Iron in PDB 5ff3: Hyde From T. Maritima in Complex with 4R-Tca

The structure of Hyde From T. Maritima in Complex with 4R-Tca, PDB code: 5ff3 was solved by R.Rohac, P.Amara, A.Benjdia, L.Martin, P.Ruffie, A.Favier, O.Berteau, J.M.Mouesca, J.C.Fontecilla-Camps, Y.Nicolet, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.90 / 1.18
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	51.000, 79.190, 86.240, 90.00, 90.00, 90.00
R / Rfree (%)	11.8 / 14.2

The structure of Hyde From T. Maritima in Complex with 4R-Tca also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Iron atom in the Hyde From T. Maritima in Complex with 4R-Tca (pdb code 5ff3). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the Hyde From T. Maritima in Complex with 4R-Tca, PDB code: 5ff3:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in the Hyde From T. Maritima in Complex with 4R-Tca


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Hyde From T. Maritima in Complex with 4R-Tca within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:11.2 occ:1.00 FE1 A:SF4401 0.0 11.2 1.0 S3 A:SF4401 2.2 11.2 1.0 SG A:CYS70 2.3 11.5 1.0 S2 A:SF4401 2.3 12.0 1.0 S4 A:SF4401 2.3 11.6 1.0 FE2 A:SF4401 2.7 11.1 1.0 FE3 A:SF4401 2.7 11.4 1.0 FE4 A:SF4401 2.9 12.7 0.8 CB A:CYS70 3.1 11.4 1.0 S1 A:SF4401 3.9 11.7 1.0 CB A:LEU72 4.2 11.8 1.0 CD2 A:LEU305 4.4 16.6 1.0 SD A:SAH410 4.5 19.6 1.0 CA A:CYS70 4.5 11.1 1.0 N A:SAH410 4.7 16.9 1.0 SG A:CYS67 4.8 12.4 1.0 CB A:CYS67 4.8 12.3 1.0 N A:ARG73 4.8 11.2 1.0 SG A:CYS63 4.8 11.0 1.0 C A:LEU72 4.8 11.4 1.0 N A:LEU72 4.9 11.1 1.0 OXT A:SAH410 4.9 15.8 1.0 CA A:LEU72 4.9 11.2 1.0

Iron binding site 2 out of 6 in the Hyde From T. Maritima in Complex with 4R-Tca


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Hyde From T. Maritima in Complex with 4R-Tca within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:11.1 occ:1.00 FE2 A:SF4401 0.0 11.1 1.0 S4 A:SF4401 2.3 11.6 1.0 SG A:CYS63 2.3 11.0 1.0 S3 A:SF4401 2.3 11.2 1.0 S1 A:SF4401 2.3 11.7 1.0 FE1 A:SF4401 2.7 11.2 1.0 FE3 A:SF4401 2.7 11.4 1.0 FE4 A:SF4401 2.9 12.7 0.8 CB A:CYS63 3.4 10.6 1.0 S2 A:SF4401 3.9 12.0 1.0 N A:SAH410 4.1 16.9 1.0 CB A:LYS65 4.2 10.8 1.0 N A:GLU110 4.4 10.0 1.0 CA A:GLY109 4.6 9.9 1.0 O A:LYS65 4.7 13.1 1.0 CA A:CYS63 4.8 10.9 1.0 SG A:CYS70 4.8 11.5 1.0 N A:LYS65 4.8 11.1 1.0 SG A:CYS67 4.8 12.4 1.0 C A:LYS65 4.8 11.4 1.0 CA A:LYS65 4.8 11.9 1.0 CB A:LEU72 4.9 11.8 1.0 OXT A:SAH410 4.9 15.8 1.0

Iron binding site 3 out of 6 in the Hyde From T. Maritima in Complex with 4R-Tca


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Hyde From T. Maritima in Complex with 4R-Tca within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:11.4 occ:1.00 FE3 A:SF4401 0.0 11.4 1.0 S1 A:SF4401 2.3 11.7 1.0 S4 A:SF4401 2.3 11.6 1.0 S2 A:SF4401 2.3 12.0 1.0 SG A:CYS67 2.3 12.4 1.0 FE2 A:SF4401 2.7 11.1 1.0 FE1 A:SF4401 2.7 11.2 1.0 FE4 A:SF4401 2.9 12.7 0.8 CB A:CYS67 3.2 12.3 1.0 S3 A:SF4401 3.9 11.2 1.0 O A:HOH570 3.9 15.7 1.0 OXT A:SAH410 4.2 15.8 1.0 N A:CYS67 4.2 11.7 1.0 CB A:LYS65 4.3 10.8 1.0 CA A:CYS67 4.4 11.9 1.0 NH2 A:ARG172 4.4 12.9 1.0 CB A:CYS70 4.5 11.4 1.0 OH A:TYR69 4.7 14.1 1.0 SG A:CYS70 4.7 11.5 1.0 SG A:CYS63 4.7 11.0 1.0 O A:HOH595 4.8 14.0 1.0 CE1 A:TYR69 4.9 11.9 1.0 N A:SAH410 4.9 16.9 1.0 CD A:LYS65 4.9 13.0 1.0 NE A:ARG172 5.0 12.3 1.0

Iron binding site 4 out of 6 in the Hyde From T. Maritima in Complex with 4R-Tca


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Hyde From T. Maritima in Complex with 4R-Tca within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:12.7 occ:0.85 FE4 A:SF4401 0.0 12.7 0.8 N A:SAH410 2.2 16.9 1.0 OXT A:SAH410 2.2 15.8 1.0 S2 A:SF4401 2.4 12.0 1.0 S1 A:SF4401 2.4 11.7 1.0 S3 A:SF4401 2.4 11.2 1.0 FE1 A:SF4401 2.9 11.2 1.0 FE2 A:SF4401 2.9 11.1 1.0 FE3 A:SF4401 2.9 11.4 1.0 C A:SAH410 3.0 13.0 1.0 CA A:SAH410 3.1 12.4 1.0 SD A:SAH410 3.3 19.6 1.0 CG A:SAH410 3.7 18.5 1.0 CB A:SAH410 3.9 16.6 1.0 O A:HOH595 4.1 14.0 1.0 S4 A:SF4401 4.1 11.6 1.0 O A:HOH570 4.1 15.7 1.0 O A:SAH410 4.3 13.4 1.0 SG A:CYS63 4.8 11.0 1.0 SG A:CYS70 4.9 11.5 1.0 C5' A:SAH410 5.0 18.5 1.0

Iron binding site 5 out of 6 in the Hyde From T. Maritima in Complex with 4R-Tca


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Hyde From T. Maritima in Complex with 4R-Tca within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe409 b:13.9 occ:0.50 FE1 A:FES409 0.0 13.9 0.5 S A:H2S412 1.5 19.5 0.3 S1 A:FES409 2.2 14.0 0.5 S2 A:FES409 2.3 17.2 0.5 SG A:CYS311 2.3 23.7 1.0 SG A:CYS319 2.4 15.8 0.7 FE2 A:FES409 2.7 16.0 0.5 SG A:CYS319 3.0 21.8 0.3 CB A:CYS311 3.3 20.6 1.0 CB A:CYS319 3.3 13.1 0.3 CB A:CYS319 3.4 12.0 0.7 CA A:CYS319 3.8 11.7 0.3 O A:HOH730 3.9 25.9 1.0 CA A:CYS319 3.9 11.2 0.7 CA A:CYS311 4.1 16.9 1.0 O A:HOH794 4.2 19.3 0.5 N A:CYS319 4.6 11.4 0.3 N A:CYS319 4.7 10.7 0.7 CB A:CYS322 4.7 11.3 0.4 CB A:CYS322 4.7 12.2 0.6 NH1 A:ARG279 4.7 16.9 1.0 SG A:CYS322 4.7 16.3 0.6 SG A:CYS322 4.8 22.0 0.4 O A:CYS319 4.9 12.1 0.3 NH2 A:ARG279 4.9 17.1 1.0 C A:CYS319 4.9 10.2 0.3 N A:CYS311 4.9 18.7 1.0 C A:CYS319 5.0 10.4 0.7 O A:CYS319 5.0 10.6 0.7

Iron binding site 6 out of 6 in the Hyde From T. Maritima in Complex with 4R-Tca


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Hyde From T. Maritima in Complex with 4R-Tca within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe409 b:16.0 occ:0.50 FE2 A:FES409 0.0 16.0 0.5 O A:HOH794 2.2 19.3 0.5 S1 A:FES409 2.3 14.0 0.5 SG A:CYS322 2.3 16.3 0.6 S2 A:FES409 2.3 17.2 0.5 FE1 A:FES409 2.7 13.9 0.5 CB A:CYS322 3.1 11.3 0.4 CB A:CYS322 3.1 12.2 0.6 SG A:CYS322 3.4 22.0 0.4 S A:H2S412 3.7 19.5 0.3 O A:HOH887 3.7 35.1 1.0 NH2 A:ARG279 4.0 17.1 1.0 S A:H2S411 4.2 24.8 0.3 SG A:CYS311 4.2 23.7 1.0 CA A:CYS322 4.5 10.2 0.4 CA A:CYS322 4.5 10.5 0.6 C A:CYS322 4.8 9.5 0.4 C A:CYS322 4.8 9.6 0.6 CA A:CYS319 4.8 11.7 0.3 SG A:CYS319 4.8 15.8 0.7 NH1 A:ARG279 4.9 16.9 1.0 CZ A:ARG279 4.9 15.5 1.0 CA A:CYS319 4.9 11.2 0.7

R.Rohac, P.Amara, A.Benjdia, L.Martin, P.Ruffie, A.Favier, O.Berteau, J.M.Mouesca, J.C.Fontecilla-Camps, Y.Nicolet. Carbon-Sulfur Bond-Forming Reaction Catalysed By the Radical Sam Enzyme Hyde. Nat.Chem. V. 8 491 2016.
ISSN: ESSN 1755-4349
PubMed: 27102684
DOI: 10.1038/NCHEM.2490