Iron in the structure of 4FE-4S-Pyruvate Formate-Lyase Activating Enzyme With Partially Disordered Adomet (pdb 3c8f)

The binding sites of Iron atom in the structure of 4FE-4S-Pyruvate Formate-Lyase Activating Enzyme With Partially Disordered Adomet (pdb code 3c8f). This binding sites where shown with 5.0 Angstroms radius around Iron atom. The 3c8f structure was solved by J.L.VEY, C.L.DRENNAN, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 30.9-2.2 Space group P3121 a (A) 58.051 b (A) 58.051 c (A) 117.466 alpha (°) 90.00 beta (°) 90.00 gamma (°) 120.00 Rfactor (%) 22.4 Rfree (%) 29.8 Iron Binding Sites: Iron binding site 1 out of 4 in 3c8f Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Iron in the PDB 3c8f. 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: Cys29, A: Met31, A: Cys33, A: Cys36, A: Lys131, A: Sf4500, A: Mt2501, conact list: Atom Atom Distance (A) Fe SG A:Cys29 4.66 Fe CB A:Met31 4.29 Fe C A:Met31 4.98 Fe N A:Cys33 3.95 Fe CB A:Cys33 3.25 Fe SG A:Cys33 2.31 Fe CA A:Cys33 4.24 Fe CB A:Cys36 4.68 Fe SG A:Cys36 4.54 Fe CA A:Cys36 4.98 Fe CE A:Lys131 4.24 Fe NZ A:Lys131 3.85 Fe S1 A:Sf4500 3.80 Fe FE1 A:Sf4500 0.00 Fe FE3 A:Sf4500 2.58 Fe S4 A:Sf4500 2.29 Fe FE2 A:Sf4500 2.75 Fe S2 A:Sf4500 2.29 Fe FE4 A:Sf4500 2.62 Fe S3 A:Sf4500 2.29 Fe CA A:Mt2501 4.89 interactive model: Iron binding site 2 out of 4 in 3c8f Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Iron in the PDB 3c8f. 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: Cys29, A: Cys33, A: Cys36, A: Gly77, A: Gly78, A: Asn106, A: Lys131, A: Sf4500, A: Mt2501, conact list: Atom Atom Distance (A) Fe SG A:Cys29 4.76 Fe SG A:Cys33 4.80 Fe SG A:Cys36 4.78 Fe O A:Gly77 5.00 Fe O A:Gly78 4.51 Fe ND2 A:Asn106 4.09 Fe OD1 A:Asn106 4.19 Fe CG A:Asn106 4.55 Fe NZ A:Lys131 4.31 Fe S1 A:Sf4500 2.31 Fe FE1 A:Sf4500 2.75 Fe FE3 A:Sf4500 2.69 Fe S4 A:Sf4500 2.29 Fe FE2 A:Sf4500 0.00 Fe S2 A:Sf4500 3.99 Fe FE4 A:Sf4500 2.78 Fe S3 A:Sf4500 2.33 Fe O A:Mt2501 2.92 Fe N A:Mt2501 3.30 Fe CB A:Mt2501 3.37 Fe C A:Mt2501 3.09 Fe CG A:Mt2501 4.78 Fe CA A:Mt2501 2.44 Fe OXT A:Mt2501 4.24 interactive model: Iron binding site 3 out of 4 in 3c8f Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Iron in the PDB 3c8f. 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: Cys29, A: Cys33, A: Cys36, A: His37, A: Asn38, A: Thr41, A: Trp42, A: Sf4500, A: Mt2501, conact list: Atom Atom Distance (A) Fe SG A:Cys29 4.90 Fe CB A:Cys33 4.76 Fe SG A:Cys33 4.62 Fe N A:Cys36 4.99 Fe CB A:Cys36 3.28 Fe SG A:Cys36 2.29 Fe C A:Cys36 4.69 Fe CA A:Cys36 3.89 Fe N A:His37 4.62 Fe O A:Asn38 4.74 Fe OG1 A:Thr41 4.90 Fe CD1 A:Trp42 4.55 Fe NE1 A:Trp42 3.88 Fe S1 A:Sf4500 2.29 Fe FE1 A:Sf4500 2.58 Fe FE3 A:Sf4500 0.00 Fe S4 A:Sf4500 2.29 Fe FE2 A:Sf4500 2.69 Fe S2 A:Sf4500 2.32 Fe FE4 A:Sf4500 2.74 Fe S3 A:Sf4500 3.85 Fe O A:Mt2501 4.96 Fe CA A:Mt2501 4.95 interactive model: Iron binding site 4 out of 4 in 3c8f Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Iron in the PDB 3c8f. 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: Cys29, A: Met31, A: Cys33, A: Cys36, A: Trp42, A: Gly78, A: Asn106, A: Sf4500, A: Mt2501, conact list: Atom Atom Distance (A) Fe CB A:Cys29 3.40 Fe SG A:Cys29 2.29 Fe CA A:Cys29 4.79 Fe O A:Met31 4.37 Fe N A:Met31 4.75 Fe CB A:Met31 4.13 Fe C A:Met31 4.62 Fe CA A:Met31 4.75 Fe SG A:Cys33 4.69 Fe SG A:Cys36 4.82 Fe CD1 A:Trp42 4.68 Fe NE1 A:Trp42 4.48 Fe O A:Gly78 4.79 Fe C A:Gly78 4.73 Fe CA A:Gly78 4.58 Fe ND2 A:Asn106 4.19 Fe S1 A:Sf4500 2.32 Fe FE1 A:Sf4500 2.62 Fe FE3 A:Sf4500 2.74 Fe S4 A:Sf4500 3.92 Fe FE2 A:Sf4500 2.78 Fe S2 A:Sf4500 2.29 Fe FE4 A:Sf4500 0.00 Fe S3 A:Sf4500 2.27 Fe O A:Mt2501 4.49 Fe CA A:Mt2501 5.00 interactive model: