Iron in the structure of The Structure of Deoxy and Oxy Hemerythrin At 2.0 Angstroms Resolution (pdb 1hmd)

The binding sites of Iron atom in the structure of The Structure of Deoxy and Oxy Hemerythrin At 2.0 Angstroms Resolution (pdb code 1hmd). This binding sites where shown with 5.0 Angstroms radius around Iron atom. The 1hmd structure was solved by M.A.HOLMES, I.LETRONG, S.TURLEY, L.C.SIEKER, R.E.STENKAMP, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 10.0-2.0 Space group P4 a (A) 86.840 b (A) 86.840 c (A) 80.820 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) n/a Rfree (%) n/a Iron Binding Sites: Iron binding site 1 out of 8 in 1hmd Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Iron in the PDB 1hmd. 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: His54, A: Phe55, A: Glu58, A: His73, A: His77, A: His101, A: Asp106, A: Tyr109, A: Feo115, A: Hoh135, conact list: Atom Atom Distance (A) Fe NE2 A:His54 4.71 Fe CD1 A:Phe55 4.96 Fe CE1 A:Phe55 4.88 Fe OE1 A:Glu58 2.32 Fe OE2 A:Glu58 3.57 Fe CD A:Glu58 3.26 Fe CG A:Glu58 4.63 Fe NE2 A:His73 2.21 Fe ND1 A:His73 4.30 Fe CD2 A:His73 3.24 Fe CE1 A:His73 3.16 Fe CG A:His73 4.37 Fe NE2 A:His77 2.23 Fe ND1 A:His77 4.25 Fe CD2 A:His77 3.27 Fe CE1 A:His77 3.13 Fe CG A:His77 4.36 Fe NE2 A:His101 2.22 Fe ND1 A:His101 4.34 Fe CD2 A:His101 3.15 Fe CE1 A:His101 3.23 Fe CG A:His101 4.30 Fe N A:Asp106 5.00 Fe CB A:Asp106 4.58 Fe OD2 A:Asp106 3.48 Fe OD1 A:Asp106 2.20 Fe CG A:Asp106 3.18 Fe CA A:Asp106 4.92 Fe CE2 A:Tyr109 4.91 Fe O A:Feo115 2.16 Fe FE1 A:Feo115 0.00 Fe FE2 A:Feo115 3.34 Fe O A:Hoh135 4.43 interactive model: Iron binding site 2 out of 8 in 1hmd Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Iron in the PDB 1hmd. 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: Ile21, A: His25, A: His54, A: Glu58, A: His77, A: His101, A: Ile102, A: Asp106, A: Tyr109, A: Feo115, A: Hoh135, conact list: Atom Atom Distance (A) Fe CG2 A:Ile21 4.43 Fe NE2 A:His25 2.13 Fe ND1 A:His25 4.25 Fe CD2 A:His25 3.12 Fe CE1 A:His25 3.12 Fe CG A:His25 4.28 Fe NE2 A:His54 2.30 Fe ND1 A:His54 4.33 Fe CD2 A:His54 3.33 Fe CE1 A:His54 3.16 Fe CG A:His54 4.42 Fe OE1 A:Glu58 3.31 Fe CB A:Glu58 4.84 Fe OE2 A:Glu58 2.14 Fe CD A:Glu58 3.01 Fe CG A:Glu58 4.30 Fe NE2 A:His77 4.78 Fe NE2 A:His101 4.62 Fe CD2 A:His101 4.53 Fe CG1 A:Ile102 4.86 Fe CB A:Asp106 4.37 Fe OD2 A:Asp106 2.14 Fe OD1 A:Asp106 3.41 Fe CG A:Asp106 3.11 Fe OH A:Tyr109 4.21 Fe O A:Feo115 1.78 Fe FE1 A:Feo115 3.34 Fe FE2 A:Feo115 0.00 Fe O A:Hoh135 3.47 interactive model: Iron binding site 3 out of 8 in 1hmd Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Iron in the PDB 1hmd. 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: His54, B: Phe55, B: Glu58, B: His73, B: His77, B: His101, B: Asp106, B: Feo115, conact list: Atom Atom Distance (A) Fe NE2 B:His54 4.68 Fe CD1 B:Phe55 4.83 Fe CE1 B:Phe55 4.78 Fe OE1 B:Glu58 2.32 Fe OE2 B:Glu58 3.63 Fe CD B:Glu58 3.29 Fe CG B:Glu58 4.66 Fe NE2 B:His73 2.25 Fe ND1 B:His73 4.36 Fe CD2 B:His73 3.20 Fe CE1 B:His73 3.28 Fe CG B:His73 4.37 Fe NE2 B:His77 2.18 Fe ND1 B:His77 4.22 Fe CD2 B:His77 3.20 Fe CE1 B:His77 3.12 Fe CG B:His77 4.31 Fe NE2 B:His101 2.23 Fe ND1 B:His101 4.35 Fe CD2 B:His101 3.11 Fe CE1 B:His101 3.26 Fe CG B:His101 4.31 Fe CB B:Asp106 4.56 Fe OD2 B:Asp106 3.51 Fe OD1 B:Asp106 2.15 Fe CG B:Asp106 3.19 Fe O B:Feo115 2.10 Fe FE1 B:Feo115 0.00 Fe FE2 B:Feo115 3.34 interactive model: Iron binding site 4 out of 8 in 1hmd Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Iron in the PDB 1hmd. 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: Ile21, B: His25, B: His54, B: Glu58, B: His77, B: His101, B: Ile102, B: Asp106, B: Tyr109, B: Feo115, conact list: Atom Atom Distance (A) Fe CG2 B:Ile21 4.47 Fe NE2 B:His25 2.12 Fe ND1 B:His25 4.22 Fe CD2 B:His25 3.15 Fe CE1 B:His25 3.09 Fe CG B:His25 4.27 Fe NE2 B:His54 2.29 Fe ND1 B:His54 4.32 Fe CD2 B:His54 3.39 Fe CE1 B:His54 3.11 Fe CG B:His54 4.45 Fe OE1 B:Glu58 3.25 Fe CB B:Glu58 4.87 Fe OE2 B:Glu58 2.14 Fe CD B:Glu58 2.96 Fe CG B:Glu58 4.26 Fe NE2 B:His77 4.73 Fe NE2 B:His101 4.68 Fe CD2 B:His101 4.58 Fe CG1 B:Ile102 4.91 Fe CB B:Asp106 4.38 Fe OD2 B:Asp106 2.12 Fe OD1 B:Asp106 3.29 Fe CG B:Asp106 3.09 Fe OH B:Tyr109 4.25 Fe O B:Feo115 1.84 Fe FE1 B:Feo115 3.34 Fe FE2 B:Feo115 0.00 interactive model: Iron binding site 5 out of 8 in 1hmd Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Iron in the PDB 1hmd. 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: His54, C: Phe55, C: Glu58, C: His73, C: His77, C: His101, C: Asp106, C: Feo115, C: Hoh147, conact list: Atom Atom Distance (A) Fe NE2 C:His54 4.70 Fe CD1 C:Phe55 4.84 Fe CE1 C:Phe55 4.78 Fe OE1 C:Glu58 2.36 Fe OE2 C:Glu58 3.62 Fe CD C:Glu58 3.28 Fe CG C:Glu58 4.69 Fe NE2 C:His73 2.23 Fe ND1 C:His73 4.33 Fe CD2 C:His73 3.22 Fe CE1 C:His73 3.23 Fe CG C:His73 4.36 Fe NE2 C:His77 2.21 Fe ND1 C:His77 4.24 Fe CD2 C:His77 3.27 Fe CE1 C:His77 3.12 Fe CG C:His77 4.36 Fe NE2 C:His101 2.26 Fe ND1 C:His101 4.39 Fe CD2 C:His101 3.21 Fe CE1 C:His101 3.27 Fe CG C:His101 4.37 Fe N C:Asp106 4.94 Fe CB C:Asp106 4.56 Fe OD2 C:Asp106 3.46 Fe OD1 C:Asp106 2.19 Fe CG C:Asp106 3.18 Fe CA C:Asp106 4.87 Fe O C:Feo115 2.06 Fe FE1 C:Feo115 0.00 Fe FE2 C:Feo115 3.34 Fe O C:Hoh147 4.32 interactive model: Iron binding site 6 out of 8 in 1hmd Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Iron in the PDB 1hmd. 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: Ile21, C: His25, C: His54, C: Glu58, C: His77, C: His101, C: Ile102, C: Asp106, C: Tyr109, C: Feo115, C: Hoh147, conact list: Atom Atom Distance (A) Fe CG2 C:Ile21 4.45 Fe NE2 C:His25 2.12 Fe ND1 C:His25 4.23 Fe CD2 C:His25 3.08 Fe CE1 C:His25 3.13 Fe CG C:His25 4.24 Fe NE2 C:His54 2.26 Fe ND1 C:His54 4.31 Fe CD2 C:His54 3.33 Fe CE1 C:His54 3.13 Fe CG C:His54 4.40 Fe OE1 C:Glu58 3.29 Fe CB C:Glu58 4.80 Fe OE2 C:Glu58 2.13 Fe CD C:Glu58 2.98 Fe CG C:Glu58 4.31 Fe NE2 C:His77 4.82 Fe NE2 C:His101 4.71 Fe CD2 C:His101 4.68 Fe CG1 C:Ile102 4.82 Fe CB C:Asp106 4.35 Fe OD2 C:Asp106 2.15 Fe OD1 C:Asp106 3.37 Fe CG C:Asp106 3.07 Fe OH C:Tyr109 4.18 Fe O C:Feo115 1.85 Fe FE1 C:Feo115 3.34 Fe FE2 C:Feo115 0.00 Fe O C:Hoh147 3.67 interactive model: Iron binding site 7 out of 8 in 1hmd Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Iron in the PDB 1hmd. 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: His54, D: Phe55, D: Glu58, D: His73, D: His77, D: His101, D: Asp106, D: Tyr109, D: Feo115, conact list: Atom Atom Distance (A) Fe NE2 D:His54 4.71 Fe CD1 D:Phe55 4.87 Fe CE1 D:Phe55 4.85 Fe OE1 D:Glu58 2.31 Fe OE2 D:Glu58 3.65 Fe CD D:Glu58 3.28 Fe CG D:Glu58 4.63 Fe NE2 D:His73 2.22 Fe ND1 D:His73 4.30 Fe CD2 D:His73 3.27 Fe CE1 D:His73 3.16 Fe CG D:His73 4.39 Fe NE2 D:His77 2.22 Fe ND1 D:His77 4.28 Fe CD2 D:His77 3.26 Fe CE1 D:His77 3.15 Fe CG D:His77 4.37 Fe NE2 D:His101 2.22 Fe ND1 D:His101 4.34 Fe CD2 D:His101 3.14 Fe CE1 D:His101 3.22 Fe CG D:His101 4.30 Fe CB D:Asp106 4.58 Fe OD2 D:Asp106 3.51 Fe OD1 D:Asp106 2.16 Fe CG D:Asp106 3.22 Fe CA D:Asp106 4.93 Fe CE2 D:Tyr109 4.94 Fe O D:Feo115 2.11 Fe FE1 D:Feo115 0.00 Fe FE2 D:Feo115 3.34 interactive model: Iron binding site 8 out of 8 in 1hmd Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Iron in the PDB 1hmd. 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: Ile21, D: His25, D: His54, D: Glu58, D: His77, D: His101, D: Ile102, D: Asp106, D: Tyr109, D: Feo115, conact list: Atom Atom Distance (A) Fe CG2 D:Ile21 4.34 Fe NE2 D:His25 2.15 Fe ND1 D:His25 4.25 Fe CD2 D:His25 3.17 Fe CE1 D:His25 3.12 Fe CG D:His25 4.30 Fe NE2 D:His54 2.24 Fe ND1 D:His54 4.28 Fe CD2 D:His54 3.30 Fe CE1 D:His54 3.12 Fe CG D:His54 4.38 Fe OE1 D:Glu58 3.22 Fe CB D:Glu58 4.82 Fe OE2 D:Glu58 2.15 Fe CD D:Glu58 2.95 Fe CG D:Glu58 4.26 Fe NE2 D:His77 4.77 Fe NE2 D:His101 4.63 Fe CD2 D:His101 4.53 Fe CG1 D:Ile102 4.82 Fe CB D:Asp106 4.41 Fe OD2 D:Asp106 2.15 Fe OD1 D:Asp106 3.30 Fe CG D:Asp106 3.10 Fe OH D:Tyr109 4.20 Fe O D:Feo115 1.81 Fe FE1 D:Feo115 3.34 Fe FE2 D:Feo115 0.00 interactive model: