Iron in the structure of Napthalene 1,2-Dioxygenase (pdb 1ndo)

The binding sites of Iron atom in the structure of Napthalene 1,2-Dioxygenase (pdb code 1ndo). This binding sites where shown with 5.0 Angstroms radius around Iron atom. The 1ndo structure was solved by S.RAMASWAMY, B.KAUPPI, E.CARREDANO, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 30.0-2.2 Space group I222 a (A) 105.000 b (A) 174.000 c (A) 282.500 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 19 Rfree (%) 24 Iron Binding Sites: Iron binding site 1 out of 9 in 1ndo Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Iron in the PDB 1ndo. 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: Asn201, A: His208, A: Thr212, A: His213, A: Asp362, A: Hoh712, conact list: Atom Atom Distance (A) Fe ND2 A:Asn201 4.30 Fe OD1 A:Asn201 3.80 Fe CG A:Asn201 4.48 Fe NE2 A:His208 2.04 Fe ND1 A:His208 4.14 Fe CD2 A:His208 3.01 Fe CE1 A:His208 3.04 Fe CG A:His208 4.16 Fe CG2 A:Thr212 4.49 Fe NE2 A:His213 2.15 Fe ND1 A:His213 4.23 Fe CD2 A:His213 3.02 Fe CE1 A:His213 3.18 Fe CG A:His213 4.20 Fe CB A:Asp362 4.32 Fe OD2 A:Asp362 2.27 Fe OD1 A:Asp362 2.65 Fe CG A:Asp362 2.82 Fe O A:Hoh712 4.55 interactive model: Iron binding site 2 out of 9 in 1ndo Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Iron in the PDB 1ndo. 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: Cys81, A: His83, A: Arg84, A: Cys101, A: Tyr103, A: His104, A: Trp106, A: Fes451, conact list: Atom Atom Distance (A) Fe SG A:Cys81 4.27 Fe NE2 A:His83 4.34 Fe CB A:His83 3.43 Fe ND1 A:His83 2.23 Fe CD2 A:His83 4.35 Fe C A:His83 4.87 Fe CE1 A:His83 3.22 Fe CG A:His83 3.18 Fe CA A:His83 4.68 Fe N A:Arg84 4.14 Fe CB A:Arg84 4.50 Fe CG A:Arg84 4.46 Fe CA A:Arg84 4.89 Fe SG A:Cys101 4.53 Fe CB A:Tyr103 4.07 Fe CD2 A:Tyr103 4.40 Fe C A:Tyr103 4.65 Fe CG A:Tyr103 4.35 Fe CA A:Tyr103 4.88 Fe NE2 A:His104 4.03 Fe N A:His104 3.77 Fe CB A:His104 3.49 Fe ND1 A:His104 1.99 Fe CD2 A:His104 4.13 Fe CE1 A:His104 2.89 Fe CG A:His104 3.05 Fe CA A:His104 4.24 Fe CD1 A:Trp106 4.98 Fe S1 A:Fes451 2.18 Fe S2 A:Fes451 2.33 Fe FE1 A:Fes451 0.00 Fe FE2 A:Fes451 2.77 interactive model: Iron binding site 3 out of 9 in 1ndo Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Iron in the PDB 1ndo. 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: Cys81, A: His83, A: Arg84, A: Lys86, A: Cys101, A: Tyr103, A: His104, A: Trp106, A: Fes451, conact list: Atom Atom Distance (A) Fe CB A:Cys81 2.99 Fe SG A:Cys81 2.17 Fe C A:Cys81 4.96 Fe CA A:Cys81 4.46 Fe N A:His83 4.86 Fe CB A:His83 4.15 Fe ND1 A:His83 4.53 Fe CG A:His83 4.85 Fe N A:Arg84 4.69 Fe N A:Lys86 4.96 Fe CB A:Lys86 4.49 Fe CB A:Cys101 3.10 Fe SG A:Cys101 2.27 Fe CA A:Cys101 4.55 Fe N A:Tyr103 4.95 Fe CB A:Tyr103 4.26 Fe N A:His104 4.68 Fe ND1 A:His104 4.47 Fe CB A:Trp106 4.98 Fe S1 A:Fes451 2.31 Fe S2 A:Fes451 2.21 Fe FE1 A:Fes451 2.77 Fe FE2 A:Fes451 0.00 interactive model: Iron binding site 4 out of 9 in 1ndo Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Iron in the PDB 1ndo. 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: C: Asn201, C: His208, C: Thr212, C: His213, C: Asp362, conact list: Atom Atom Distance (A) Fe ND2 C:Asn201 4.28 Fe OD1 C:Asn201 3.68 Fe CG C:Asn201 4.41 Fe NE2 C:His208 2.08 Fe ND1 C:His208 4.24 Fe CD2 C:His208 3.01 Fe CE1 C:His208 3.12 Fe CG C:His208 4.20 Fe CG2 C:Thr212 4.43 Fe NE2 C:His213 2.19 Fe ND1 C:His213 4.31 Fe CD2 C:His213 3.09 Fe CE1 C:His213 3.21 Fe CG C:His213 4.28 Fe CB C:Asp362 4.20 Fe OD2 C:Asp362 2.18 Fe OD1 C:Asp362 2.58 Fe CG C:Asp362 2.70 interactive model: Iron binding site 5 out of 9 in 1ndo Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Iron in the PDB 1ndo. 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: C: Cys81, C: His83, C: Arg84, C: Cys101, C: Tyr103, C: His104, C: Trp106, C: Fes451, conact list: Atom Atom Distance (A) Fe SG C:Cys81 4.33 Fe NE2 C:His83 4.30 Fe CB C:His83 3.41 Fe ND1 C:His83 2.17 Fe CD2 C:His83 4.30 Fe C C:His83 4.87 Fe CE1 C:His83 3.18 Fe CG C:His83 3.15 Fe CA C:His83 4.72 Fe N C:Arg84 4.18 Fe CB C:Arg84 4.67 Fe CG C:Arg84 4.52 Fe CA C:Arg84 4.99 Fe SG C:Cys101 4.47 Fe CB C:Tyr103 4.07 Fe CD2 C:Tyr103 4.52 Fe C C:Tyr103 4.62 Fe CG C:Tyr103 4.38 Fe CA C:Tyr103 4.92 Fe NE2 C:His104 3.98 Fe N C:His104 3.66 Fe CB C:His104 3.36 Fe ND1 C:His104 1.98 Fe CD2 C:His104 4.07 Fe C C:His104 4.89 Fe CE1 C:His104 2.91 Fe CG C:His104 2.97 Fe CA C:His104 4.07 Fe CD1 C:Trp106 4.88 Fe S1 C:Fes451 2.19 Fe S2 C:Fes451 2.35 Fe FE1 C:Fes451 0.00 Fe FE2 C:Fes451 2.69 interactive model: Iron binding site 6 out of 9 in 1ndo Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Iron in the PDB 1ndo. 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: C: Cys81, C: His83, C: Arg84, C: Lys86, C: Cys101, C: Tyr103, C: His104, C: Trp106, C: Fes451, conact list: Atom Atom Distance (A) Fe CB C:Cys81 3.16 Fe SG C:Cys81 2.29 Fe CA C:Cys81 4.65 Fe N C:His83 4.98 Fe CB C:His83 4.14 Fe ND1 C:His83 4.45 Fe CG C:His83 4.80 Fe N C:Arg84 4.70 Fe CB C:Lys86 4.57 Fe CB C:Cys101 3.05 Fe SG C:Cys101 2.24 Fe C C:Cys101 4.95 Fe CA C:Cys101 4.49 Fe N C:Tyr103 4.91 Fe CB C:Tyr103 4.21 Fe CA C:Tyr103 4.98 Fe N C:His104 4.44 Fe ND1 C:His104 4.37 Fe CB C:Trp106 4.80 Fe S1 C:Fes451 2.28 Fe S2 C:Fes451 2.21 Fe FE1 C:Fes451 2.69 Fe FE2 C:Fes451 0.00 interactive model: Iron binding site 7 out of 9 in 1ndo Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Iron in the PDB 1ndo. 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: E: Asn201, E: His208, E: Thr212, E: His213, E: Asp362, E: Hoh563, conact list: Atom Atom Distance (A) Fe ND2 E:Asn201 4.43 Fe OD1 E:Asn201 3.98 Fe CG E:Asn201 4.65 Fe NE2 E:His208 2.15 Fe ND1 E:His208 4.28 Fe CD2 E:His208 3.06 Fe CE1 E:His208 3.19 Fe CG E:His208 4.25 Fe CG2 E:Thr212 4.54 Fe NE2 E:His213 2.00 Fe ND1 E:His213 4.11 Fe CD2 E:His213 2.95 Fe CE1 E:His213 3.02 Fe CG E:His213 4.09 Fe CB E:Asp362 4.24 Fe OD2 E:Asp362 2.23 Fe OD1 E:Asp362 2.64 Fe CG E:Asp362 2.73 Fe O E:Hoh563 4.03 interactive model: Iron binding site 8 out of 9 in 1ndo Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Iron in the PDB 1ndo. 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: E: Cys81, E: His83, E: Arg84, E: Cys101, E: Tyr103, E: His104, E: Trp106, E: Fes451, conact list: Atom Atom Distance (A) Fe SG E:Cys81 4.36 Fe NE2 E:His83 4.21 Fe CB E:His83 3.42 Fe ND1 E:His83 2.07 Fe CD2 E:His83 4.24 Fe C E:His83 4.78 Fe CE1 E:His83 3.08 Fe CG E:His83 3.09 Fe CA E:His83 4.66 Fe N E:Arg84 4.08 Fe CB E:Arg84 4.57 Fe CG E:Arg84 4.41 Fe CA E:Arg84 4.87 Fe SG E:Cys101 4.55 Fe CB E:Tyr103 4.12 Fe CD2 E:Tyr103 4.40 Fe C E:Tyr103 4.66 Fe CG E:Tyr103 4.39 Fe CA E:Tyr103 4.94 Fe NE2 E:His104 4.03 Fe N E:His104 3.79 Fe CB E:His104 3.51 Fe ND1 E:His104 2.05 Fe CD2 E:His104 4.12 Fe CE1 E:His104 2.91 Fe CG E:His104 3.07 Fe CA E:His104 4.22 Fe CD1 E:Trp106 4.94 Fe S1 E:Fes451 2.23 Fe S2 E:Fes451 2.34 Fe FE1 E:Fes451 0.00 Fe FE2 E:Fes451 2.77 interactive model: Iron binding site 9 out of 9 in 1ndo Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 9 of Iron in the PDB 1ndo. 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: E: Cys81, E: His83, E: Arg84, E: Lys86, E: Cys101, E: Tyr103, E: His104, E: Trp106, E: Fes451, conact list: Atom Atom Distance (A) Fe CB E:Cys81 3.08 Fe SG E:Cys81 2.28 Fe CA E:Cys81 4.55 Fe N E:His83 4.96 Fe CB E:His83 4.19 Fe ND1 E:His83 4.43 Fe CG E:His83 4.81 Fe N E:Arg84 4.64 Fe CB E:Lys86 4.44 Fe CB E:Cys101 3.11 Fe SG E:Cys101 2.25 Fe C E:Cys101 4.97 Fe CA E:Cys101 4.55 Fe N E:Tyr103 4.91 Fe CB E:Tyr103 4.21 Fe N E:His104 4.59 Fe ND1 E:His104 4.45 Fe CB E:Trp106 4.89 Fe S1 E:Fes451 2.35 Fe S2 E:Fes451 2.27 Fe FE1 E:Fes451 2.77 Fe FE2 E:Fes451 0.00 interactive model: