Iron in the structure of Crystal Structure and Biochemical Characterization of Gdosp, A Gentisate 1,2-Dioxygenase From Silicibacter Pomeroyi (pdb 3bu7)

The binding sites of Iron atom in the structure of Crystal Structure and Biochemical Characterization of Gdosp, A Gentisate 1,2-Dioxygenase From Silicibacter Pomeroyi (pdb code 3bu7). This binding sites where shown with 5.0 Angstroms radius around Iron atom. The 3bu7 structure was solved by J.CHEN, M.Z.WANG, G.Y.ZHU, X.C.ZHANG, Z.H.RAO, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 41.9-2.8 Space group H32 a (A) 129.999 b (A) 129.999 c (A) 246.255 alpha (°) 90.00 beta (°) 90.00 gamma (°) 120.00 Rfactor (%) 21 Rfree (%) 24.5 Iron Binding Sites: Iron binding site 1 out of 4 in 3bu7 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Iron in the PDB 3bu7. 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: His119, A: His121, A: His160, A: Hoh501, A: Hoh502, conact list: Atom Atom Distance (A) Fe NE2 A:His119 2.37 Fe ND1 A:His119 4.46 Fe CD2 A:His119 3.34 Fe CE1 A:His119 3.34 Fe CG A:His119 4.50 Fe NE2 A:His121 2.20 Fe ND1 A:His121 4.27 Fe CD2 A:His121 3.16 Fe CE1 A:His121 3.16 Fe CG A:His121 4.30 Fe NE2 A:His160 2.23 Fe ND1 A:His160 4.27 Fe CD2 A:His160 3.30 Fe CE1 A:His160 3.11 Fe CG A:His160 4.40 Fe O A:Hoh501 2.54 Fe O A:Hoh502 2.65 interactive model: Iron binding site 2 out of 4 in 3bu7 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Iron in the PDB 3bu7. 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: Asp255, A: His290, A: His292, A: Tyr298, A: His330, conact list: Atom Atom Distance (A) Fe OD2 A:Asp255 3.99 Fe OD1 A:Asp255 4.04 Fe CG A:Asp255 4.45 Fe NE2 A:His290 2.35 Fe ND1 A:His290 4.37 Fe CD2 A:His290 3.38 Fe CE1 A:His290 3.23 Fe CG A:His290 4.47 Fe NE2 A:His292 2.34 Fe ND1 A:His292 4.46 Fe CD2 A:His292 3.23 Fe CE1 A:His292 3.38 Fe CG A:His292 4.43 Fe OH A:Tyr298 3.95 Fe NE2 A:His330 2.18 Fe ND1 A:His330 4.26 Fe CD2 A:His330 3.19 Fe CE1 A:His330 3.12 Fe CG A:His330 4.32 interactive model: Iron binding site 3 out of 4 in 3bu7 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Iron in the PDB 3bu7. 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: B: His119, B: His121, B: His160, B: His162, conact list: Atom Atom Distance (A) Fe NE2 B:His119 2.25 Fe ND1 B:His119 4.37 Fe CD2 B:His119 3.14 Fe CE1 B:His119 3.29 Fe CG B:His119 4.33 Fe NE2 B:His121 2.35 Fe ND1 B:His121 4.46 Fe CD2 B:His121 3.28 Fe CE1 B:His121 3.35 Fe CG B:His121 4.45 Fe NE2 B:His160 2.23 Fe ND1 B:His160 4.27 Fe CD2 B:His160 3.30 Fe CE1 B:His160 3.11 Fe CG B:His160 4.39 Fe NE2 B:His162 5.00 interactive model: Iron binding site 4 out of 4 in 3bu7 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Iron in the PDB 3bu7. 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: B: Asp255, B: His290, B: His292, B: Tyr298, B: His330, B: Hoh501, B: Hoh502, conact list: Atom Atom Distance (A) Fe OD2 B:Asp255 4.06 Fe OD1 B:Asp255 4.06 Fe CG B:Asp255 4.50 Fe NE2 B:His290 2.40 Fe ND1 B:His290 4.31 Fe CD2 B:His290 3.44 Fe CE1 B:His290 3.18 Fe CG B:His290 4.47 Fe NE2 B:His292 2.28 Fe ND1 B:His292 4.37 Fe CD2 B:His292 3.23 Fe CE1 B:His292 3.26 Fe CG B:His292 4.38 Fe OH B:Tyr298 3.90 Fe NE2 B:His330 2.07 Fe ND1 B:His330 4.16 Fe CD2 B:His330 3.05 Fe CE1 B:His330 3.05 Fe CG B:His330 4.20 Fe O B:Hoh501 2.24 Fe O B:Hoh502 2.28 interactive model: