Chlorine in PDB 4jy9: 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: 4jy9 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)	58.22 / 1.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	51.247, 78.950, 86.145, 90.00, 90.00, 90.00
R / Rfree (%)	10.2 / 15.6

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)

6 atoms

The binding sites of Chlorine atom in the X-Ray Snapshots of Possible Intermediates in the Time Course of Synthesis and Degradation of Protein-Bound FE4S4 Clusters (pdb code 4jy9). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine 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: 4jy9:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine 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 Chlorine with other atoms in the Cl 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:Cl411 b:13.3 occ:1.00 OG1 A:THR134 3.0 9.9 1.0 NH1 A:ARG155 3.3 9.3 1.0 O A:HOH538 3.3 16.2 1.0 NE A:ARG54 3.5 11.3 1.0 CD A:ARG54 3.7 12.6 1.0 SD A:MET224 3.7 8.6 0.2 CD A:ARG155 3.7 9.2 1.0 CB A:THR134 3.8 9.2 1.0 CG2 A:THR134 3.9 10.2 1.0 CG2 A:THR103 3.9 9.8 1.0 CG A:ARG54 4.0 12.8 1.0 CZ A:ARG54 4.0 9.6 1.0 CZ A:ARG155 4.3 10.2 1.0 NH2 A:ARG54 4.3 11.7 1.0 CG2 A:VAL105 4.4 10.5 1.0 O A:HOH762 4.4 38.8 1.0 NE A:ARG155 4.4 9.5 1.0 CB A:ARG54 4.5 10.6 1.0 CE A:MET224 4.5 18.4 0.8 CG A:ARG155 4.7 8.5 1.0 CD2 A:LEU157 4.7 21.9 1.0 NH1 A:ARG54 4.8 10.1 1.0 CB A:ARG155 4.8 9.5 1.0 CB A:THR103 4.9 8.8 1.0 CE A:MET224 4.9 9.3 0.2 OG1 A:THR103 5.0 8.7 1.0

Chlorine 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 Chlorine with other atoms in the Cl 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:Cl412 b:27.1 occ:0.50 O A:HOH643 2.7 24.3 1.0 O A:HOH845 3.0 48.1 1.0 NH2 A:ARG159 3.2 26.6 1.0 CE A:MET291 3.6 36.4 0.5 CG A:PRO266 3.8 15.1 1.0 O A:HOH841 3.8 38.9 1.0 O A:HOH712 3.8 28.7 1.0 NE A:ARG159 3.9 24.0 1.0 CA A:GLY226 3.9 10.5 1.0 CG2 A:THR268 4.0 12.2 1.0 CZ A:ARG159 4.0 22.1 1.0 SD A:MET291 4.1 25.1 0.5 O A:HOH531 4.5 20.2 1.0 CB A:PRO266 4.6 9.8 1.0 O A:HOH843 4.6 36.8 1.0 CE A:MET291 4.7 29.8 0.5 CD1 A:LEU157 4.7 19.4 1.0 C A:GLY226 4.7 10.7 1.0 O A:HOH600 4.8 18.4 1.0 N A:GLY226 4.8 10.3 1.0 O A:HOH844 4.8 29.2 1.0 O A:HOH762 4.8 38.8 1.0 CD A:PRO266 4.9 10.0 1.0

Chlorine 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 Chlorine with other atoms in the Cl 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:Cl413 b:24.5 occ:0.50 CL A:CL413 0.0 24.5 0.5 CL A:CL413 1.3 31.0 0.5 O A:HOH842 1.8 23.6 0.5 O A:HOH842 2.7 31.3 0.5 O A:HOH843 2.8 36.8 1.0 O A:HOH829 3.0 37.7 1.0 N A:ALA270 3.4 10.3 1.0 NH2 A:ARG159 3.4 26.6 1.0 O A:HOH652 3.4 25.7 1.0 CB A:ALA270 3.5 12.0 1.0 CB A:THR268 3.6 11.6 1.0 OH A:TYR306 3.7 21.9 1.0 OG1 A:THR268 4.0 11.4 1.0 N A:THR269 4.0 13.4 1.0 CA A:ALA270 4.0 10.0 1.0 CE2 A:TYR306 4.2 14.9 1.0 CZ A:ARG159 4.2 22.1 1.0 NH1 A:ARG159 4.3 24.8 1.0 CG2 A:THR268 4.4 12.2 1.0 CZ A:TYR306 4.4 17.0 1.0 C A:THR269 4.4 13.1 1.0 C A:THR268 4.5 11.4 1.0 CA A:THR269 4.5 13.8 1.0 CA A:THR268 4.6 12.3 1.0 O A:HOH844 4.6 29.2 1.0 CB A:THR269 4.7 19.0 1.0 O A:HOH845 4.9 48.1 1.0 O A:HOH841 4.9 38.9 1.0 N3 A:SAH402 5.0 13.8 1.0

Chlorine 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 Chlorine with other atoms in the Cl 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:Cl413 b:31.0 occ:0.50 CL A:CL413 0.0 31.0 0.5 CL A:CL413 1.3 24.5 0.5 O A:HOH842 1.6 31.3 0.5 O A:HOH843 1.9 36.8 1.0 O A:HOH829 3.0 37.7 1.0 O A:HOH842 3.1 23.6 0.5 OH A:TYR306 3.2 21.9 1.0 N A:ALA270 3.5 10.3 1.0 N A:THR269 3.5 13.4 1.0 CB A:THR269 3.6 19.0 1.0 O A:HOH844 3.8 29.2 1.0 CA A:THR269 3.9 13.8 1.0 O A:HOH763 4.0 32.7 1.0 CB A:THR268 4.0 11.6 1.0 C A:THR269 4.1 13.1 1.0 CZ A:TYR306 4.2 17.0 1.0 NH2 A:ARG159 4.2 26.6 1.0 CE2 A:TYR306 4.2 14.9 1.0 CB A:ALA270 4.2 12.0 1.0 C A:THR268 4.3 11.4 1.0 OG1 A:THR269 4.3 21.5 1.0 O A:HOH845 4.4 48.1 1.0 CA A:ALA270 4.4 10.0 1.0 CA A:THR268 4.6 12.3 1.0 O A:HOH841 4.6 38.9 1.0 OG1 A:THR268 4.7 11.4 1.0 O A:HOH652 4.7 25.7 1.0 CG2 A:THR269 4.8 24.7 1.0 CG2 A:THR268 4.8 12.2 1.0 O A:HOH537 5.0 18.3 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