Iron in the structure of 4FE-4S-Pyruvate Formate-Lyase Activating Enzyme in Complex With Adomet and A Peptide Substrate (pdb 3cb8)

The binding sites of Iron atom in the structure of 4FE-4S-Pyruvate Formate-Lyase Activating Enzyme in Complex With Adomet and A Peptide Substrate (pdb code 3cb8). This binding sites where shown with 5.0 Angstroms radius around Iron atom. The 3cb8 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) 38.0-2.8 Space group P6122 a (A) 74.494 b (A) 74.494 c (A) 187.737 alpha (°) 90.00 beta (°) 90.00 gamma (°) 120.00 Rfactor (%) 22.9 Rfree (%) 25.4 Iron Binding Sites: Iron binding site 1 out of 4 in 3cb8 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Iron in the PDB 3cb8. 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: Sam501, conact list: Atom Atom Distance (A) Fe SG A:Cys29 4.68 Fe CB A:Met31 4.29 Fe N A:Cys33 3.94 Fe CB A:Cys33 3.20 Fe SG A:Cys33 2.25 Fe CA A:Cys33 4.21 Fe CB A:Cys36 4.66 Fe SG A:Cys36 4.70 Fe CE A:Lys131 4.13 Fe CD A:Lys131 4.89 Fe NZ A:Lys131 3.96 Fe S1 A:Sf4500 3.82 Fe FE1 A:Sf4500 0.00 Fe FE3 A:Sf4500 2.70 Fe S4 A:Sf4500 2.30 Fe FE2 A:Sf4500 2.74 Fe S2 A:Sf4500 2.30 Fe FE4 A:Sf4500 2.68 Fe S3 A:Sf4500 2.30 Fe N A:Sam501 4.51 Fe C A:Sam501 4.97 Fe O A:Sam501 3.92 interactive model: Iron binding site 2 out of 4 in 3cb8 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Iron in the PDB 3cb8. 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: Gly78, A: Asn106, A: Lys131, A: Sf4500, A: Sam501, conact list: Atom Atom Distance (A) Fe SG A:Cys29 4.60 Fe SG A:Cys33 4.75 Fe O A:Gly78 4.59 Fe ND2 A:Asn106 5.00 Fe CE A:Lys131 4.77 Fe NZ A:Lys131 4.29 Fe S1 A:Sf4500 2.31 Fe FE1 A:Sf4500 2.74 Fe FE3 A:Sf4500 2.88 Fe S4 A:Sf4500 2.31 Fe FE2 A:Sf4500 0.00 Fe S2 A:Sf4500 3.99 Fe FE4 A:Sf4500 2.74 Fe S3 A:Sf4500 2.31 Fe N A:Sam501 2.17 Fe CB A:Sam501 3.83 Fe C A:Sam501 2.94 Fe CG A:Sam501 3.42 Fe SD A:Sam501 3.22 Fe CA A:Sam501 3.04 Fe O A:Sam501 2.12 Fe CE A:Sam501 3.52 Fe C5' A:Sam501 4.97 Fe C2' A:Sam501 4.70 Fe OXT A:Sam501 4.16 interactive model: Iron binding site 3 out of 4 in 3cb8 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Iron in the PDB 3cb8. 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: Asn38, A: Trp42, A: Sf4500, A: Sam501, conact list: Atom Atom Distance (A) Fe SG A:Cys29 4.84 Fe CB A:Cys33 4.73 Fe SG A:Cys33 4.66 Fe N A:Cys36 5.00 Fe CB A:Cys36 3.16 Fe SG A:Cys36 2.31 Fe C A:Cys36 4.87 Fe CA A:Cys36 3.98 Fe O A:Asn38 4.98 Fe CD1 A:Trp42 4.51 Fe CE2 A:Trp42 4.73 Fe NE1 A:Trp42 3.71 Fe S1 A:Sf4500 2.29 Fe FE1 A:Sf4500 2.70 Fe FE3 A:Sf4500 0.00 Fe S4 A:Sf4500 2.29 Fe FE2 A:Sf4500 2.88 Fe S2 A:Sf4500 2.29 Fe FE4 A:Sf4500 2.76 Fe S3 A:Sf4500 3.97 Fe N A:Sam501 4.70 Fe SD A:Sam501 4.98 Fe O A:Sam501 4.79 Fe CE A:Sam501 4.08 interactive model: Iron binding site 4 out of 4 in 3cb8 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Iron in the PDB 3cb8. 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: Sam501, conact list: Atom Atom Distance (A) Fe CB A:Cys29 3.41 Fe SG A:Cys29 2.23 Fe CA A:Cys29 4.77 Fe O A:Met31 4.39 Fe N A:Met31 4.72 Fe CB A:Met31 4.18 Fe C A:Met31 4.61 Fe CG A:Met31 5.00 Fe CA A:Met31 4.74 Fe SG A:Cys33 4.72 Fe SG A:Cys36 4.83 Fe CD1 A:Trp42 4.73 Fe NE1 A:Trp42 4.44 Fe O A:Gly78 4.99 Fe C A:Gly78 4.88 Fe CA A:Gly78 4.88 Fe ND2 A:Asn106 4.54 Fe S1 A:Sf4500 2.30 Fe FE1 A:Sf4500 2.68 Fe FE3 A:Sf4500 2.76 Fe S4 A:Sf4500 3.86 Fe FE2 A:Sf4500 2.74 Fe S2 A:Sf4500 2.31 Fe FE4 A:Sf4500 0.00 Fe S3 A:Sf4500 2.29 Fe N A:Sam501 3.50 Fe CA A:Sam501 4.89 Fe O A:Sam501 4.62 interactive model: