Zinc in the structure of 5'-Nucleotidase From E. Coli (pdb 2ush)

The binding sites of Zinc atom in the structure of 5'-Nucleotidase From E. Coli (pdb code 2ush). This binding sites where shown with 5.0 Angstroms radius around Zinc atom. The 2ush structure was solved by T.KNOFEL, N.STRATER, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 8.0-2.2 Space group P212121 a (A) 93.210 b (A) 116.290 c (A) 132.770 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 19.8 Rfree (%) 25.4 Zinc Binding Sites: Zinc binding site 1 out of 9 in 2ush Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Zinc in the PDB 2ush. 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: Asp41, A: His43, A: Asp84, A: Asn116, A: His117, A: His217, A: His252, A: Gln254, A: Zn602, A: Hoh844, A: Hoh883, conact list: Atom Atom Distance (A) Zn CB A:Asp41 3.64 Zn OD2 A:Asp41 2.12 Zn OD1 A:Asp41 4.29 Zn CG A:Asp41 3.20 Zn CA A:Asp41 4.34 Zn NE2 A:His43 2.18 Zn ND1 A:His43 4.22 Zn CD2 A:His43 3.20 Zn CE1 A:His43 3.10 Zn CG A:His43 4.31 Zn CB A:Asp84 3.45 Zn OD2 A:Asp84 2.33 Zn OD1 A:Asp84 4.38 Zn CG A:Asp84 3.23 Zn CA A:Asp84 4.98 Zn OD1 A:Asn116 4.81 Zn NE2 A:His117 4.99 Zn CD2 A:His117 4.31 Zn NE2 A:His217 4.32 Zn CE1 A:His217 4.22 Zn O A:His252 4.28 Zn N A:His252 4.92 Zn ND1 A:His252 4.95 Zn C A:His252 4.82 Zn CA A:His252 4.49 Zn NE2 A:Gln254 4.37 Zn OE1 A:Gln254 2.27 Zn CD A:Gln254 3.31 Zn CG A:Gln254 3.91 Zn ZN A:Zn602 3.33 Zn O A:Hoh844 4.36 Zn O A:Hoh883 2.04 interactive model: Zinc binding site 2 out of 9 in 2ush Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Zinc in the PDB 2ush. 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: Asp41, A: Asp84, A: Asn116, A: His117, A: His217, A: His252, A: Zn601, A: Hoh844, A: Hoh883, conact list: Atom Atom Distance (A) Zn OD2 A:Asp41 3.89 Zn CB A:Asp84 4.45 Zn OD2 A:Asp84 2.25 Zn OD1 A:Asp84 3.67 Zn CG A:Asp84 3.24 Zn N A:Asn116 4.30 Zn CB A:Asn116 4.32 Zn ND2 A:Asn116 3.63 Zn OD1 A:Asn116 1.99 Zn CG A:Asn116 3.07 Zn CA A:Asn116 4.86 Zn NE2 A:His117 4.96 Zn N A:His117 4.93 Zn CD2 A:His117 4.25 Zn NE2 A:His217 2.06 Zn ND1 A:His217 4.14 Zn CD2 A:His217 3.07 Zn CE1 A:His217 3.02 Zn CG A:His217 4.19 Zn O A:His252 4.11 Zn NE2 A:His252 4.21 Zn N A:His252 4.45 Zn CB A:His252 3.61 Zn ND1 A:His252 2.17 Zn CD2 A:His252 4.32 Zn C A:His252 4.29 Zn CE1 A:His252 3.05 Zn CG A:His252 3.23 Zn CA A:His252 3.50 Zn ZN A:Zn601 3.33 Zn O A:Hoh844 3.55 Zn O A:Hoh883 2.13 interactive model: Zinc binding site 3 out of 9 in 2ush Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Zinc in the PDB 2ush. 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: Asp374, A: Asp376, B: Asp374, B: Asp376, conact list: Atom Atom Distance (A) Zn CB A:Asp374 4.22 Zn OD2 A:Asp374 1.93 Zn OD1 A:Asp374 2.95 Zn CG A:Asp374 2.78 Zn N A:Asp376 4.98 Zn CB A:Asp376 4.20 Zn OD2 A:Asp376 2.36 Zn OD1 A:Asp376 4.37 Zn CG A:Asp376 3.47 Zn CB B:Asp374 4.91 Zn OD2 B:Asp374 4.00 Zn CG B:Asp374 4.80 Zn CB B:Asp376 3.73 Zn OD2 B:Asp376 1.83 Zn OD1 B:Asp376 3.30 Zn CG B:Asp376 2.71 interactive model: Zinc binding site 4 out of 9 in 2ush Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Zinc in the PDB 2ush. 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: His289, A: Glu290, A: Lys293, B: Glu326, B: Asp327, A: Hoh902, conact list: Atom Atom Distance (A) Zn NE2 A:His289 2.43 Zn ND1 A:His289 4.50 Zn CD2 A:His289 3.43 Zn CE1 A:His289 3.36 Zn CG A:His289 4.56 Zn OE2 A:Glu290 3.59 Zn CD A:Glu290 4.46 Zn CG A:Glu290 4.80 Zn CE A:Lys293 3.23 Zn CD A:Lys293 3.48 Zn CG A:Lys293 4.95 Zn NZ A:Lys293 2.00 Zn O B:Glu326 4.12 Zn OE1 B:Glu326 2.32 Zn OE2 B:Glu326 2.73 Zn CD B:Glu326 2.86 Zn C B:Glu326 4.50 Zn CG B:Glu326 4.36 Zn N B:Asp327 4.74 Zn CA B:Asp327 4.61 Zn O A:Hoh902 4.63 interactive model: Zinc binding site 5 out of 9 in 2ush Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Zinc in the PDB 2ush. 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: Arg410, A: Wo4703, B: Wo4701, B: Wo4704, conact list: Atom Atom Distance (A) Zn NH2 A:Arg410 4.71 Zn O1 A:Wo4703 4.17 Zn W A:Wo4703 3.80 Zn O2 A:Wo4703 4.89 Zn O4 A:Wo4703 2.32 Zn O3 A:Wo4703 4.93 Zn O4 B:Wo4701 3.96 Zn O3 B:Wo4704 4.15 interactive model: Zinc binding site 6 out of 9 in 2ush Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Zinc in the PDB 2ush. 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: Asp41, B: His43, B: Asp84, B: Asn116, B: His117, B: His217, B: His252, B: Gln254, B: Zn602, B: Hoh833, B: Hoh880, conact list: Atom Atom Distance (A) Zn CB B:Asp41 3.55 Zn OD2 B:Asp41 4.25 Zn OD1 B:Asp41 2.24 Zn CG B:Asp41 3.17 Zn CA B:Asp41 4.34 Zn NE2 B:His43 2.17 Zn ND1 B:His43 4.25 Zn CD2 B:His43 3.13 Zn CE1 B:His43 3.15 Zn CG B:His43 4.28 Zn CB B:Asp84 3.57 Zn OD2 B:Asp84 2.43 Zn OD1 B:Asp84 4.50 Zn CG B:Asp84 3.34 Zn OD1 B:Asn116 4.83 Zn NE2 B:His117 4.87 Zn CD2 B:His117 4.28 Zn NE2 B:His217 4.38 Zn CE1 B:His217 4.17 Zn O B:His252 4.23 Zn N B:His252 4.88 Zn ND1 B:His252 4.86 Zn C B:His252 4.78 Zn CA B:His252 4.42 Zn NE2 B:Gln254 4.34 Zn OE1 B:Gln254 2.23 Zn CD B:Gln254 3.27 Zn CG B:Gln254 3.85 Zn ZN B:Zn602 3.29 Zn O B:Hoh833 4.32 Zn O B:Hoh880 1.90 interactive model: Zinc binding site 7 out of 9 in 2ush Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Zinc in the PDB 2ush. 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: Asp41, B: His43, B: Asp84, B: Asn116, B: His117, B: His217, B: His252, B: Zn601, B: Hoh833, B: Hoh880, conact list: Atom Atom Distance (A) Zn OD1 B:Asp41 3.69 Zn CG B:Asp41 4.89 Zn NE2 B:His43 4.97 Zn CB B:Asp84 4.42 Zn OD2 B:Asp84 2.20 Zn OD1 B:Asp84 3.72 Zn CG B:Asp84 3.22 Zn N B:Asn116 4.36 Zn CB B:Asn116 4.39 Zn ND2 B:Asn116 3.65 Zn OD1 B:Asn116 2.09 Zn CG B:Asn116 3.14 Zn CA B:Asn116 4.91 Zn NE2 B:His117 4.87 Zn N B:His117 4.90 Zn CD2 B:His117 4.15 Zn NE2 B:His217 1.96 Zn ND1 B:His217 3.98 Zn CD2 B:His217 3.08 Zn CE1 B:His217 2.81 Zn CG B:His217 4.14 Zn O B:His252 4.18 Zn NE2 B:His252 4.18 Zn N B:His252 4.45 Zn CB B:His252 3.60 Zn ND1 B:His252 2.14 Zn CD2 B:His252 4.29 Zn C B:His252 4.34 Zn CE1 B:His252 3.01 Zn CG B:His252 3.22 Zn CA B:His252 3.54 Zn ZN B:Zn601 3.29 Zn O B:Hoh833 3.65 Zn O B:Hoh880 1.71 interactive model: Zinc binding site 8 out of 9 in 2ush Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Zinc in the PDB 2ush. 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: Gly224, B: His226, B: Pro231, B: Glu235, conact list: Atom Atom Distance (A) Zn O B:Gly224 4.42 Zn NE2 B:His226 2.14 Zn ND1 B:His226 4.26 Zn CD2 B:His226 3.02 Zn CE1 B:His226 3.20 Zn CG B:His226 4.22 Zn CB B:Pro231 4.97 Zn CG B:Pro231 4.37 Zn OE1 B:Glu235 2.81 Zn OE2 B:Glu235 1.77 Zn CD B:Glu235 2.60 Zn CG B:Glu235 4.04 interactive model: Zinc binding site 9 out of 9 in 2ush Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 9 of Zinc in the PDB 2ush. 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: Glu225, conact list: Atom Atom Distance (A) Zn OE1 B:Glu225 2.31 Zn CB B:Glu225 4.83 Zn OE2 B:Glu225 2.36 Zn CD B:Glu225 2.63 Zn CG B:Glu225 4.08 interactive model: