Iron in the structure of Crystal Structure of A Dps Protein From Bacillus Brevis (pdb 1n1q)

The binding sites of Iron atom in the structure of Crystal Structure of A Dps Protein From Bacillus Brevis (pdb code 1n1q). This binding sites where shown with 5.0 Angstroms radius around Iron atom. The 1n1q structure was solved by B.REN, G.TIBBELIN, T.KAJINO, O.ASAMI, R.LADENSTEIN, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 24.5-2.2 Space group H3 a (A) 86.911 b (A) 86.911 c (A) 220.808 alpha (°) 90.00 beta (°) 90.00 gamma (°) 120.00 Rfactor (%) 19.6 Rfree (%) 20.8 Iron Binding Sites: Iron binding site 1 out of 8 in 1n1q Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Iron in the PDB 1n1q. 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: Asp58, A: Glu62, B: His31, B: Trp32, B: His43, B: Tyr50, A: Feo516, B: Hoh611, B: Hoh612, conact list: Atom Atom Distance (A) Fe CB A:Asp58 4.34 Fe OD2 A:Asp58 2.24 Fe OD1 A:Asp58 2.75 Fe CG A:Asp58 2.84 Fe OE1 A:Glu62 3.34 Fe OE2 A:Glu62 2.07 Fe CD A:Glu62 2.97 Fe CG A:Glu62 4.21 Fe NE2 B:His31 2.18 Fe ND1 B:His31 4.30 Fe CD2 B:His31 3.11 Fe CE1 B:His31 3.20 Fe CG B:His31 4.29 Fe CD1 B:Trp32 4.87 Fe NE1 B:Trp32 4.69 Fe NE2 B:His43 4.01 Fe CE1 B:His43 3.94 Fe OH B:Tyr50 3.93 Fe O A:Feo516 1.90 Fe FE1 A:Feo516 0.00 Fe FE2 A:Feo516 3.34 Fe O B:Hoh611 4.40 Fe O B:Hoh612 4.25 interactive model: Iron binding site 2 out of 8 in 1n1q Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Iron in the PDB 1n1q. 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: Asp58, A: Glu62, B: His31, B: His43, A: Feo516, B: Hoh611, B: Hoh612, conact list: Atom Atom Distance (A) Fe OD2 A:Asp58 4.35 Fe OE1 A:Glu62 3.62 Fe OE2 A:Glu62 3.84 Fe CD A:Glu62 4.14 Fe NE2 B:His31 4.76 Fe NE2 B:His43 3.84 Fe CD2 B:His43 4.79 Fe CE1 B:His43 4.70 Fe O A:Feo516 1.98 Fe FE1 A:Feo516 3.34 Fe FE2 A:Feo516 0.00 Fe O B:Hoh611 2.19 Fe O B:Hoh612 3.93 interactive model: Iron binding site 3 out of 8 in 1n1q Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Iron in the PDB 1n1q. 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: His31, A: Trp32, A: His43, A: Tyr50, B: Asp58, B: Glu62, B: Feo515, A: Hoh640, A: Hoh641, conact list: Atom Atom Distance (A) Fe NE2 A:His31 2.18 Fe ND1 A:His31 4.31 Fe CD2 A:His31 3.05 Fe CE1 A:His31 3.25 Fe CG A:His31 4.25 Fe CD1 A:Trp32 4.77 Fe NE1 A:Trp32 4.56 Fe NE2 A:His43 4.15 Fe CE1 A:His43 4.05 Fe OH A:Tyr50 3.86 Fe CB B:Asp58 4.20 Fe OD2 B:Asp58 2.08 Fe OD1 B:Asp58 2.66 Fe CG B:Asp58 2.70 Fe OE1 B:Glu62 3.29 Fe OE2 B:Glu62 2.12 Fe CD B:Glu62 2.96 Fe CG B:Glu62 4.20 Fe O B:Feo515 1.96 Fe FE1 B:Feo515 0.00 Fe FE2 B:Feo515 3.32 Fe O A:Hoh640 4.09 Fe O A:Hoh641 4.08 interactive model: Iron binding site 4 out of 8 in 1n1q Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Iron in the PDB 1n1q. 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: His31, A: His43, B: Asp58, B: Glu62, B: Feo515, A: Hoh640, A: Hoh641, conact list: Atom Atom Distance (A) Fe NE2 A:His31 4.55 Fe CE1 A:His31 4.86 Fe NE2 A:His43 3.69 Fe CD2 A:His43 4.65 Fe CE1 A:His43 4.53 Fe OD2 B:Asp58 4.32 Fe OE1 B:Glu62 3.64 Fe OE2 B:Glu62 3.86 Fe CD B:Glu62 4.16 Fe O B:Feo515 2.04 Fe FE1 B:Feo515 3.32 Fe FE2 B:Feo515 0.00 Fe O A:Hoh640 2.16 Fe O A:Hoh641 3.62 interactive model: Iron binding site 5 out of 8 in 1n1q Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Iron in the PDB 1n1q. 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: Asp58, C: Glu62, D: His31, D: Trp32, D: His43, D: Tyr50, C: Feo518, D: Hoh633, D: Hoh634, conact list: Atom Atom Distance (A) Fe CB C:Asp58 4.22 Fe OD2 C:Asp58 2.09 Fe OD1 C:Asp58 2.70 Fe CG C:Asp58 2.72 Fe OE1 C:Glu62 3.24 Fe OE2 C:Glu62 2.11 Fe CD C:Glu62 2.93 Fe CG C:Glu62 4.18 Fe NE2 D:His31 2.15 Fe ND1 D:His31 4.26 Fe CD2 D:His31 3.09 Fe CE1 D:His31 3.16 Fe CG D:His31 4.26 Fe CD1 D:Trp32 4.88 Fe NE1 D:Trp32 4.70 Fe NE2 D:His43 4.00 Fe CE1 D:His43 3.94 Fe OH D:Tyr50 3.91 Fe O C:Feo518 1.98 Fe FE1 C:Feo518 0.00 Fe FE2 C:Feo518 3.32 Fe O D:Hoh633 3.76 Fe O D:Hoh634 4.31 interactive model: Iron binding site 6 out of 8 in 1n1q Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Iron in the PDB 1n1q. 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: Lys139, C: Asp58, C: Glu62, D: His31, D: His43, C: Feo518, C: Hoh532, D: Hoh633, D: Hoh634, conact list: Atom Atom Distance (A) Fe CE B:Lys139 4.35 Fe NZ B:Lys139 3.84 Fe OD2 C:Asp58 4.22 Fe OE1 C:Glu62 3.76 Fe OE2 C:Glu62 4.04 Fe CD C:Glu62 4.33 Fe NE2 D:His31 4.72 Fe CE1 D:His31 4.98 Fe NE2 D:His43 3.96 Fe CD2 D:His43 4.86 Fe CE1 D:His43 4.83 Fe O C:Feo518 2.02 Fe FE1 C:Feo518 3.32 Fe FE2 C:Feo518 0.00 Fe O C:Hoh532 4.84 Fe O D:Hoh633 2.14 Fe O D:Hoh634 3.61 interactive model: Iron binding site 7 out of 8 in 1n1q Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Iron in the PDB 1n1q. 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: His31, C: Trp32, C: His43, C: Tyr50, D: Asp58, D: Glu62, D: Feo517, C: Hoh657, C: Hoh658, D: Hoh527, conact list: Atom Atom Distance (A) Fe NE2 C:His31 2.13 Fe ND1 C:His31 4.24 Fe CD2 C:His31 3.06 Fe CE1 C:His31 3.15 Fe CG C:His31 4.23 Fe CD1 C:Trp32 4.84 Fe NE1 C:Trp32 4.67 Fe NE2 C:His43 3.99 Fe CE1 C:His43 3.92 Fe OH C:Tyr50 3.91 Fe CB D:Asp58 4.20 Fe OD2 D:Asp58 2.07 Fe OD1 D:Asp58 2.74 Fe CG D:Asp58 2.72 Fe OE1 D:Glu62 3.20 Fe OE2 D:Glu62 2.10 Fe CD D:Glu62 2.90 Fe CG D:Glu62 4.17 Fe O D:Feo517 1.98 Fe FE1 D:Feo517 0.00 Fe FE2 D:Feo517 3.31 Fe O C:Hoh657 4.72 Fe O C:Hoh658 4.48 Fe O D:Hoh527 4.57 interactive model: Iron binding site 8 out of 8 in 1n1q Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Iron in the PDB 1n1q. 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: His31, C: His43, D: Asp58, D: Glu62, D: Feo517, C: Hoh628, C: Hoh657, C: Hoh658, D: Hoh527, conact list: Atom Atom Distance (A) Fe NE2 C:His31 4.66 Fe CE1 C:His31 4.95 Fe NE2 C:His43 3.72 Fe CD2 C:His43 4.66 Fe CE1 C:His43 4.58 Fe OD2 D:Asp58 4.35 Fe OE1 D:Glu62 3.60 Fe OE2 D:Glu62 3.93 Fe CD D:Glu62 4.17 Fe O D:Feo517 1.99 Fe FE1 D:Feo517 3.31 Fe FE2 D:Feo517 0.00 Fe O C:Hoh628 3.84 Fe O C:Hoh657 2.32 Fe O C:Hoh658 3.76 Fe O D:Hoh527 4.62 interactive model: