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Bromine in PDB 2byd: Structure of Aminoadipate-Semialdehyde Dehydrogenase- Phosphopantetheinyl Transferase

Enzymatic activity of Structure of Aminoadipate-Semialdehyde Dehydrogenase- Phosphopantetheinyl Transferase

All present enzymatic activity of Structure of Aminoadipate-Semialdehyde Dehydrogenase- Phosphopantetheinyl Transferase:
1.2.1.31;

Protein crystallography data

The structure of Structure of Aminoadipate-Semialdehyde Dehydrogenase- Phosphopantetheinyl Transferase, PDB code: 2byd was solved by G.Bunkoczi, X.Wu, E.Dubinina, C.Johansson, C.Smee, A.Turnbull, U.Oppermann, F.Von Delft, C.Arrowsmith, A.Edwards, M.Sundstrom, J.Weigelt, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.94 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 63.780, 69.948, 71.239, 90.00, 90.00, 90.00
R / Rfree (%) 17.3 / 24.2

Bromine Binding Sites:

The binding sites of Bromine atom in the Structure of Aminoadipate-Semialdehyde Dehydrogenase- Phosphopantetheinyl Transferase (pdb code 2byd). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 9 binding sites of Bromine where determined in the Structure of Aminoadipate-Semialdehyde Dehydrogenase- Phosphopantetheinyl Transferase, PDB code: 2byd:
Jump to Bromine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Bromine binding site 1 out of 9 in 2byd

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Bromine binding site 1 out of 9 in the Structure of Aminoadipate-Semialdehyde Dehydrogenase- Phosphopantetheinyl Transferase


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Structure of Aminoadipate-Semialdehyde Dehydrogenase- Phosphopantetheinyl Transferase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br1319

b:20.6
occ:1.00
 NH2 A:ARG74 3.3 11.6 1.0
N A:GLN51 3.4 14.9 1.0
NH1 A:ARG78 3.4 12.9 1.0
NE A:ARG74 3.4 8.8 1.0
CB A:ILE50 3.7 9.7 1.0
CG A:GLN51 3.8 8.6 1.0
CG A:GLU54 3.8 19.2 1.0
CD A:ARG78 3.8 18.3 1.0
CZ A:ARG74 3.8 6.3 1.0
CB A:GLN51 3.9 17.4 1.0
CA A:ILE50 4.0 13.9 1.0
CB A:GLU54 4.0 12.4 1.0
CD A:GLN51 4.1 11.6 1.0
CD1 A:LEU94 4.1 22.9 1.0
C A:ILE50 4.2 11.0 1.0
CA A:GLN51 4.3 11.9 1.0
CZ A:ARG78 4.3 12.9 1.0
CG A:ARG78 4.3 13.5 1.0
OE1 A:GLN51 4.4 19.0 1.0
CG2 A:ILE50 4.4 8.9 1.0
CB A:ARG74 4.4 8.2 1.0
NE A:ARG78 4.4 11.9 1.0
NE2 A:GLN51 4.6 12.4 1.0
CD A:ARG74 4.6 10.3 1.0
CG A:ARG74 4.6 14.2 1.0
CG1 A:ILE50 4.9 12.9 1.0
O A:ARG74 5.0 8.7 1.0

Bromine binding site 2 out of 9 in 2byd

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Bromine binding site 2 out of 9 in the Structure of Aminoadipate-Semialdehyde Dehydrogenase- Phosphopantetheinyl Transferase


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Structure of Aminoadipate-Semialdehyde Dehydrogenase- Phosphopantetheinyl Transferase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br1320

b:23.6
occ:0.90
 O A:HOH2048 3.2 20.2 1.0
N A:THR308 3.4 14.5 1.0
N A:ARG65 3.4 14.1 1.0
CB A:ARG65 3.6 18.8 1.0
CA A:PHE307 3.7 17.0 1.0
CG A:ARG65 3.8 15.1 1.0
OG1 A:THR308 3.8 25.7 1.0
CG2 A:THR308 3.9 19.4 1.0
CA A:ARG65 4.0 18.6 1.0
C A:PHE307 4.0 17.6 1.0
N A:ALA64 4.0 8.0 1.0
CB A:ALA64 4.1 11.4 1.0
O A:CYS306 4.1 12.9 1.0
CD A:ARG65 4.2 18.6 1.0
CB A:THR308 4.2 11.3 1.0
C A:ALA64 4.3 14.7 1.0
CA A:ALA64 4.4 12.5 1.0
CA A:THR308 4.4 16.7 1.0
CD1 A:PHE307 4.5 15.2 1.0
CB A:PHE307 4.5 18.0 1.0
CB A:PHE63 4.5 11.6 1.0
CD1 A:PHE63 4.5 10.2 1.0
N A:PHE307 4.7 15.2 1.0
C A:CYS306 4.8 13.5 1.0
C A:PHE63 4.8 12.8 1.0
OE1 A:GLU309 4.9 38.0 1.0
CG A:PHE307 4.9 15.1 1.0
NE A:ARG65 4.9 38.4 1.0
CG A:PHE63 5.0 15.7 1.0

Bromine binding site 3 out of 9 in 2byd

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Bromine binding site 3 out of 9 in the Structure of Aminoadipate-Semialdehyde Dehydrogenase- Phosphopantetheinyl Transferase


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of Structure of Aminoadipate-Semialdehyde Dehydrogenase- Phosphopantetheinyl Transferase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br1321

b:26.3
occ:0.80
 NZ A:LYS84 3.3 19.9 1.0
NE1 A:TRP29 3.5 8.7 1.0
O A:HOH2006 3.6 18.8 1.0
O A:HOH2005 3.6 22.5 1.0
CE A:LYS84 3.8 17.6 1.0
CE2 A:TRP29 4.2 14.2 1.0
CZ2 A:TRP29 4.2 17.0 1.0
CD1 A:TRP29 4.6 8.7 1.0
CG2 A:VAL27 4.7 25.5 1.0
CG1 A:VAL27 4.8 23.2 1.0

Bromine binding site 4 out of 9 in 2byd

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Bromine binding site 4 out of 9 in the Structure of Aminoadipate-Semialdehyde Dehydrogenase- Phosphopantetheinyl Transferase


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 4 of Structure of Aminoadipate-Semialdehyde Dehydrogenase- Phosphopantetheinyl Transferase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br1322

b:28.9
occ:0.40
 N A:GLN276 3.2 58.5 1.0
N A:GLN278 3.6 23.4 1.0
C A:GLN276 3.8 55.3 1.0
CB A:GLN278 3.9 25.6 1.0
N A:ARG277 3.9 45.2 1.0
CA A:GLN276 4.0 57.9 1.0
O A:GLN276 4.2 56.9 1.0
CA A:GLN278 4.3 23.6 1.0
O A:GLN278 4.5 15.4 1.0
O A:HOH2162 4.5 28.8 1.0
CG A:GLN278 4.6 24.8 1.0
C A:ARG277 4.6 29.5 1.0
CA A:ARG277 4.8 41.3 1.0
CB A:GLN276 4.9 59.7 1.0
C A:GLN278 4.9 15.4 1.0

Bromine binding site 5 out of 9 in 2byd

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Bromine binding site 5 out of 9 in the Structure of Aminoadipate-Semialdehyde Dehydrogenase- Phosphopantetheinyl Transferase


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 5 of Structure of Aminoadipate-Semialdehyde Dehydrogenase- Phosphopantetheinyl Transferase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br1323

b:26.6
occ:0.30
 NH2 A:ARG48 3.5 22.1 1.0
C A:THR295 3.5 15.8 1.0
O A:THR295 3.6 13.4 1.0
N A:PRO296 3.6 19.9 1.0
CA A:PRO296 4.0 20.2 1.0
N A:THR295 4.1 19.6 1.0
CA A:THR295 4.1 18.1 1.0
CD A:PRO296 4.2 17.6 1.0
C A:MET294 4.2 18.7 1.0
O A:MET294 4.4 19.1 1.0
CG A:PRO296 4.4 21.6 1.0
CZ A:ARG48 4.4 25.6 1.0
CB A:PRO293 4.5 14.2 1.0
NE A:ARG48 4.5 22.6 1.0
O A:PRO293 4.7 16.4 1.0
C A:PRO293 4.7 16.7 1.0
N A:MET294 4.8 20.5 1.0
CB A:PRO296 4.8 22.0 1.0
CA A:MET294 4.8 22.2 1.0
CG A:PRO293 5.0 18.0 1.0

Bromine binding site 6 out of 9 in 2byd

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Bromine binding site 6 out of 9 in the Structure of Aminoadipate-Semialdehyde Dehydrogenase- Phosphopantetheinyl Transferase


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 6 of Structure of Aminoadipate-Semialdehyde Dehydrogenase- Phosphopantetheinyl Transferase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br1324

b:20.5
occ:0.30
 OG A:SER120 2.9 12.3 1.0
O A:HOH2081 3.2 36.9 1.0
N A:HIS121 3.6 8.4 1.0
CA A:SER120 3.6 8.7 1.0
CB A:SER120 3.7 16.4 1.0
O A:HIS121 3.8 13.1 1.0
OD1 A:ASP139 4.0 15.7 1.0
C A:SER120 4.1 5.8 1.0
NZ A:LYS195 4.1 23.3 1.0
O A:HOH2090 4.2 20.2 1.0
CD2 A:HIS121 4.2 32.1 1.0
CE A:LYS195 4.3 21.0 1.0
NE2 A:HIS121 4.6 39.4 1.0
O A:ILE119 4.6 11.8 1.0
C A:HIS121 4.7 14.6 1.0
CA A:HIS121 4.7 16.0 1.0
CG A:HIS121 4.8 16.2 1.0
N A:SER120 4.8 12.6 1.0

Bromine binding site 7 out of 9 in 2byd

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Bromine binding site 7 out of 9 in the Structure of Aminoadipate-Semialdehyde Dehydrogenase- Phosphopantetheinyl Transferase


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 7 of Structure of Aminoadipate-Semialdehyde Dehydrogenase- Phosphopantetheinyl Transferase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br1325

b:12.5
occ:0.30
 ND2 A:ASN118 3.2 29.2 1.0
CE A:LYS195 3.5 21.0 1.0
CB A:LYS195 3.9 14.5 1.0
CG A:LYS195 4.0 8.2 1.0
CG A:ASN118 4.1 8.6 1.0
CD A:LYS101 4.1 30.4 1.0
NZ A:LYS195 4.1 23.3 1.0
OD1 A:ASN118 4.2 18.8 1.0
CG A:LYS101 4.3 23.1 1.0
CD A:LYS195 4.4 19.6 1.0
CA A:LYS195 4.5 19.5 1.0
O A:LYS195 4.5 15.1 1.0
BR A:BR1327 4.6 12.4 0.2
CB A:LYS101 4.8 27.0 1.0
O A:ILE119 4.8 11.8 1.0
C A:LYS195 4.9 15.0 1.0
O A:HOH2025 4.9 28.1 1.0

Bromine binding site 8 out of 9 in 2byd

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Bromine binding site 8 out of 9 in the Structure of Aminoadipate-Semialdehyde Dehydrogenase- Phosphopantetheinyl Transferase


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 8 of Structure of Aminoadipate-Semialdehyde Dehydrogenase- Phosphopantetheinyl Transferase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br1326

b:2.0
occ:0.20
 O A:HOH2011 3.2 20.5 1.0
N A:PHE284 3.2 14.3 1.0
CB A:ASN283 3.6 18.6 1.0
CA A:ASN283 3.8 13.9 1.0
CD1 A:TRP36 3.8 16.4 1.0
CB A:PHE284 3.9 15.1 1.0
CE1 A:PHE31 4.0 15.0 1.0
C A:ASN283 4.0 10.9 1.0
O A:HOH2013 4.1 21.3 1.0
O A:HOH2012 4.1 22.5 1.0
CA A:PHE284 4.2 14.2 1.0
CZ A:PHE31 4.3 8.0 1.0
CG A:TRP36 4.4 14.2 1.0
NE1 A:TRP36 4.5 12.7 1.0
O A:HOH2165 4.5 9.9 1.0
CB A:TRP36 4.7 9.2 1.0
CG A:ASN283 4.8 20.4 1.0
CA A:TRP36 4.9 11.0 1.0

Bromine binding site 9 out of 9 in 2byd

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Bromine binding site 9 out of 9 in the Structure of Aminoadipate-Semialdehyde Dehydrogenase- Phosphopantetheinyl Transferase


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 9 of Structure of Aminoadipate-Semialdehyde Dehydrogenase- Phosphopantetheinyl Transferase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br1327

b:12.4
occ:0.20
 ND2 A:ASN118 3.2 29.2 1.0
CD A:PRO102 3.4 26.7 1.0
N A:ILE119 3.5 9.9 1.0
CA A:ASN118 3.6 9.8 1.0
CG1 A:ILE119 3.8 23.4 1.0
CG A:PRO102 3.8 27.1 1.0
CE1 A:PHE117 3.8 16.9 1.0
O A:PRO102 3.9 20.9 1.0
C A:ASN118 3.9 6.6 1.0
O A:HOH2025 4.0 28.1 1.0
CD1 A:PHE117 4.0 11.0 1.0
O A:PHE117 4.1 13.1 1.0
CB A:PRO102 4.1 24.6 1.0
CG A:LYS101 4.1 23.1 1.0
N A:PRO102 4.2 26.0 1.0
CG A:ASN118 4.3 8.6 1.0
N A:ASN118 4.5 10.1 1.0
CA A:ILE119 4.5 14.6 1.0
CB A:ASN118 4.5 10.0 1.0
CB A:ILE119 4.5 14.0 1.0
C A:PHE117 4.6 10.6 1.0
CD1 A:ILE119 4.6 17.6 1.0
CA A:PRO102 4.6 23.6 1.0
BR A:BR1325 4.6 12.5 0.3
CG2 A:ILE119 4.7 17.7 1.0
C A:PRO102 4.7 21.1 1.0
O A:ILE119 4.8 11.8 1.0
CD A:LYS101 4.8 30.4 1.0
CZ A:PHE117 4.9 12.9 1.0

Reference:

G.Bunkoczi, S.Pasta, A.Joshi, X.Wu, K.L.Kavanagh, S.Smith, U.Oppermann. Mechanism and Substrate Recognition of Human Holo Acp Synthase. Chem. Biol. V. 14 1243 2007.
ISSN: ISSN 1074-5521
PubMed: 18022563
DOI: 10.1016/J.CHEMBIOL.2007.10.013
Page generated: Wed Jul 10 17:51:00 2024

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