Iron in the structure of Crystal Structure of Biphenyl 2,3-Dioxygenase From Sphingomonas Yanoikuyae B1 (pdb 2gbw)

The binding sites of Iron atom in the structure of Crystal Structure of Biphenyl 2,3-Dioxygenase From Sphingomonas Yanoikuyae B1 (pdb code 2gbw). This binding sites where shown with 5.0 Angstroms radius around Iron atom. The 2gbw structure was solved by D.J.FERRARO, E.N.BROWN, C.YU, R.E.PARALES, D.T.GIBSON, S.RAMASWAMY, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 19.8-1.7 Space group P3121 a (A) 134.958 b (A) 134.958 c (A) 219.887 alpha (°) 90.00 beta (°) 90.00 gamma (°) 120.00 Rfactor (%) 18.8 Rfree (%) 22.8 Iron Binding Sites: Iron binding site 1 out of 9 in 2gbw Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Iron in the PDB 2gbw. 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: Asn200, A: His207, A: Thr211, A: His212, A: Phe350, A: Asp360, A: Oxy457, A: Hoh663, A: Hoh959, conact list: Atom Atom Distance (A) Fe ND2 A:Asn200 4.08 Fe OD1 A:Asn200 4.61 Fe CG A:Asn200 4.80 Fe NE2 A:His207 2.04 Fe ND1 A:His207 4.14 Fe CD2 A:His207 3.01 Fe CE1 A:His207 3.04 Fe CG A:His207 4.16 Fe CG2 A:Thr211 4.77 Fe NE2 A:His212 2.04 Fe ND1 A:His212 4.10 Fe CD2 A:His212 3.10 Fe CE1 A:His212 2.94 Fe CG A:His212 4.20 Fe CE1 A:Phe350 4.89 Fe CB A:Asp360 4.13 Fe OD2 A:Asp360 1.75 Fe OD1 A:Asp360 2.97 Fe CG A:Asp360 2.69 Fe O1 A:Oxy457 2.30 Fe O2 A:Oxy457 2.35 Fe O A:Hoh663 3.50 Fe O A:Hoh959 2.29 interactive model: Iron binding site 2 out of 9 in 2gbw Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Iron in the PDB 2gbw. 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: Cys80, A: His82, A: Arg83, A: Cys100, A: Tyr102, A: His103, A: Fes455, conact list: Atom Atom Distance (A) Fe SG A:Cys80 4.45 Fe NE2 A:His82 4.16 Fe CB A:His82 3.35 Fe ND1 A:His82 2.07 Fe CD2 A:His82 4.19 Fe C A:His82 4.92 Fe CE1 A:His82 3.05 Fe CG A:His82 3.05 Fe CA A:His82 4.67 Fe N A:Arg83 4.25 Fe CB A:Arg83 4.75 Fe CG A:Arg83 4.36 Fe SG A:Cys100 4.61 Fe CB A:Tyr102 4.15 Fe CD2 A:Tyr102 4.40 Fe C A:Tyr102 4.63 Fe CG A:Tyr102 4.36 Fe CA A:Tyr102 4.91 Fe NE2 A:His103 4.14 Fe N A:His103 3.79 Fe CB A:His103 3.46 Fe ND1 A:His103 2.11 Fe CD2 A:His103 4.20 Fe CE1 A:His103 3.04 Fe CG A:His103 3.11 Fe CA A:His103 4.22 Fe S1 A:Fes455 2.21 Fe S2 A:Fes455 2.22 Fe FE1 A:Fes455 0.00 Fe FE2 A:Fes455 2.73 interactive model: Iron binding site 3 out of 9 in 2gbw Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Iron in the PDB 2gbw. 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: Cys80, A: His82, A: Arg83, A: Asn85, A: Cys100, A: Tyr102, A: His103, A: Trp105, A: Fes455, conact list: Atom Atom Distance (A) Fe CB A:Cys80 3.12 Fe SG A:Cys80 2.35 Fe CA A:Cys80 4.59 Fe N A:His82 4.85 Fe CB A:His82 3.93 Fe ND1 A:His82 4.33 Fe CG A:His82 4.64 Fe CA A:His82 4.94 Fe N A:Arg83 4.66 Fe N A:Asn85 4.92 Fe CB A:Asn85 4.33 Fe CB A:Cys100 3.21 Fe SG A:Cys100 2.36 Fe C A:Cys100 4.91 Fe CA A:Cys100 4.61 Fe N A:Tyr102 4.97 Fe CB A:Tyr102 4.51 Fe N A:His103 4.64 Fe ND1 A:His103 4.57 Fe CB A:Trp105 4.71 Fe CG A:Trp105 4.94 Fe S1 A:Fes455 2.21 Fe S2 A:Fes455 2.21 Fe FE1 A:Fes455 2.73 Fe FE2 A:Fes455 0.00 interactive model: Iron binding site 4 out of 9 in 2gbw Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Iron in the PDB 2gbw. 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: Asn200, C: His207, C: Thr211, C: His212, C: Phe350, C: Asp360, E: Oxy457, C: Hoh675, E: Hoh811, conact list: Atom Atom Distance (A) Fe ND2 C:Asn200 4.57 Fe OD1 C:Asn200 4.00 Fe CG C:Asn200 4.72 Fe NE2 C:His207 2.05 Fe ND1 C:His207 4.14 Fe CD2 C:His207 3.06 Fe CE1 C:His207 3.01 Fe CG C:His207 4.19 Fe CG2 C:Thr211 4.84 Fe NE2 C:His212 2.02 Fe ND1 C:His212 4.10 Fe CD2 C:His212 3.06 Fe CE1 C:His212 2.96 Fe CG C:His212 4.18 Fe CE1 C:Phe350 4.85 Fe CB C:Asp360 4.18 Fe OD2 C:Asp360 1.80 Fe OD1 C:Asp360 3.05 Fe CG C:Asp360 2.76 Fe O1 E:Oxy457 2.34 Fe O2 E:Oxy457 2.26 Fe O C:Hoh675 4.19 Fe O E:Hoh811 2.28 interactive model: Iron binding site 5 out of 9 in 2gbw Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Iron in the PDB 2gbw. 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: Cys80, C: His82, C: Arg83, C: Cys100, C: Tyr102, C: His103, C: Trp105, C: Fes455, conact list: Atom Atom Distance (A) Fe SG C:Cys80 4.39 Fe NE2 C:His82 4.20 Fe CB C:His82 3.37 Fe ND1 C:His82 2.10 Fe CD2 C:His82 4.21 Fe C C:His82 4.95 Fe CE1 C:His82 3.09 Fe CG C:His82 3.07 Fe CA C:His82 4.69 Fe N C:Arg83 4.25 Fe CB C:Arg83 4.80 Fe CG C:Arg83 4.39 Fe SG C:Cys100 4.54 Fe CB C:Tyr102 4.19 Fe CD2 C:Tyr102 4.43 Fe C C:Tyr102 4.67 Fe CG C:Tyr102 4.43 Fe CA C:Tyr102 4.96 Fe NE2 C:His103 4.16 Fe N C:His103 3.84 Fe CB C:His103 3.46 Fe ND1 C:His103 2.13 Fe CD2 C:His103 4.22 Fe CE1 C:His103 3.05 Fe CG C:His103 3.13 Fe CA C:His103 4.23 Fe CD1 C:Trp105 5.00 Fe S1 C:Fes455 2.24 Fe S2 C:Fes455 2.25 Fe FE1 C:Fes455 0.00 Fe FE2 C:Fes455 2.74 interactive model: Iron binding site 6 out of 9 in 2gbw Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Iron in the PDB 2gbw. 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: Cys80, C: His82, C: Arg83, C: Asn85, C: Cys100, C: Tyr102, C: His103, C: Trp105, C: Fes455, conact list: Atom Atom Distance (A) Fe CB C:Cys80 3.10 Fe SG C:Cys80 2.31 Fe CA C:Cys80 4.56 Fe N C:His82 4.87 Fe CB C:His82 4.00 Fe ND1 C:His82 4.38 Fe CG C:His82 4.69 Fe CA C:His82 4.97 Fe N C:Arg83 4.69 Fe N C:Asn85 4.95 Fe CB C:Asn85 4.53 Fe CB C:Cys100 3.10 Fe SG C:Cys100 2.29 Fe C C:Cys100 4.89 Fe CA C:Cys100 4.52 Fe N C:Tyr102 4.97 Fe CB C:Tyr102 4.51 Fe N C:His103 4.71 Fe ND1 C:His103 4.62 Fe CB C:Trp105 4.74 Fe CG C:Trp105 4.98 Fe S1 C:Fes455 2.22 Fe S2 C:Fes455 2.22 Fe FE1 C:Fes455 2.74 Fe FE2 C:Fes455 0.00 interactive model: Iron binding site 7 out of 9 in 2gbw Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Iron in the PDB 2gbw. 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: Asn200, E: His207, E: Thr211, E: His212, E: Asp360, C: Oxy457, C: Hoh898, conact list: Atom Atom Distance (A) Fe ND2 E:Asn200 4.62 Fe OD1 E:Asn200 4.04 Fe CG E:Asn200 4.77 Fe NE2 E:His207 2.02 Fe ND1 E:His207 4.12 Fe CD2 E:His207 2.99 Fe CE1 E:His207 3.02 Fe CG E:His207 4.14 Fe CG2 E:Thr211 4.82 Fe NE2 E:His212 1.93 Fe ND1 E:His212 4.02 Fe CD2 E:His212 2.97 Fe CE1 E:His212 2.89 Fe CG E:His212 4.09 Fe CB E:Asp360 4.19 Fe OD2 E:Asp360 1.85 Fe OD1 E:Asp360 2.99 Fe CG E:Asp360 2.76 Fe O1 C:Oxy457 2.36 Fe O2 C:Oxy457 2.19 Fe O C:Hoh898 2.34 interactive model: Iron binding site 8 out of 9 in 2gbw Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Iron in the PDB 2gbw. 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: Cys80, E: His82, E: Arg83, E: Cys100, E: Tyr102, E: His103, E: Trp105, E: Fes455, conact list: Atom Atom Distance (A) Fe SG E:Cys80 4.41 Fe NE2 E:His82 4.30 Fe CB E:His82 3.36 Fe ND1 E:His82 2.20 Fe CD2 E:His82 4.29 Fe C E:His82 4.94 Fe CE1 E:His82 3.20 Fe CG E:His82 3.13 Fe CA E:His82 4.68 Fe N E:Arg83 4.29 Fe CB E:Arg83 4.81 Fe CG E:Arg83 4.44 Fe SG E:Cys100 4.47 Fe CB E:Tyr102 4.14 Fe CD2 E:Tyr102 4.46 Fe C E:Tyr102 4.75 Fe CG E:Tyr102 4.44 Fe CA E:Tyr102 4.98 Fe NE2 E:His103 4.11 Fe N E:His103 3.95 Fe CB E:His103 3.45 Fe ND1 E:His103 2.11 Fe CD2 E:His103 4.17 Fe CE1 E:His103 3.00 Fe CG E:His103 3.10 Fe CA E:His103 4.29 Fe CD1 E:Trp105 4.94 Fe S1 E:Fes455 2.22 Fe S2 E:Fes455 2.28 Fe FE1 E:Fes455 0.00 Fe FE2 E:Fes455 2.69 interactive model: Iron binding site 9 out of 9 in 2gbw Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 9 of Iron in the PDB 2gbw. 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: Cys80, E: His82, E: Arg83, E: Asn85, E: Cys100, E: Tyr102, E: His103, E: Trp105, E: Fes455, conact list: Atom Atom Distance (A) Fe CB E:Cys80 3.15 Fe SG E:Cys80 2.34 Fe CA E:Cys80 4.61 Fe N E:His82 4.86 Fe CB E:His82 3.96 Fe ND1 E:His82 4.43 Fe CG E:His82 4.71 Fe CA E:His82 4.95 Fe N E:Arg83 4.69 Fe N E:Asn85 4.96 Fe CB E:Asn85 4.32 Fe CB E:Cys100 3.14 Fe SG E:Cys100 2.24 Fe C E:Cys100 4.86 Fe CA E:Cys100 4.54 Fe N E:Tyr102 4.99 Fe CB E:Tyr102 4.47 Fe N E:His103 4.73 Fe ND1 E:His103 4.51 Fe CB E:Trp105 4.68 Fe CG E:Trp105 4.89 Fe S1 E:Fes455 2.20 Fe S2 E:Fes455 2.23 Fe FE1 E:Fes455 2.69 Fe FE2 E:Fes455 0.00 interactive model: