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 |
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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:
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