Iron in the structure of Napa Protein From Borrelia Burgdorferi (pdb 2pyb)

The binding sites of Iron atom in the structure of Napa Protein From Borrelia Burgdorferi (pdb code 2pyb). This binding sites where shown with 5.0 Angstroms radius around Iron atom. The 2pyb structure was solved by G.ZANOTTI, E.PAPINUTTO, M.DE BERNARD, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 38.0-2.6 Space group H3 a (A) 93.078 b (A) 93.078 c (A) 227.500 alpha (°) 90.00 beta (°) 90.00 gamma (°) 120.00 Rfactor (%) 24.2 Rfree (%) 27.5 Iron Binding Sites: Iron binding site 1 out of 8 in 2pyb Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Iron in the PDB 2pyb. 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: His38, A: His50, A: Gln54, B: Asp65, B: Glu69, C: Lys148, C: Trp151, B: Fe501, B: Hoh503, B: Hoh510, conact list: Atom Atom Distance (A) Fe NE2 A:His38 3.98 Fe CE1 A:His38 4.22 Fe NE2 A:His50 2.92 Fe ND1 A:His50 4.67 Fe CD2 A:His50 3.89 Fe CE1 A:His50 3.57 Fe CG A:His50 4.87 Fe NE2 A:Gln54 4.50 Fe OD2 B:Asp65 4.43 Fe OE1 B:Glu69 3.63 Fe OE2 B:Glu69 3.05 Fe CD B:Glu69 3.72 Fe NZ C:Lys148 4.44 Fe CZ3 C:Trp151 5.00 Fe CH2 C:Trp151 4.56 Fe FE B:Fe501 2.91 Fe O B:Hoh503 1.92 Fe O B:Hoh510 4.17 interactive model: Iron binding site 2 out of 8 in 2pyb Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Iron in the PDB 2pyb. 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: Asp65, A: Glu69, B: His38, B: Trp39, B: His50, B: Gln54, B: Tyr57, A: Fe504, B: Hoh502, B: Hoh505, conact list: Atom Atom Distance (A) Fe CB A:Asp65 4.15 Fe OD2 A:Asp65 2.38 Fe OD1 A:Asp65 2.42 Fe CG A:Asp65 2.69 Fe OE1 A:Glu69 4.26 Fe OE2 A:Glu69 2.37 Fe CD A:Glu69 3.59 Fe CG A:Glu69 4.66 Fe NE2 B:His38 2.54 Fe ND1 B:His38 4.66 Fe CD2 B:His38 3.42 Fe CE1 B:His38 3.55 Fe CG B:His38 4.61 Fe CD1 B:Trp39 4.74 Fe NE1 B:Trp39 4.50 Fe NE2 B:His50 4.56 Fe CE1 B:His50 4.45 Fe NE2 B:Gln54 4.75 Fe OE1 B:Gln54 4.89 Fe CD B:Gln54 4.84 Fe OH B:Tyr57 4.29 Fe FE A:Fe504 2.73 Fe O B:Hoh502 3.30 Fe O B:Hoh505 4.65 interactive model: Iron binding site 3 out of 8 in 2pyb Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Iron in the PDB 2pyb. 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: Asp65, A: Glu69, B: His38, B: His50, B: Gln54, A: Fe503, B: Hoh502, B: Hoh505, conact list: Atom Atom Distance (A) Fe OD2 A:Asp65 4.18 Fe OE1 A:Glu69 3.75 Fe OE2 A:Glu69 3.19 Fe CD A:Glu69 3.89 Fe NE2 B:His38 4.13 Fe CE1 B:His38 4.40 Fe NE2 B:His50 3.42 Fe CD2 B:His50 4.30 Fe CE1 B:His50 4.13 Fe NE2 B:Gln54 4.41 Fe FE A:Fe503 2.73 Fe O B:Hoh502 1.80 Fe O B:Hoh505 3.97 interactive model: Iron binding site 4 out of 8 in 2pyb Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Iron in the PDB 2pyb. 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: His38, A: Trp39, A: His50, A: Gln54, A: Tyr57, B: Asp65, B: Glu69, A: Fe502, B: Hoh503, B: Hoh510, conact list: Atom Atom Distance (A) Fe NE2 A:His38 2.63 Fe ND1 A:His38 4.76 Fe CD2 A:His38 3.45 Fe CE1 A:His38 3.69 Fe CG A:His38 4.67 Fe CD1 A:Trp39 4.65 Fe NE1 A:Trp39 4.39 Fe NE2 A:His50 4.75 Fe CE1 A:His50 4.55 Fe NE2 A:Gln54 4.82 Fe OE1 A:Gln54 4.98 Fe CD A:Gln54 4.93 Fe OH A:Tyr57 4.27 Fe CB B:Asp65 4.03 Fe OD2 B:Asp65 2.23 Fe OD1 B:Asp65 2.40 Fe CG B:Asp65 2.58 Fe OE1 B:Glu69 4.25 Fe OE2 B:Glu69 2.32 Fe CD B:Glu69 3.55 Fe CG B:Glu69 4.57 Fe FE A:Fe502 2.91 Fe O B:Hoh503 2.27 Fe O B:Hoh510 4.04 interactive model: Iron binding site 5 out of 8 in 2pyb Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Iron in the PDB 2pyb. 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: His38, C: His50, C: Gln54, D: Asp65, D: Glu69, D: Fe505, C: Hoh510, C: Hoh511, conact list: Atom Atom Distance (A) Fe NE2 C:His38 4.22 Fe CE1 C:His38 4.38 Fe NE2 C:His50 2.71 Fe ND1 C:His50 4.62 Fe CD2 C:His50 3.61 Fe CE1 C:His50 3.55 Fe CG C:His50 4.69 Fe NE2 C:Gln54 4.50 Fe OD2 D:Asp65 4.81 Fe OE1 D:Glu69 3.78 Fe OE2 D:Glu69 3.34 Fe CD D:Glu69 3.95 Fe FE D:Fe505 3.26 Fe O C:Hoh510 2.38 Fe O C:Hoh511 2.11 interactive model: Iron binding site 6 out of 8 in 2pyb Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Iron in the PDB 2pyb. 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: Asp65, C: Glu69, D: His38, D: Trp39, D: His50, D: Gln54, D: Tyr57, C: Fe508, C: Hoh512, D: Hoh511, conact list: Atom Atom Distance (A) Fe CB C:Asp65 4.16 Fe OD2 C:Asp65 2.41 Fe OD1 C:Asp65 2.34 Fe CG C:Asp65 2.67 Fe OE1 C:Glu69 4.22 Fe OE2 C:Glu69 2.30 Fe CD C:Glu69 3.53 Fe CG C:Glu69 4.57 Fe NE2 D:His38 2.42 Fe ND1 D:His38 4.52 Fe CD2 D:His38 3.24 Fe CE1 D:His38 3.48 Fe CG D:His38 4.45 Fe CD1 D:Trp39 4.49 Fe NE1 D:Trp39 4.29 Fe NE2 D:His50 4.48 Fe CE1 D:His50 4.28 Fe NE2 D:Gln54 4.78 Fe OE1 D:Gln54 4.99 Fe CD D:Gln54 4.89 Fe OH D:Tyr57 4.25 Fe FE C:Fe508 3.00 Fe O C:Hoh512 3.07 Fe O D:Hoh511 2.28 interactive model: Iron binding site 7 out of 8 in 2pyb Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Iron in the PDB 2pyb. 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: Asp65, C: Glu69, D: His38, D: His50, D: Gln54, C: Fe507, C: Hoh512, D: Hoh511, conact list: Atom Atom Distance (A) Fe OD2 C:Asp65 4.34 Fe OE1 C:Glu69 3.70 Fe OE2 C:Glu69 3.30 Fe CD C:Glu69 3.91 Fe NE2 D:His38 4.26 Fe CE1 D:His38 4.50 Fe NE2 D:His50 3.25 Fe CD2 D:His50 4.17 Fe CE1 D:His50 3.99 Fe NE2 D:Gln54 4.47 Fe FE C:Fe507 3.00 Fe O C:Hoh512 2.01 Fe O D:Hoh511 2.31 interactive model: Iron binding site 8 out of 8 in 2pyb Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Iron in the PDB 2pyb. 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: His38, C: Trp39, C: His50, C: Gln54, C: Tyr57, D: Asp65, D: Glu69, C: Fe506, C: Hoh510, C: Hoh511, conact list: Atom Atom Distance (A) Fe NE2 C:His38 2.58 Fe ND1 C:His38 4.70 Fe CD2 C:His38 3.43 Fe CE1 C:His38 3.63 Fe CG C:His38 4.64 Fe CD1 C:Trp39 4.71 Fe NE1 C:Trp39 4.45 Fe NE2 C:His50 4.65 Fe CE1 C:His50 4.51 Fe NE2 C:Gln54 4.70 Fe OE1 C:Gln54 4.79 Fe CD C:Gln54 4.76 Fe OH C:Tyr57 4.24 Fe CB D:Asp65 4.06 Fe OD2 D:Asp65 2.33 Fe OD1 D:Asp65 2.34 Fe CG D:Asp65 2.60 Fe OE1 D:Glu69 4.29 Fe OE2 D:Glu69 2.44 Fe CD D:Glu69 3.64 Fe CG D:Glu69 4.69 Fe FE C:Fe506 3.26 Fe O C:Hoh510 2.37 Fe O C:Hoh511 3.68 interactive model: