Bromine in PDB 2fcv: SYRB2 with Fe(II), Bromide, and Alpha-Ketoglutarate

The structure of SYRB2 with Fe(II), Bromide, and Alpha-Ketoglutarate, PDB code: 2fcv was solved by L.C.Blasiak, C.L.Drennan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.18 / 1.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	57.120, 89.350, 125.060, 90.00, 90.00, 90.00
R / Rfree (%)	17.1 / 21

The structure of SYRB2 with Fe(II), Bromide, and Alpha-Ketoglutarate also contains other interesting chemical elements:

Iron

(Fe)

2 atoms

The binding sites of Bromine atom in the SYRB2 with Fe(II), Bromide, and Alpha-Ketoglutarate (pdb code 2fcv). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 4 binding sites of Bromine where determined in the SYRB2 with Fe(II), Bromide, and Alpha-Ketoglutarate, PDB code: 2fcv:
Jump to Bromine binding site number: 1; 2; 3; 4;

Bromine binding site 1 out of 4 in the SYRB2 with Fe(II), Bromide, and Alpha-Ketoglutarate


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of SYRB2 with Fe(II), Bromide, and Alpha-Ketoglutarate within 5.0Å range: probe atom residue distance (Å) B Occ A:Br901 b:27.1 occ:1.00 FE A:FE2900 2.5 11.6 1.0 O A:HOH915 3.1 17.8 1.0 O A:HOH1068 3.2 16.8 1.0 O2 A:AKG897 3.4 15.3 1.0 O A:HOH946 3.4 24.0 1.0 CE1 A:HIS235 3.5 13.8 1.0 NE2 A:HIS235 3.5 12.3 1.0 NE2 A:HIS116 3.6 9.8 1.0 CD2 A:HIS116 3.6 12.0 1.0 NH2 A:ARG254 3.8 14.3 1.0 CB A:ALA118 3.9 12.6 1.0 CZ A:PHE121 3.9 13.6 1.0 CB A:SER231 4.0 10.7 1.0 CE1 A:PHE121 4.2 16.7 1.0 O A:SER231 4.3 9.9 1.0 NH1 A:ARG254 4.3 13.4 1.0 CZ A:ARG254 4.3 13.1 1.0 CA A:SER231 4.5 9.9 1.0 N A:ALA118 4.5 12.2 1.0 C1 A:AKG897 4.6 14.7 1.0 O5 A:AKG897 4.7 10.6 1.0 CE2 A:PHE121 4.8 15.1 1.0 CE1 A:HIS116 4.8 10.8 1.0 CA A:ALA118 4.8 12.7 1.0 ND1 A:HIS235 4.8 10.7 1.0 C A:SER231 4.9 9.4 1.0 CD2 A:HIS235 4.9 7.5 1.0 CG A:HIS116 4.9 9.0 1.0

Bromine binding site 2 out of 4 in the SYRB2 with Fe(II), Bromide, and Alpha-Ketoglutarate


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of SYRB2 with Fe(II), Bromide, and Alpha-Ketoglutarate within 5.0Å range: probe atom residue distance (Å) B Occ A:Br903 b:26.6 occ:1.00 O A:HOH1100 3.4 21.7 1.0 N A:ASP212 3.4 12.9 1.0 O A:HOH1009 3.5 24.8 1.0 CZ2 A:TRP209 3.9 13.3 1.0 CB A:ASP212 3.9 12.7 1.0 CG A:MET234 4.0 9.9 1.0 CG2 A:THR164 4.1 13.4 1.0 CE A:MET234 4.1 10.0 1.0 CD1 A:ILE161 4.1 11.2 1.0 CA A:PRO211 4.2 12.1 1.0 CA A:ASP212 4.2 12.8 1.0 ND2 A:ASN169 4.3 15.2 1.0 C A:PRO211 4.3 13.0 1.0 CG2 A:ILE161 4.4 9.5 1.0 SD A:MET234 4.5 12.0 1.0 CH2 A:TRP209 4.7 13.3 1.0 CE2 A:TRP209 4.7 12.7 1.0 CB A:ILE161 4.8 9.8 1.0 O A:HOH970 4.8 25.7 1.0 NE1 A:TRP209 4.8 14.4 1.0 CB A:PRO211 4.9 11.8 1.0 CB A:MET234 4.9 9.4 1.0 CB A:THR164 4.9 12.3 1.0 CG1 A:ILE161 5.0 10.5 1.0

Bromine binding site 3 out of 4 in the SYRB2 with Fe(II), Bromide, and Alpha-Ketoglutarate


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of SYRB2 with Fe(II), Bromide, and Alpha-Ketoglutarate within 5.0Å range: probe atom residue distance (Å) B Occ B:Br902 b:38.8 occ:1.00 FE B:FE2899 2.5 13.6 1.0 O B:HOH1009 3.1 19.5 1.0 O B:HOH926 3.1 16.6 1.0 O2 B:AKG898 3.5 15.5 1.0 NE2 B:HIS235 3.5 14.6 1.0 NE2 B:HIS116 3.5 13.8 1.0 CD2 B:HIS116 3.6 16.5 1.0 CE1 B:HIS235 3.6 16.7 1.0 CB B:ALA118 3.7 16.3 1.0 CZ B:PHE121 4.0 19.9 1.0 NH2 B:ARG254 4.1 18.8 1.0 CB B:SER231 4.2 13.0 1.0 CE2 B:PHE121 4.3 20.6 1.0 NH1 B:ARG254 4.3 14.6 1.0 O B:SER231 4.4 12.3 1.0 CZ B:ARG254 4.4 15.7 1.0 N B:ALA118 4.6 14.7 1.0 C1 B:AKG898 4.7 17.9 1.0 O5 B:AKG898 4.7 16.0 1.0 CA B:SER231 4.7 12.0 1.0 CA B:ALA118 4.8 16.2 1.0 CE1 B:HIS116 4.8 13.2 1.0 CD2 B:HIS235 4.9 14.3 1.0 CG B:HIS116 4.9 14.2 1.0 ND1 B:HIS235 4.9 13.1 1.0 CE1 B:PHE121 4.9 19.5 1.0 C B:SER231 5.0 12.3 1.0

Bromine binding site 4 out of 4 in the SYRB2 with Fe(II), Bromide, and Alpha-Ketoglutarate


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 4 of SYRB2 with Fe(II), Bromide, and Alpha-Ketoglutarate within 5.0Å range: probe atom residue distance (Å) B Occ B:Br904 b:29.7 occ:1.00 O B:HOH907 3.3 23.5 1.0 N B:ASP212 3.4 18.2 1.0 O B:HOH1012 3.5 32.9 1.0 CZ2 B:TRP209 3.9 20.1 1.0 CB B:ASP212 3.9 18.8 1.0 CG2 B:THR164 4.0 14.4 1.0 CD1 B:ILE161 4.0 14.6 1.0 O B:HOH1078 4.0 45.5 1.0 CE B:MET234 4.0 16.6 1.0 CG B:MET234 4.1 13.7 1.0 CA B:PRO211 4.1 19.4 1.0 ND2 B:ASN169 4.2 19.4 1.0 C B:PRO211 4.3 18.6 1.0 CA B:ASP212 4.3 18.3 1.0 CG2 B:ILE161 4.3 11.5 1.0 SD B:MET234 4.6 15.4 1.0 O B:HOH1095 4.6 34.0 1.0 CH2 B:TRP209 4.6 18.4 1.0 CB B:PRO211 4.7 19.1 1.0 CB B:ILE161 4.8 12.6 1.0 CE2 B:TRP209 4.8 22.0 1.0 CB B:MET234 4.9 12.3 1.0 NE1 B:TRP209 5.0 23.0 1.0 CB B:THR164 5.0 14.0 1.0 CG1 B:ILE161 5.0 14.0 1.0

L.C.Blasiak, F.H.Vaillancourt, C.T.Walsh, C.L.Drennan. Crystal Structure of the Non-Haem Iron Halogenase SYRB2 in Syringomycin Biosynthesis. Nature V. 440 368 2006.
ISSN: ISSN 0028-0836
PubMed: 16541079
DOI: 10.1038/NATURE04544