Bromine in PDB 2b4g: Dihydroorotate Dehydrogenase

All present enzymatic activity of Dihydroorotate Dehydrogenase:
1.3.99.11;

The structure of Dihydroorotate Dehydrogenase, PDB code: 2b4g was solved by T.L.Arakaki, E.A.Merritt, Structural Genomics Of Pathogenic Protozoaconsortium (Sgpp), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 1.95
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	81.605, 162.630, 163.070, 90.00, 90.00, 90.00
R / Rfree (%)	18.9 / 24.2

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 11;

Binding sites:

The binding sites of Bromine atom in the Dihydroorotate Dehydrogenase (pdb code 2b4g). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 11 binding sites of Bromine where determined in the Dihydroorotate Dehydrogenase, PDB code: 2b4g:
Jump to Bromine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Bromine binding site 1 out of 11 in the Dihydroorotate Dehydrogenase


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Dihydroorotate Dehydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Br1411 b:28.4 occ:0.50 OE1 A:GLN139 2.7 22.6 1.0 ND2 A:ASN199 3.0 8.3 1.0 O A:HOH1434 3.1 20.6 1.0 N B:ILE172 3.2 11.6 1.0 CD A:GLN139 3.7 20.0 1.0 CA B:ASP171 3.7 11.9 1.0 OD2 B:ASP171 3.8 18.0 0.8 CG1 B:ILE172 3.8 10.9 1.0 O A:PRO132 3.9 13.0 1.0 C B:ASP171 4.0 11.8 1.0 CB B:ILE172 4.1 11.4 1.0 CG A:ASN199 4.1 10.2 1.0 NE2 A:GLN139 4.1 19.5 1.0 CA B:ILE172 4.2 11.6 1.0 CA A:PRO138 4.3 19.2 1.0 CG B:ASP171 4.3 12.7 0.8 OD1 A:ASN199 4.4 12.2 1.0 NZ A:LYS215 4.4 12.9 1.0 O B:PHE170 4.4 9.7 1.0 CA A:PRO132 4.4 13.1 1.0 C A:PRO132 4.5 13.6 1.0 O A:HOH1444 4.5 18.8 1.0 CB B:ASP171 4.5 12.9 1.0 CB A:PRO138 4.6 19.8 1.0 N A:GLN139 4.6 17.5 1.0 O A:HOH1515 4.7 25.5 1.0 N B:ASP171 4.8 11.6 1.0 CB A:PRO132 4.8 13.3 1.0 CG A:GLN139 4.9 17.5 1.0 CD1 B:ILE172 4.9 13.4 1.0

Bromine binding site 2 out of 11 in the Dihydroorotate Dehydrogenase


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Dihydroorotate Dehydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Br1412 b:28.6 occ:0.50 N A:PHE170 3.1 9.6 1.0 ND1 A:HIS174 3.2 15.1 1.0 CA A:TYR169 3.6 10.4 1.0 O A:HOH1589 3.7 20.2 1.0 CD1 A:PHE170 3.7 9.8 1.0 C A:TYR169 3.9 10.0 1.0 CB A:TYR169 4.0 11.0 1.0 CA A:PHE170 4.0 10.3 1.0 CB A:ASP171 4.0 11.1 1.0 CB A:PHE170 4.1 10.3 1.0 N A:ASP171 4.1 10.5 1.0 CE1 A:HIS174 4.1 17.8 1.0 CG A:HIS174 4.1 14.2 1.0 CD1 A:TYR169 4.2 11.7 1.0 CB A:HIS174 4.2 13.1 1.0 C A:PHE170 4.3 10.3 1.0 CG A:PHE170 4.4 10.0 1.0 CE2 B:TYR142 4.6 10.1 1.0 CG A:TYR169 4.6 11.8 1.0 O B:HOH2548 4.6 21.1 1.0 O A:PRO168 4.7 10.8 1.0 CE1 A:PHE170 4.7 10.4 1.0 CA A:ASP171 4.8 11.0 1.0 CD2 B:TYR142 4.8 11.2 1.0 CE1 A:TYR142 4.9 11.1 1.0 N A:TYR169 4.9 10.2 1.0 CZ B:TYR142 4.9 11.4 1.0

Bromine binding site 3 out of 11 in the Dihydroorotate Dehydrogenase


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of Dihydroorotate Dehydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Br1414 b:32.1 occ:0.30 O A:HOH1515 3.0 25.5 1.0 CD A:PRO138 3.8 20.3 1.0 CB A:PRO138 3.8 19.8 1.0 N B:ALA173 3.9 11.5 1.0 CB B:ILE172 4.0 11.4 1.0 CG A:PRO138 4.0 20.2 1.0 CA A:GLY136 4.1 19.8 1.0 N A:GLY136 4.1 19.6 1.0 N A:PRO138 4.1 20.0 1.0 C A:GLY136 4.2 20.3 1.0 CG2 B:ILE172 4.2 11.0 1.0 N A:LYS137 4.2 20.4 1.0 CB B:ALA173 4.3 12.4 1.0 CA A:PRO138 4.4 19.2 1.0 CA B:ALA173 4.4 12.0 1.0 C B:ILE172 4.5 11.3 1.0 O B:HOH2489 4.5 20.1 1.0 CA B:ILE172 4.7 11.6 1.0 O A:GLY136 4.8 20.6 1.0 C A:LYS137 4.8 20.5 1.0 O A:HOH1434 4.9 20.6 1.0 OD2 B:ASP171 4.9 18.0 0.8 CG1 B:ILE172 5.0 10.9 1.0

Bromine binding site 4 out of 11 in the Dihydroorotate Dehydrogenase


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 4 of Dihydroorotate Dehydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Br1415 b:41.8 occ:0.40 O A:HOH1500 3.0 24.0 1.0 CB A:PRO161 3.6 15.2 1.0 CA A:LEU8 3.8 18.8 1.0 CG A:PRO161 3.8 15.6 1.0 CD2 A:LEU8 3.9 16.5 1.0 CG A:LYS189 4.0 16.2 1.0 C A:LEU8 4.2 19.3 1.0 CB A:LEU8 4.4 18.7 1.0 CD A:LYS189 4.4 18.1 1.0 CB A:LYS189 4.4 14.9 1.0 O A:LEU8 4.5 19.7 1.0 N A:LEU8 4.7 18.7 1.0 CG A:LEU8 4.8 17.1 1.0 NZ A:LYS189 4.8 22.0 1.0 CE A:LYS189 4.8 20.1 1.0 O A:HOH1538 4.9 23.4 1.0 N A:GLY9 4.9 19.5 1.0

Bromine binding site 5 out of 11 in the Dihydroorotate Dehydrogenase


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 5 of Dihydroorotate Dehydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ B:Br1413 b:27.3 occ:0.30 O B:HOH2447 3.7 20.0 1.0 CG B:PRO138 3.8 17.6 1.0 CB A:ILE172 3.9 11.9 1.0 CA B:GLY136 3.9 17.8 1.0 C B:GLY136 4.0 17.8 1.0 N A:ALA173 4.1 12.3 1.0 CG2 A:ILE172 4.1 13.0 1.0 O B:GLY136 4.2 18.0 1.0 CD B:PRO138 4.3 17.5 1.0 N B:GLY136 4.4 17.8 1.0 CB B:PRO138 4.4 17.0 1.0 N B:PRO138 4.5 17.3 1.0 N B:LYS137 4.6 18.1 1.0 C A:ILE172 4.6 11.8 1.0 CA A:ALA173 4.6 12.5 1.0 CB A:ALA173 4.7 12.9 1.0 CG1 A:ILE172 4.8 12.5 1.0 CA A:ILE172 4.8 12.0 1.0 CA B:PRO138 4.9 16.6 1.0

Bromine binding site 6 out of 11 in the Dihydroorotate Dehydrogenase


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 6 of Dihydroorotate Dehydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ B:Br2410 b:21.6 occ:0.50 ND2 B:ASN296 3.1 20.4 1.0 O D:HOH4557 3.2 13.3 1.0 N D:GLU27 3.5 14.4 1.0 CB B:ASN296 3.5 19.1 1.0 CG B:ASN296 3.8 19.8 1.0 CD1 D:LEU75 3.8 13.3 1.0 CB D:THR26 3.8 13.4 1.0 O A:HOH1579 3.9 28.3 1.0 CB D:GLU27 4.1 14.9 1.0 CA D:THR26 4.1 13.3 1.0 O A:HOH1586 4.2 28.4 1.0 CG2 D:THR26 4.2 14.9 1.0 C D:THR26 4.4 13.5 1.0 CA D:GLU27 4.4 14.9 1.0 CE2 D:PHE79 4.6 12.3 1.0 CG1 B:ILE293 4.6 20.1 1.0 CA B:ILE293 4.7 19.1 1.0 CG2 B:ILE293 4.8 19.4 1.0 CZ D:PHE79 4.8 12.1 1.0 O B:ILE293 4.9 18.5 1.0 OD1 B:ASN296 5.0 20.6 1.0 CB B:ILE293 5.0 19.0 1.0

Bromine binding site 7 out of 11 in the Dihydroorotate Dehydrogenase


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 7 of Dihydroorotate Dehydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ C:Br3410 b:16.6 occ:0.50 O A:HOH1575 3.3 15.0 1.0 ND2 C:ASN296 3.4 16.0 1.0 N A:GLU27 3.7 13.0 1.0 CB C:ASN296 3.8 15.9 1.0 CD1 A:LEU75 3.8 14.7 1.0 CB A:THR26 3.8 13.3 1.0 CG C:ASN296 4.1 16.0 1.0 CA A:THR26 4.2 13.4 1.0 CB A:GLU27 4.2 13.1 1.0 CG2 A:THR26 4.3 14.7 1.0 C A:THR26 4.5 13.2 1.0 CA A:GLU27 4.6 13.2 1.0 CG2 C:ILE293 4.6 15.7 1.0 CA C:ILE293 4.7 14.8 1.0 CE2 A:PHE79 4.7 13.6 1.0 CG1 C:ILE293 4.8 15.4 1.0 CE C:LYS297 4.9 22.1 1.0 CZ A:PHE79 4.9 12.0 1.0 OG1 A:THR26 4.9 13.2 1.0 O C:ILE293 4.9 13.8 1.0 CB C:ILE293 5.0 15.0 1.0

Bromine binding site 8 out of 11 in the Dihydroorotate Dehydrogenase


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 8 of Dihydroorotate Dehydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ C:Br3411 b:32.7 occ:0.40 O C:HOH4552 3.1 26.4 1.0 O C:HOH4567 3.2 27.8 1.0 O C:HOH4556 3.4 13.4 1.0 O3 C:GOL3401 3.4 55.7 1.0 N C:LEU23 3.5 10.2 1.0 CA C:VAL22 3.7 10.6 1.0 O C:HOH4459 3.7 16.6 1.0 O C:GLY21 3.7 9.5 1.0 CG1 C:VAL22 4.0 10.9 1.0 C C:VAL22 4.2 10.2 1.0 C3 C:GOL3401 4.3 55.9 1.0 CB C:VAL22 4.4 10.9 1.0 CA C:LEU23 4.6 11.0 1.0 C C:GLY21 4.6 10.6 1.0 N C:VAL22 4.6 11.1 1.0 C7M C:FMN3400 4.8 13.7 1.0 CG2 C:VAL22 4.8 11.6 1.0

Bromine binding site 9 out of 11 in the Dihydroorotate Dehydrogenase


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 9 of Dihydroorotate Dehydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ C:Br4410 b:36.6 occ:0.30 O C:HOH4569 3.3 31.2 1.0 CB D:ILE172 3.7 15.0 1.0 CG C:PRO138 3.8 20.1 1.0 CG2 D:ILE172 3.9 14.8 1.0 CA C:GLY136 3.9 20.4 1.0 C C:GLY136 3.9 20.6 1.0 CD C:PRO138 4.1 19.9 1.0 N D:ALA173 4.2 15.8 1.0 N C:PRO138 4.2 19.5 1.0 O C:GLY136 4.3 20.6 1.0 N C:LYS137 4.3 20.3 1.0 N C:GLY136 4.3 20.4 1.0 CB C:PRO138 4.5 19.5 1.0 CG1 D:ILE172 4.5 15.1 1.0 CA C:PRO138 4.6 19.0 1.0 C D:ILE172 4.6 15.3 1.0 CA D:ILE172 4.6 15.0 1.0 C C:LYS137 4.7 20.2 1.0 CB D:ALA173 4.7 16.1 1.0 CA D:ALA173 4.8 15.6 1.0 O C:HOH4480 4.8 21.1 1.0 O C:HOH4450 5.0 12.1 1.0 CA C:LYS137 5.0 20.2 1.0 OD2 D:ASP171 5.0 20.2 0.8

Bromine binding site 10 out of 11 in the Dihydroorotate Dehydrogenase


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 10 of Dihydroorotate Dehydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ D:Br4411 b:30.4 occ:0.30 CD D:PRO138 3.8 20.2 1.0 CB C:ILE172 3.9 13.8 1.0 CB D:PRO138 4.0 20.0 1.0 N C:ALA173 4.0 14.4 1.0 CG D:PRO138 4.0 20.2 1.0 C D:GLY136 4.0 21.4 1.0 CA D:GLY136 4.1 20.8 1.0 N D:PRO138 4.1 20.3 1.0 CG2 C:ILE172 4.1 13.3 1.0 N D:GLY136 4.2 20.8 1.0 N D:LYS137 4.2 21.3 1.0 CA D:PRO138 4.4 19.6 1.0 CB C:ALA173 4.4 15.4 1.0 O D:GLY136 4.5 21.6 1.0 CA C:ALA173 4.5 14.9 1.0 C C:ILE172 4.6 14.0 1.0 C D:LYS137 4.6 20.6 1.0 O C:HOH4439 4.7 31.0 1.0 CA C:ILE172 4.7 14.2 1.0 CG1 C:ILE172 4.8 14.7 1.0 OD2 C:ASP171 4.9 20.9 0.8 O D:HOH4426 4.9 5.9 1.0 CA D:LYS137 4.9 20.8 1.0 O C:HOH4545 5.0 23.6 1.0

T.L.Arakaki, F.S.Buckner, J.R.Gillespie, N.A.Malmquist, M.A.Phillips, O.Kalyuzhniy, J.R.Luft, G.T.Detitta, C.L.Verlinde, W.C.Van Voorhis, W.G.Hol, E.A.Merritt. Characterization of Trypanosoma Brucei Dihydroorotate Dehydrogenase As A Possible Drug Target; Structural, Kinetic and Rnai Studies Mol.Microbiol. V. 68 37 2008.
ISSN: ISSN 0950-382X
PubMed: 18312275
DOI: 10.1111/J.1365-2958.2008.06131.X