Bromine in PDB 4jyd: X-Ray Snapshots of Possible Intermediates in the Time Course of Synthesis and Degradation of Protein-Bound FE4S4 Clusters.

The structure of X-Ray Snapshots of Possible Intermediates in the Time Course of Synthesis and Degradation of Protein-Bound FE4S4 Clusters., PDB code: 4jyd was solved by Y.Nicolet, R.Rohac, L.Martin, J.C.Fontecilla-Camps, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.60 / 1.71
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	50.598, 78.699, 85.960, 90.00, 90.00, 90.00
R / Rfree (%)	18.9 / 25.1

The structure of X-Ray Snapshots of Possible Intermediates in the Time Course of Synthesis and Degradation of Protein-Bound FE4S4 Clusters. also contains other interesting chemical elements:

Iron

(Fe)

5 atoms

The binding sites of Bromine atom in the X-Ray Snapshots of Possible Intermediates in the Time Course of Synthesis and Degradation of Protein-Bound FE4S4 Clusters. (pdb code 4jyd). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 4 binding sites of Bromine where determined in the X-Ray Snapshots of Possible Intermediates in the Time Course of Synthesis and Degradation of Protein-Bound FE4S4 Clusters., PDB code: 4jyd:
Jump to Bromine binding site number: 1; 2; 3; 4;

Bromine binding site 1 out of 4 in the X-Ray Snapshots of Possible Intermediates in the Time Course of Synthesis and Degradation of Protein-Bound FE4S4 Clusters.


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of X-Ray Snapshots of Possible Intermediates in the Time Course of Synthesis and Degradation of Protein-Bound FE4S4 Clusters. within 5.0Å range: probe atom residue distance (Å) B Occ A:Br411 b:29.4 occ:0.50 O A:HOH585 2.7 35.6 1.0 O A:HOH567 3.1 25.4 1.0 NH1 A:ARG64 3.2 15.4 1.0 CD A:PRO141 3.6 18.6 1.0 CE3 A:TRP140 3.7 16.0 1.0 CG A:PRO141 3.8 19.5 1.0 CZ3 A:TRP140 3.8 15.8 1.0 NH2 A:ARG64 3.9 17.9 1.0 CZ A:ARG64 4.0 17.4 1.0 O A:HOH742 4.4 30.4 1.0 O A:HOH850 4.6 64.9 1.0 CD2 A:TRP140 4.9 15.4 1.0 N A:PRO141 4.9 18.6 1.0 CE2 A:TYR144 4.9 19.7 1.0

Bromine binding site 2 out of 4 in the X-Ray Snapshots of Possible Intermediates in the Time Course of Synthesis and Degradation of Protein-Bound FE4S4 Clusters.


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of X-Ray Snapshots of Possible Intermediates in the Time Course of Synthesis and Degradation of Protein-Bound FE4S4 Clusters. within 5.0Å range: probe atom residue distance (Å) B Occ A:Br412 b:21.5 occ:0.90 OG1 A:THR134 3.2 12.9 1.0 NH1 A:ARG155 3.4 15.7 1.0 O A:HOH539 3.4 19.5 1.0 NE A:ARG54 3.5 18.7 1.0 SD A:MET224 3.8 16.3 0.6 CD A:ARG54 3.8 16.4 1.0 CD A:ARG155 3.8 13.5 1.0 CG2 A:THR134 3.8 10.9 1.0 CG A:ARG54 3.9 12.8 1.0 CB A:THR134 3.9 11.1 1.0 CG2 A:THR103 4.0 12.6 1.0 CZ A:ARG54 4.0 15.2 1.0 CE A:MET291 4.2 14.1 0.4 NH2 A:ARG54 4.4 14.7 1.0 CB A:ARG54 4.4 13.8 1.0 CZ A:ARG155 4.4 14.6 1.0 CG2 A:VAL105 4.4 11.9 1.0 CE A:MET224 4.5 14.9 0.4 NE A:ARG155 4.6 15.5 1.0 NH1 A:ARG54 4.8 14.0 1.0 CG A:ARG155 4.8 12.7 1.0 CB A:ARG155 4.8 12.2 1.0 CD2 A:LEU157 4.8 18.3 1.0 O A:HOH739 4.8 28.5 1.0 CB A:THR103 4.9 12.4 1.0 CE A:MET224 4.9 14.7 0.6 CD1 A:LEU157 4.9 15.5 1.0

Bromine binding site 3 out of 4 in the X-Ray Snapshots of Possible Intermediates in the Time Course of Synthesis and Degradation of Protein-Bound FE4S4 Clusters.


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of X-Ray Snapshots of Possible Intermediates in the Time Course of Synthesis and Degradation of Protein-Bound FE4S4 Clusters. within 5.0Å range: probe atom residue distance (Å) B Occ A:Br413 b:28.9 occ:0.50 O A:HOH638 2.9 20.2 1.0 O A:HOH816 3.0 37.9 1.0 NH2 A:ARG159 3.4 22.1 1.0 CG A:PRO266 3.5 13.7 0.5 O A:HOH700 3.5 23.3 1.0 CG A:PRO266 3.8 13.3 0.5 SD A:MET291 3.8 22.0 0.6 CA A:GLY226 3.8 14.8 1.0 O A:HOH712 3.9 31.8 1.0 CG2 A:THR268 3.9 12.9 1.0 NE A:ARG159 4.1 18.4 1.0 CB A:PRO266 4.2 12.8 0.5 CZ A:ARG159 4.2 20.0 1.0 CE A:MET291 4.2 14.1 0.4 CE A:MET291 4.4 20.1 0.6 CB A:PRO266 4.4 12.7 0.5 CD A:PRO266 4.5 13.2 0.5 SD A:MET291 4.5 16.1 0.4 CD A:PRO266 4.6 13.4 0.5 N A:GLY226 4.7 13.7 1.0 O A:HOH532 4.7 17.5 1.0 O A:HOH741 4.8 21.3 1.0 CD1 A:LEU157 4.8 15.5 1.0 C A:GLY226 4.8 15.2 1.0 O A:HOH601 4.9 17.4 1.0

Bromine binding site 4 out of 4 in the X-Ray Snapshots of Possible Intermediates in the Time Course of Synthesis and Degradation of Protein-Bound FE4S4 Clusters.


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 4 of X-Ray Snapshots of Possible Intermediates in the Time Course of Synthesis and Degradation of Protein-Bound FE4S4 Clusters. within 5.0Å range: probe atom residue distance (Å) B Occ A:Br414 b:27.1 occ:0.50 O A:HOH803 3.1 22.3 1.0 OH A:TYR306 3.4 23.2 1.0 O A:HOH529 3.4 18.5 1.0 N A:ALA270 3.5 14.6 1.0 NH2 A:ARG159 3.7 22.1 1.0 CB A:ALA270 3.8 13.9 1.0 CB A:THR268 3.9 12.6 1.0 N A:THR269 3.9 14.5 1.0 CE2 A:TYR306 4.0 20.8 1.0 CZ A:TYR306 4.1 22.5 1.0 O A:HOH741 4.2 21.3 1.0 CA A:ALA270 4.2 14.2 1.0 CB A:THR269 4.3 16.5 1.0 C A:THR269 4.3 14.3 1.0 CA A:THR269 4.4 15.5 1.0 OG1 A:THR268 4.4 12.8 1.0 NH1 A:ARG159 4.5 19.7 1.0 C A:THR268 4.5 13.0 1.0 CZ A:ARG159 4.5 20.0 1.0 CG2 A:THR268 4.6 12.9 1.0 O A:HOH804 4.6 33.6 1.0 CA A:THR268 4.7 12.8 1.0 O A:HOH740 4.8 34.5 1.0

Y.Nicolet, R.Rohac, L.Martin, J.C.Fontecilla-Camps. X-Ray Snapshots of Possible Intermediates in the Time Course of Synthesis and Degradation of Protein-Bound FE4S4 Clusters. Proc.Natl.Acad.Sci.Usa V. 110 7188 2013.
ISSN: ISSN 0027-8424
PubMed: 23596207
DOI: 10.1073/PNAS.1302388110