Iron 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:

Bromine

(Br)

4 atoms

The binding sites of Iron 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 Iron atom.
In total 5 binding sites of Iron 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 Iron binding site number: 1; 2; 3; 4; 5;

Iron binding site 1 out of 5 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 Iron with other atoms in the Fe 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:Fe401 b:19.9 occ:1.00 FE1 A:SF4401 0.0 19.9 1.0 S2 A:SF4401 2.3 20.9 1.0 S3 A:SF4401 2.3 22.9 1.0 S4 A:SF4401 2.3 21.0 1.0 SG A:CYS67 2.3 17.3 1.0 FE4 A:SF4401 2.7 20.4 1.0 FE3 A:SF4401 2.8 20.0 1.0 FE2 A:SF4401 2.9 21.2 1.0 CB A:CYS67 3.2 16.7 1.0 S1 A:SF4401 4.0 22.0 1.0 O A:HOH568 4.0 25.0 1.0 OXT A:SAH402 4.2 20.5 1.0 N A:CYS67 4.2 16.2 1.0 NH2 A:ARG172 4.3 20.3 1.0 CA A:CYS67 4.3 16.4 1.0 CB A:LYS65 4.4 17.4 1.0 CB A:CYS70 4.4 16.4 1.0 OH A:TYR69 4.5 19.0 1.0 SG A:CYS70 4.6 17.3 1.0 CE1 A:TYR69 4.7 17.8 1.0 SG A:CYS63 4.7 19.4 1.0 O A:HOH520 4.8 17.9 1.0 NE A:ARG172 4.9 19.1 1.0 CZ A:TYR69 4.9 16.9 1.0 CD A:LYS65 5.0 17.9 1.0

Iron binding site 2 out of 5 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 Iron with other atoms in the Fe 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:Fe401 b:21.2 occ:1.00 FE2 A:SF4401 0.0 21.2 1.0 N A:SAH402 2.3 18.9 1.0 S3 A:SF4401 2.3 22.9 1.0 S1 A:SF4401 2.3 22.0 1.0 OXT A:SAH402 2.3 20.5 1.0 S4 A:SF4401 2.3 21.0 1.0 FE4 A:SF4401 2.8 20.4 1.0 FE3 A:SF4401 2.8 20.0 1.0 FE1 A:SF4401 2.9 19.9 1.0 C A:SAH402 3.1 19.9 1.0 CA A:SAH402 3.2 20.0 1.0 SD A:SAH402 3.4 26.2 1.0 CG A:SAH402 3.8 21.9 1.0 CB A:SAH402 4.0 19.9 1.0 S2 A:SF4401 4.1 20.9 1.0 O A:HOH520 4.1 17.9 1.0 O A:HOH568 4.2 25.0 1.0 O A:SAH402 4.2 19.1 1.0 SG A:CYS63 4.7 19.4 1.0 SG A:CYS70 4.9 17.3 1.0 SG A:CYS67 5.0 17.3 1.0

Iron binding site 3 out of 5 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 Iron with other atoms in the Fe 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:Fe401 b:20.0 occ:1.00 FE3 A:SF4401 0.0 20.0 1.0 SG A:CYS63 2.2 19.4 1.0 S4 A:SF4401 2.3 21.0 1.0 S2 A:SF4401 2.3 20.9 1.0 S1 A:SF4401 2.4 22.0 1.0 FE4 A:SF4401 2.7 20.4 1.0 FE1 A:SF4401 2.8 19.9 1.0 FE2 A:SF4401 2.8 21.2 1.0 CB A:CYS63 3.4 17.3 1.0 S3 A:SF4401 3.9 22.9 1.0 CB A:LYS65 4.1 17.4 1.0 N A:SAH402 4.2 18.9 1.0 N A:GLU110 4.4 17.8 1.0 CA A:GLY109 4.5 16.3 1.0 O A:LYS65 4.6 17.9 1.0 SG A:CYS70 4.7 17.3 1.0 N A:LYS65 4.7 16.6 1.0 CA A:CYS63 4.7 17.4 1.0 CA A:LYS65 4.8 16.7 1.0 SG A:CYS67 4.8 17.3 1.0 C A:LYS65 4.8 16.9 1.0 OXT A:SAH402 4.9 20.5 1.0 CB A:LEU72 4.9 17.0 1.0 O A:LEU72 5.0 16.4 1.0

Iron binding site 4 out of 5 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 Iron with other atoms in the Fe 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:Fe401 b:20.4 occ:1.00 FE4 A:SF4401 0.0 20.4 1.0 SG A:CYS70 2.3 17.3 1.0 S2 A:SF4401 2.3 20.9 1.0 S1 A:SF4401 2.3 22.0 1.0 S3 A:SF4401 2.3 22.9 1.0 FE3 A:SF4401 2.7 20.0 1.0 FE1 A:SF4401 2.7 19.9 1.0 FE2 A:SF4401 2.8 21.2 1.0 CB A:CYS70 3.0 16.4 1.0 S4 A:SF4401 3.8 21.0 1.0 CB A:LEU72 4.3 17.0 1.0 SD A:SAH402 4.5 26.2 1.0 CA A:CYS70 4.5 16.2 1.0 CD2 A:LEU305 4.5 20.9 1.0 N A:SAH402 4.7 18.9 1.0 SG A:CYS67 4.8 17.3 1.0 SG A:CYS63 4.8 19.4 1.0 N A:ARG73 4.8 16.8 1.0 CB A:CYS67 4.8 16.7 1.0 N A:LEU72 4.9 17.4 1.0 C A:LEU72 4.9 16.2 1.0 OXT A:SAH402 4.9 20.5 1.0 CA A:LEU72 5.0 16.8 1.0

Iron binding site 5 out of 5 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 Iron with other atoms in the Fe binding site number 5 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:Fe408 b:23.2 occ:0.50 S A:H2S410 2.3 32.9 0.5 SG A:CYS319 2.3 15.7 0.7 S A:H2S409 2.3 21.4 0.5 SG A:CYS311 2.4 34.7 1.0 CB A:CYS311 3.2 32.8 1.0 CB A:CYS319 3.3 14.1 1.0 CA A:CYS319 3.6 13.7 1.0 O A:HOH501 3.7 16.0 1.0 O A:HOH772 4.1 36.0 1.0 CA A:CYS311 4.2 32.7 1.0 N A:CYS319 4.3 13.6 1.0 CB A:CYS322 4.6 18.3 1.0 SG A:CYS322 4.6 24.2 1.0 NH1 A:ARG279 4.7 21.9 1.0 C A:CYS319 4.8 14.2 1.0 NH2 A:ARG279 4.8 19.6 1.0 O A:CYS319 4.9 13.9 1.0 C A:ALA318 5.0 15.6 1.0 N A:CYS311 5.0 32.3 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