Iron in the structure of Crystal Structure of A Putative Hd Superfamily Hydrolase (BH1327) From Bacillus Halodurans At 1.90 A Resolution (pdb 2o08)

The binding sites of Iron atom in the structure of Crystal Structure of A Putative Hd Superfamily Hydrolase (BH1327) From Bacillus Halodurans At 1.90 A Resolution (pdb code 2o08). This binding sites where shown with 5.0 Angstroms radius around Iron atom. The 2o08 structure was solved by JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG), with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 28.9-1.9 Space group C2221 a (A) 86.830 b (A) 166.510 c (A) 73.410 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 17.4 Rfree (%) 22.3 Iron Binding Sites: Iron binding site 1 out of 4 in 2o08 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Iron in the PDB 2o08. 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: Arg18, A: His21, A: Val25, A: His50, A: Asp51, A: His109, A: Asp127, A: Arg133, A: Fe401, A: Po4500, A: Hoh622, conact list: Atom Atom Distance (A) Fe NH2 A:Arg18 4.11 Fe NE2 A:His21 2.15 Fe ND1 A:His21 4.20 Fe CD2 A:His21 3.22 Fe CE1 A:His21 3.03 Fe CG A:His21 4.31 Fe CG2 A:Val25 4.67 Fe NE2 A:His50 2.17 Fe ND1 A:His50 4.29 Fe CD2 A:His50 3.03 Fe CE1 A:His50 3.23 Fe CG A:His50 4.23 Fe CB A:Asp51 4.38 Fe OD2 A:Asp51 2.16 Fe OD1 A:Asp51 3.44 Fe CG A:Asp51 3.10 Fe NE2 A:His109 4.65 Fe CD2 A:His109 4.81 Fe CB A:Asp127 4.36 Fe OD2 A:Asp127 3.50 Fe OD1 A:Asp127 2.17 Fe CG A:Asp127 3.11 Fe CA A:Asp127 4.92 Fe CZ A:Arg133 4.79 Fe NH2 A:Arg133 3.96 Fe NH1 A:Arg133 4.96 Fe FE A:Fe401 3.61 Fe O1 A:Po4500 4.49 Fe O2 A:Po4500 3.60 Fe P A:Po4500 3.40 Fe O4 A:Po4500 4.25 Fe O3 A:Po4500 2.13 Fe O A:Hoh622 1.83 interactive model: Iron binding site 2 out of 4 in 2o08 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Iron in the PDB 2o08. 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: His50, A: Asp51, A: Lys54, A: His83, A: His109, A: Thr110, A: Asp127, A: Fe400, A: Po4500, A: Hoh507, A: Hoh622, A: Hoh661, A: Hoh662, conact list: Atom Atom Distance (A) Fe O A:His50 4.94 Fe NE2 A:His50 4.47 Fe CD2 A:His50 4.11 Fe CB A:Asp51 4.49 Fe OD2 A:Asp51 3.41 Fe OD1 A:Asp51 2.13 Fe CG A:Asp51 3.12 Fe CA A:Asp51 4.87 Fe CD A:Lys54 4.92 Fe NE2 A:His83 2.22 Fe ND1 A:His83 4.30 Fe CD2 A:His83 3.23 Fe CE1 A:His83 3.16 Fe CG A:His83 4.36 Fe NE2 A:His109 2.24 Fe ND1 A:His109 4.36 Fe CD2 A:His109 3.16 Fe CE1 A:His109 3.27 Fe CG A:His109 4.34 Fe OG1 A:Thr110 3.92 Fe OD2 A:Asp127 4.20 Fe OD1 A:Asp127 4.73 Fe CG A:Asp127 4.77 Fe FE A:Fe400 3.61 Fe O1 A:Po4500 4.59 Fe O2 A:Po4500 2.12 Fe P A:Po4500 3.38 Fe O4 A:Po4500 4.06 Fe O3 A:Po4500 3.72 Fe O A:Hoh507 2.29 Fe O A:Hoh622 2.07 Fe O A:Hoh661 3.98 Fe O A:Hoh662 4.20 interactive model: Iron binding site 3 out of 4 in 2o08 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Iron in the PDB 2o08. 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: Arg18, B: His50, B: Asp51, B: Lys54, B: His83, B: His109, B: Thr110, B: Asp127, B: Fe401, B: Dgi500, B: Hoh625, conact list: Atom Atom Distance (A) Fe NH1 B:Arg18 4.93 Fe O B:His50 4.96 Fe NE2 B:His50 4.52 Fe CD2 B:His50 4.16 Fe CB B:Asp51 4.59 Fe OD2 B:Asp51 3.55 Fe OD1 B:Asp51 2.25 Fe CG B:Asp51 3.24 Fe CA B:Asp51 4.88 Fe CD B:Lys54 4.54 Fe NZ B:Lys54 4.63 Fe NE2 B:His83 2.18 Fe ND1 B:His83 4.29 Fe CD2 B:His83 3.17 Fe CE1 B:His83 3.16 Fe CG B:His83 4.32 Fe NE2 B:His109 2.29 Fe ND1 B:His109 4.41 Fe CD2 B:His109 3.16 Fe CE1 B:His109 3.34 Fe CG B:His109 4.36 Fe OG1 B:Thr110 3.81 Fe OD2 B:Asp127 4.21 Fe OD1 B:Asp127 4.79 Fe CG B:Asp127 4.86 Fe FE B:Fe401 3.51 Fe O3B B:Dgi500 4.49 Fe PA B:Dgi500 3.28 Fe O2A B:Dgi500 4.43 Fe O1B B:Dgi500 2.07 Fe PB B:Dgi500 3.20 Fe O5' B:Dgi500 4.24 Fe O2B B:Dgi500 3.69 Fe O3A B:Dgi500 3.31 Fe O1A B:Dgi500 2.27 Fe O B:Hoh625 1.92 interactive model: Iron binding site 4 out of 4 in 2o08 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Iron in the PDB 2o08. 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: Arg18, B: His21, B: Val25, B: His50, B: Asp51, B: His109, B: Asp127, B: Arg133, B: Fe400, B: Dgi500, B: Hoh625, conact list: Atom Atom Distance (A) Fe NH1 B:Arg18 4.16 Fe NE2 B:His21 2.11 Fe ND1 B:His21 4.20 Fe CD2 B:His21 3.03 Fe CE1 B:His21 3.12 Fe CG B:His21 4.19 Fe CG2 B:Val25 4.68 Fe NE2 B:His50 2.19 Fe ND1 B:His50 4.31 Fe CD2 B:His50 2.98 Fe CE1 B:His50 3.29 Fe CG B:His50 4.20 Fe CB B:Asp51 4.39 Fe OD2 B:Asp51 2.24 Fe OD1 B:Asp51 3.36 Fe CG B:Asp51 3.07 Fe NE2 B:His109 4.56 Fe CD2 B:His109 4.66 Fe CB B:Asp127 4.43 Fe OD2 B:Asp127 3.43 Fe OD1 B:Asp127 2.20 Fe CG B:Asp127 3.13 Fe CA B:Asp127 4.97 Fe CZ B:Arg133 4.93 Fe NH2 B:Arg133 4.07 Fe FE B:Fe400 3.51 Fe O3B B:Dgi500 4.88 Fe O1B B:Dgi500 3.63 Fe PB B:Dgi500 3.49 Fe O2B B:Dgi500 2.37 Fe O3A B:Dgi500 3.87 Fe O1A B:Dgi500 4.89 Fe O B:Hoh625 2.01 interactive model: