Iron in the structure of Structural Genomics, Protein Ybgi, Unknown Function (pdb 1nmo)

The binding sites of Iron atom in the structure of Structural Genomics, Protein Ybgi, Unknown Function (pdb code 1nmo). This binding sites where shown with 5.0 Angstroms radius around Iron atom. The 1nmo structure was solved by J.E.LADNER, G.OBMOLOVA, A.TEPLYAKOV, P.P.KHIL, R.D.CAMERINI-OTERO, G.L.GILLILAND, STRUCTURE 2 FUNCTION PROJECT (S2F), with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 19.6-2.2 Space group P3 a (A) 154.660 b (A) 154.660 c (A) 57.520 alpha (°) 90.00 beta (°) 90.00 gamma (°) 120.00 Rfactor (%) 21.1 Rfree (%) 25.9 Iron Binding Sites: Iron binding site 1 out of 12 in 1nmo Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Iron in the PDB 1nmo. 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: His63, A: His64, A: His97, A: Gly173, A: Gly174, A: His215, A: Glu219, A: Fe302, A: Hoh409, A: Hoh448, conact list: Atom Atom Distance (A) Fe NE2 A:His63 3.74 Fe CD2 A:His63 3.81 Fe CE1 A:His63 4.89 Fe NE2 A:His64 2.14 Fe ND1 A:His64 3.93 Fe CD2 A:His64 3.41 Fe CE1 A:His64 2.67 Fe CG A:His64 4.31 Fe NE2 A:His97 4.62 Fe CD2 A:His97 4.92 Fe CA A:Gly173 4.49 Fe N A:Gly174 5.00 Fe NE2 A:His215 2.26 Fe ND1 A:His215 4.21 Fe CD2 A:His215 3.39 Fe CE1 A:His215 3.02 Fe CG A:His215 4.42 Fe OE1 A:Glu219 2.30 Fe CB A:Glu219 4.96 Fe OE2 A:Glu219 3.46 Fe CD A:Glu219 3.19 Fe CG A:Glu219 4.50 Fe FE A:Fe302 3.17 Fe O A:Hoh409 4.61 Fe O A:Hoh448 3.19 interactive model: Iron binding site 2 out of 12 in 1nmo Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Iron in the PDB 1nmo. 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: His63, A: His64, A: His97, A: Asp101, A: Asn108, A: Thr172, A: Gly173, A: His215, A: Glu219, A: Fe301, A: Hoh409, A: Hoh432, A: Hoh448, conact list: Atom Atom Distance (A) Fe NE2 A:His63 2.53 Fe ND1 A:His63 4.58 Fe CD2 A:His63 3.61 Fe CE1 A:His63 3.38 Fe CG A:His63 4.72 Fe NE2 A:His64 4.65 Fe NE2 A:His97 4.31 Fe CD2 A:His97 4.53 Fe CB A:Asp101 4.34 Fe OD2 A:Asp101 2.44 Fe OD1 A:Asp101 2.68 Fe CG A:Asp101 2.87 Fe ND2 A:Asn108 3.98 Fe O A:Thr172 4.38 Fe OG1 A:Thr172 4.19 Fe C A:Thr172 4.89 Fe CA A:Gly173 4.87 Fe NE2 A:His215 4.99 Fe OE1 A:Glu219 3.08 Fe OE2 A:Glu219 2.29 Fe CD A:Glu219 2.95 Fe CG A:Glu219 4.31 Fe FE A:Fe301 3.17 Fe O A:Hoh409 2.37 Fe O A:Hoh432 4.46 Fe O A:Hoh448 3.72 interactive model: Iron binding site 3 out of 12 in 1nmo Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Iron in the PDB 1nmo. 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: His63, B: His64, B: His97, B: Gly173, B: His215, B: Glu219, B: Fe302, B: Hoh483, B: Hoh1002, conact list: Atom Atom Distance (A) Fe NE2 B:His63 3.93 Fe CD2 B:His63 4.06 Fe NE2 B:His64 2.10 Fe ND1 B:His64 3.96 Fe CD2 B:His64 3.34 Fe CE1 B:His64 2.69 Fe CG B:His64 4.28 Fe NE2 B:His97 4.70 Fe CA B:Gly173 4.52 Fe NE2 B:His215 2.21 Fe ND1 B:His215 4.30 Fe CD2 B:His215 3.20 Fe CE1 B:His215 3.17 Fe CG B:His215 4.34 Fe OE1 B:Glu219 2.21 Fe CB B:Glu219 4.90 Fe OE2 B:Glu219 3.53 Fe CD B:Glu219 3.20 Fe CG B:Glu219 4.48 Fe FE B:Fe302 3.36 Fe O B:Hoh483 4.58 Fe O B:Hoh1002 4.58 interactive model: Iron binding site 4 out of 12 in 1nmo Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Iron in the PDB 1nmo. 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: His63, B: His64, B: His97, B: Asp101, B: Asn108, B: Thr172, B: Glu219, B: Fe301, B: Hoh483, B: Hoh941, conact list: Atom Atom Distance (A) Fe NE2 B:His63 2.45 Fe ND1 B:His63 4.45 Fe CD2 B:His63 3.57 Fe CE1 B:His63 3.24 Fe CG B:His63 4.64 Fe NE2 B:His64 4.71 Fe NE2 B:His97 4.25 Fe CD2 B:His97 4.43 Fe CB B:Asp101 4.39 Fe OD2 B:Asp101 2.45 Fe OD1 B:Asp101 2.61 Fe CG B:Asp101 2.89 Fe ND2 B:Asn108 3.98 Fe O B:Thr172 4.78 Fe OG1 B:Thr172 4.39 Fe OE1 B:Glu219 2.90 Fe OE2 B:Glu219 2.26 Fe CD B:Glu219 2.90 Fe CG B:Glu219 4.35 Fe FE B:Fe301 3.36 Fe O B:Hoh483 2.33 Fe O B:Hoh941 3.91 interactive model: Iron binding site 5 out of 12 in 1nmo Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Iron in the PDB 1nmo. 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: His63, C: His64, C: His97, C: Gly173, C: Gly174, C: His215, C: Glu219, C: Fe302, C: Hoh562, C: Hoh644, D: Hoh891, conact list: Atom Atom Distance (A) Fe NE2 C:His63 3.89 Fe CD2 C:His63 3.94 Fe NE2 C:His64 2.21 Fe ND1 C:His64 3.96 Fe CD2 C:His64 3.52 Fe CE1 C:His64 2.67 Fe CG C:His64 4.39 Fe NE2 C:His97 4.77 Fe CA C:Gly173 4.37 Fe N C:Gly174 4.89 Fe NE2 C:His215 2.10 Fe ND1 C:His215 4.17 Fe CD2 C:His215 3.10 Fe CE1 C:His215 3.05 Fe CG C:His215 4.23 Fe OE1 C:Glu219 2.15 Fe CB C:Glu219 4.97 Fe OE2 C:Glu219 3.29 Fe CD C:Glu219 3.03 Fe CG C:Glu219 4.35 Fe FE C:Fe302 3.35 Fe O C:Hoh562 3.19 Fe O C:Hoh644 4.86 Fe O D:Hoh891 4.72 interactive model: Iron binding site 6 out of 12 in 1nmo Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Iron in the PDB 1nmo. 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: His63, C: His64, C: His97, C: Asp101, C: Asn108, C: Thr172, C: Gly173, C: Glu219, C: Fe301, C: Hoh562, C: Hoh644, C: Hoh1008, conact list: Atom Atom Distance (A) Fe NE2 C:His63 2.55 Fe ND1 C:His63 4.61 Fe CD2 C:His63 3.64 Fe CE1 C:His63 3.41 Fe CG C:His63 4.75 Fe NE2 C:His64 4.66 Fe NE2 C:His97 4.21 Fe CD2 C:His97 4.38 Fe CB C:Asp101 4.43 Fe OD2 C:Asp101 2.36 Fe OD1 C:Asp101 2.72 Fe CG C:Asp101 2.90 Fe ND2 C:Asn108 4.09 Fe O C:Thr172 4.69 Fe OG1 C:Thr172 4.23 Fe CA C:Gly173 4.87 Fe OE1 C:Glu219 3.42 Fe OE2 C:Glu219 2.30 Fe CD C:Glu219 3.17 Fe CG C:Glu219 4.51 Fe FE C:Fe301 3.35 Fe O C:Hoh562 3.68 Fe O C:Hoh644 2.52 Fe O C:Hoh1008 3.79 interactive model: Iron binding site 7 out of 12 in 1nmo Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Iron in the PDB 1nmo. 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: His63, D: His64, D: His97, D: Gly173, D: Gly174, D: His215, D: Glu219, D: Fe302, D: Hoh628, D: Hoh865, conact list: Atom Atom Distance (A) Fe NE2 D:His63 4.11 Fe CD2 D:His63 4.08 Fe NE2 D:His64 2.08 Fe ND1 D:His64 3.96 Fe CD2 D:His64 3.33 Fe CE1 D:His64 2.71 Fe CG D:His64 4.28 Fe NE2 D:His97 4.51 Fe CA D:Gly173 4.51 Fe N D:Gly174 4.82 Fe NE2 D:His215 2.06 Fe ND1 D:His215 4.06 Fe CD2 D:His215 3.19 Fe CE1 D:His215 2.88 Fe CG D:His215 4.24 Fe OE1 D:Glu219 2.24 Fe OE2 D:Glu219 3.61 Fe CD D:Glu219 3.27 Fe CG D:Glu219 4.60 Fe FE D:Fe302 3.44 Fe O D:Hoh628 3.24 Fe O D:Hoh865 4.62 interactive model: Iron binding site 8 out of 12 in 1nmo Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Iron in the PDB 1nmo. 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: His63, D: His64, D: His97, D: Asp101, D: Asn108, D: Thr172, D: Glu219, D: Fe301, D: Hoh628, D: Hoh865, conact list: Atom Atom Distance (A) Fe NE2 D:His63 2.41 Fe ND1 D:His63 4.47 Fe CD2 D:His63 3.47 Fe CE1 D:His63 3.28 Fe CG D:His63 4.59 Fe NE2 D:His64 4.58 Fe NE2 D:His97 3.97 Fe CD2 D:His97 4.30 Fe CE1 D:His97 4.97 Fe CB D:Asp101 4.29 Fe OD2 D:Asp101 2.32 Fe OD1 D:Asp101 2.51 Fe CG D:Asp101 2.77 Fe ND2 D:Asn108 4.28 Fe O D:Thr172 4.66 Fe OG1 D:Thr172 4.39 Fe OE1 D:Glu219 3.23 Fe OE2 D:Glu219 2.28 Fe CD D:Glu219 3.09 Fe CG D:Glu219 4.48 Fe FE D:Fe301 3.44 Fe O D:Hoh628 3.97 Fe O D:Hoh865 2.29 interactive model: Iron binding site 9 out of 12 in 1nmo Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 9 of Iron in the PDB 1nmo. 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: E: His63, E: His64, E: His97, E: Gly173, E: His215, E: Glu219, E: Fe302, E: Hoh694, F: Hoh898, conact list: Atom Atom Distance (A) Fe NE2 E:His63 3.98 Fe CD2 E:His63 4.06 Fe NE2 E:His64 2.16 Fe ND1 E:His64 4.22 Fe CD2 E:His64 3.22 Fe CE1 E:His64 3.06 Fe CG E:His64 4.33 Fe NE2 E:His97 4.32 Fe CD2 E:His97 4.87 Fe CA E:Gly173 4.34 Fe NE2 E:His215 2.20 Fe ND1 E:His215 4.24 Fe CD2 E:His215 3.29 Fe CE1 E:His215 3.07 Fe CG E:His215 4.38 Fe OE1 E:Glu219 2.13 Fe CB E:Glu219 4.94 Fe OE2 E:Glu219 3.64 Fe CD E:Glu219 3.19 Fe CG E:Glu219 4.46 Fe FE E:Fe302 3.39 Fe O E:Hoh694 4.62 Fe O F:Hoh898 4.37 interactive model: Iron binding site 10 out of 12 in 1nmo Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 10 of Iron in the PDB 1nmo. 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: E: His63, E: His64, E: His97, E: Asp101, E: Asn108, E: Thr172, E: Gly173, E: Glu219, E: Fe301, E: Hoh694, E: Hoh738, conact list: Atom Atom Distance (A) Fe NE2 E:His63 2.54 Fe ND1 E:His63 4.58 Fe CD2 E:His63 3.63 Fe CE1 E:His63 3.38 Fe CG E:His63 4.73 Fe NE2 E:His64 4.90 Fe NE2 E:His97 4.07 Fe CD2 E:His97 4.44 Fe CE1 E:His97 4.93 Fe CB E:Asp101 4.19 Fe OD2 E:Asp101 2.34 Fe OD1 E:Asp101 2.30 Fe CG E:Asp101 2.66 Fe ND2 E:Asn108 4.16 Fe O E:Thr172 4.43 Fe OG1 E:Thr172 4.08 Fe C E:Thr172 4.85 Fe CA E:Gly173 4.80 Fe OE1 E:Glu219 2.98 Fe OE2 E:Glu219 2.27 Fe CD E:Glu219 2.92 Fe CG E:Glu219 4.34 Fe FE E:Fe301 3.39 Fe O E:Hoh694 2.28 Fe O E:Hoh738 4.39 interactive model: Iron binding site 11 out of 12 in 1nmo Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 11 of Iron in the PDB 1nmo. 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: F: His63, F: His64, F: His97, F: Gly173, F: Gly174, F: His215, F: Glu219, F: Fe302, F: Hoh802, F: Hoh866, conact list: Atom Atom Distance (A) Fe NE2 F:His63 3.97 Fe CD2 F:His63 4.18 Fe NE2 F:His64 2.32 Fe ND1 F:His64 4.33 Fe CD2 F:His64 3.45 Fe CE1 F:His64 3.13 Fe CG F:His64 4.51 Fe NE2 F:His97 4.65 Fe CD2 F:His97 4.91 Fe CA F:Gly173 4.49 Fe N F:Gly174 4.86 Fe NE2 F:His215 2.35 Fe ND1 F:His215 4.38 Fe CD2 F:His215 3.44 Fe CE1 F:His215 3.19 Fe CG F:His215 4.53 Fe OE1 F:Glu219 2.24 Fe OE2 F:Glu219 3.48 Fe CD F:Glu219 3.20 Fe CG F:Glu219 4.55 Fe FE F:Fe302 3.12 Fe O F:Hoh802 3.17 Fe O F:Hoh866 4.31 interactive model: Iron binding site 12 out of 12 in 1nmo Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 12 of Iron in the PDB 1nmo. 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: F: His63, F: His64, F: His97, F: Asp101, F: Asn108, F: Thr172, F: Gly173, F: Glu219, F: Fe301, F: Hoh800, F: Hoh802, F: Hoh866, conact list: Atom Atom Distance (A) Fe NE2 F:His63 2.64 Fe ND1 F:His63 4.66 Fe CD2 F:His63 3.72 Fe CE1 F:His63 3.47 Fe CG F:His63 4.81 Fe NE2 F:His64 4.69 Fe NE2 F:His97 4.32 Fe CD2 F:His97 4.44 Fe CB F:Asp101 4.30 Fe OD2 F:Asp101 2.24 Fe OD1 F:Asp101 2.61 Fe CG F:Asp101 2.78 Fe ND2 F:Asn108 4.10 Fe O F:Thr172 4.56 Fe OG1 F:Thr172 4.33 Fe CA F:Gly173 4.99 Fe OE1 F:Glu219 3.09 Fe OE2 F:Glu219 2.32 Fe CD F:Glu219 3.05 Fe CG F:Glu219 4.48 Fe FE F:Fe301 3.12 Fe O F:Hoh800 4.25 Fe O F:Hoh802 3.86 Fe O F:Hoh866 2.13 interactive model: