Iron in the structure of Bovine Milk Xanthine Dehydrogenase Y-700 Bound Form (pdb 1vdv)

The binding sites of Iron atom in the structure of Bovine Milk Xanthine Dehydrogenase Y-700 Bound Form (pdb code 1vdv). This binding sites where shown with 5.0 Angstroms radius around Iron atom. The 1vdv structure was solved by A.FUKUNARI, K.OKAMOTO, T.NISHINO, B.T.EGER, E.F.PAI, M.KAMEZAWA, I.YAMADA, N.KATO, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 20.0-2.0 Space group C121 a (A) 166.817 b (A) 123.940 c (A) 148.888 alpha (°) 90.00 beta (°) 91.16 gamma (°) 90.00 Rfactor (%) 17.8 Rfree (%) 21.5 Iron Binding Sites: Iron binding site 1 out of 8 in 1vdv Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Iron in the PDB 1vdv. 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: Fes3001, A: Hoh5391, conact list: Atom Atom Distance (A) Fe CB A:Gln112 4.81 Fe C A:Gln112 4.70 Fe N A:Cys113 3.56 Fe CB A:Cys113 3.36 Fe SG A:Cys113 2.36 Fe C A:Cys113 4.26 Fe CA A:Cys113 3.90 Fe N A:Gly114 3.85 Fe CA A:Gly114 4.82 Fe N A:Phe115 4.44 Fe N A:Cys116 4.93 Fe SG A:Cys116 4.74 Fe SG A:Cys148 4.45 Fe N A:Arg149 4.79 Fe N A:Cys150 4.05 Fe CB A:Cys150 3.37 Fe SG A:Cys150 2.39 Fe CA A:Cys150 4.35 Fe S1 A:Fes3001 2.25 Fe S2 A:Fes3001 2.21 Fe FE1 A:Fes3001 0.00 Fe FE2 A:Fes3001 2.72 Fe O A:Hoh5391 3.52 interactive model: Iron binding site 2 out of 8 in 1vdv Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Iron in the PDB 1vdv. 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: Cys116, A: Leu147, A: Cys148, A: Arg149, A: Cys150, A: Thr151, A: Fes3001, A: Hoh5320, conact list: Atom Atom Distance (A) Fe SG A:Cys113 4.74 Fe N A:Cys116 4.24 Fe CB A:Cys116 3.40 Fe SG A:Cys116 2.37 Fe C A:Cys116 4.97 Fe CA A:Cys116 4.39 Fe O A:Leu147 4.86 Fe CB A:Cys148 3.43 Fe SG A:Cys148 2.40 Fe C A:Cys148 4.34 Fe CA A:Cys148 3.72 Fe N A:Arg149 4.08 Fe N A:Cys150 4.34 Fe CB A:Cys150 4.54 Fe SG A:Cys150 4.53 Fe CA A:Cys150 5.00 Fe CG2 A:Thr151 4.70 Fe S1 A:Fes3001 2.19 Fe S2 A:Fes3001 2.16 Fe FE1 A:Fes3001 2.72 Fe FE2 A:Fes3001 0.00 Fe O A:Hoh5320 4.31 interactive model: Iron binding site 3 out of 8 in 1vdv Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Iron in the PDB 1vdv. 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: Fes3002, conact list: Atom Atom Distance (A) Fe SG A:Cys43 4.38 Fe N A:Gly44 4.40 Fe CA A:Gly44 4.70 Fe N A:Glu45 4.92 Fe N A:Gly46 4.25 Fe CA A:Gly46 4.42 Fe SG A:Cys48 4.69 Fe N A:Gly49 4.80 Fe N A:Ala50 4.90 Fe N A:Cys51 4.21 Fe CB A:Cys51 3.41 Fe SG A:Cys51 2.37 Fe CA A:Cys51 4.43 Fe CB A:Asn71 4.25 Fe OD1 A:Asn71 4.42 Fe CG A:Asn71 4.55 Fe CA A:Asn71 4.99 Fe N A:Cys73 4.31 Fe CB A:Cys73 3.33 Fe SG A:Cys73 2.37 Fe CA A:Cys73 4.43 Fe S1 A:Fes3002 2.21 Fe S2 A:Fes3002 2.22 Fe FE1 A:Fes3002 0.00 Fe FE2 A:Fes3002 2.73 interactive model: Iron binding site 4 out of 8 in 1vdv Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Iron in the PDB 1vdv. 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: Fes3002, conact list: Atom Atom Distance (A) Fe O A:Gly42 4.87 Fe N A:Gly42 4.22 Fe C A:Gly42 4.00 Fe CA A:Gly42 4.27 Fe N A:Cys43 3.34 Fe CB A:Cys43 3.45 Fe SG A:Cys43 2.39 Fe C A:Cys43 4.26 Fe CA A:Cys43 3.84 Fe N A:Gly44 3.81 Fe CA A:Gly44 4.84 Fe N A:Glu45 4.66 Fe N A:Gly46 4.42 Fe C A:Gly46 4.79 Fe CA A:Gly46 4.75 Fe N A:Gly47 4.39 Fe C A:Gly47 4.70 Fe N A:Cys48 3.56 Fe CB A:Cys48 3.43 Fe SG A:Cys48 2.38 Fe C A:Cys48 4.25 Fe CA A:Cys48 3.90 Fe N A:Gly49 3.89 Fe CA A:Gly49 4.86 Fe N A:Ala50 4.36 Fe CB A:Ala50 4.90 Fe SG A:Cys51 4.72 Fe SG A:Cys73 4.53 Fe S1 A:Fes3002 2.21 Fe S2 A:Fes3002 2.18 Fe FE1 A:Fes3002 2.73 Fe FE2 A:Fes3002 0.00 interactive model: Iron binding site 5 out of 8 in 1vdv Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Iron in the PDB 1vdv. 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: Fes4001, B: Hoh6323, conact list: Atom Atom Distance (A) Fe N B:Gln112 4.97 Fe CB B:Gln112 4.74 Fe C B:Gln112 4.64 Fe N B:Cys113 3.53 Fe CB B:Cys113 3.37 Fe SG B:Cys113 2.36 Fe C B:Cys113 4.23 Fe CA B:Cys113 3.89 Fe N B:Gly114 3.77 Fe C B:Gly114 4.97 Fe CA B:Gly114 4.71 Fe N B:Phe115 4.38 Fe N B:Cys116 4.92 Fe SG B:Cys116 4.70 Fe SG B:Cys148 4.46 Fe N B:Arg149 4.81 Fe N B:Cys150 4.10 Fe CB B:Cys150 3.36 Fe SG B:Cys150 2.39 Fe CA B:Cys150 4.37 Fe S1 B:Fes4001 2.24 Fe S2 B:Fes4001 2.21 Fe FE1 B:Fes4001 0.00 Fe FE2 B:Fes4001 2.72 Fe O B:Hoh6323 3.58 interactive model: Iron binding site 6 out of 8 in 1vdv Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Iron in the PDB 1vdv. 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: Cys116, B: Leu147, B: Cys148, B: Arg149, B: Cys150, B: Thr151, B: Fes4001, B: Hoh5370, conact list: Atom Atom Distance (A) Fe SG B:Cys113 4.72 Fe N B:Cys116 4.24 Fe CB B:Cys116 3.41 Fe SG B:Cys116 2.37 Fe C B:Cys116 4.95 Fe CA B:Cys116 4.40 Fe O B:Leu147 4.85 Fe N B:Cys148 4.97 Fe CB B:Cys148 3.41 Fe SG B:Cys148 2.38 Fe C B:Cys148 4.31 Fe CA B:Cys148 3.67 Fe N B:Arg149 4.07 Fe N B:Cys150 4.33 Fe CB B:Cys150 4.51 Fe SG B:Cys150 4.51 Fe CA B:Cys150 4.98 Fe N B:Thr151 4.98 Fe CG2 B:Thr151 4.81 Fe S1 B:Fes4001 2.19 Fe S2 B:Fes4001 2.17 Fe FE1 B:Fes4001 2.72 Fe FE2 B:Fes4001 0.00 Fe O B:Hoh5370 4.32 interactive model: Iron binding site 7 out of 8 in 1vdv Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Iron in the PDB 1vdv. 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: Ala50, B: Cys51, B: Asn71, B: Cys73, B: Fes4002, conact list: Atom Atom Distance (A) Fe SG B:Cys43 4.40 Fe N B:Gly44 4.41 Fe CA B:Gly44 4.69 Fe N B:Glu45 4.90 Fe N B:Gly46 4.19 Fe CA B:Gly46 4.37 Fe SG B:Cys48 4.70 Fe N B:Gly49 4.81 Fe N B:Ala50 4.98 Fe N B:Cys51 4.30 Fe CB B:Cys51 3.43 Fe SG B:Cys51 2.37 Fe CA B:Cys51 4.49 Fe CB B:Asn71 4.22 Fe OD1 B:Asn71 4.41 Fe CG B:Asn71 4.48 Fe CA B:Asn71 4.97 Fe N B:Cys73 4.28 Fe CB B:Cys73 3.29 Fe SG B:Cys73 2.37 Fe CA B:Cys73 4.39 Fe S1 B:Fes4002 2.22 Fe S2 B:Fes4002 2.21 Fe FE1 B:Fes4002 0.00 Fe FE2 B:Fes4002 2.73 interactive model: Iron binding site 8 out of 8 in 1vdv Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Iron in the PDB 1vdv. 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: Fes4002, conact list: Atom Atom Distance (A) Fe O B:Gly42 4.90 Fe N B:Gly42 4.23 Fe C B:Gly42 4.03 Fe CA B:Gly42 4.28 Fe N B:Cys43 3.36 Fe CB B:Cys43 3.49 Fe SG B:Cys43 2.40 Fe C B:Cys43 4.29 Fe CA B:Cys43 3.87 Fe N B:Gly44 3.82 Fe CA B:Gly44 4.83 Fe N B:Glu45 4.55 Fe N B:Gly46 4.28 Fe C B:Gly46 4.78 Fe CA B:Gly46 4.75 Fe N B:Gly47 4.37 Fe C B:Gly47 4.70 Fe N B:Cys48 3.56 Fe CB B:Cys48 3.45 Fe SG B:Cys48 2.38 Fe C B:Cys48 4.26 Fe CA B:Cys48 3.91 Fe N B:Gly49 3.90 Fe CA B:Gly49 4.87 Fe N B:Ala50 4.43 Fe CB B:Ala50 4.99 Fe SG B:Cys51 4.70 Fe SG B:Cys73 4.54 Fe S1 B:Fes4002 2.20 Fe S2 B:Fes4002 2.18 Fe FE1 B:Fes4002 2.73 Fe FE2 B:Fes4002 0.00 interactive model: