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Bromine in PDB 1kgj: Rat Transthyretin (Also Called Prealbumin) Complex with 3', 5'-Dibromoflavone (EMD21388)

Protein crystallography data

The structure of Rat Transthyretin (Also Called Prealbumin) Complex with 3', 5'-Dibromoflavone (EMD21388), PDB code: 1kgj was solved by A.Wojtczak, P.Neumann, T.Muziol, V.Cody, J.R.Luft, W.Pangborn, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 12.00 / 2.30
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 82.545, 82.545, 161.741, 90.00, 90.00, 90.00
R / Rfree (%) 20.3 / 28.8

Bromine Binding Sites:

The binding sites of Bromine atom in the Rat Transthyretin (Also Called Prealbumin) Complex with 3', 5'-Dibromoflavone (EMD21388) (pdb code 1kgj). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 6 binding sites of Bromine where determined in the Rat Transthyretin (Also Called Prealbumin) Complex with 3', 5'-Dibromoflavone (EMD21388), PDB code: 1kgj:
Jump to Bromine binding site number: 1; 2; 3; 4; 5; 6;

Bromine binding site 1 out of 6 in 1kgj

Go back to Bromine Binding Sites List in 1kgj
Bromine binding site 1 out of 6 in the Rat Transthyretin (Also Called Prealbumin) Complex with 3', 5'-Dibromoflavone (EMD21388)


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Rat Transthyretin (Also Called Prealbumin) Complex with 3', 5'-Dibromoflavone (EMD21388) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br328

b:15.2
occ:0.40
 BR3 B:FL8328 0.0 15.2 0.4
C3' B:FL8328 1.9 10.5 0.4
C4' B:FL8328 2.8 11.2 0.4
C2' B:FL8328 2.9 10.3 0.4
O4' B:FL8328 3.0 6.3 0.4
OG1 B:THR319 3.2 7.0 1.0
O B:ALA308 3.4 3.0 1.0
O B:SER317 3.4 1.8 1.0
OG B:SER317 3.5 3.6 1.0
C B:SER317 3.8 1.8 1.0
C B:ALA308 4.1 5.2 1.0
C5' B:FL8328 4.1 11.9 0.4
CB B:LEU310 4.1 5.5 1.0
N B:LEU310 4.1 3.6 1.0
C B:THR318 4.2 1.8 1.0
CB B:THR319 4.2 3.8 1.0
C1' B:FL8328 4.2 9.8 0.4
CA B:THR318 4.2 1.8 1.0
N B:THR318 4.2 1.9 1.0
CB B:SER317 4.2 3.0 1.0
N B:THR319 4.3 2.1 1.0
CD2 D:LEU710 4.4 1.8 1.0
C B:ALA309 4.4 1.8 1.0
CA B:ALA309 4.4 2.2 1.0
N B:ALA309 4.5 3.7 1.0
CB B:ALA308 4.6 7.4 1.0
O B:THR318 4.6 2.8 1.0
C6' B:FL8328 4.6 11.1 0.4
CA B:SER317 4.6 1.8 1.0
CA B:LEU310 4.8 3.5 1.0
CA B:THR319 4.9 2.4 1.0
CA B:ALA308 5.0 6.3 1.0

Bromine binding site 2 out of 6 in 1kgj

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Bromine binding site 2 out of 6 in the Rat Transthyretin (Also Called Prealbumin) Complex with 3', 5'-Dibromoflavone (EMD21388)


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Rat Transthyretin (Also Called Prealbumin) Complex with 3', 5'-Dibromoflavone (EMD21388) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br328

b:21.1
occ:0.40
 BR5 B:FL8328 0.0 21.1 0.4
C5' B:FL8328 1.9 11.9 0.4
C4' B:FL8328 2.8 11.2 0.4
C6' B:FL8328 2.9 11.1 0.4
O4' B:FL8328 3.0 6.3 0.4
O D:SER717 3.3 2.5 1.0
CG2 D:THR719 3.8 3.4 1.0
OG D:SER717 3.8 10.6 1.0
C D:SER717 3.8 2.9 1.0
O D:ALA708 3.8 8.6 1.0
N D:LEU710 3.9 4.4 1.0
C D:ALA708 4.0 6.8 1.0
C3' B:FL8328 4.1 10.5 0.4
N D:THR719 4.1 1.8 1.0
CA D:ALA709 4.1 5.5 1.0
N D:ALA709 4.1 5.6 1.0
CA D:THR718 4.1 3.0 1.0
CB D:LEU710 4.1 1.8 1.0
C1' B:FL8328 4.2 9.8 0.4
N D:THR718 4.2 3.2 1.0
C D:THR718 4.2 1.8 1.0
CB D:ALA708 4.2 7.0 1.0
CB D:THR719 4.2 3.1 1.0
CB D:SER717 4.2 4.6 1.0
C D:ALA709 4.3 4.5 1.0
C2' B:FL8328 4.6 10.3 0.4
CA D:LEU710 4.7 3.0 1.0
CA D:SER717 4.7 4.5 1.0
CA D:ALA708 4.8 6.6 1.0
CA D:THR719 4.8 2.4 1.0
O D:THR718 4.8 1.8 1.0
CD2 B:LEU310 4.9 8.6 1.0

Bromine binding site 3 out of 6 in 1kgj

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Bromine binding site 3 out of 6 in the Rat Transthyretin (Also Called Prealbumin) Complex with 3', 5'-Dibromoflavone (EMD21388)


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of Rat Transthyretin (Also Called Prealbumin) Complex with 3', 5'-Dibromoflavone (EMD21388) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Br128

b:20.6
occ:0.25
 BR3 C:FL8128 0.0 20.6 0.2
BR3 C:FL8128 1.7 18.5 0.3
C3' C:FL8128 1.8 17.6 0.3
C3' C:FL8128 1.9 17.8 0.2
C2' C:FL8128 1.9 18.0 0.3
C4' C:FL8128 2.8 17.2 0.2
C2' C:FL8128 2.8 18.7 0.2
O4' C:FL8128 3.1 15.6 0.2
C4' C:FL8128 3.1 17.3 0.3
C1' C:FL8128 3.2 18.2 0.3
O A:ALA108 3.4 1.8 1.0
C A:ALA108 3.5 1.9 1.0
CB A:ALA108 3.6 1.9 1.0
N A:ALA109 3.8 1.8 1.0
C A:ALA109 3.8 2.7 1.0
N A:LEU110 3.8 3.2 1.0
O4' C:FL8128 3.9 16.1 0.3
OG1 A:THR119 3.9 7.2 1.0
O A:SER117 3.9 2.0 1.0
CA A:ALA109 3.9 1.8 1.0
C5' C:FL8128 4.0 17.8 0.3
CB A:LEU110 4.0 2.8 1.0
C6' C:FL8128 4.1 18.1 0.3
C5' C:FL8128 4.1 17.4 0.2
C1' C:FL8128 4.1 18.5 0.2
CA A:ALA108 4.2 1.8 1.0
C2 C:FL8128 4.2 19.0 0.3
O A:ALA109 4.2 1.8 1.0
C3B C:FL8128 4.3 19.2 0.3
N A:THR119 4.4 4.3 1.0
CA A:LEU110 4.4 3.3 1.0
CB A:THR119 4.4 5.8 1.0
C A:SER117 4.5 2.9 1.0
C6' C:FL8128 4.6 18.2 0.2
C3 C:FL8128 4.7 19.7 0.3
CA A:THR118 4.7 4.0 1.0
C A:THR118 4.7 4.4 1.0
CB A:SER117 4.8 1.8 1.0
N A:THR118 4.8 2.9 1.0

Bromine binding site 4 out of 6 in 1kgj

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Bromine binding site 4 out of 6 in the Rat Transthyretin (Also Called Prealbumin) Complex with 3', 5'-Dibromoflavone (EMD21388)


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 4 of Rat Transthyretin (Also Called Prealbumin) Complex with 3', 5'-Dibromoflavone (EMD21388) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Br128

b:18.5
occ:0.29
 BR3 C:FL8128 0.0 18.5 0.3
BR3 C:FL8128 1.7 20.6 0.2
C3' C:FL8128 1.9 17.6 0.3
O4' C:FL8128 2.8 15.6 0.2
C2' C:FL8128 2.8 18.0 0.3
C4' C:FL8128 2.8 17.3 0.3
OG1 A:THR119 2.9 7.2 1.0
C3' C:FL8128 2.9 17.8 0.2
O4' C:FL8128 3.1 16.1 0.3
C4' C:FL8128 3.3 17.2 0.2
O A:SER117 3.4 2.0 1.0
CB A:SER117 3.4 1.8 1.0
C A:SER117 3.5 2.9 1.0
N A:THR118 3.8 2.9 1.0
O A:ALA108 3.8 1.8 1.0
C A:THR118 3.8 4.4 1.0
N A:THR119 3.8 4.3 1.0
CB A:THR119 3.9 5.8 1.0
CA A:THR118 4.0 4.0 1.0
C5' C:FL8128 4.1 17.8 0.3
CA A:SER117 4.1 2.3 1.0
C2' C:FL8128 4.1 18.7 0.2
C1' C:FL8128 4.1 18.2 0.3
O A:THR118 4.3 7.5 1.0
CD2 C:LEU510 4.3 3.9 1.0
CB A:LEU110 4.3 2.8 1.0
C A:ALA108 4.3 1.9 1.0
N A:LEU110 4.4 3.2 1.0
CA A:THR119 4.5 4.4 1.0
OG A:SER117 4.6 1.8 1.0
C5' C:FL8128 4.6 17.4 0.2
CA A:ALA109 4.6 1.8 1.0
C6' C:FL8128 4.6 18.1 0.3
C A:ALA109 4.7 2.7 1.0
N A:ALA109 4.8 1.8 1.0
CB A:ALA108 4.8 1.9 1.0
OG B:SER315 4.8 4.5 1.0

Bromine binding site 5 out of 6 in 1kgj

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Bromine binding site 5 out of 6 in the Rat Transthyretin (Also Called Prealbumin) Complex with 3', 5'-Dibromoflavone (EMD21388)


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 5 of Rat Transthyretin (Also Called Prealbumin) Complex with 3', 5'-Dibromoflavone (EMD21388) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Br128

b:18.0
occ:0.25
 BR5 C:FL8128 0.0 18.0 0.2
C5' C:FL8128 1.9 17.4 0.2
C6' C:FL8128 1.9 18.1 0.3
C5' C:FL8128 2.0 17.8 0.3
BR5 C:FL8128 2.2 19.8 0.3
C4' C:FL8128 2.8 17.2 0.2
C6' C:FL8128 2.8 18.2 0.2
O4' C:FL8128 3.1 15.6 0.2
C1' C:FL8128 3.1 18.2 0.3
C4' C:FL8128 3.2 17.3 0.3
O C:ALA508 3.3 2.7 1.0
C C:ALA508 3.5 2.7 1.0
N C:LEU510 3.5 1.8 1.0
N C:ALA509 3.7 1.8 1.0
CB C:ALA508 3.7 1.8 1.0
C C:ALA509 3.8 1.8 1.0
CA C:ALA509 3.8 1.8 1.0
C2 C:FL8128 4.0 19.0 0.3
C2' C:FL8128 4.0 18.0 0.3
C3' C:FL8128 4.0 17.6 0.3
CB C:LEU510 4.0 1.8 1.0
O4' C:FL8128 4.1 16.1 0.3
O1 C:FL8128 4.1 20.1 0.3
C3' C:FL8128 4.1 17.8 0.2
C1' C:FL8128 4.1 18.5 0.2
CG2 C:THR519 4.1 1.8 1.0
O C:SER517 4.1 2.1 1.0
N C:THR519 4.2 2.5 1.0
CA C:ALA508 4.2 2.1 1.0
CA C:LEU510 4.3 1.8 1.0
OG C:SER517 4.3 12.3 1.0
CA C:THR518 4.4 2.4 1.0
O C:ALA509 4.6 2.0 1.0
C2' C:FL8128 4.6 18.7 0.2
C C:SER517 4.6 4.2 1.0
CB C:THR519 4.7 1.8 1.0
C C:THR518 4.7 1.8 1.0
N C:THR518 4.8 3.6 1.0

Bromine binding site 6 out of 6 in 1kgj

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Bromine binding site 6 out of 6 in the Rat Transthyretin (Also Called Prealbumin) Complex with 3', 5'-Dibromoflavone (EMD21388)


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 6 of Rat Transthyretin (Also Called Prealbumin) Complex with 3', 5'-Dibromoflavone (EMD21388) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Br128

b:19.8
occ:0.29
 BR5 C:FL8128 0.0 19.8 0.3
C5' C:FL8128 1.9 17.8 0.3
BR5 C:FL8128 2.2 18.0 0.2
C4' C:FL8128 2.8 17.3 0.3
C6' C:FL8128 2.8 18.1 0.3
O4' C:FL8128 2.9 15.6 0.2
O4' C:FL8128 3.1 16.1 0.3
OG C:SER517 3.1 12.3 1.0
C5' C:FL8128 3.3 17.4 0.2
N C:THR519 3.4 2.5 1.0
C4' C:FL8128 3.4 17.2 0.2
C C:THR518 3.5 1.8 1.0
CA C:THR518 3.6 2.4 1.0
N C:THR518 3.6 3.6 1.0
C C:SER517 3.7 4.2 1.0
CB C:THR519 3.7 1.8 1.0
O C:SER517 3.8 2.1 1.0
CG2 C:THR519 3.9 1.8 1.0
O C:ALA508 4.0 2.7 1.0
CB C:SER517 4.0 7.2 1.0
CD2 A:LEU110 4.1 1.8 1.0
C3' C:FL8128 4.1 17.6 0.3
CA C:THR519 4.1 2.7 1.0
C1' C:FL8128 4.2 18.2 0.3
O C:THR518 4.2 1.8 1.0
OG D:SER715 4.2 9.1 1.0
C6' C:FL8128 4.5 18.2 0.2
CA C:SER517 4.5 5.7 1.0
N C:LEU510 4.6 1.8 1.0
C2' C:FL8128 4.7 18.0 0.3
CB C:LEU510 4.7 1.8 1.0
C C:ALA508 4.7 2.7 1.0
C3' C:FL8128 4.8 17.8 0.2
OG1 C:THR519 5.0 1.8 1.0

Reference:

T.Muziol, V.Cody, A.Wojtczak. Comparison of Binding Interactions of Dibromoflavonoids with Transthyretin. Acta Biochim.Pol. V. 48 885 2001.
ISSN: ISSN 0001-527X
PubMed: 11995999
Page generated: Wed Jul 10 16:48:39 2024

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