1 A:ARG85 5.0 47.9 1.0

Bromine binding site 2 out of 8 in 4g86

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Bromine binding site 2 out of 8 in the Crystal Structure of the Redox-Active Cofactor Dbmib Bound to the Full Length Circadian Clock Protein Kaia From Synechococcus Elongatus


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 the Redox-Active Cofactor Dbmib Bound to the Full Length Circadian Clock Protein Kaia From Synechococcus Elongatus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br301

b:75.5
occ:0.70
 BRAI A:BNT301 0.0 75.5 0.7
CAJ A:BNT301 1.9 58.2 0.7
N A:ARG64 2.6 31.8 1.0
N A:ALA65 2.8 33.9 1.0
CAE A:BNT301 2.9 61.7 0.7
CB A:ARG64 2.9 45.3 1.0
CAK A:BNT301 3.0 53.2 0.7
CA A:ARG64 3.0 37.8 1.0
OAN A:BNT301 3.1 45.0 0.7
C A:SER62 3.1 33.8 1.0
CAC A:BNT301 3.2 57.4 0.7
CAD A:BNT301 3.2 62.5 0.7
N A:PHE63 3.3 33.1 1.0
CAA A:BNT301 3.3 65.8 0.7
C A:ARG64 3.4 35.5 1.0
CA A:SER62 3.5 37.4 1.0
O A:SER62 3.5 36.3 1.0
C A:PHE63 3.5 30.2 1.0
CG A:ARG64 3.7 53.7 1.0
CA A:PHE63 3.9 31.9 1.0
CA A:ALA65 4.0 29.6 1.0
CB A:ALA65 4.0 29.7 1.0
CAF A:BNT301 4.3 63.8 0.7
CAL A:BNT301 4.4 62.5 0.7
CB A:SER62 4.4 32.6 1.0
CD A:ARG64 4.4 62.9 1.0
O A:PHE63 4.4 25.8 1.0
N A:SER62 4.5 36.3 1.0
O A:ARG64 4.6 29.4 1.0
CB A:PHE63 4.7 33.0 1.0
CAG A:BNT301 4.9 65.9 0.7

Bromine binding site 3 out of 8 in 4g86

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Bromine binding site 3 out of 8 in the Crystal Structure of the Redox-Active Cofactor Dbmib Bound to the Full Length Circadian Clock Protein Kaia From Synechococcus Elongatus


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 the Redox-Active Cofactor Dbmib Bound to the Full Length Circadian Clock Protein Kaia From Synechococcus Elongatus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br304

b:56.9
occ:0.70
 BRAH A:BNT304 0.0 56.9 0.7
CAG A:BNT304 1.9 50.9 0.7
CAL A:BNT304 2.9 50.5 0.7
CAF A:BNT304 3.0 48.5 0.7
CAM A:BNT304 3.1 48.0 0.7
OAB A:BNT304 3.1 49.3 0.7
O B:HOH1434 3.1 37.1 1.0
OE1 B:GLU274 3.6 30.6 1.0
CD B:GLU274 3.8 33.7 1.0
NH2 B:ARG277 4.1 30.4 1.0
OE2 B:GLU274 4.2 33.3 1.0
CAK A:BNT304 4.3 45.8 0.7
CG B:GLU274 4.3 32.3 1.0
O B:HOH1442 4.3 32.9 1.0
CAE A:BNT304 4.4 46.6 0.7
CB B:GLU274 4.8 24.9 1.0
CAJ A:BNT304 4.9 50.1 0.7
CB A:PRO229 4.9 36.3 1.0

Bromine binding site 4 out of 8 in 4g86

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Bromine binding site 4 out of 8 in the Crystal Structure of the Redox-Active Cofactor Dbmib Bound to the Full Length Circadian Clock Protein Kaia From Synechococcus Elongatus


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 the Redox-Active Cofactor Dbmib Bound to the Full Length Circadian Clock Protein Kaia From Synechococcus Elongatus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br304

b:55.6
occ:0.70
 BRAI A:BNT304 0.0 55.6 0.7
CAJ A:BNT304 1.9 50.1 0.7
CAE A:BNT304 2.9 46.6 0.7
CAK A:BNT304 3.0 45.8 0.7
CAD A:BNT304 3.0 44.2 0.7
OAN A:BNT304 3.1 47.3 0.7
CAC A:BNT304 3.7 42.4 0.7
CG A:PRO229 4.0 35.5 1.0
CAA A:BNT304 4.3 41.7 0.7
CAF A:BNT304 4.3 48.5 0.7
CAL A:BNT304 4.4 50.5 0.7
CD A:PRO229 4.8 34.3 1.0
CAG A:BNT304 4.9 50.9 0.7
CB A:PRO229 4.9 36.3 1.0

Bromine binding site 5 out of 8 in 4g86

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Bromine binding site 5 out of 8 in the Crystal Structure of the Redox-Active Cofactor Dbmib Bound to the Full Length Circadian Clock Protein Kaia From Synechococcus Elongatus


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 the Redox-Active Cofactor Dbmib Bound to the Full Length Circadian Clock Protein Kaia From Synechococcus Elongatus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br1301

b:59.4
occ:0.70
 BRAH B:BNT1301 0.0 59.4 0.7
CAG B:BNT1301 1.9 43.5 0.7
CAL B:BNT1301 2.9 43.9 0.7
CAF B:BNT1301 3.0 43.5 0.7
OE2 A:GLU112 3.0 45.0 1.0
OAB B:BNT1301 3.1 34.1 0.7
CAM B:BNT1301 3.1 43.8 0.7
O B:LYS189 3.3 27.0 1.0
CB B:ALA193 3.4 24.7 1.0
CG A:GLU112 3.5 36.8 1.0
C B:LYS189 3.7 29.5 1.0
O A:HOH433 3.7 38.4 1.0
CD A:GLU112 3.7 42.7 1.0
CB B:LYS189 4.0 32.9 1.0
CB A:GLU112 4.1 34.0 1.0
CD B:LYS189 4.1 43.6 1.0
N B:LEU190 4.2 21.3 1.0
O A:GLU112 4.2 30.0 1.0
CAK B:BNT1301 4.3 45.4 0.7
CAE B:BNT1301 4.3 44.8 0.7
CA B:LYS189 4.4 30.0 1.0
CA B:LEU190 4.4 25.1 1.0
CG B:LYS189 4.6 39.7 1.0
C A:GLU112 4.6 28.7 1.0
CA B:ALA193 4.6 27.1 1.0
N B:ALA193 4.7 26.4 1.0
CAJ B:BNT1301 4.8 43.8 0.7
OE1 A:GLU112 5.0 39.6 1.0

Bromine binding site 6 out of 8 in 4g86

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Bromine binding site 6 out of 8 in the Crystal Structure of the Redox-Active Cofactor Dbmib Bound to the Full Length Circadian Clock Protein Kaia From Synechococcus Elongatus


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 the Redox-Active Cofactor Dbmib Bound to the Full Length Circadian Clock Protein Kaia From Synechococcus Elongatus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br1301

b:60.1
occ:0.70
 BRAI B:BNT1301 0.0 60.1 0.7
CAJ B:BNT1301 1.9 43.8 0.7
CAE B:BNT1301 2.9 44.8 0.7
CAK B:BNT1301 3.0 45.4 0.7
OAN B:BNT1301 3.1 52.8 0.7
CAD B:BNT1301 3.1 34.6 0.7
OH7 A:1PE302 3.2 38.6 1.0
CG B:GLU186 3.3 27.2 1.0
CAA B:BNT1301 4.0 24.4 0.7
OE1 B:GLU186 4.1 37.5 1.0
CD B:GLU186 4.2 36.6 1.0
CAC B:BNT1301 4.2 33.6 0.7
C16 A:1PE302 4.3 40.5 1.0
CAF B:BNT1301 4.3 43.5 0.7
CAL B:BNT1301 4.4 43.9 0.7
O A:HOH472 4.4 48.3 1.0
CB B:GLU186 4.4 31.0 1.0
C26 A:1PE302 4.6 37.0 1.0
C6 A:2PE303 4.8 53.8 1.0
CAG B:BNT1301 4.8 43.5 0.7
CA B:GLU186 4.8 27.6 1.0
O7 A:2PE303 5.0 54.9 1.0

Bromine binding site 7 out of 8 in 4g86

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Bromine binding site 7 out of 8 in the Crystal Structure of the Redox-Active Cofactor Dbmib Bound to the Full Length Circadian Clock Protein Kaia From Synechococcus Elongatus


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 the Redox-Active Cofactor Dbmib Bound to the Full Length Circadian Clock Protein Kaia From Synechococcus Elongatus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br1302

b:51.0
occ:0.70
 BRAH B:BNT1302 0.0 51.0 0.7
CAG B:BNT1302 1.9 60.3 0.7
CAL B:BNT1302 2.9 55.9 0.7
CAF B:BNT1302 3.0 68.1 0.7
CAM B:BNT1302 3.1 63.0 0.7
OAB B:BNT1302 3.1 68.9 0.7
CA B:SER62 4.0 48.9 1.0
OG B:SER62 4.2 48.7 1.0
CAK B:BNT1302 4.3 54.6 0.7
CAE B:BNT1302 4.4 67.4 0.7
CB B:SER62 4.4 48.7 1.0
N B:SER62 4.6 47.5 1.0
CAJ B:BNT1302 4.9 58.9 0.7
NH1 B:ARG64 4.9 57.4 1.0
C B:SER62 4.9 47.1 1.0

Bromine binding site 8 out of 8 in 4g86

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Bromine binding site 8 out of 8 in the Crystal Structure of the Redox-Active Cofactor Dbmib Bound to the Full Length Circadian Clock Protein Kaia From Synechococcus Elongatus


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 the Redox-Active Cofactor Dbmib Bound to the Full Length Circadian Clock Protein Kaia From Synechococcus Elongatus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br1302

b:58.1
occ:0.70
 BRAI B:BNT1302 0.0 58.1 0.7
CAJ B:BNT1302 1.9 58.9 0.7
CAE B:BNT1302 2.9 67.4 0.7
CAK B:BNT1302 3.0 54.6 0.7
OAN B:BNT1302 3.1 52.2 0.7
CAA B:BNT1302 3.2 63.4 0.7
CAD B:BNT1302 3.2 64.7 0.7
CAC B:BNT1302 3.3 57.1 0.7
O B:ALA58 3.6 47.0 1.0
CB B:ARG85 3.7 57.8 1.0
CG B:ARG85 3.8 57.9 1.0
O B:ALA59 3.9 48.5 1.0
O B:ASN60 3.9 51.2 1.0
CD B:ARG85 3.9 63.4 1.0
C B:ALA59 4.1 45.2 1.0
CA B:ALA59 4.2 46.2 1.0
O B:HOH1444 4.2 44.4 1.0
CB B:PHE63 4.3 49.9 1.0
CAF B:BNT1302 4.3 68.1 0.7
OD1 B:ASP86 4.3 69.2 1.0
CAL B:BNT1302 4.4 55.9 0.7
CA B:ARG85 4.4 58.9 1.0
C B:ALA58 4.6 45.7 1.0
C B:ASN60 4.8 50.3 1.0
N B:PHE63 4.8 43.9 1.0
N B:ASN60 4.8 45.8 1.0
CAG B:BNT1302 4.9 60.3 0.7
NE B:ARG85 4.9 65.9 1.0
N B:ASP86 4.9 66.2 1.0
N B:ALA59 4.9 41.4 1.0

Reference:

R.Pattanayek, S.K.Sidiqi, M.Egli. Crystal Structure of the Redox-Active Cofactor Dibromothymoquinone Bound to Circadian Clock Protein Kaia and Structural Basis For Dibromothymoquinone'S Ability to Prevent Stimulation of Kaic Phosphorylation By Kaia. Biochemistry V. 51 8050 2012.
ISSN: ISSN 0006-2960
PubMed: 23020633
DOI: 10.1021/BI301222T
Page generated: Wed Jul 10 21:21:28 2024

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