Zinc in the structure of Crystal Structure Of the Tpr Domain of Xanthomonas Campestris Ybgf (pdb 2xev)

The binding sites of Zinc atom in the structure of Crystal Structure Of the Tpr Domain of Xanthomonas Campestris Ybgf (pdb code 2xev). This binding sites where shown with 5.0 Angstroms radius around Zinc atom. The 2xev structure was solved by A.M.KRACHLER, A.SHARMA, C.KLEANTHOUS, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 18.8-1.6 Space group P1211 a (A) 86.360 b (A) 37.120 c (A) 90.610 alpha (°) 90.00 beta (°) 117.14 gamma (°) 90.00 Rfactor (%) 20.407 Rfree (%) 22.813 Zinc Binding Sites: Zinc binding site 1 out of 6 in 2xev Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Zinc in the PDB 2xev. 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: Glu58, A: Arg62, A: Gln85, A: Glu88, A: Lys90, A: Glu93, A: Hoh2033, conact list: Atom Atom Distance (A) Zn OE1 A:Glu58 3.15 Zn CB A:Glu58 4.95 Zn OE2 A:Glu58 1.90 Zn CD A:Glu58 2.84 Zn CG A:Glu58 4.20 Zn NH2 A:Arg62 4.56 Zn NE2 A:Gln85 4.42 Zn CB A:Gln85 4.58 Zn CD A:Gln85 4.65 Zn CG A:Gln85 3.92 Zn CA A:Gln85 4.73 Zn OE1 A:Glu88 1.89 Zn CB A:Glu88 4.68 Zn OE2 A:Glu88 3.27 Zn CD A:Glu88 2.91 Zn CG A:Glu88 4.27 Zn CB A:Lys90 4.82 Zn CG A:Lys90 4.31 Zn OE1 A:Glu93 2.24 Zn OE2 A:Glu93 3.97 Zn CD A:Glu93 3.41 Zn CG A:Glu93 4.60 Zn O A:Hoh2033 3.87 interactive model: Zinc binding site 2 out of 6 in 2xev Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Zinc in the PDB 2xev. 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: Gln22, B: Arg52, B: Asn53, B: Phe54, B: Gln55, B: Leu56, B: Hoh2036, conact list: Atom Atom Distance (A) Zn OE1 A:Gln22 3.19 Zn CB A:Gln22 4.86 Zn CD A:Gln22 4.15 Zn CG A:Gln22 4.42 Zn O B:Arg52 4.88 Zn O B:Asn53 3.61 Zn N B:Asn53 4.68 Zn CB B:Asn53 3.48 Zn C B:Asn53 3.19 Zn OD1 B:Asn53 3.46 Zn CG B:Asn53 3.91 Zn CA B:Asn53 3.27 Zn N B:Phe54 3.51 Zn C B:Phe54 4.22 Zn CA B:Phe54 4.44 Zn N B:Gln55 3.29 Zn OE1 B:Gln55 4.28 Zn CB B:Gln55 3.64 Zn CD B:Gln55 4.65 Zn C B:Gln55 4.09 Zn CG B:Gln55 4.28 Zn CA B:Gln55 3.84 Zn N B:Leu56 3.33 Zn CB B:Leu56 4.06 Zn CD1 B:Leu56 4.29 Zn CD2 B:Leu56 4.70 Zn CG B:Leu56 3.64 Zn CA B:Leu56 4.29 Zn O B:Hoh2036 2.84 interactive model: Zinc binding site 3 out of 6 in 2xev Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Zinc in the PDB 2xev. 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: Asp19, B: Gln55, B: Glu58, B: Glu88, B: Lys90, B: Zn1127, A: Hoh2010, B: Hoh2037, conact list: Atom Atom Distance (A) Zn CB A:Asp19 4.14 Zn OD2 A:Asp19 2.46 Zn OD1 A:Asp19 2.13 Zn CG A:Asp19 2.61 Zn CA A:Asp19 4.91 Zn NE2 B:Gln55 4.66 Zn CB B:Gln55 4.70 Zn CG B:Gln55 4.31 Zn CA B:Gln55 4.81 Zn OE1 B:Glu58 2.12 Zn CB B:Glu58 4.92 Zn OE2 B:Glu58 3.55 Zn CD B:Glu58 3.17 Zn CG B:Glu58 4.50 Zn OE1 B:Glu88 3.16 Zn OE2 B:Glu88 1.92 Zn CD B:Glu88 2.89 Zn CG B:Glu88 4.30 Zn CE B:Lys90 4.59 Zn CD B:Lys90 4.83 Zn NZ B:Lys90 3.81 Zn ZN B:Zn1127 2.99 Zn O A:Hoh2010 4.61 Zn O B:Hoh2037 4.02 interactive model: Zinc binding site 4 out of 6 in 2xev Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Zinc in the PDB 2xev. 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: Asp19, B: Glu58, B: Arg62, B: Gln85, B: Glu88, B: Lys90, B: Glu93, B: Zn1126, conact list: Atom Atom Distance (A) Zn OD2 A:Asp19 4.68 Zn OE1 B:Glu58 3.02 Zn OE2 B:Glu58 2.05 Zn CD B:Glu58 2.84 Zn CG B:Glu58 4.23 Zn NH2 B:Arg62 4.73 Zn NE2 B:Gln85 4.10 Zn CB B:Gln85 4.29 Zn CD B:Gln85 4.31 Zn CG B:Gln85 3.68 Zn CA B:Gln85 4.63 Zn OE1 B:Glu88 1.91 Zn CB B:Glu88 4.80 Zn OE2 B:Glu88 3.23 Zn CD B:Glu88 2.92 Zn CG B:Glu88 4.31 Zn CB B:Lys90 4.73 Zn CE B:Lys90 4.34 Zn CD B:Lys90 3.59 Zn CG B:Lys90 4.49 Zn NZ B:Lys90 4.09 Zn OE1 B:Glu93 2.08 Zn CB B:Glu93 4.96 Zn OE2 B:Glu93 2.98 Zn CD B:Glu93 2.87 Zn CG B:Glu93 4.32 Zn ZN B:Zn1126 2.99 interactive model: Zinc binding site 5 out of 6 in 2xev Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Zinc in the PDB 2xev. 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: Lys16, B: Asp19, C: Gln55, C: Glu58, C: Gln85, C: Glu88, C: Lys90, C: Cl1125, B: Hoh2015, C: Hoh2032, conact list: Atom Atom Distance (A) Zn CE B:Lys16 4.72 Zn NZ B:Lys16 3.72 Zn CB B:Asp19 4.31 Zn CB B:Asp19 4.28 Zn OD2 B:Asp19 2.02 Zn OD2 B:Asp19 2.03 Zn OD1 B:Asp19 3.14 Zn OD1 B:Asp19 3.09 Zn CG B:Asp19 2.91 Zn CG B:Asp19 2.88 Zn CB C:Gln55 4.89 Zn CG C:Gln55 4.17 Zn CA C:Gln55 4.75 Zn OE1 C:Glu58 1.95 Zn CB C:Glu58 4.55 Zn OE2 C:Glu58 3.11 Zn CD C:Glu58 2.82 Zn CG C:Glu58 4.20 Zn NE2 C:Gln85 4.86 Zn CG C:Gln85 4.25 Zn CA C:Gln85 4.95 Zn OE1 C:Glu88 1.86 Zn CB C:Glu88 4.92 Zn OE2 C:Glu88 3.12 Zn CD C:Glu88 2.83 Zn CG C:Glu88 4.20 Zn CG C:Lys90 4.65 Zn NZ C:Lys90 3.89 Zn CL C:Cl1125 2.24 Zn O B:Hoh2015 4.42 Zn O C:Hoh2032 4.08 interactive model: Zinc binding site 6 out of 6 in 2xev Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Zinc in the PDB 2xev. 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: Asp19, C: Hoh2011, C: Hoh2013, C: Hoh2014, conact list: Atom Atom Distance (A) Zn CB C:Asp19 4.04 Zn OD2 C:Asp19 2.29 Zn OD1 C:Asp19 2.18 Zn CG C:Asp19 2.52 Zn CA C:Asp19 4.87 Zn O C:Hoh2011 4.24 Zn O C:Hoh2013 4.66 Zn O C:Hoh2014 4.37 interactive model: