Iron in the structure of Crystal Structure of Bovine Milk Xanthine Dehydrogenase With Nad Bound (pdb 3una)

The binding sites of Iron atom in the structure of Crystal Structure of Bovine Milk Xanthine Dehydrogenase With Nad Bound (pdb code 3una). This binding sites where shown with 5.0 Angstroms radius around Iron atom. The 3una structure was solved by B.T.EGER, K.OKAMOTO, T.NISHINO, E.F.PAI, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 20.0-1.9 Space group C121 a (A) 166.028 b (A) 123.182 c (A) 147.624 alpha (°) 90.00 beta (°) 91.02 gamma (°) 90.00 Rfactor (%) 18.1 Rfree (%) 21.4 Iron Binding Sites: Iron binding site 1 out of 8 in 3una Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Iron in the PDB 3una. 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: Gln112, A: Cys113, A: Gly114, A: Phe115, A: Cys116, A: Cys148, A: Arg149, A: Cys150, A: Fes1333, A: Hoh1836, conact list: Atom Atom Distance (A) Fe CB A:Gln112 4.81 Fe C A:Gln112 4.65 Fe N A:Cys113 3.51 Fe CB A:Cys113 3.22 Fe SG A:Cys113 2.23 Fe C A:Cys113 4.20 Fe CA A:Cys113 3.81 Fe N A:Gly114 3.80 Fe CA A:Gly114 4.79 Fe N A:Phe115 4.40 Fe N A:Cys116 4.87 Fe SG A:Cys116 4.58 Fe SG A:Cys148 4.43 Fe N A:Arg149 4.75 Fe N A:Cys150 4.05 Fe CB A:Cys150 3.31 Fe SG A:Cys150 2.41 Fe CA A:Cys150 4.33 Fe S1 A:Fes1333 2.25 Fe S2 A:Fes1333 2.19 Fe FE1 A:Fes1333 0.00 Fe FE2 A:Fes1333 2.69 Fe O A:Hoh1836 3.49 interactive model: Iron binding site 2 out of 8 in 3una Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Iron in the PDB 3una. 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: Cys113, A: Gly114, A: Cys116, A: Thr117, A: Leu147, A: Cys148, A: Arg149, A: Cys150, A: Thr151, A: Fes1333, A: Hoh1936, conact list: Atom Atom Distance (A) Fe SG A:Cys113 4.58 Fe N A:Gly114 4.98 Fe N A:Cys116 4.20 Fe CB A:Cys116 3.34 Fe SG A:Cys116 2.23 Fe C A:Cys116 4.92 Fe CA A:Cys116 4.35 Fe N A:Thr117 4.96 Fe O A:Leu147 4.87 Fe N A:Cys148 4.97 Fe CB A:Cys148 3.37 Fe SG A:Cys148 2.41 Fe C A:Cys148 4.30 Fe CA A:Cys148 3.66 Fe N A:Arg149 4.07 Fe N A:Cys150 4.30 Fe CB A:Cys150 4.41 Fe SG A:Cys150 4.50 Fe CA A:Cys150 4.92 Fe N A:Thr151 4.95 Fe CG2 A:Thr151 4.71 Fe S1 A:Fes1333 2.19 Fe S2 A:Fes1333 2.18 Fe FE1 A:Fes1333 2.69 Fe FE2 A:Fes1333 0.00 Fe O A:Hoh1936 4.37 interactive model: Iron binding site 3 out of 8 in 3una Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Iron in the PDB 3una. 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: Cys43, A: Gly44, A: Glu45, A: Gly46, A: Cys48, A: Gly49, A: Ala50, A: Cys51, A: Asn71, A: Cys73, A: Fes1334, conact list: Atom Atom Distance (A) Fe SG A:Cys43 4.38 Fe N A:Gly44 4.36 Fe CA A:Gly44 4.63 Fe N A:Glu45 4.81 Fe N A:Gly46 4.21 Fe CA A:Gly46 4.41 Fe SG A:Cys48 4.59 Fe N A:Gly49 4.79 Fe N A:Ala50 4.99 Fe N A:Cys51 4.24 Fe CB A:Cys51 3.39 Fe SG A:Cys51 2.26 Fe CA A:Cys51 4.42 Fe CB A:Asn71 4.17 Fe ND2 A:Asn71 4.25 Fe CG A:Asn71 4.59 Fe CA A:Asn71 4.87 Fe N A:Cys73 4.25 Fe CB A:Cys73 3.19 Fe SG A:Cys73 2.34 Fe CA A:Cys73 4.33 Fe S1 A:Fes1334 2.14 Fe S2 A:Fes1334 2.25 Fe FE1 A:Fes1334 0.00 Fe FE2 A:Fes1334 2.79 interactive model: Iron binding site 4 out of 8 in 3una Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Iron in the PDB 3una. 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: Gly42, A: Cys43, A: Gly44, A: Glu45, A: Gly46, A: Gly47, A: Cys48, A: Gly49, A: Ala50, A: Cys51, A: Cys73, A: Fes1334, conact list: Atom Atom Distance (A) Fe O A:Gly42 4.83 Fe N A:Gly42 4.15 Fe C A:Gly42 3.94 Fe CA A:Gly42 4.19 Fe N A:Cys43 3.27 Fe CB A:Cys43 3.46 Fe SG A:Cys43 2.33 Fe C A:Cys43 4.23 Fe CA A:Cys43 3.81 Fe N A:Gly44 3.80 Fe CA A:Gly44 4.83 Fe N A:Glu45 4.62 Fe N A:Gly46 4.45 Fe C A:Gly46 4.79 Fe CA A:Gly46 4.80 Fe N A:Gly47 4.37 Fe C A:Gly47 4.64 Fe N A:Cys48 3.46 Fe CB A:Cys48 3.40 Fe SG A:Cys48 2.21 Fe C A:Cys48 4.19 Fe CA A:Cys48 3.83 Fe N A:Gly49 3.80 Fe CA A:Gly49 4.80 Fe N A:Ala50 4.37 Fe CB A:Ala50 4.99 Fe SG A:Cys51 4.62 Fe SG A:Cys73 4.55 Fe S1 A:Fes1334 2.32 Fe S2 A:Fes1334 2.26 Fe FE1 A:Fes1334 2.79 Fe FE2 A:Fes1334 0.00 interactive model: Iron binding site 5 out of 8 in 3una Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Iron in the PDB 3una. 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: Gln112, B: Cys113, B: Gly114, B: Phe115, B: Cys116, B: Cys148, B: Arg149, B: Cys150, B: Fes1333, B: Hoh1961, conact list: Atom Atom Distance (A) Fe N B:Gln112 5.00 Fe CB B:Gln112 4.80 Fe C B:Gln112 4.67 Fe N B:Cys113 3.55 Fe CB B:Cys113 3.30 Fe SG B:Cys113 2.24 Fe C B:Cys113 4.20 Fe CA B:Cys113 3.86 Fe N B:Gly114 3.76 Fe C B:Gly114 4.97 Fe CA B:Gly114 4.73 Fe N B:Phe115 4.36 Fe N B:Cys116 4.86 Fe SG B:Cys116 4.56 Fe SG B:Cys148 4.40 Fe N B:Arg149 4.74 Fe N B:Cys150 4.05 Fe CB B:Cys150 3.32 Fe SG B:Cys150 2.45 Fe CA B:Cys150 4.33 Fe S1 B:Fes1333 2.28 Fe S2 B:Fes1333 2.21 Fe FE1 B:Fes1333 0.00 Fe FE2 B:Fes1333 2.70 Fe O B:Hoh1961 3.45 interactive model: Iron binding site 6 out of 8 in 3una Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Iron in the PDB 3una. 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: Cys113, B: Gly114, B: Cys116, B: Thr117, B: Leu147, B: Cys148, B: Arg149, B: Cys150, B: Thr151, B: Fes1333, B: Hoh1902, conact list: Atom Atom Distance (A) Fe SG B:Cys113 4.62 Fe N B:Gly114 4.96 Fe N B:Cys116 4.20 Fe CB B:Cys116 3.32 Fe SG B:Cys116 2.22 Fe C B:Cys116 4.92 Fe CA B:Cys116 4.34 Fe N B:Thr117 4.96 Fe O B:Leu147 4.82 Fe N B:Cys148 4.96 Fe CB B:Cys148 3.35 Fe SG B:Cys148 2.36 Fe C B:Cys148 4.29 Fe CA B:Cys148 3.66 Fe N B:Arg149 4.07 Fe N B:Cys150 4.30 Fe CB B:Cys150 4.44 Fe SG B:Cys150 4.55 Fe CA B:Cys150 4.93 Fe N B:Thr151 4.97 Fe CG2 B:Thr151 4.77 Fe S1 B:Fes1333 2.21 Fe S2 B:Fes1333 2.22 Fe FE1 B:Fes1333 2.70 Fe FE2 B:Fes1333 0.00 Fe O B:Hoh1902 4.29 interactive model: Iron binding site 7 out of 8 in 3una Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Iron in the PDB 3una. 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: Cys43, B: Gly44, B: Glu45, B: Gly46, B: Cys48, B: Gly49, B: Cys51, B: Asn71, B: Cys73, B: Fes1334, conact list: Atom Atom Distance (A) Fe SG B:Cys43 4.37 Fe N B:Gly44 4.35 Fe C B:Gly44 4.97 Fe CA B:Gly44 4.62 Fe N B:Glu45 4.86 Fe N B:Gly46 4.19 Fe CA B:Gly46 4.36 Fe SG B:Cys48 4.61 Fe N B:Gly49 4.82 Fe N B:Cys51 4.29 Fe CB B:Cys51 3.37 Fe SG B:Cys51 2.26 Fe CA B:Cys51 4.44 Fe CB B:Asn71 4.21 Fe OD1 B:Asn71 4.28 Fe CG B:Asn71 4.56 Fe CA B:Asn71 4.89 Fe N B:Cys73 4.23 Fe CB B:Cys73 3.11 Fe SG B:Cys73 2.31 Fe CA B:Cys73 4.27 Fe S1 B:Fes1334 2.15 Fe S2 B:Fes1334 2.25 Fe FE1 B:Fes1334 0.00 Fe FE2 B:Fes1334 2.78 interactive model: Iron binding site 8 out of 8 in 3una Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Iron in the PDB 3una. 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: Gly42, B: Cys43, B: Gly44, B: Glu45, B: Gly46, B: Gly47, B: Cys48, B: Gly49, B: Ala50, B: Cys51, B: Cys73, B: Fes1334, conact list: Atom Atom Distance (A) Fe O B:Gly42 4.87 Fe N B:Gly42 4.14 Fe C B:Gly42 4.00 Fe CA B:Gly42 4.24 Fe N B:Cys43 3.35 Fe CB B:Cys43 3.50 Fe SG B:Cys43 2.34 Fe C B:Cys43 4.29 Fe CA B:Cys43 3.87 Fe N B:Gly44 3.78 Fe CA B:Gly44 4.81 Fe N B:Glu45 4.66 Fe N B:Gly46 4.44 Fe C B:Gly46 4.76 Fe CA B:Gly46 4.76 Fe N B:Gly47 4.32 Fe C B:Gly47 4.63 Fe CA B:Gly47 4.99 Fe N B:Cys48 3.46 Fe CB B:Cys48 3.41 Fe SG B:Cys48 2.24 Fe C B:Cys48 4.20 Fe CA B:Cys48 3.84 Fe N B:Gly49 3.78 Fe CA B:Gly49 4.77 Fe N B:Ala50 4.39 Fe SG B:Cys51 4.59 Fe SG B:Cys73 4.53 Fe S1 B:Fes1334 2.25 Fe S2 B:Fes1334 2.27 Fe FE1 B:Fes1334 2.78 Fe FE2 B:Fes1334 0.00 interactive model: