Iron in the structure of X-Ray Structures of Moorella Thermoacetica Fpra. Novel Diiron Site Structure and Mechanistic Insights Into A Scavenging Nitric Oxide Reductase (pdb 1ycg)

The binding sites of Iron atom in the structure of X-Ray Structures of Moorella Thermoacetica Fpra. Novel Diiron Site Structure and Mechanistic Insights Into A Scavenging Nitric Oxide Reductase (pdb code 1ycg). This binding sites where shown with 5.0 Angstroms radius around Iron atom. The 1ycg structure was solved by R.SILAGHI-DUMITRESCU, D.M.KURTZ, W.N.LANZILOTTA, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 49.7-2.8 Space group P43212 a (A) 159.680 b (A) 159.680 c (A) 278.136 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 22.7 Rfree (%) 24.5 Iron Binding Sites: Iron binding site 1 out of 8 in 1ycg Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Iron in the PDB 1ycg. 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: Phe24, A: His81, A: Glu83, A: Asp85, A: His86, A: Asn166, A: Asp167, A: Tyr195, A: Ser227, A: His228, A: Feo501, A: Edo602, conact list: Atom Atom Distance (A) Fe CZ A:Phe24 4.73 Fe CE1 A:Phe24 4.70 Fe CD2 A:His81 4.60 Fe OE2 A:Glu83 4.62 Fe CD A:Glu83 4.99 Fe CB A:Asp85 4.56 Fe OD2 A:Asp85 2.22 Fe OD1 A:Asp85 3.79 Fe CG A:Asp85 3.32 Fe NE2 A:His86 2.00 Fe ND1 A:His86 4.02 Fe CD2 A:His86 2.93 Fe CE1 A:His86 2.97 Fe CG A:His86 4.04 Fe ND2 A:Asn166 4.94 Fe CB A:Asp167 4.38 Fe OD2 A:Asp167 3.12 Fe OD1 A:Asp167 2.10 Fe CG A:Asp167 2.95 Fe CA A:Asp167 4.96 Fe OH A:Tyr195 4.82 Fe CB A:Ser227 4.94 Fe OG A:Ser227 3.94 Fe NE2 A:His228 1.91 Fe ND1 A:His228 3.99 Fe CD2 A:His228 2.89 Fe CE1 A:His228 2.90 Fe CG A:His228 4.02 Fe O A:Feo501 2.45 Fe FE1 A:Feo501 0.00 Fe FE2 A:Feo501 3.75 Fe O1 A:Edo602 4.52 Fe O2 A:Edo602 4.11 Fe C2 A:Edo602 2.93 Fe C1 A:Edo602 3.30 interactive model: Iron binding site 2 out of 8 in 1ycg Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Iron in the PDB 1ycg. 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: His81, A: Glu83, A: Asp85, A: His86, A: His148, A: Asn166, A: Asp167, A: Feo501, A: Edo602, conact list: Atom Atom Distance (A) Fe NE2 A:His81 2.22 Fe ND1 A:His81 4.25 Fe CD2 A:His81 2.90 Fe CE1 A:His81 3.30 Fe CG A:His81 4.08 Fe OE1 A:Glu83 4.12 Fe CB A:Glu83 4.02 Fe OE2 A:Glu83 2.21 Fe CD A:Glu83 3.36 Fe CG A:Glu83 4.30 Fe OD1 A:Asp85 4.90 Fe NE2 A:His86 4.80 Fe CD2 A:His86 4.71 Fe NE2 A:His148 1.95 Fe CB A:His148 4.50 Fe ND1 A:His148 3.89 Fe CD2 A:His148 1.99 Fe CE1 A:His148 3.27 Fe CG A:His148 3.33 Fe ND2 A:Asn166 4.70 Fe CB A:Asp167 4.23 Fe OD2 A:Asp167 2.00 Fe OD1 A:Asp167 3.85 Fe CG A:Asp167 3.17 Fe O A:Feo501 2.45 Fe FE1 A:Feo501 3.75 Fe FE2 A:Feo501 0.00 Fe O1 A:Edo602 4.07 Fe O2 A:Edo602 3.08 Fe C2 A:Edo602 3.35 Fe C1 A:Edo602 3.97 interactive model: Iron binding site 3 out of 8 in 1ycg Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Iron in the PDB 1ycg. 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: His81, B: Glu83, B: Asp85, B: His86, B: His148, B: Asn166, B: Asp167, B: Feo511, B: Edo612, conact list: Atom Atom Distance (A) Fe NE2 B:His81 2.08 Fe ND1 B:His81 4.17 Fe CD2 B:His81 2.75 Fe CE1 B:His81 3.23 Fe CG B:His81 3.98 Fe OE1 B:Glu83 4.10 Fe CB B:Glu83 3.68 Fe OE2 B:Glu83 2.02 Fe CD B:Glu83 3.20 Fe CG B:Glu83 4.01 Fe OD2 B:Asp85 4.82 Fe OD1 B:Asp85 4.52 Fe NE2 B:His86 4.55 Fe CD2 B:His86 4.49 Fe NE2 B:His148 2.07 Fe CB B:His148 4.66 Fe ND1 B:His148 4.04 Fe CD2 B:His148 2.15 Fe CE1 B:His148 3.39 Fe CG B:His148 3.49 Fe ND2 B:Asn166 4.87 Fe CB B:Asp167 4.46 Fe OD2 B:Asp167 2.24 Fe OD1 B:Asp167 3.82 Fe CG B:Asp167 3.30 Fe O B:Feo511 2.42 Fe FE1 B:Feo511 0.00 Fe FE2 B:Feo511 3.80 Fe O1 B:Edo612 4.05 Fe O2 B:Edo612 2.83 Fe C2 B:Edo612 3.36 Fe C1 B:Edo612 4.06 interactive model: Iron binding site 4 out of 8 in 1ycg Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Iron in the PDB 1ycg. 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: Phe24, B: His81, B: Glu83, B: Asp85, B: His86, B: Asn166, B: Asp167, B: Tyr195, B: Ser227, B: His228, B: Feo511, B: Edo612, conact list: Atom Atom Distance (A) Fe CZ B:Phe24 4.94 Fe CE1 B:Phe24 4.74 Fe CD2 B:His81 4.73 Fe OE2 B:Glu83 4.76 Fe CB B:Asp85 4.65 Fe OD2 B:Asp85 2.29 Fe OD1 B:Asp85 3.87 Fe CG B:Asp85 3.41 Fe NE2 B:His86 2.04 Fe ND1 B:His86 4.01 Fe CD2 B:His86 3.13 Fe CE1 B:His86 2.86 Fe CG B:His86 4.17 Fe ND2 B:Asn166 4.94 Fe CB B:Asp167 4.34 Fe OD2 B:Asp167 3.33 Fe OD1 B:Asp167 2.03 Fe CG B:Asp167 3.00 Fe CA B:Asp167 4.83 Fe OH B:Tyr195 4.51 Fe CB B:Ser227 4.89 Fe OG B:Ser227 3.80 Fe NE2 B:His228 1.82 Fe ND1 B:His228 3.86 Fe CD2 B:His228 2.74 Fe CE1 B:His228 2.82 Fe CG B:His228 3.85 Fe O B:Feo511 2.41 Fe FE1 B:Feo511 3.80 Fe FE2 B:Feo511 0.00 Fe O1 B:Edo612 4.29 Fe O2 B:Edo612 3.84 Fe C2 B:Edo612 2.73 Fe C1 B:Edo612 3.12 interactive model: Iron binding site 5 out of 8 in 1ycg Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Iron in the PDB 1ycg. 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: C: His81, C: Glu83, C: Asp85, C: His86, C: His148, C: Asn166, C: Asp167, C: Feo521, C: Edo622, conact list: Atom Atom Distance (A) Fe NE2 C:His81 2.04 Fe ND1 C:His81 4.15 Fe CD2 C:His81 2.84 Fe CE1 C:His81 3.14 Fe CG C:His81 4.04 Fe OE1 C:Glu83 4.02 Fe CB C:Glu83 3.82 Fe OE2 C:Glu83 1.96 Fe CD C:Glu83 3.18 Fe CG C:Glu83 4.10 Fe OD2 C:Asp85 4.78 Fe OD1 C:Asp85 4.54 Fe NE2 C:His86 4.88 Fe CD2 C:His86 4.75 Fe NE2 C:His148 2.09 Fe CB C:His148 4.66 Fe ND1 C:His148 4.04 Fe CD2 C:His148 2.19 Fe CE1 C:His148 3.39 Fe CG C:His148 3.51 Fe ND2 C:Asn166 4.83 Fe CB C:Asp167 4.45 Fe OD2 C:Asp167 2.16 Fe OD1 C:Asp167 3.80 Fe CG C:Asp167 3.27 Fe O C:Feo521 2.37 Fe FE1 C:Feo521 0.00 Fe FE2 C:Feo521 3.74 Fe O1 C:Edo622 3.46 Fe O2 C:Edo622 3.55 Fe C2 C:Edo622 3.58 Fe C1 C:Edo622 3.53 interactive model: Iron binding site 6 out of 8 in 1ycg Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Iron in the PDB 1ycg. 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: C: Phe24, C: His81, C: Glu83, C: Asp85, C: His86, C: Asp167, C: Tyr195, C: Ser227, C: His228, C: Feo521, C: Edo622, conact list: Atom Atom Distance (A) Fe CE1 C:Phe24 4.58 Fe NE2 C:His81 4.96 Fe CD2 C:His81 4.65 Fe OE2 C:Glu83 4.54 Fe CB C:Asp85 4.65 Fe OD2 C:Asp85 2.31 Fe OD1 C:Asp85 3.88 Fe CG C:Asp85 3.42 Fe NE2 C:His86 2.39 Fe ND1 C:His86 4.31 Fe CD2 C:His86 3.32 Fe CE1 C:His86 3.24 Fe CG C:His86 4.38 Fe CB C:Asp167 4.44 Fe OD2 C:Asp167 3.31 Fe OD1 C:Asp167 2.10 Fe CG C:Asp167 3.05 Fe CA C:Asp167 4.90 Fe OH C:Tyr195 4.37 Fe OG C:Ser227 3.92 Fe NE2 C:His228 1.76 Fe ND1 C:His228 3.87 Fe CD2 C:His228 2.70 Fe CE1 C:His228 2.81 Fe CG C:His228 3.86 Fe O C:Feo521 2.32 Fe FE1 C:Feo521 3.74 Fe FE2 C:Feo521 0.00 Fe O1 C:Edo622 4.16 Fe O2 C:Edo622 4.78 Fe C2 C:Edo622 3.60 Fe C1 C:Edo622 3.10 interactive model: Iron binding site 7 out of 8 in 1ycg Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Iron in the PDB 1ycg. 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: D: His81, D: Glu83, D: Asp85, D: His86, D: His148, D: Asn166, D: Asp167, D: Feo531, D: Edo632, conact list: Atom Atom Distance (A) Fe NE2 D:His81 2.09 Fe ND1 D:His81 4.19 Fe CD2 D:His81 2.75 Fe CE1 D:His81 3.25 Fe CG D:His81 3.99 Fe OE1 D:Glu83 3.71 Fe CB D:Glu83 3.78 Fe OE2 D:Glu83 1.62 Fe CD D:Glu83 2.70 Fe CG D:Glu83 3.34 Fe OD2 D:Asp85 4.86 Fe OD1 D:Asp85 4.62 Fe NE2 D:His86 4.72 Fe CD2 D:His86 4.63 Fe NE2 D:His148 2.01 Fe CB D:His148 4.65 Fe ND1 D:His148 3.93 Fe CD2 D:His148 2.23 Fe CE1 D:His148 3.25 Fe CG D:His148 3.49 Fe ND2 D:Asn166 4.91 Fe CB D:Asp167 4.54 Fe OD2 D:Asp167 2.26 Fe OD1 D:Asp167 4.06 Fe CG D:Asp167 3.45 Fe O D:Feo531 2.46 Fe FE1 D:Feo531 0.00 Fe FE2 D:Feo531 4.04 Fe O1 D:Edo632 4.35 Fe O2 D:Edo632 3.36 Fe C2 D:Edo632 4.12 Fe C1 D:Edo632 4.65 interactive model: Iron binding site 8 out of 8 in 1ycg Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Iron in the PDB 1ycg. 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: D: Phe24, D: His81, D: Glu83, D: Asp85, D: His86, D: Asp167, D: Tyr195, D: Ser227, D: His228, D: Feo531, D: Edo632, conact list: Atom Atom Distance (A) Fe CE1 D:Phe24 4.64 Fe CD2 D:His81 4.85 Fe OE2 D:Glu83 4.60 Fe CB D:Asp85 4.31 Fe OD2 D:Asp85 2.01 Fe OD1 D:Asp85 3.72 Fe CG D:Asp85 3.15 Fe NE2 D:His86 1.98 Fe ND1 D:His86 3.96 Fe CD2 D:His86 3.03 Fe CE1 D:His86 2.84 Fe CG D:His86 4.08 Fe CB D:Asp167 4.64 Fe OD2 D:Asp167 3.43 Fe OD1 D:Asp167 2.37 Fe CG D:Asp167 3.24 Fe OH D:Tyr195 4.73 Fe CB D:Ser227 4.99 Fe OG D:Ser227 3.88 Fe NE2 D:His228 1.81 Fe ND1 D:His228 3.87 Fe CD2 D:His228 2.77 Fe CE1 D:His228 2.81 Fe CG D:His228 3.89 Fe O D:Feo531 2.33 Fe FE1 D:Feo531 4.04 Fe FE2 D:Feo531 0.00 Fe O1 D:Edo632 4.65 Fe O2 D:Edo632 3.47 Fe C2 D:Edo632 2.75 Fe C1 D:Edo632 3.66 interactive model: