Zinc in the structure of The Structure of the Helicobacter Pylori Ferric Uptake Regulator Fur Reveals Three Functional Metal Binding Sites (pdb 2xig)

The binding sites of Zinc atom in the structure of The Structure of the Helicobacter Pylori Ferric Uptake Regulator Fur Reveals Three Functional Metal Binding Sites (pdb code 2xig). This binding sites where shown with 5.0 Angstroms radius around Zinc atom. The 2xig structure was solved by C.DIAN, S.VITALE, G.A.LEONARD, F.FAUQUANT, C.MULLER, C.BAHLAWANE, H.DE REUSE, I.MICHAUD-SORET, L.TERRADOT, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 35.1-1.9 Space group P1 a (A) 48.150 b (A) 48.290 c (A) 72.250 alpha (°) 83.32 beta (°) 77.82 gamma (°) 87.65 Rfactor (%) 19.81 Rfree (%) 23.39 Zinc Binding Sites: Zinc binding site 1 out of 12 in 2xig Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Zinc in the PDB 2xig. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Zinc atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: His96, A: His97, A: Asp98, A: Glu117, A: Gln120, A: His134, A: Hoh2064, A: Hoh2073, conact list: Atom Atom Distance (A) Zn NE2 A:His96 2.08 Zn ND1 A:His96 4.12 Zn CD2 A:His96 3.17 Zn CE1 A:His96 2.96 Zn CG A:His96 4.25 Zn C A:His97 4.87 Zn N A:Asp98 4.73 Zn CB A:Asp98 4.19 Zn OD2 A:Asp98 2.12 Zn OD1 A:Asp98 2.62 Zn CG A:Asp98 2.70 Zn CA A:Asp98 4.97 Zn OE1 A:Glu117 3.06 Zn OE2 A:Glu117 2.15 Zn CD A:Glu117 2.94 Zn CG A:Glu117 4.38 Zn NE2 A:Gln120 4.63 Zn OE1 A:Gln120 4.48 Zn CD A:Gln120 4.99 Zn NE2 A:His134 2.14 Zn ND1 A:His134 4.22 Zn CD2 A:His134 3.15 Zn CE1 A:His134 3.09 Zn CG A:His134 4.28 Zn O A:Hoh2064 4.94 Zn O A:Hoh2073 3.65 interactive model: Zinc binding site 2 out of 12 in 2xig Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Zinc in the PDB 2xig. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Zinc atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: His42, A: Glu90, A: Lys94, A: His97, A: His99, A: Glu110, A: Hoh2062, conact list: Atom Atom Distance (A) Zn NE2 A:His42 2.14 Zn ND1 A:His42 4.27 Zn CD2 A:His42 2.95 Zn CE1 A:His42 3.25 Zn CG A:His42 4.17 Zn OE1 A:Glu90 2.26 Zn CB A:Glu90 4.81 Zn OE2 A:Glu90 2.46 Zn CD A:Glu90 2.66 Zn CG A:Glu90 4.13 Zn CE A:Lys94 4.88 Zn NZ A:Lys94 4.57 Zn NE2 A:His97 2.16 Zn ND1 A:His97 4.25 Zn CD2 A:His97 3.16 Zn CE1 A:His97 3.12 Zn CG A:His97 4.30 Zn NE2 A:His99 2.19 Zn ND1 A:His99 4.29 Zn CD2 A:His99 3.10 Zn CE1 A:His99 3.22 Zn CG A:His99 4.27 Zn OE1 A:Glu110 4.69 Zn OE2 A:Glu110 2.64 Zn CD A:Glu110 3.62 Zn CG A:Glu110 3.96 Zn O A:Hoh2062 4.98 interactive model: Zinc binding site 3 out of 12 in 2xig Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Zinc in the PDB 2xig. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Zinc atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Cys102, A: His104, A: Cys105, A: Gly106, A: Lys107, A: Cys142, A: Cys145, A: Hoh2094, conact list: Atom Atom Distance (A) Zn CB A:Cys102 3.21 Zn SG A:Cys102 2.38 Zn CA A:Cys102 4.66 Zn CB A:His104 4.71 Zn C A:His104 4.83 Zn N A:Cys105 3.76 Zn CB A:Cys105 3.29 Zn SG A:Cys105 2.31 Zn C A:Cys105 4.86 Zn CA A:Cys105 4.09 Zn N A:Gly106 4.92 Zn CB A:Lys107 4.75 Zn CE A:Lys107 4.93 Zn CD A:Lys107 4.94 Zn O A:Cys142 4.78 Zn N A:Cys142 4.02 Zn CB A:Cys142 3.41 Zn SG A:Cys142 2.37 Zn C A:Cys142 4.78 Zn CA A:Cys142 4.24 Zn N A:Cys145 4.23 Zn CB A:Cys145 3.26 Zn SG A:Cys145 2.35 Zn CA A:Cys145 4.32 Zn O A:Hoh2094 4.40 interactive model: Zinc binding site 4 out of 12 in 2xig Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Zinc in the PDB 2xig. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Zinc atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: B: His42, B: Glu90, B: Lys94, B: His97, B: His99, B: Glu110, B: Hoh2025, B: Hoh2030, conact list: Atom Atom Distance (A) Zn NE2 B:His42 2.10 Zn ND1 B:His42 4.23 Zn CD2 B:His42 2.99 Zn CE1 B:His42 3.17 Zn CG B:His42 4.18 Zn OE1 B:Glu90 2.44 Zn CB B:Glu90 4.76 Zn OE2 B:Glu90 2.13 Zn CD B:Glu90 2.57 Zn CG B:Glu90 4.05 Zn NZ B:Lys94 4.56 Zn NE2 B:His97 2.11 Zn ND1 B:His97 4.18 Zn CD2 B:His97 3.05 Zn CE1 B:His97 3.09 Zn CG B:His97 4.19 Zn NE2 B:His99 2.21 Zn ND1 B:His99 4.32 Zn CD2 B:His99 3.02 Zn CE1 B:His99 3.29 Zn CG B:His99 4.23 Zn OE2 B:Glu110 4.24 Zn CD B:Glu110 4.53 Zn CG B:Glu110 4.40 Zn O B:Hoh2025 4.27 Zn O B:Hoh2030 4.86 interactive model: Zinc binding site 5 out of 12 in 2xig Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Zinc in the PDB 2xig. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Zinc atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: B: His96, B: His97, B: Asp98, B: Glu117, B: Gln120, B: His134, B: Hoh2032, B: Hoh2033, conact list: Atom Atom Distance (A) Zn NE2 B:His96 2.11 Zn ND1 B:His96 4.12 Zn CD2 B:His96 3.23 Zn CE1 B:His96 2.94 Zn CG B:His96 4.29 Zn C B:His97 4.80 Zn N B:Asp98 4.63 Zn CB B:Asp98 4.21 Zn OD2 B:Asp98 2.66 Zn OD1 B:Asp98 2.17 Zn CG B:Asp98 2.73 Zn CA B:Asp98 4.92 Zn OE1 B:Glu117 2.11 Zn OE2 B:Glu117 3.06 Zn CD B:Glu117 2.93 Zn CG B:Glu117 4.36 Zn OE1 B:Gln120 4.42 Zn NE2 B:His134 2.11 Zn ND1 B:His134 4.14 Zn CD2 B:His134 3.22 Zn CE1 B:His134 2.97 Zn CG B:His134 4.29 Zn O B:Hoh2032 3.85 Zn O B:Hoh2033 4.94 interactive model: Zinc binding site 6 out of 12 in 2xig Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Zinc in the PDB 2xig. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Zinc atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: B: Cys102, B: His104, B: Cys105, B: Gly106, B: Lys107, B: Cys142, B: Cys145, conact list: Atom Atom Distance (A) Zn CB B:Cys102 3.29 Zn SG B:Cys102 2.33 Zn CA B:Cys102 4.70 Zn N B:His104 4.87 Zn CB B:His104 4.18 Zn C B:His104 4.65 Zn CA B:His104 4.81 Zn N B:Cys105 3.60 Zn CB B:Cys105 3.29 Zn SG B:Cys105 2.41 Zn C B:Cys105 4.79 Zn CA B:Cys105 4.02 Zn N B:Gly106 4.75 Zn N B:Lys107 4.99 Zn CB B:Lys107 4.67 Zn CE B:Lys107 4.49 Zn O B:Cys142 4.94 Zn N B:Cys142 4.11 Zn CB B:Cys142 3.51 Zn SG B:Cys142 2.18 Zn C B:Cys142 4.98 Zn CA B:Cys142 4.36 Zn N B:Cys145 4.34 Zn CB B:Cys145 3.22 Zn SG B:Cys145 2.40 Zn CA B:Cys145 4.34 interactive model: Zinc binding site 7 out of 12 in 2xig Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Zinc in the PDB 2xig. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Zinc atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: C: His42, C: Glu90, C: Lys94, C: His97, C: His99, C: Glu110, C: Hoh2088, C: Hoh2089, conact list: Atom Atom Distance (A) Zn NE2 C:His42 2.18 Zn ND1 C:His42 4.31 Zn CD2 C:His42 3.05 Zn CE1 C:His42 3.25 Zn CG C:His42 4.25 Zn OE1 C:Glu90 2.57 Zn CB C:Glu90 4.80 Zn OE2 C:Glu90 2.04 Zn CD C:Glu90 2.58 Zn CG C:Glu90 4.04 Zn NZ C:Lys94 4.39 Zn NE2 C:His97 2.10 Zn ND1 C:His97 4.22 Zn CD2 C:His97 3.01 Zn CE1 C:His97 3.14 Zn CG C:His97 4.19 Zn NE2 C:His99 2.10 Zn ND1 C:His99 4.20 Zn CD2 C:His99 3.05 Zn CE1 C:His99 3.11 Zn CG C:His99 4.21 Zn OE2 C:Glu110 3.90 Zn CD C:Glu110 4.20 Zn CG C:Glu110 4.11 Zn O C:Hoh2088 3.84 Zn O C:Hoh2089 4.30 interactive model: Zinc binding site 8 out of 12 in 2xig Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Zinc in the PDB 2xig. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Zinc atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: C: Cys102, C: His104, C: Cys105, C: Gly106, C: Lys107, C: Cys142, C: Cys145, conact list: Atom Atom Distance (A) Zn CB C:Cys102 3.24 Zn SG C:Cys102 2.38 Zn CA C:Cys102 4.68 Zn N C:His104 4.97 Zn CB C:His104 4.63 Zn C C:His104 4.72 Zn N C:Cys105 3.68 Zn CB C:Cys105 3.18 Zn SG C:Cys105 2.33 Zn C C:Cys105 4.74 Zn CA C:Cys105 3.99 Zn N C:Gly106 4.90 Zn CB C:Lys107 4.79 Zn CE C:Lys107 4.87 Zn NZ C:Lys107 4.89 Zn O C:Cys142 4.87 Zn N C:Cys142 4.00 Zn CB C:Cys142 3.47 Zn SG C:Cys142 2.45 Zn C C:Cys142 4.83 Zn CA C:Cys142 4.27 Zn N C:Cys145 4.14 Zn CB C:Cys145 3.34 Zn SG C:Cys145 2.38 Zn CA C:Cys145 4.34 interactive model: Zinc binding site 9 out of 12 in 2xig Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 9 of Zinc in the PDB 2xig. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Zinc atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: C: His96, C: His97, C: Asp98, C: Glu117, C: Gln120, C: His134, C: Hoh2097, C: Hoh2098, conact list: Atom Atom Distance (A) Zn NE2 C:His96 2.14 Zn ND1 C:His96 4.22 Zn CD2 C:His96 3.15 Zn CE1 C:His96 3.09 Zn CG C:His96 4.28 Zn C C:His97 4.83 Zn N C:Asp98 4.66 Zn CB C:Asp98 4.15 Zn OD2 C:Asp98 2.14 Zn OD1 C:Asp98 2.53 Zn CG C:Asp98 2.65 Zn CA C:Asp98 4.90 Zn OE1 C:Glu117 3.15 Zn OE2 C:Glu117 2.02 Zn CD C:Glu117 2.93 Zn CG C:Glu117 4.33 Zn OE1 C:Gln120 4.77 Zn NE2 C:His134 2.04 Zn ND1 C:His134 4.07 Zn CD2 C:His134 3.14 Zn CE1 C:His134 2.91 Zn CG C:His134 4.21 Zn O C:Hoh2097 3.91 Zn O C:Hoh2098 4.97 interactive model: Zinc binding site 10 out of 12 in 2xig Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 10 of Zinc in the PDB 2xig. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Zinc atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: D: Cys102, D: His104, D: Cys105, D: Gly106, D: Lys107, D: Cys142, D: Cys145, D: Hoh2090, conact list: Atom Atom Distance (A) Zn CB D:Cys102 3.31 Zn SG D:Cys102 2.42 Zn CA D:Cys102 4.74 Zn CB D:His104 4.71 Zn C D:His104 4.66 Zn N D:Cys105 3.68 Zn CB D:Cys105 3.23 Zn SG D:Cys105 2.28 Zn C D:Cys105 4.86 Zn CA D:Cys105 4.02 Zn N D:Gly106 4.90 Zn CB D:Lys107 4.74 Zn CE D:Lys107 4.65 Zn NZ D:Lys107 4.80 Zn O D:Cys142 4.85 Zn N D:Cys142 3.98 Zn CB D:Cys142 3.45 Zn SG D:Cys142 2.37 Zn C D:Cys142 4.85 Zn CA D:Cys142 4.25 Zn N D:Cys145 4.26 Zn CB D:Cys145 3.35 Zn SG D:Cys145 2.39 Zn CA D:Cys145 4.40 Zn O D:Hoh2090 4.52 interactive model: Zinc binding site 11 out of 12 in 2xig Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 11 of Zinc in the PDB 2xig. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Zinc atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: D: His96, D: His97, D: Asp98, D: Glu117, D: Gln120, D: His134, D: Hoh2071, conact list: Atom Atom Distance (A) Zn NE2 D:His96 2.06 Zn ND1 D:His96 4.10 Zn CD2 D:His96 3.17 Zn CE1 D:His96 2.92 Zn CG D:His96 4.24 Zn C D:His97 4.78 Zn N D:Asp98 4.56 Zn CB D:Asp98 4.15 Zn OD2 D:Asp98 2.09 Zn OD1 D:Asp98 2.66 Zn CG D:Asp98 2.68 Zn CA D:Asp98 4.88 Zn OE1 D:Glu117 3.03 Zn OE2 D:Glu117 2.10 Zn CD D:Glu117 2.91 Zn CG D:Glu117 4.35 Zn OE1 D:Gln120 4.48 Zn NE2 D:His134 2.12 Zn ND1 D:His134 4.11 Zn CD2 D:His134 3.27 Zn CE1 D:His134 2.91 Zn CG D:His134 4.31 Zn O D:Hoh2071 3.88 interactive model: Zinc binding site 12 out of 12 in 2xig Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 12 of Zinc in the PDB 2xig. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Zinc atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: D: His42, D: Glu90, D: Lys94, D: His97, D: His99, D: Glu110, D: Hoh2046, D: Hoh2048, conact list: Atom Atom Distance (A) Zn NE2 D:His42 2.05 Zn ND1 D:His42 4.16 Zn CD2 D:His42 2.99 Zn CE1 D:His42 3.07 Zn CG D:His42 4.15 Zn OE1 D:Glu90 2.54 Zn CB D:Glu90 4.83 Zn OE2 D:Glu90 2.09 Zn CD D:Glu90 2.61 Zn CG D:Glu90 4.09 Zn NZ D:Lys94 4.62 Zn NE2 D:His97 2.08 Zn ND1 D:His97 4.15 Zn CD2 D:His97 3.07 Zn CE1 D:His97 3.04 Zn CG D:His97 4.20 Zn NE2 D:His99 2.10 Zn ND1 D:His99 4.19 Zn CD2 D:His99 3.07 Zn CE1 D:His99 3.08 Zn CG D:His99 4.21 Zn OE2 D:Glu110 4.10 Zn CD D:Glu110 4.54 Zn CG D:Glu110 4.32 Zn O D:Hoh2046 4.56 Zn O D:Hoh2048 4.14 interactive model: