Iron in the structure of Hybrid Cluster Protein From Desulfovibrio Vulgaris (pdb 1e1d)

The binding sites of Iron atom in the structure of Hybrid Cluster Protein From Desulfovibrio Vulgaris (pdb code 1e1d). This binding sites where shown with 5.0 Angstroms radius around Iron atom. The 1e1d structure was solved by A.F.ARENDSEN, S.J.COOPER, S.BAILEY, C.D.GARNER, W.R.HAGEN, P.F.LINDLEY, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 12.0-1.7 Space group P212121 a (A) 64.500 b (A) 65.500 c (A) 155.200 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 17.1 Rfree (%) 20.8 Iron Binding Sites: Iron binding site 1 out of 8 in 1e1d Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Iron in the PDB 1e1d. 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: His244, A: Glu268, A: Trp292, A: Cys312, A: Cys406, A: Cys434, A: Fso600, A: Hoh2277, conact list: Atom Atom Distance (A) Fe NE2 A:His244 4.87 Fe CE1 A:His244 4.88 Fe OE2 A:Glu268 4.48 Fe CD A:Glu268 4.51 Fe CG A:Glu268 3.94 Fe CD1 A:Trp292 3.98 Fe CG A:Trp292 4.89 Fe NE1 A:Trp292 4.47 Fe SG A:Cys312 4.91 Fe CB A:Cys406 4.38 Fe SG A:Cys406 4.21 Fe CA A:Cys406 4.78 Fe N A:Cys434 4.41 Fe CB A:Cys434 3.50 Fe SG A:Cys434 2.34 Fe CA A:Cys434 4.58 Fe S6 A:Fso600 2.20 Fe O10 A:Fso600 2.08 Fe O9 A:Fso600 4.23 Fe FE6 A:Fso600 2.71 Fe FE7 A:Fso600 3.75 Fe FE5 A:Fso600 0.00 Fe O8 A:Fso600 3.59 Fe FE8 A:Fso600 3.17 Fe S5 A:Fso600 2.20 Fe S7 A:Fso600 4.52 Fe O A:Hoh2277 3.92 interactive model: Iron binding site 2 out of 8 in 1e1d Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Iron in the PDB 1e1d. 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: His244, A: Trp292, A: Asn311, A: Cys312, A: Cys434, A: Glu494, A: Fso600, conact list: Atom Atom Distance (A) Fe CE1 A:His244 4.69 Fe CB A:Trp292 4.74 Fe CD1 A:Trp292 4.10 Fe CD2 A:Trp292 4.90 Fe CG A:Trp292 4.37 Fe CE2 A:Trp292 4.96 Fe NE1 A:Trp292 4.49 Fe O A:Asn311 4.36 Fe ND2 A:Asn311 4.09 Fe C A:Asn311 4.27 Fe CG A:Asn311 4.54 Fe N A:Cys312 3.83 Fe CB A:Cys312 3.52 Fe SG A:Cys312 2.37 Fe CA A:Cys312 4.23 Fe SG A:Cys434 4.73 Fe OE2 A:Glu494 4.11 Fe CD A:Glu494 4.91 Fe CG A:Glu494 4.76 Fe S6 A:Fso600 2.26 Fe O10 A:Fso600 3.79 Fe O9 A:Fso600 4.44 Fe FE6 A:Fso600 0.00 Fe FE5 A:Fso600 2.71 Fe O8 A:Fso600 1.98 Fe FE8 A:Fso600 3.05 Fe S5 A:Fso600 2.20 interactive model: Iron binding site 3 out of 8 in 1e1d Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Iron in the PDB 1e1d. 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: His244, A: Glu268, A: Cys406, A: Cys459, A: Glu494, A: Lys496, A: Fso600, conact list: Atom Atom Distance (A) Fe NE2 A:His244 2.16 Fe ND1 A:His244 4.22 Fe CD2 A:His244 3.18 Fe CE1 A:His244 3.08 Fe CG A:His244 4.29 Fe OE1 A:Glu268 4.30 Fe CB A:Glu268 4.33 Fe OE2 A:Glu268 2.18 Fe CD A:Glu268 3.16 Fe CG A:Glu268 3.48 Fe SG A:Cys406 4.46 Fe N A:Cys459 4.03 Fe CB A:Cys459 3.47 Fe SG A:Cys459 2.42 Fe CA A:Cys459 4.39 Fe OE2 A:Glu494 5.00 Fe NZ A:Lys496 4.44 Fe S6 A:Fso600 4.94 Fe O10 A:Fso600 1.71 Fe O9 A:Fso600 2.10 Fe FE7 A:Fso600 0.00 Fe FE5 A:Fso600 3.75 Fe O8 A:Fso600 4.10 Fe FE8 A:Fso600 3.31 Fe S5 A:Fso600 4.65 Fe S7 A:Fso600 4.51 interactive model: Iron binding site 4 out of 8 in 1e1d Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Iron in the PDB 1e1d. 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: His244, A: Asn311, A: Cys312, A: Cys406, A: Cys459, A: Glu494, A: Lys496, A: Fso600, conact list: Atom Atom Distance (A) Fe NE2 A:His244 4.42 Fe CE1 A:His244 4.36 Fe ND2 A:Asn311 4.20 Fe CG A:Asn311 4.95 Fe SG A:Cys312 4.86 Fe CB A:Cys406 4.59 Fe SG A:Cys406 3.70 Fe SG A:Cys459 4.63 Fe OE1 A:Glu494 4.17 Fe OE2 A:Glu494 2.10 Fe CD A:Glu494 3.14 Fe CG A:Glu494 3.62 Fe CB A:Lys496 4.80 Fe CE A:Lys496 4.32 Fe CD A:Lys496 4.90 Fe NZ A:Lys496 4.07 Fe S6 A:Fso600 2.58 Fe O10 A:Fso600 2.59 Fe O9 A:Fso600 2.04 Fe FE6 A:Fso600 3.05 Fe FE7 A:Fso600 3.31 Fe FE5 A:Fso600 3.17 Fe O8 A:Fso600 2.17 Fe FE8 A:Fso600 0.00 Fe S5 A:Fso600 4.23 Fe S7 A:Fso600 2.48 interactive model: Iron binding site 5 out of 8 in 1e1d Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Iron in the PDB 1e1d. 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: Cys3, A: Phe4, A: Gln5, A: Cys6, A: Cys15, A: Cys21, A: Lys23, A: Sf4650, conact list: Atom Atom Distance (A) Fe O A:Cys3 4.17 Fe CB A:Cys3 3.28 Fe SG A:Cys3 2.29 Fe C A:Cys3 4.06 Fe CA A:Cys3 4.27 Fe N A:Phe4 4.46 Fe CA A:Phe4 4.95 Fe NE2 A:Gln5 4.83 Fe N A:Gln5 4.30 Fe CG A:Gln5 4.22 Fe N A:Cys6 4.86 Fe SG A:Cys6 4.89 Fe SG A:Cys15 4.76 Fe SG A:Cys21 4.90 Fe CE A:Lys23 4.25 Fe NZ A:Lys23 4.07 Fe S1 A:Sf4650 3.93 Fe FE1 A:Sf4650 0.00 Fe FE3 A:Sf4650 2.77 Fe S4 A:Sf4650 2.25 Fe FE2 A:Sf4650 2.79 Fe S2 A:Sf4650 2.33 Fe FE4 A:Sf4650 2.77 Fe S3 A:Sf4650 2.34 interactive model: Iron binding site 6 out of 8 in 1e1d Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Iron in the PDB 1e1d. 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: Cys3, A: Cys6, A: Cys15, A: Gly19, A: Met20, A: Cys21, A: Lys23, A: Thr71, A: Sf4650, A: Hoh2075, conact list: Atom Atom Distance (A) Fe SG A:Cys3 4.84 Fe SG A:Cys6 4.55 Fe SG A:Cys15 4.76 Fe C A:Gly19 4.70 Fe CA A:Gly19 4.32 Fe N A:Met20 4.55 Fe N A:Cys21 3.93 Fe CB A:Cys21 3.30 Fe SG A:Cys21 2.26 Fe CA A:Cys21 4.25 Fe CB A:Lys23 4.60 Fe CE A:Lys23 4.38 Fe NZ A:Lys23 4.93 Fe CG2 A:Thr71 4.90 Fe S1 A:Sf4650 2.36 Fe FE1 A:Sf4650 2.79 Fe FE3 A:Sf4650 2.75 Fe S4 A:Sf4650 2.39 Fe FE2 A:Sf4650 0.00 Fe S2 A:Sf4650 3.94 Fe FE4 A:Sf4650 2.79 Fe S3 A:Sf4650 2.28 Fe O A:Hoh2075 4.52 interactive model: Iron binding site 7 out of 8 in 1e1d Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Iron in the PDB 1e1d. 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: Cys3, A: Gln5, A: Cys6, A: Glu8, A: Thr9, A: Cys15, A: Cys21, A: Thr71, A: Sf4650, A: Hoh2010, conact list: Atom Atom Distance (A) Fe SG A:Cys3 4.91 Fe N A:Gln5 4.84 Fe C A:Gln5 4.86 Fe O A:Cys6 4.49 Fe N A:Cys6 3.77 Fe CB A:Cys6 3.27 Fe SG A:Cys6 2.21 Fe C A:Cys6 4.42 Fe CA A:Cys6 3.98 Fe C A:Glu8 4.95 Fe N A:Thr9 4.63 Fe CB A:Thr9 4.88 Fe CA A:Thr9 4.72 Fe SG A:Cys15 4.87 Fe CB A:Cys21 4.93 Fe SG A:Cys21 4.70 Fe CG2 A:Thr71 4.60 Fe OG1 A:Thr71 4.50 Fe S1 A:Sf4650 2.32 Fe FE1 A:Sf4650 2.77 Fe FE3 A:Sf4650 0.00 Fe S4 A:Sf4650 2.35 Fe FE2 A:Sf4650 2.75 Fe S2 A:Sf4650 2.29 Fe FE4 A:Sf4650 2.78 Fe S3 A:Sf4650 3.95 Fe O A:Hoh2010 4.74 interactive model: Iron binding site 8 out of 8 in 1e1d Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Iron in the PDB 1e1d. 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: Cys3, A: Cys6, A: Thr9, A: Ala10, A: Cys15, A: Gly19, A: Met20, A: Cys21, A: Sf4650, conact list: Atom Atom Distance (A) Fe O A:Cys3 4.12 Fe CB A:Cys3 4.78 Fe SG A:Cys3 4.70 Fe C A:Cys3 4.79 Fe SG A:Cys6 4.69 Fe N A:Thr9 4.82 Fe CB A:Thr9 4.40 Fe OG1 A:Thr9 4.13 Fe CA A:Thr9 4.11 Fe N A:Ala10 4.99 Fe N A:Cys15 4.66 Fe CB A:Cys15 3.29 Fe SG A:Cys15 2.25 Fe CA A:Cys15 4.59 Fe C A:Gly19 4.64 Fe CA A:Gly19 4.17 Fe N A:Met20 4.07 Fe CB A:Met20 4.94 Fe N A:Cys21 4.93 Fe SG A:Cys21 4.79 Fe S1 A:Sf4650 2.26 Fe FE1 A:Sf4650 2.77 Fe FE3 A:Sf4650 2.78 Fe S4 A:Sf4650 3.97 Fe FE2 A:Sf4650 2.79 Fe S2 A:Sf4650 2.34 Fe FE4 A:Sf4650 0.00 Fe S3 A:Sf4650 2.39 interactive model: