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

The structure of Hyde From T. Maritima in Complex with (2R,4R)-Mesetda, PDB code: 5fes 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)	43.95 / 1.27
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	51.070, 79.100, 86.260, 90.00, 90.00, 90.00
R / Rfree (%)	10.8 / 13.5

The structure of Hyde From T. Maritima in Complex with (2R,4R)-Mesetda 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 (pdb code 5fes). 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, PDB code: 5fes:
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


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:13.3 occ:1.00 FE1 A:SF4401 0.0 13.3 1.0 S3 A:SF4401 2.2 12.7 1.0 SG A:CYS70 2.3 13.2 1.0 S2 A:SF4401 2.3 14.1 1.0 S4 A:SF4401 2.3 13.5 1.0 FE2 A:SF4401 2.7 12.8 1.0 FE3 A:SF4401 2.7 13.1 1.0 FE4 A:SF4401 2.9 13.7 1.0 CB A:CYS70 3.1 12.8 1.0 S1 A:SF4401 3.9 13.4 1.0 CE A:SAM408 4.1 19.9 1.0 CB A:LEU72 4.2 12.9 1.0 SD A:SAM408 4.4 16.3 1.0 CA A:CYS70 4.5 12.0 1.0 OXT A:SAM408 4.8 14.7 1.0 N A:ARG73 4.8 11.5 1.0 C A:LEU72 4.8 12.6 1.0 SG A:CYS67 4.8 13.6 1.0 SG A:CYS63 4.8 11.9 1.0 N A:SAM408 4.8 14.6 1.0 CD2 A:LEU305 4.8 37.5 1.0 CB A:CYS67 4.8 12.5 1.0 CA A:LEU72 4.8 12.0 1.0 N A:LEU72 4.8 12.2 1.0 CG A:LEU72 4.9 16.2 1.0 C8 A:SAM408 4.9 15.3 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:12.8 occ:1.00 FE2 A:SF4401 0.0 12.8 1.0 SG A:CYS63 2.3 11.9 1.0 S4 A:SF4401 2.3 13.5 1.0 S3 A:SF4401 2.3 12.7 1.0 S1 A:SF4401 2.3 13.4 1.0 FE1 A:SF4401 2.7 13.3 1.0 FE3 A:SF4401 2.7 13.1 1.0 FE4 A:SF4401 2.8 13.7 1.0 CB A:CYS63 3.4 11.7 1.0 S2 A:SF4401 3.9 14.1 1.0 N A:SAM408 4.1 14.6 1.0 CB A:LYS65 4.2 11.3 1.0 N A:GLU110 4.4 10.5 1.0 O A:LYS65 4.6 14.5 1.0 CA A:GLY109 4.6 10.9 1.0 CA A:CYS63 4.8 11.2 1.0 SG A:CYS70 4.8 13.2 1.0 SG A:CYS67 4.8 13.6 1.0 C A:LYS65 4.8 12.5 1.0 N A:LYS65 4.8 11.3 1.0 CA A:LYS65 4.8 12.8 1.0 OXT A:SAM408 4.9 14.7 1.0 CB A:LEU72 4.9 12.9 1.0 O A:LEU72 5.0 12.5 1.0 CG A:GLU110 5.0 10.8 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:13.1 occ:1.00 FE3 A:SF4401 0.0 13.1 1.0 S1 A:SF4401 2.3 13.4 1.0 S4 A:SF4401 2.3 13.5 1.0 S2 A:SF4401 2.3 14.1 1.0 SG A:CYS67 2.3 13.6 1.0 FE1 A:SF4401 2.7 13.3 1.0 FE2 A:SF4401 2.7 12.8 1.0 FE4 A:SF4401 2.9 13.7 1.0 CB A:CYS67 3.2 12.5 1.0 O A:HOH587 3.9 17.2 1.0 S3 A:SF4401 3.9 12.7 1.0 OXT A:SAM408 4.2 14.7 1.0 N A:CYS67 4.3 12.1 1.0 CA A:CYS67 4.4 12.7 1.0 CB A:LYS65 4.4 11.3 1.0 CB A:CYS70 4.4 12.8 1.0 NH2 A:ARG172 4.5 13.0 1.0 SG A:CYS70 4.6 13.2 1.0 OH A:TYR69 4.7 14.7 1.0 SG A:CYS63 4.7 11.9 1.0 CE1 A:TYR69 4.8 13.2 1.0 O A:HOH582 4.9 14.8 1.0 N A:SAM408 4.9 14.6 1.0 CZ A:TYR69 5.0 12.9 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:13.7 occ:1.00 FE4 A:SF4401 0.0 13.7 1.0 OXT A:SAM408 2.2 14.7 1.0 N A:SAM408 2.3 14.6 1.0 S1 A:SF4401 2.4 13.4 1.0 S3 A:SF4401 2.4 12.7 1.0 S2 A:SF4401 2.4 14.1 1.0 FE2 A:SF4401 2.8 12.8 1.0 FE3 A:SF4401 2.9 13.1 1.0 FE1 A:SF4401 2.9 13.3 1.0 C A:SAM408 3.1 14.7 1.0 CA A:SAM408 3.2 13.6 1.0 SD A:SAM408 3.2 16.3 1.0 CG A:SAM408 3.7 16.1 1.0 O A:HOH582 4.0 14.8 1.0 CB A:SAM408 4.0 14.0 1.0 S4 A:SF4401 4.1 13.5 1.0 O A:HOH587 4.1 17.2 1.0 CE A:SAM408 4.1 19.9 1.0 O A:SAM408 4.2 15.2 1.0 SG A:CYS63 4.7 11.9 1.0 C5' A:SAM408 4.8 18.6 1.0 SG A:CYS70 4.9 13.2 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