Iron in the structure of The Three-Dimensional Structure of the N-Acetylglucosamine- 6-Phosphate Deacetylase From Bacillus Subtilis (pdb 2vhl)

The binding sites of Iron atom in the structure of The Three-Dimensional Structure of the N-Acetylglucosamine- 6-Phosphate Deacetylase From Bacillus Subtilis (pdb code 2vhl). This binding sites where shown with 5.0 Angstroms radius around Iron atom. The 2vhl structure was solved by F.VINCENT, D.YATES, E.GARMAN, G.J.DAVIES, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 21.8-2.0 Space group P21212 a (A) 51.680 b (A) 107.740 c (A) 188.250 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 20.5 Rfree (%) 26 Iron Binding Sites: Iron binding site 1 out of 4 in 2vhl Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Iron in the PDB 2vhl. 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: His65, A: Thr98, A: Glu136, A: Gln148, A: His223, A: Asp281, A: Glp1395, A: Fe1398, A: Hoh2319, A: Hoh2321, conact list: Atom Atom Distance (A) Fe NE2 A:His63 2.15 Fe ND1 A:His63 4.23 Fe CD2 A:His63 3.15 Fe CE1 A:His63 3.11 Fe CG A:His63 4.28 Fe NE2 A:His65 2.10 Fe ND1 A:His65 4.22 Fe CD2 A:His65 3.02 Fe CE1 A:His65 3.13 Fe CG A:His65 4.19 Fe CG2 A:Thr98 4.68 Fe OE1 A:Glu136 2.17 Fe CB A:Glu136 4.86 Fe OE2 A:Glu136 3.40 Fe CD A:Glu136 3.09 Fe CG A:Glu136 4.44 Fe OE1 A:Gln148 4.72 Fe NE2 A:His223 4.55 Fe CD2 A:His223 4.39 Fe CB A:Asp281 4.46 Fe OD2 A:Asp281 3.56 Fe OD1 A:Asp281 2.16 Fe CG A:Asp281 3.16 Fe CA A:Asp281 4.85 Fe N2 A:Glp1395 4.04 Fe FE A:Fe1398 3.56 Fe O A:Hoh2319 3.94 Fe O A:Hoh2321 1.98 interactive model: Iron binding site 2 out of 4 in 2vhl Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Iron in the PDB 2vhl. 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: Glu136, A: Gln148, A: His202, A: Thr222, A: His223, A: Asp281, A: Glp1395, A: Fe1397, A: Hoh2319, A: Hoh2321, conact list: Atom Atom Distance (A) Fe NE2 A:His63 4.50 Fe CE1 A:His63 4.34 Fe OE1 A:Glu136 3.44 Fe OE2 A:Glu136 2.14 Fe CD A:Glu136 3.09 Fe CG A:Glu136 4.37 Fe OE1 A:Gln148 3.86 Fe CD A:Gln148 4.71 Fe CG A:Gln148 4.89 Fe NE2 A:His202 2.16 Fe ND1 A:His202 4.24 Fe CD2 A:His202 3.16 Fe CE1 A:His202 3.12 Fe CG A:His202 4.29 Fe CG2 A:Thr222 4.81 Fe NE2 A:His223 2.10 Fe ND1 A:His223 4.19 Fe CD2 A:His223 3.06 Fe CE1 A:His223 3.10 Fe CG A:His223 4.21 Fe OD2 A:Asp281 4.49 Fe OD1 A:Asp281 4.85 Fe N2 A:Glp1395 3.50 Fe C1 A:Glp1395 4.65 Fe O3 A:Glp1395 4.01 Fe C2 A:Glp1395 3.53 Fe C3 A:Glp1395 4.41 Fe FE A:Fe1397 3.56 Fe O A:Hoh2319 3.19 Fe O A:Hoh2321 1.94 interactive model: Iron binding site 3 out of 4 in 2vhl Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Iron in the PDB 2vhl. 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: Glu136, B: Gln148, B: His202, B: Thr222, B: His223, B: Asp281, B: Glp1395, B: Fe1398, B: Hoh2224, B: Hoh2301, conact list: Atom Atom Distance (A) Fe NE2 B:His63 4.38 Fe CE1 B:His63 4.21 Fe OE1 B:Glu136 3.27 Fe OE2 B:Glu136 2.05 Fe CD B:Glu136 2.97 Fe CG B:Glu136 4.30 Fe OE1 B:Gln148 3.73 Fe CD B:Gln148 4.76 Fe NE2 B:His202 2.15 Fe ND1 B:His202 4.20 Fe CD2 B:His202 3.21 Fe CE1 B:His202 3.04 Fe CG B:His202 4.31 Fe CG2 B:Thr222 4.80 Fe NE2 B:His223 2.15 Fe ND1 B:His223 4.23 Fe CD2 B:His223 3.16 Fe CE1 B:His223 3.11 Fe CG B:His223 4.30 Fe OD2 B:Asp281 4.48 Fe OD1 B:Asp281 4.89 Fe N2 B:Glp1395 3.72 Fe C1 B:Glp1395 4.69 Fe O3 B:Glp1395 3.86 Fe C2 B:Glp1395 3.60 Fe C3 B:Glp1395 4.38 Fe FE B:Fe1398 3.50 Fe O B:Hoh2224 2.06 Fe O B:Hoh2301 2.70 interactive model: Iron binding site 4 out of 4 in 2vhl Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Iron in the PDB 2vhl. 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: His65, B: Thr98, B: Glu136, B: His223, B: Asp281, B: Glp1395, B: Fe1397, B: Hoh2224, B: Hoh2301, conact list: Atom Atom Distance (A) Fe NE2 B:His63 2.06 Fe ND1 B:His63 4.13 Fe CD2 B:His63 3.05 Fe CE1 B:His63 3.03 Fe CG B:His63 4.18 Fe NE2 B:His65 2.12 Fe ND1 B:His65 4.24 Fe CD2 B:His65 3.02 Fe CE1 B:His65 3.17 Fe CG B:His65 4.20 Fe CG2 B:Thr98 4.77 Fe OE1 B:Glu136 2.17 Fe CB B:Glu136 4.78 Fe OE2 B:Glu136 3.50 Fe CD B:Glu136 3.14 Fe CG B:Glu136 4.46 Fe NE2 B:His223 4.50 Fe CD2 B:His223 4.43 Fe CB B:Asp281 4.37 Fe OD2 B:Asp281 3.47 Fe OD1 B:Asp281 2.15 Fe CG B:Asp281 3.09 Fe CA B:Asp281 4.86 Fe N2 B:Glp1395 4.24 Fe FE B:Fe1397 3.50 Fe O B:Hoh2224 1.98 Fe O B:Hoh2301 3.81 interactive model: