Iron in the structure of X-Ray Structure of the Fefe-Hydrogenase Maturase Hyde From T. Maritima in Complex With S-Adenosyl-L-Methionine (pdb 3iiz)

The binding sites of Iron atom in the structure of X-Ray Structure of the Fefe-Hydrogenase Maturase Hyde From T. Maritima in Complex With S-Adenosyl-L-Methionine (pdb code 3iiz). This binding sites where shown with 5.0 Angstroms radius around Iron atom. The 3iiz structure was solved by Y.NICOLET, P.AMARA, J.M.MOUESCA, J.C.FONTECILLA-CAMPS, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 38.2-1.6 Space group P212121 a (A) 50.628 b (A) 78.780 c (A) 85.943 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 13.8 Rfree (%) 18.4 Iron Binding Sites: Iron binding site 1 out of 6 in 3iiz Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Iron in the PDB 3iiz. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Iron atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Cys63, A: Lys65, A: Cys67, A: Tyr69, A: Cys70, A: Arg172, A: Sf42460, A: Sam1501, A: Hoh466, A: Hoh514, conact list: Atom Atom Distance (A) Fe SG A:Cys63 4.70 Fe CB A:Lys65 4.41 Fe N A:Cys67 4.25 Fe CB A:Cys67 3.21 Fe SG A:Cys67 2.34 Fe CA A:Cys67 4.35 Fe CZ A:Tyr69 5.00 Fe CE1 A:Tyr69 4.76 Fe OH A:Tyr69 4.66 Fe CB A:Cys70 4.43 Fe SG A:Cys70 4.64 Fe NH2 A:Arg172 4.50 Fe S1 A:Sf42460 3.88 Fe FE1 A:Sf42460 0.00 Fe FE3 A:Sf42460 2.71 Fe S4 A:Sf42460 2.26 Fe FE2 A:Sf42460 2.83 Fe S2 A:Sf42460 2.30 Fe FE4 A:Sf42460 2.72 Fe S3 A:Sf42460 2.33 Fe N A:Sam1501 4.97 Fe O A:Sam1501 4.18 Fe O A:Hoh466 4.79 Fe O A:Hoh514 3.91 interactive model: Iron binding site 2 out of 6 in 3iiz Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Iron in the PDB 3iiz. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Iron atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Cys63, A: Cys67, A: Cys70, A: Sf42460, A: Sam1501, A: Hoh466, A: Hoh514, conact list: Atom Atom Distance (A) Fe SG A:Cys63 4.74 Fe SG A:Cys67 4.98 Fe SG A:Cys70 4.88 Fe S1 A:Sf42460 2.35 Fe FE1 A:Sf42460 2.83 Fe FE3 A:Sf42460 2.84 Fe S4 A:Sf42460 2.33 Fe FE2 A:Sf42460 0.00 Fe S2 A:Sf42460 4.04 Fe FE4 A:Sf42460 2.83 Fe S3 A:Sf42460 2.28 Fe N A:Sam1501 2.33 Fe CB A:Sam1501 4.02 Fe C A:Sam1501 3.06 Fe CG A:Sam1501 3.73 Fe SD A:Sam1501 3.25 Fe CA A:Sam1501 3.22 Fe O A:Sam1501 2.25 Fe CE A:Sam1501 4.10 Fe C5' A:Sam1501 4.92 Fe OXT A:Sam1501 4.22 Fe O A:Hoh466 4.04 Fe O A:Hoh514 4.07 interactive model: Iron binding site 3 out of 6 in 3iiz Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Iron in the PDB 3iiz. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Iron atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Cys63, A: Lys65, A: Cys67, A: Cys70, A: Leu72, A: Gly109, A: Glu110, A: Sf42460, A: Sam1501, conact list: Atom Atom Distance (A) Fe CB A:Cys63 3.35 Fe SG A:Cys63 2.28 Fe CA A:Cys63 4.73 Fe O A:Lys65 4.59 Fe N A:Lys65 4.83 Fe CB A:Lys65 4.27 Fe C A:Lys65 4.83 Fe CA A:Lys65 4.89 Fe SG A:Cys67 4.80 Fe SG A:Cys70 4.74 Fe O A:Leu72 4.95 Fe CB A:Leu72 4.96 Fe CA A:Gly109 4.60 Fe N A:Glu110 4.38 Fe S1 A:Sf42460 2.30 Fe FE1 A:Sf42460 2.71 Fe FE3 A:Sf42460 0.00 Fe S4 A:Sf42460 2.32 Fe FE2 A:Sf42460 2.84 Fe S2 A:Sf42460 2.24 Fe FE4 A:Sf42460 2.67 Fe S3 A:Sf42460 3.86 Fe N A:Sam1501 4.12 Fe O A:Sam1501 4.92 interactive model: Iron binding site 4 out of 6 in 3iiz Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Iron in the PDB 3iiz. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Iron atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Cys63, A: Cys67, A: Cys70, A: Leu72, A: Arg73, A: Leu305, A: Sf42460, A: Sam1501, conact list: Atom Atom Distance (A) Fe SG A:Cys63 4.83 Fe CB A:Cys67 4.79 Fe SG A:Cys67 4.78 Fe CB A:Cys70 3.03 Fe SG A:Cys70 2.26 Fe C A:Cys70 5.00 Fe CA A:Cys70 4.49 Fe N A:Leu72 4.86 Fe CB A:Leu72 4.34 Fe C A:Leu72 4.85 Fe CG A:Leu72 4.86 Fe CA A:Leu72 4.92 Fe N A:Arg73 4.76 Fe CD2 A:Leu305 4.88 Fe S1 A:Sf42460 2.24 Fe FE1 A:Sf42460 2.72 Fe FE3 A:Sf42460 2.67 Fe S4 A:Sf42460 3.86 Fe FE2 A:Sf42460 2.83 Fe S2 A:Sf42460 2.32 Fe FE4 A:Sf42460 0.00 Fe S3 A:Sf42460 2.31 Fe N A:Sam1501 4.83 Fe SD A:Sam1501 4.42 Fe O A:Sam1501 4.84 Fe CE A:Sam1501 4.08 interactive model: Iron binding site 5 out of 6 in 3iiz Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Iron in the PDB 3iiz. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Iron atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Arg279, A: Cys311, A: Cys319, A: Cys322, A: Fes2648, A: H2s2649, A: H2s2650, A: Hoh569, conact list: Atom Atom Distance (A) Fe CZ A:Arg279 4.85 Fe NH2 A:Arg279 4.46 Fe NH1 A:Arg279 4.37 Fe N A:Cys311 4.33 Fe CB A:Cys311 3.27 Fe SG A:Cys311 2.05 Fe CA A:Cys311 3.81 Fe CB A:Cys319 3.73 Fe SG A:Cys319 3.21 Fe CA A:Cys319 4.30 Fe SG A:Cys322 4.96 Fe S1 A:Fes2648 2.25 Fe S2 A:Fes2648 2.17 Fe FE1 A:Fes2648 0.00 Fe FE2 A:Fes2648 2.77 Fe S A:H2s2649 2.11 Fe S A:H2s2650 4.60 Fe O A:Hoh569 3.31 interactive model: Iron binding site 6 out of 6 in 3iiz Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Iron in the PDB 3iiz. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Iron atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Arg279, A: Ile310, A: Cys311, A: Cys322, A: Val323, A: Met326, A: Fes2648, A: H2s2649, A: H2s2650, A: Hoh569, A: Hoh585, conact list: Atom Atom Distance (A) Fe CZ A:Arg279 2.95 Fe NE A:Arg279 4.24 Fe NH2 A:Arg279 2.24 Fe NH1 A:Arg279 2.91 Fe CD1 A:Ile310 4.63 Fe SG A:Cys311 4.24 Fe CB A:Cys322 4.39 Fe CB A:Cys322 4.43 Fe SG A:Cys322 3.63 Fe CG1 A:Val323 4.24 Fe CE A:Met326 4.36 Fe S1 A:Fes2648 2.16 Fe S2 A:Fes2648 2.19 Fe FE1 A:Fes2648 2.77 Fe FE2 A:Fes2648 0.00 Fe S A:H2s2649 4.43 Fe S A:H2s2650 2.27 Fe O A:Hoh569 4.35 Fe O A:Hoh585 4.80 interactive model: