Iron in PDB 5fez: Hyde From T. Maritima in Complex with (2R,4R)-Mesetda, 5'- Deoxyadenosine and Methionine

The structure of Hyde From T. Maritima in Complex with (2R,4R)-Mesetda, 5'- Deoxyadenosine and Methionine, PDB code: 5fez 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)	38.27 / 1.35
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	50.800, 78.870, 86.250, 90.00, 90.00, 90.00
R / Rfree (%)	11.9 / 13.5

The structure of Hyde From T. Maritima in Complex with (2R,4R)-Mesetda, 5'- Deoxyadenosine and Methionine 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)-Mesetda, 5'- Deoxyadenosine and Methionine (pdb code 5fez). 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)-Mesetda, 5'- Deoxyadenosine and Methionine, PDB code: 5fez:
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)-Mesetda, 5'- Deoxyadenosine and Methionine


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)-Mesetda, 5'- Deoxyadenosine and Methionine within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:11.8 occ:1.00 FE1 A:SFS401 0.0 11.8 1.0 SG A:CYS70 2.3 11.9 1.0 SE3 A:SFS401 2.3 14.3 1.0 SE2 A:SFS401 2.4 15.2 1.0 SE4 A:SFS401 2.4 14.2 1.0 FE2 A:SFS401 2.7 11.2 1.0 FE3 A:SFS401 2.7 11.7 1.0 FE4 A:SFS401 2.9 13.1 1.0 CB A:CYS70 3.1 11.1 1.0 SE1 A:SFS401 4.0 14.4 1.0 SD A:MET409 4.1 14.6 1.0 CB A:LEU72 4.3 11.6 1.0 CA A:CYS70 4.6 10.5 1.0 CE A:MET409 4.7 16.6 1.0 SG A:CYS67 4.8 12.0 1.0 N A:ARG73 4.8 11.1 1.0 C A:LEU72 4.8 11.0 1.0 CB A:CYS67 4.8 10.8 1.0 SG A:CYS63 4.9 10.6 1.0 N A:LEU72 4.9 11.1 1.0 CA A:LEU72 4.9 11.5 1.0 N A:MET409 4.9 12.8 1.0 OXT A:MET409 4.9 13.5 1.0

Iron binding site 2 out of 4 in the Hyde From T. Maritima in Complex with (2R,4R)-Mesetda, 5'- Deoxyadenosine and Methionine


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)-Mesetda, 5'- Deoxyadenosine and Methionine within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:11.7 occ:1.00 FE3 A:SFS401 0.0 11.7 1.0 SG A:CYS67 2.3 12.0 1.0 SE1 A:SFS401 2.4 14.4 1.0 SE2 A:SFS401 2.4 15.2 1.0 SE4 A:SFS401 2.4 14.2 1.0 FE1 A:SFS401 2.7 11.8 1.0 FE2 A:SFS401 2.7 11.2 1.0 FE4 A:SFS401 3.0 13.1 1.0 CB A:CYS67 3.2 10.8 1.0 O A:HOH621 3.9 16.7 1.0 SE3 A:SFS401 4.0 14.3 1.0 N A:CYS67 4.2 11.2 1.0 OXT A:MET409 4.3 13.5 1.0 CA A:CYS67 4.4 10.8 1.0 CB A:LYS65 4.4 10.4 1.0 NH2 A:ARG172 4.5 12.3 1.0 CB A:CYS70 4.5 11.1 1.0 SG A:CYS70 4.6 11.9 1.0 OH A:TYR69 4.7 13.1 1.0 SG A:CYS63 4.8 10.6 1.0 CE1 A:TYR69 4.9 11.9 1.0 NE A:ARG172 5.0 12.0 1.0 O A:HOH569 5.0 13.5 1.0 CD A:LYS65 5.0 11.2 1.0

Iron binding site 3 out of 4 in the Hyde From T. Maritima in Complex with (2R,4R)-Mesetda, 5'- Deoxyadenosine and Methionine


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)-Mesetda, 5'- Deoxyadenosine and Methionine within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:11.2 occ:1.00 FE2 A:SFS401 0.0 11.2 1.0 SG A:CYS63 2.3 10.6 1.0 SE4 A:SFS401 2.3 14.2 1.0 SE3 A:SFS401 2.3 14.3 1.0 SE1 A:SFS401 2.4 14.4 1.0 FE1 A:SFS401 2.7 11.8 1.0 FE3 A:SFS401 2.7 11.7 1.0 FE4 A:SFS401 3.0 13.1 1.0 CB A:CYS63 3.4 10.9 1.0 SE2 A:SFS401 4.0 15.2 1.0 N A:MET409 4.2 12.8 1.0 CB A:LYS65 4.2 10.4 1.0 N A:GLU110 4.5 9.5 1.0 O A:LYS65 4.6 12.4 1.0 CA A:GLY109 4.7 9.9 1.0 N A:LYS65 4.7 10.8 1.0 C A:LYS65 4.8 10.4 1.0 CA A:CYS63 4.8 10.8 1.0 CA A:LYS65 4.8 10.7 1.0 SG A:CYS70 4.8 11.9 1.0 SG A:CYS67 4.8 12.0 1.0 OXT A:MET409 4.9 13.5 1.0

Iron binding site 4 out of 4 in the Hyde From T. Maritima in Complex with (2R,4R)-Mesetda, 5'- Deoxyadenosine and Methionine


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)-Mesetda, 5'- Deoxyadenosine and Methionine within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:13.1 occ:1.00 FE4 A:SFS401 0.0 13.1 1.0 N A:MET409 2.2 12.8 1.0 OXT A:MET409 2.3 13.5 1.0 SE3 A:SFS401 2.5 14.3 1.0 SE2 A:SFS401 2.5 15.2 1.0 SE1 A:SFS401 2.6 14.4 1.0 SD A:MET409 2.6 14.6 1.0 FE1 A:SFS401 2.9 11.8 1.0 FE2 A:SFS401 3.0 11.2 1.0 FE3 A:SFS401 3.0 11.7 1.0 C A:MET409 3.2 12.6 1.0 CA A:MET409 3.2 12.2 1.0 CE A:MET409 3.7 16.6 1.0 CG A:MET409 3.7 16.5 1.0 CB A:MET409 3.9 13.4 1.0 O A:HOH621 4.2 16.7 1.0 O A:HOH569 4.3 13.5 1.0 SE4 A:SFS401 4.3 14.2 1.0 O A:MET409 4.3 13.1 1.0 SG A:CYS63 4.8 10.6 1.0 SG A:CYS70 4.9 11.9 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