Iron in the structure of Steric and Conformational Features of the Aconitase Mechanism (pdb 1ami)

The binding sites of Iron atom in the structure of Steric and Conformational Features of the Aconitase Mechanism (pdb code 1ami). This binding sites where shown with 5.0 Angstroms radius around Iron atom. The 1ami structure was solved by C.D.STOUT, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 8.0-2.0 Space group B2 a (A) 185.900 b (A) 71.800 c (A) 73.200 alpha (°) 90.00 beta (°) 90.00 gamma (°) 77.70 Rfactor (%) 18.2 Rfree (%) n/a Iron Binding Sites: Iron binding site 1 out of 4 in 1ami Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Iron in the PDB 1ami. 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: Ile145, A: His147, A: His167, A: Ser357, A: Cys358, A: Cys421, A: Cys424, A: Asn446, A: Sf4999, A: Hoh1000, conact list: Atom Atom Distance (A) Fe CG2 A:Ile145 4.27 Fe CD2 A:His147 4.53 Fe CB A:His167 4.87 Fe ND1 A:His167 4.59 Fe CG A:His167 4.93 Fe CB A:Ser357 4.86 Fe C A:Ser357 4.95 Fe N A:Cys358 3.87 Fe CB A:Cys358 3.48 Fe SG A:Cys358 2.31 Fe CA A:Cys358 4.37 Fe SG A:Cys421 4.88 Fe SG A:Cys424 4.62 Fe ND2 A:Asn446 4.59 Fe S1 A:Sf4999 3.71 Fe FE1 A:Sf4999 0.00 Fe FE3 A:Sf4999 2.65 Fe S4 A:Sf4999 2.30 Fe FE2 A:Sf4999 2.59 Fe S2 A:Sf4999 2.30 Fe FE4 A:Sf4999 2.69 Fe S3 A:Sf4999 2.28 Fe O A:Hoh1000 4.02 interactive model: Iron binding site 2 out of 4 in 1ami Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Iron in the PDB 1ami. 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: Ser357, A: Cys358, A: Cys421, A: Cys424, A: Asn446, A: Arg452, A: Sf4999, A: Mic755, A: Hoh1000, conact list: Atom Atom Distance (A) Fe CB A:Ser357 4.36 Fe OG A:Ser357 4.96 Fe SG A:Cys358 4.58 Fe CB A:Cys421 4.58 Fe SG A:Cys421 4.69 Fe O A:Cys424 4.73 Fe CB A:Cys424 3.22 Fe SG A:Cys424 2.31 Fe C A:Cys424 4.55 Fe CA A:Cys424 4.43 Fe ND2 A:Asn446 4.74 Fe NH2 A:Arg452 4.32 Fe S1 A:Sf4999 2.25 Fe FE1 A:Sf4999 2.59 Fe FE3 A:Sf4999 2.66 Fe S4 A:Sf4999 2.29 Fe FE2 A:Sf4999 0.00 Fe S2 A:Sf4999 3.91 Fe FE4 A:Sf4999 2.88 Fe S3 A:Sf4999 2.34 Fe O2 A:Mic755 4.43 Fe O A:Hoh1000 4.74 interactive model: Iron binding site 3 out of 4 in 1ami Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Iron in the PDB 1ami. 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: His101, A: Ile145, A: Cys358, A: Cys421, A: Cys424, A: Ile425, A: Sf4999, A: Mic755, A: Hoh1000, conact list: Atom Atom Distance (A) Fe NE2 A:His101 3.97 Fe ND1 A:His101 4.58 Fe CD2 A:His101 4.75 Fe CE1 A:His101 3.85 Fe CG2 A:Ile145 4.20 Fe SG A:Cys358 4.80 Fe N A:Cys421 4.71 Fe CB A:Cys421 3.14 Fe SG A:Cys421 2.35 Fe CA A:Cys421 3.89 Fe CB A:Cys424 4.89 Fe SG A:Cys424 4.75 Fe CG1 A:Ile425 4.91 Fe S1 A:Sf4999 2.27 Fe FE1 A:Sf4999 2.65 Fe FE3 A:Sf4999 0.00 Fe S4 A:Sf4999 2.30 Fe FE2 A:Sf4999 2.66 Fe S2 A:Sf4999 2.31 Fe FE4 A:Sf4999 2.81 Fe S3 A:Sf4999 3.89 Fe O7 A:Mic755 4.39 Fe O A:Hoh1000 4.84 interactive model: Iron binding site 4 out of 4 in 1ami Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Iron in the PDB 1ami. 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: His101, A: Asp165, A: His167, A: Cys358, A: Cys421, A: Cys424, A: Arg452, A: Sf4999, A: Mic755, A: Hoh1000, conact list: Atom Atom Distance (A) Fe NE2 A:His101 4.16 Fe CE1 A:His101 4.47 Fe OD2 A:Asp165 4.02 Fe OD1 A:Asp165 4.05 Fe CG A:Asp165 4.48 Fe ND1 A:His167 4.01 Fe CE1 A:His167 4.90 Fe CG A:His167 4.87 Fe SG A:Cys358 4.66 Fe SG A:Cys421 4.87 Fe SG A:Cys424 4.98 Fe NH2 A:Arg452 4.44 Fe S1 A:Sf4999 2.32 Fe FE1 A:Sf4999 2.69 Fe FE3 A:Sf4999 2.81 Fe S4 A:Sf4999 4.06 Fe FE2 A:Sf4999 2.88 Fe S2 A:Sf4999 2.33 Fe FE4 A:Sf4999 0.00 Fe S3 A:Sf4999 2.30 Fe C1 A:Mic755 3.62 Fe O1 A:Mic755 4.84 Fe CM2 A:Mic755 4.28 Fe C2 A:Mic755 3.58 Fe C6 A:Mic755 4.95 Fe O2 A:Mic755 2.80 Fe C3 A:Mic755 4.71 Fe O7 A:Mic755 2.55 Fe O6 A:Mic755 4.48 Fe O A:Hoh1000 2.14 interactive model: