Iron in PDB 5ff4: Hyde From T. Maritima in Complex with (2R,4R)-Tmetda

The structure of Hyde From T. Maritima in Complex with (2R,4R)-Tmetda, PDB code: 5ff4 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)	43.08 / 1.35
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	51.110, 79.380, 86.160, 90.00, 90.00, 90.00
R / Rfree (%)	11.6 / 15.3

The structure of Hyde From T. Maritima in Complex with (2R,4R)-Tmetda also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Iron atom in the Hyde From T. Maritima in Complex with (2R,4R)-Tmetda (pdb code 5ff4). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Hyde From T. Maritima in Complex with (2R,4R)-Tmetda, PDB code: 5ff4:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Hyde From T. Maritima in Complex with (2R,4R)-Tmetda


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 (2R,4R)-Tmetda within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:16.6 occ:1.00 FE1 A:SFS401 0.0 16.6 1.0 SG A:CYS70 2.3 16.8 1.0 SE3 A:SFS401 2.3 16.9 0.9 SE2 A:SFS401 2.4 17.1 0.9 SE4 A:SFS401 2.4 16.7 0.9 FE2 A:SFS401 2.7 15.9 1.0 FE3 A:SFS401 2.7 16.2 1.0 FE4 A:SFS401 2.9 18.9 1.0 CB A:CYS70 3.1 14.4 1.0 SE1 A:SFS401 4.0 16.6 0.8 CB A:LEU72 4.3 15.2 1.0 CD2 A:LEU305 4.4 21.9 1.0 SD A:SAH408 4.5 18.2 1.0 CA A:CYS70 4.5 14.4 1.0 N A:ARG73 4.8 14.0 1.0 SG A:CYS67 4.8 17.4 1.0 N A:SAH408 4.8 17.4 1.0 SG A:CYS63 4.8 14.9 1.0 C A:LEU72 4.8 14.7 1.0 N A:LEU72 4.8 14.0 1.0 CB A:CYS67 4.8 16.0 1.0 OXT A:SAH408 4.9 21.1 1.0 CA A:LEU72 4.9 15.3 1.0

Iron binding site 2 out of 4 in the Hyde From T. Maritima in Complex with (2R,4R)-Tmetda


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 (2R,4R)-Tmetda within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:16.2 occ:1.00 FE3 A:SFS401 0.0 16.2 1.0 SG A:CYS67 2.3 17.4 1.0 SE1 A:SFS401 2.4 16.6 0.8 SE2 A:SFS401 2.4 17.1 0.9 SE4 A:SFS401 2.4 16.7 0.9 FE1 A:SFS401 2.7 16.6 1.0 FE2 A:SFS401 2.8 15.9 1.0 FE4 A:SFS401 3.0 18.9 1.0 CB A:CYS67 3.2 16.0 1.0 O A:HOH639 3.9 20.6 1.0 SE3 A:SFS401 4.1 16.9 0.9 OXT A:SAH408 4.2 21.1 1.0 N A:CYS67 4.3 14.9 1.0 CB A:LYS65 4.4 12.8 1.0 CA A:CYS67 4.4 14.2 1.0 CB A:CYS70 4.5 14.4 1.0 NH2 A:ARG172 4.6 15.9 1.0 OH A:TYR69 4.7 16.4 1.0 SG A:CYS70 4.7 16.8 1.0 SG A:CYS63 4.8 14.9 1.0 CE1 A:TYR69 4.9 14.4 1.0 O A:HOH580 5.0 18.1 1.0

Iron binding site 3 out of 4 in the Hyde From T. Maritima in Complex with (2R,4R)-Tmetda


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 (2R,4R)-Tmetda within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:15.9 occ:1.00 FE2 A:SFS401 0.0 15.9 1.0 SG A:CYS63 2.3 14.9 1.0 SE4 A:SFS401 2.3 16.7 0.9 SE3 A:SFS401 2.4 16.9 0.9 SE1 A:SFS401 2.4 16.6 0.8 FE1 A:SFS401 2.7 16.6 1.0 FE3 A:SFS401 2.8 16.2 1.0 FE4 A:SFS401 2.9 18.9 1.0 CB A:CYS63 3.4 14.9 1.0 SE2 A:SFS401 4.0 17.1 0.9 N A:SAH408 4.1 17.4 1.0 CB A:LYS65 4.3 12.8 1.0 N A:GLU110 4.4 12.4 1.0 CA A:GLY109 4.6 12.6 1.0 O A:LYS65 4.7 16.6 1.0 SG A:CYS70 4.8 16.8 1.0 CA A:CYS63 4.8 13.5 1.0 N A:LYS65 4.9 13.9 1.0 C A:LYS65 4.9 14.9 1.0 SG A:CYS67 4.9 17.4 1.0 CA A:LYS65 4.9 15.0 1.0 CB A:LEU72 4.9 15.2 1.0 OXT A:SAH408 4.9 21.1 1.0 O A:LEU72 5.0 14.9 1.0

Iron binding site 4 out of 4 in the Hyde From T. Maritima in Complex with (2R,4R)-Tmetda


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 (2R,4R)-Tmetda within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:18.9 occ:1.00 FE4 A:SFS401 0.0 18.9 1.0 OXT A:SAH408 2.2 21.1 1.0 N A:SAH408 2.2 17.4 1.0 SE2 A:SFS401 2.5 17.1 0.9 SE3 A:SFS401 2.5 16.9 0.9 SE1 A:SFS401 2.5 16.6 0.8 FE1 A:SFS401 2.9 16.6 1.0 FE2 A:SFS401 2.9 15.9 1.0 C A:SAH408 3.0 17.5 1.0 FE3 A:SFS401 3.0 16.2 1.0 CA A:SAH408 3.2 15.9 1.0 SD A:SAH408 3.3 18.2 1.0 CG A:SAH408 3.7 14.9 1.0 CB A:SAH408 3.9 15.8 1.0 O A:HOH639 4.1 20.6 1.0 O A:HOH580 4.2 18.1 1.0 O A:SAH408 4.2 16.3 1.0 SE4 A:SFS401 4.3 16.7 0.9 SG A:CYS63 4.8 14.9 1.0 C5' A:SAH408 4.8 17.7 1.0 SG A:CYS70 4.9 16.8 1.0

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