Zinc in the structure of Crystal Structure of Allantoinase From Bacillus Halodurans C-125 (pdb 3hm7)

The binding sites of Zinc atom in the structure of Crystal Structure of Allantoinase From Bacillus Halodurans C-125 (pdb code 3hm7). This binding sites where shown with 5.0 Angstroms radius around Zinc atom. The 3hm7 structure was solved by Y.PATSKOVSKY, R.ROMERO, M.RUTTER, S.MILLER, S.R.WASSERMAN, J.M.SAUDER, F.M.RAUSHEL, S.K.BURLEY, S.C.ALMO, NEW YORK STRUCTURAL GENOMIX RESEARCHCONSORTIUM (NYSGXRC), NEW YORK SGX RESEARCH CENTER FOR STRUCTURALGENOMICS (NYSGXRC), with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 20.0-2.6 Space group P6122 a (A) 157.658 b (A) 157.658 c (A) 418.026 alpha (°) 90.00 beta (°) 90.00 gamma (°) 120.00 Rfactor (%) 24 Rfree (%) 26.7 Zinc Binding Sites: Zinc binding site 1 out of 6 in 3hm7 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Zinc in the PDB 3hm7. 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: His63, A: His65, A: Lys150, A: His242, A: Asp315, A: Hoh480, conact list: Atom Atom Distance (A) Zn NE2 A:His63 2.31 Zn ND1 A:His63 4.32 Zn CD2 A:His63 3.32 Zn CE1 A:His63 3.19 Zn CG A:His63 4.42 Zn NE2 A:His65 2.22 Zn ND1 A:His65 4.18 Zn CD2 A:His65 3.35 Zn CE1 A:His65 2.99 Zn CG A:His65 4.38 Zn NZ A:Lys150 4.20 Zn NE2 A:His242 3.93 Zn CD2 A:His242 4.22 Zn CB A:Asp315 4.43 Zn OD2 A:Asp315 3.74 Zn OD1 A:Asp315 2.21 Zn CG A:Asp315 3.23 Zn CA A:Asp315 4.82 Zn O A:Hoh480 3.08 interactive model: Zinc binding site 2 out of 6 in 3hm7 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Zinc in the PDB 3hm7. 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: His63, B: His65, B: Lys150, B: Phe152, B: His242, B: Asp315, B: Hoh449, conact list: Atom Atom Distance (A) Zn NE2 B:His63 2.38 Zn ND1 B:His63 4.29 Zn CD2 B:His63 3.47 Zn CE1 B:His63 3.12 Zn CG B:His63 4.49 Zn NE2 B:His65 2.40 Zn ND1 B:His65 4.31 Zn CD2 B:His65 3.59 Zn CE1 B:His65 3.07 Zn CG B:His65 4.58 Zn NZ B:Lys150 4.82 Zn CZ B:Phe152 4.81 Zn NE2 B:His242 3.79 Zn CD2 B:His242 4.19 Zn CE1 B:His242 5.00 Zn CB B:Asp315 4.50 Zn OD2 B:Asp315 3.50 Zn OD1 B:Asp315 2.33 Zn CG B:Asp315 3.20 Zn CA B:Asp315 4.97 Zn O B:Hoh449 3.07 interactive model: Zinc binding site 3 out of 6 in 3hm7 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Zinc in the PDB 3hm7. 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: His63, C: His65, C: Lys150, C: His242, C: Asp315, C: Ser317, C: Hoh455, conact list: Atom Atom Distance (A) Zn NE2 C:His63 2.25 Zn ND1 C:His63 4.16 Zn CD2 C:His63 3.05 Zn CE1 C:His63 3.18 Zn CG C:His63 4.13 Zn NE2 C:His65 2.30 Zn ND1 C:His65 4.35 Zn CD2 C:His65 3.24 Zn CE1 C:His65 3.25 Zn CG C:His65 4.37 Zn NZ C:Lys150 4.65 Zn NE2 C:His242 4.72 Zn ND1 C:His242 3.93 Zn CE1 C:His242 3.51 Zn CB C:Asp315 4.62 Zn OD2 C:Asp315 3.89 Zn OD1 C:Asp315 2.31 Zn CG C:Asp315 3.40 Zn CA C:Asp315 4.76 Zn CB C:Ser317 4.96 Zn O C:Hoh455 4.94 interactive model: Zinc binding site 4 out of 6 in 3hm7 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Zinc in the PDB 3hm7. 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: His63, D: His65, D: Lys150, D: His242, D: Asp315, D: Ser317, D: Hoh486, conact list: Atom Atom Distance (A) Zn NE2 D:His63 2.38 Zn ND1 D:His63 4.23 Zn CD2 D:His63 3.35 Zn CE1 D:His63 3.15 Zn CG D:His63 4.36 Zn NE2 D:His65 2.50 Zn ND1 D:His65 4.41 Zn CD2 D:His65 3.65 Zn CE1 D:His65 3.20 Zn CG D:His65 4.66 Zn NZ D:Lys150 4.88 Zn NE2 D:His242 3.90 Zn CD2 D:His242 4.24 Zn CB D:Asp315 4.61 Zn OD2 D:Asp315 3.65 Zn OD1 D:Asp315 2.31 Zn CG D:Asp315 3.30 Zn OG D:Ser317 4.10 Zn O D:Hoh486 3.19 interactive model: Zinc binding site 5 out of 6 in 3hm7 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Zinc in the PDB 3hm7. 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: E: His63, E: His65, E: Met95, E: Lys150, E: Phe152, E: His242, E: Asp315, E: Hoh459, E: Hoh487, conact list: Atom Atom Distance (A) Zn NE2 E:His63 2.21 Zn ND1 E:His63 4.24 Zn CD2 E:His63 3.28 Zn CE1 E:His63 3.08 Zn CG E:His63 4.36 Zn NE2 E:His65 2.39 Zn ND1 E:His65 4.29 Zn CD2 E:His65 3.56 Zn CE1 E:His65 3.06 Zn CG E:His65 4.55 Zn CG E:Met95 4.73 Zn NZ E:Lys150 4.68 Zn CZ E:Phe152 4.64 Zn NE2 E:His242 4.13 Zn CD2 E:His242 4.37 Zn CB E:Asp315 4.64 Zn OD2 E:Asp315 4.15 Zn OD1 E:Asp315 2.45 Zn CG E:Asp315 3.54 Zn O E:Hoh459 4.53 Zn O E:Hoh487 2.52 interactive model: Zinc binding site 6 out of 6 in 3hm7 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Zinc in the PDB 3hm7. 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: F: His63, F: His65, F: His242, F: Asp315, F: Hoh463, conact list: Atom Atom Distance (A) Zn NE2 F:His63 2.24 Zn ND1 F:His63 4.25 Zn CD2 F:His63 3.32 Zn CE1 F:His63 3.08 Zn CG F:His63 4.39 Zn NE2 F:His65 2.37 Zn ND1 F:His65 4.29 Zn CD2 F:His65 3.55 Zn CE1 F:His65 3.06 Zn CG F:His65 4.56 Zn NE2 F:His242 4.04 Zn CD2 F:His242 4.31 Zn CB F:Asp315 4.61 Zn OD2 F:Asp315 3.76 Zn OD1 F:Asp315 2.44 Zn CG F:Asp315 3.37 Zn O F:Hoh463 3.45 interactive model: