Iron in PDB 5ff2: Hyde From T. Maritima in Complex with (2R,4R)-Tda

The structure of Hyde From T. Maritima in Complex with (2R,4R)-Tda, PDB code: 5ff2 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)	38.47 / 1.47
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	51.230, 79.090, 86.100, 90.00, 90.00, 90.00
R / Rfree (%)	16.5 / 18.7

The structure of Hyde From T. Maritima in Complex with (2R,4R)-Tda 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)-Tda (pdb code 5ff2). 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)-Tda, PDB code: 5ff2:
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)-Tda


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)-Tda within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:12.3 occ:1.00 FE1 A:SF4401 0.0 12.3 1.0 S3 A:SF4401 2.2 11.2 1.0 S2 A:SF4401 2.3 12.7 1.0 SG A:CYS70 2.3 11.6 1.0 S4 A:SF4401 2.3 13.1 1.0 FE2 A:SF4401 2.7 12.2 1.0 FE3 A:SF4401 2.7 12.3 1.0 FE4 A:SF4401 2.8 18.5 1.0 CB A:CYS70 3.1 10.4 1.0 S1 A:SF4401 3.8 12.3 1.0 CB A:LEU72 4.3 12.8 1.0 CD2 A:LEU305 4.5 18.0 1.0 CA A:CYS70 4.6 12.5 1.0 SD A:SAH408 4.6 22.6 1.0 SG A:CYS67 4.8 13.9 1.0 CB A:CYS67 4.8 11.5 1.0 N A:ARG73 4.8 12.0 1.0 SG A:CYS63 4.8 12.1 1.0 N A:SAH408 4.8 15.5 1.0 C A:LEU72 4.8 12.5 1.0 OXT A:SAH408 4.9 19.6 1.0 N A:LEU72 4.9 11.7 1.0 CA A:LEU72 4.9 12.2 1.0 CG A:LEU72 5.0 15.7 1.0

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


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)-Tda within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:12.2 occ:1.00 FE2 A:SF4401 0.0 12.2 1.0 SG A:CYS63 2.3 12.1 1.0 S4 A:SF4401 2.3 13.1 1.0 S3 A:SF4401 2.3 11.2 1.0 S1 A:SF4401 2.3 12.3 1.0 FE1 A:SF4401 2.7 12.3 1.0 FE3 A:SF4401 2.7 12.3 1.0 FE4 A:SF4401 2.9 18.5 1.0 CB A:CYS63 3.4 12.3 1.0 S2 A:SF4401 3.9 12.7 1.0 N A:SAH408 4.2 15.5 1.0 CB A:LYS65 4.2 12.1 1.0 N A:GLU110 4.4 9.9 1.0 CA A:GLY109 4.6 9.5 1.0 O A:LYS65 4.6 14.6 1.0 SG A:CYS70 4.7 11.6 1.0 CA A:CYS63 4.8 12.6 1.0 SG A:CYS67 4.8 13.9 1.0 N A:LYS65 4.8 11.8 1.0 C A:LYS65 4.8 11.8 1.0 CA A:LYS65 4.8 12.0 1.0 CB A:LEU72 4.9 12.8 1.0 OXT A:SAH408 5.0 19.6 1.0

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


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)-Tda within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:12.3 occ:1.00 FE3 A:SF4401 0.0 12.3 1.0 S2 A:SF4401 2.3 12.7 1.0 S4 A:SF4401 2.3 13.1 1.0 S1 A:SF4401 2.3 12.3 1.0 SG A:CYS67 2.3 13.9 1.0 FE1 A:SF4401 2.7 12.3 1.0 FE2 A:SF4401 2.7 12.2 1.0 FE4 A:SF4401 2.9 18.5 1.0 CB A:CYS67 3.2 11.5 1.0 S3 A:SF4401 3.9 11.2 1.0 O A:HOH633 3.9 18.5 1.0 OXT A:SAH408 4.2 19.6 1.0 N A:CYS67 4.2 12.8 1.0 CA A:CYS67 4.3 11.0 1.0 CB A:LYS65 4.4 12.1 1.0 CB A:CYS70 4.5 10.4 1.0 NH2 A:ARG172 4.5 11.8 1.0 SG A:CYS70 4.6 11.6 1.0 OH A:TYR69 4.6 13.2 1.0 SG A:CYS63 4.7 12.1 1.0 CE1 A:TYR69 4.8 14.0 1.0 O A:HOH589 4.9 15.3 1.0 CZ A:TYR69 5.0 13.6 1.0

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


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)-Tda within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:18.5 occ:1.00 FE4 A:SF4401 0.0 18.5 1.0 N A:SAH408 2.3 15.5 1.0 OXT A:SAH408 2.3 19.6 1.0 S2 A:SF4401 2.3 12.7 1.0 S3 A:SF4401 2.4 11.2 1.0 S1 A:SF4401 2.4 12.3 1.0 FE1 A:SF4401 2.8 12.3 1.0 FE2 A:SF4401 2.9 12.2 1.0 FE3 A:SF4401 2.9 12.3 1.0 C A:SAH408 3.1 18.0 1.0 CA A:SAH408 3.2 17.2 1.0 SD A:SAH408 3.5 22.6 1.0 CG A:SAH408 3.7 22.4 1.0 CB A:SAH408 3.8 17.9 1.0 S4 A:SF4401 4.1 13.1 1.0 O A:HOH633 4.1 18.5 1.0 O A:HOH589 4.2 15.3 1.0 O A:SAH408 4.3 14.6 1.0 SG A:CYS63 4.7 12.1 1.0 SG A:CYS70 4.9 11.6 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