Bromine in PDB 3md9: Structure of Apo Form of A Periplasmic Heme Binding Protein

The structure of Structure of Apo Form of A Periplasmic Heme Binding Protein, PDB code: 3md9 was solved by D.Mattle, B.A.Goetz, K.P.Locher, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.12 / 1.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	61.710, 66.740, 62.270, 90.00, 110.70, 90.00
R / Rfree (%)	15.2 / 18.1

The binding sites of Bromine atom in the Structure of Apo Form of A Periplasmic Heme Binding Protein (pdb code 3md9). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 7 binding sites of Bromine where determined in the Structure of Apo Form of A Periplasmic Heme Binding Protein, PDB code: 3md9:
Jump to Bromine binding site number: 1; 2; 3; 4; 5; 6; 7;

Bromine binding site 1 out of 7 in the Structure of Apo Form of A Periplasmic Heme Binding Protein


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Structure of Apo Form of A Periplasmic Heme Binding Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Br401 b:21.6 occ:0.78 OH A:TYR200 3.1 28.3 1.0 O A:HOH496 3.5 45.0 1.0 N A:ALA181 3.5 10.1 1.0 O A:HOH341 3.5 27.8 1.0 N A:ALA180 3.8 11.0 1.0 CB A:ALA181 3.8 11.8 1.0 CE2 A:TYR200 3.9 19.1 1.0 CB A:THR179 3.9 13.2 1.0 CD2 A:LEU258 3.9 14.6 1.0 CZ A:TYR200 3.9 26.1 1.0 CB A:ALA180 4.0 12.9 1.0 CE2 A:PHE163 4.1 11.0 1.0 CD1 A:LEU258 4.2 14.5 1.0 CA A:ALA180 4.2 11.7 1.0 CA A:ALA181 4.2 10.9 1.0 C A:ALA180 4.3 10.8 1.0 OG1 A:THR179 4.4 12.0 1.0 CD2 A:PHE163 4.5 10.6 1.0 C A:THR179 4.5 10.9 1.0 CG A:LEU258 4.6 11.4 1.0 CA A:THR179 4.6 13.9 1.0 CG2 A:THR179 4.7 13.9 1.0 CB A:ALA175 4.8 12.6 1.0 CZ A:PHE163 4.8 9.5 1.0

Bromine binding site 2 out of 7 in the Structure of Apo Form of A Periplasmic Heme Binding Protein


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Structure of Apo Form of A Periplasmic Heme Binding Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Br402 b:34.6 occ:0.68 NH1 A:ARG72 3.5 24.0 1.0 N A:ARG72 3.6 17.7 1.0 CG A:ARG72 3.7 21.2 1.0 N A:MET71 3.8 19.5 1.0 CB A:ARG72 3.9 21.4 1.0 CG2 A:THR55 4.0 21.6 1.0 CB A:MET71 4.1 17.6 1.0 CB A:TYR70 4.1 39.4 0.0 CD A:ARG72 4.1 20.8 1.0 CA A:MET71 4.3 17.5 1.0 CA A:ARG72 4.3 17.5 1.0 C A:MET71 4.4 18.3 1.0 C A:TYR70 4.5 20.5 0.0 CZ A:ARG72 4.6 28.7 1.0 CA A:TYR70 4.7 25.3 1.0 O A:HOH538 4.7 48.5 1.0 CD2 A:TYR70 4.8 65.5 0.0 NE A:ARG72 4.8 24.0 1.0 CE A:MET71 4.9 23.3 1.0 CG A:TYR70 4.9 58.1 0.0

Bromine binding site 3 out of 7 in the Structure of Apo Form of A Periplasmic Heme Binding Protein


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of Structure of Apo Form of A Periplasmic Heme Binding Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Br403 b:23.7 occ:0.76 O A:HOH491 2.6 31.1 1.0 NZ A:LYS274 3.0 18.0 1.0 O B:HOH3 3.0 11.7 1.0 N A:LEU249 3.6 9.1 1.0 O A:LYS247 3.8 11.7 1.0 CA A:ARG248 3.8 9.0 1.0 O A:LEU249 3.8 10.5 1.0 CE A:LYS274 3.8 15.7 1.0 O B:HOH523 4.0 43.2 1.0 CD2 A:LEU249 4.2 19.5 1.0 C A:ARG248 4.2 9.7 1.0 O B:HOH299 4.4 13.7 1.0 CB B:LYS247 4.5 11.1 1.0 CD B:LYS247 4.5 14.1 1.0 O A:HOH16 4.6 12.6 1.0 O A:HOH9 4.6 13.7 1.0 C A:LYS247 4.6 10.5 1.0 CB A:ARG248 4.6 12.4 1.0 N A:ARG248 4.7 8.8 1.0 C A:LEU249 4.7 9.5 1.0 CA A:LEU249 4.7 11.2 1.0 O A:HOH343 4.7 27.5 1.0 CG A:ARG248 4.9 26.5 1.0

Bromine binding site 4 out of 7 in the Structure of Apo Form of A Periplasmic Heme Binding Protein


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 4 of Structure of Apo Form of A Periplasmic Heme Binding Protein within 5.0Å range: probe atom residue distance (Å) B Occ B:Br401 b:23.1 occ:0.77 O B:HOH423 2.9 39.5 1.0 NZ B:LYS274 3.0 18.5 1.0 O A:HOH9 3.1 13.7 1.0 O B:HOH523 3.6 43.2 1.0 N B:LEU249 3.6 9.3 1.0 O B:LYS247 3.8 10.5 1.0 CA B:ARG248 3.8 8.5 1.0 O B:LEU249 3.9 10.1 1.0 CE B:LYS274 3.9 15.0 1.0 CD2 B:LEU249 4.1 21.4 1.0 C B:ARG248 4.2 7.9 1.0 CG B:ARG248 4.3 22.7 1.0 O A:HOH282 4.3 14.0 1.0 CD A:LYS247 4.5 15.4 1.0 CB A:LYS247 4.5 12.5 1.0 O A:HOH5 4.6 12.1 1.0 O B:HOH3 4.6 11.7 1.0 CB B:ARG248 4.6 13.7 1.0 C B:LYS247 4.6 10.0 1.0 O B:HOH361 4.6 31.9 1.0 C B:LEU249 4.7 8.3 1.0 CA B:LEU249 4.7 10.7 1.0 N B:ARG248 4.7 9.8 1.0 CD B:ARG248 4.8 40.9 1.0

Bromine binding site 5 out of 7 in the Structure of Apo Form of A Periplasmic Heme Binding Protein


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 5 of Structure of Apo Form of A Periplasmic Heme Binding Protein within 5.0Å range: probe atom residue distance (Å) B Occ B:Br402 b:29.3 occ:0.69 O B:HOH495 3.1 39.2 1.0 N B:SER204 3.4 14.6 1.0 O B:HOH522 3.4 33.6 1.0 CE B:MET194 3.6 10.6 1.0 CA B:GLY207 3.8 11.9 1.0 CA B:LEU203 3.8 11.2 1.0 O B:PRO202 3.8 14.8 1.0 OG B:SER204 3.8 15.8 1.0 C B:GLY207 3.9 9.8 1.0 N B:VAL208 3.9 9.6 1.0 O B:SER204 4.0 11.9 1.0 C B:LEU203 4.1 14.9 1.0 CG2 B:VAL208 4.2 11.8 1.0 SD B:MET194 4.3 13.2 1.0 CA B:SER204 4.4 14.5 1.0 CD2 B:LEU203 4.5 14.8 1.0 CB B:SER204 4.5 17.0 1.0 N B:GLY207 4.5 12.2 1.0 O B:GLY207 4.5 11.5 1.0 C B:PRO202 4.6 13.4 1.0 N B:LEU203 4.6 12.5 1.0 C B:SER204 4.7 11.7 1.0 CB B:ALA174 4.7 12.4 1.0 O B:HOH372 4.7 34.2 1.0 CA B:VAL208 4.8 9.4 1.0 CB B:LEU203 4.8 11.8 1.0 O B:HOH408 4.8 30.3 1.0

Bromine binding site 6 out of 7 in the Structure of Apo Form of A Periplasmic Heme Binding Protein


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 6 of Structure of Apo Form of A Periplasmic Heme Binding Protein within 5.0Å range: probe atom residue distance (Å) B Occ B:Br403 b:46.7 occ:0.60 NH1 B:ARG72 3.1 44.6 1.0 N B:ARG72 3.7 32.6 1.0 CG B:ARG72 3.8 37.1 1.0 CD B:ARG72 3.9 38.3 1.0 N B:MET71 3.9 35.8 1.0 CB B:ARG72 4.0 35.8 1.0 CG2 B:THR55 4.0 35.4 1.0 CB B:MET71 4.2 31.9 1.0 CB B:TYR70 4.2 80.3 0.0 CZ B:ARG72 4.2 44.1 1.0 CE B:MET71 4.4 73.6 1.0 CA B:MET71 4.4 32.0 1.0 CA B:ARG72 4.5 33.9 1.0 NE B:ARG72 4.5 40.4 1.0 C B:MET71 4.5 36.3 1.0 CD2 B:TYR70 4.5 0.3 0.0 C B:TYR70 4.6 46.9 0.0 CA B:TYR70 4.6 59.5 1.0 CG B:TYR70 4.9 0.4 0.0

Bromine binding site 7 out of 7 in the Structure of Apo Form of A Periplasmic Heme Binding Protein


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 7 of Structure of Apo Form of A Periplasmic Heme Binding Protein within 5.0Å range: probe atom residue distance (Å) B Occ B:Br404 b:44.8 occ:0.52 O B:HOH510 3.2 48.9 1.0 CD B:PRO172 3.9 27.7 1.0 O B:HOH483 3.9 42.2 1.0 CD B:PRO236 4.0 17.5 1.0 CD2 B:LEU235 4.1 20.9 1.0 CG2 B:THR171 4.1 30.3 1.0 OG1 B:THR171 4.2 32.3 1.0 CA B:THR171 4.3 26.3 1.0 CG B:PRO236 4.3 17.2 1.0 CB B:THR171 4.4 28.9 1.0 N B:PRO172 4.9 22.7 1.0 O B:HOH398 4.9 31.1 1.0 CG B:PRO172 5.0 28.5 1.0

D.Mattle, A.Zeltina, J.S.Woo, B.A.Goetz, K.P.Locher. Two Stacked Heme Molecules in the Binding Pocket of the Periplasmic Heme-Binding Protein Hmut From Yersinia Pestis. J.Mol.Biol. V. 404 220 2010.
ISSN: ISSN 0022-2836
PubMed: 20888343
DOI: 10.1016/J.JMB.2010.09.005