Zinc in the structure of Crystal Structure of L-Rhamnose Isomerase From Pseudomonas Stutzeri With L-Rhamnose (pdb 2i56)

The binding sites of Zinc atom in the structure of Crystal Structure of L-Rhamnose Isomerase From Pseudomonas Stutzeri With L-Rhamnose (pdb code 2i56). This binding sites where shown with 5.0 Angstroms radius around Zinc atom. The 2i56 structure was solved by H.YOSHIDA, M.YAMADA, G.TAKADA, K.IZUMORI, S.KAMITORI, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 33.2-2.0 Space group P1211 a (A) 74.616 b (A) 104.757 c (A) 114.292 alpha (°) 90.00 beta (°) 107.96 gamma (°) 90.00 Rfactor (%) 17 Rfree (%) 20.5 Zinc Binding Sites: Zinc binding site 1 out of 8 in 2i56 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Zinc in the PDB 2i56. 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: Glu219, A: Leu252, A: Asp254, A: His257, A: His281, A: Asp327, A: Rns2001, A: Zn502, A: Hoh2205, conact list: Atom Atom Distance (A) Zn OE1 A:Glu219 3.21 Zn OE2 A:Glu219 2.14 Zn CD A:Glu219 3.03 Zn CG A:Glu219 4.45 Zn CD2 A:Leu252 4.86 Zn CB A:Asp254 3.73 Zn OD2 A:Asp254 4.38 Zn OD1 A:Asp254 2.21 Zn CG A:Asp254 3.28 Zn CA A:Asp254 4.99 Zn NE2 A:His257 4.09 Zn ND1 A:His257 4.83 Zn CE1 A:His257 3.88 Zn NE2 A:His281 4.04 Zn CB A:His281 3.62 Zn ND1 A:His281 2.02 Zn CD2 A:His281 4.19 Zn CE1 A:His281 2.86 Zn CG A:His281 3.15 Zn CB A:Asp327 3.67 Zn OD2 A:Asp327 2.08 Zn OD1 A:Asp327 4.25 Zn CG A:Asp327 3.17 Zn O2 A:Rns2001 2.33 Zn C4 A:Rns2001 4.37 Zn C1 A:Rns2001 4.59 Zn C3 A:Rns2001 3.46 Zn O3 A:Rns2001 2.61 Zn O4 A:Rns2001 4.09 Zn C2 A:Rns2001 3.20 Zn ZN A:Zn502 4.29 Zn O A:Hoh2205 3.72 interactive model: Zinc binding site 2 out of 8 in 2i56 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Zinc in the PDB 2i56. 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: Glu219, A: Lys221, A: Asp254, A: His257, A: Asp289, A: Asp291, A: Asp327, B: Arg65, B: Phe66, A: Rns2001, A: Zn501, A: Hoh2164, A: Hoh2205, conact list: Atom Atom Distance (A) Zn OE2 A:Glu219 4.96 Zn CE A:Lys221 4.02 Zn CD A:Lys221 4.42 Zn NZ A:Lys221 3.87 Zn OD2 A:Asp254 4.56 Zn OD1 A:Asp254 3.88 Zn CG A:Asp254 4.37 Zn NE2 A:His257 2.13 Zn ND1 A:His257 4.17 Zn CD2 A:His257 3.15 Zn CE1 A:His257 3.05 Zn CG A:His257 4.25 Zn CB A:Asp289 4.26 Zn OD2 A:Asp289 2.19 Zn OD1 A:Asp289 2.95 Zn CG A:Asp289 2.86 Zn OD2 A:Asp291 3.99 Zn OD1 A:Asp291 3.72 Zn CG A:Asp291 4.29 Zn OD2 A:Asp327 4.42 Zn NH2 B:Arg65 4.49 Zn CZ B:Phe66 4.96 Zn O2 A:Rns2001 2.43 Zn C4 A:Rns2001 4.83 Zn C1 A:Rns2001 2.93 Zn O1 A:Rns2001 2.15 Zn C3 A:Rns2001 4.50 Zn O4 A:Rns2001 4.14 Zn C2 A:Rns2001 3.15 Zn ZN A:Zn501 4.29 Zn O A:Hoh2164 2.57 Zn O A:Hoh2205 2.03 interactive model: Zinc binding site 3 out of 8 in 2i56 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Zinc in the PDB 2i56. 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: Glu219, B: Asp254, B: His257, B: His281, B: Asp327, B: Rns2002, B: Zn504, conact list: Atom Atom Distance (A) Zn OE1 B:Glu219 3.16 Zn OE2 B:Glu219 2.23 Zn CD B:Glu219 2.98 Zn CG B:Glu219 4.32 Zn CB B:Asp254 3.66 Zn OD2 B:Asp254 2.21 Zn OD1 B:Asp254 4.37 Zn CG B:Asp254 3.26 Zn CA B:Asp254 4.82 Zn NE2 B:His257 4.40 Zn ND1 B:His257 4.81 Zn CE1 B:His257 3.99 Zn NE2 B:His281 4.41 Zn CB B:His281 3.54 Zn ND1 B:His281 2.32 Zn CD2 B:His281 4.43 Zn CE1 B:His281 3.29 Zn CG B:His281 3.29 Zn CB B:Asp327 3.63 Zn OD2 B:Asp327 2.24 Zn OD1 B:Asp327 4.39 Zn CG B:Asp327 3.27 Zn O2 B:Rns2002 3.17 Zn C3 B:Rns2002 3.95 Zn O3 B:Rns2002 3.04 Zn O4 B:Rns2002 4.97 Zn C2 B:Rns2002 3.65 Zn ZN B:Zn504 4.67 interactive model: Zinc binding site 4 out of 8 in 2i56 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Zinc in the PDB 2i56. 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: Arg65, B: Lys221, B: Asp254, B: His257, B: Asn283, B: Asp289, B: Asp291, B: Asp327, B: Rns2002, B: Zn503, B: Hoh2057, conact list: Atom Atom Distance (A) Zn NH2 A:Arg65 4.81 Zn NZ B:Lys221 4.99 Zn OD2 B:Asp254 3.52 Zn OD1 B:Asp254 3.73 Zn CG B:Asp254 3.88 Zn NE2 B:His257 2.52 Zn ND1 B:His257 4.63 Zn CD2 B:His257 3.28 Zn CE1 B:His257 3.60 Zn CG B:His257 4.51 Zn ND2 B:Asn283 4.36 Zn CB B:Asp289 4.37 Zn OD2 B:Asp289 2.68 Zn OD1 B:Asp289 2.37 Zn CG B:Asp289 2.87 Zn CB B:Asp291 4.64 Zn OD2 B:Asp291 3.37 Zn OD1 B:Asp291 2.37 Zn CG B:Asp291 3.22 Zn O B:Asp327 4.72 Zn OD2 B:Asp327 4.20 Zn OD1 B:Asp327 4.92 Zn CG B:Asp327 4.60 Zn O2 B:Rns2002 2.88 Zn C1 B:Rns2002 4.13 Zn O1 B:Rns2002 3.42 Zn O4 B:Rns2002 4.80 Zn C2 B:Rns2002 3.94 Zn ZN B:Zn503 4.67 Zn O B:Hoh2057 4.56 interactive model: Zinc binding site 5 out of 8 in 2i56 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Zinc in the PDB 2i56. 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: Glu219, C: Asp254, C: His257, C: His281, C: Asp327, C: Rns2003, C: Zn506, C: Hoh2302, conact list: Atom Atom Distance (A) Zn OE1 C:Glu219 3.23 Zn OE2 C:Glu219 2.20 Zn CD C:Glu219 3.04 Zn CG C:Glu219 4.42 Zn CB C:Asp254 3.76 Zn OD2 C:Asp254 2.21 Zn OD1 C:Asp254 4.37 Zn CG C:Asp254 3.29 Zn CA C:Asp254 4.99 Zn NE2 C:His257 4.27 Zn ND1 C:His257 4.80 Zn CE1 C:His257 3.94 Zn NE2 C:His281 4.24 Zn CB C:His281 3.68 Zn ND1 C:His281 2.21 Zn CD2 C:His281 4.37 Zn CE1 C:His281 3.07 Zn CG C:His281 3.29 Zn CB C:Asp327 3.64 Zn OD2 C:Asp327 2.13 Zn OD1 C:Asp327 4.27 Zn CG C:Asp327 3.18 Zn O2 C:Rns2003 2.61 Zn C4 C:Rns2003 4.51 Zn C1 C:Rns2003 4.75 Zn C3 C:Rns2003 3.57 Zn O3 C:Rns2003 2.71 Zn O4 C:Rns2003 4.22 Zn C2 C:Rns2003 3.31 Zn ZN C:Zn506 4.51 Zn O C:Hoh2302 3.82 interactive model: Zinc binding site 6 out of 8 in 2i56 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Zinc in the PDB 2i56. 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: Glu219, C: Lys221, C: Asp254, C: His257, C: Asp289, C: Asp291, C: Asp327, D: Arg65, D: Phe66, C: Rns2003, C: Zn505, C: Hoh2302, conact list: Atom Atom Distance (A) Zn OE2 C:Glu219 4.93 Zn CE C:Lys221 4.03 Zn CD C:Lys221 4.51 Zn NZ C:Lys221 3.83 Zn OD2 C:Asp254 3.98 Zn OD1 C:Asp254 4.48 Zn CG C:Asp254 4.41 Zn NE2 C:His257 2.12 Zn ND1 C:His257 4.20 Zn CD2 C:His257 3.12 Zn CE1 C:His257 3.08 Zn CG C:His257 4.26 Zn CB C:Asp289 4.21 Zn OD2 C:Asp289 2.20 Zn OD1 C:Asp289 2.76 Zn CG C:Asp289 2.78 Zn OD2 C:Asp291 3.85 Zn OD1 C:Asp291 3.49 Zn CG C:Asp291 4.09 Zn OD2 C:Asp327 4.65 Zn NH1 D:Arg65 4.44 Zn CZ D:Phe66 4.93 Zn O2 C:Rns2003 2.55 Zn C1 C:Rns2003 3.21 Zn O1 C:Rns2003 2.46 Zn C3 C:Rns2003 4.71 Zn O4 C:Rns2003 4.46 Zn C2 C:Rns2003 3.32 Zn ZN C:Zn505 4.51 Zn O C:Hoh2302 1.91 interactive model: Zinc binding site 7 out of 8 in 2i56 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Zinc in the PDB 2i56. 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: Glu219, D: Leu252, D: Asp254, D: His257, D: His281, D: Asp327, D: Rns2004, D: Zn508, D: Hoh2358, conact list: Atom Atom Distance (A) Zn OE1 D:Glu219 3.31 Zn OE2 D:Glu219 2.13 Zn CD D:Glu219 3.07 Zn CG D:Glu219 4.46 Zn CD2 D:Leu252 4.83 Zn CB D:Asp254 3.75 Zn OD2 D:Asp254 2.20 Zn OD1 D:Asp254 4.38 Zn CG D:Asp254 3.29 Zn CA D:Asp254 4.99 Zn NE2 D:His257 4.13 Zn ND1 D:His257 4.73 Zn CE1 D:His257 3.81 Zn NE2 D:His281 4.10 Zn CB D:His281 3.54 Zn ND1 D:His281 2.05 Zn CD2 D:His281 4.21 Zn CE1 D:His281 2.95 Zn CG D:His281 3.13 Zn CB D:Asp327 3.73 Zn OD2 D:Asp327 2.13 Zn OD1 D:Asp327 4.32 Zn CG D:Asp327 3.24 Zn O2 D:Rns2004 2.40 Zn C4 D:Rns2004 4.37 Zn C1 D:Rns2004 4.65 Zn C3 D:Rns2004 3.46 Zn O3 D:Rns2004 2.59 Zn O4 D:Rns2004 4.13 Zn C2 D:Rns2004 3.24 Zn ZN D:Zn508 4.28 Zn O D:Hoh2358 4.04 interactive model: Zinc binding site 8 out of 8 in 2i56 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Zinc in the PDB 2i56. 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: Arg65, C: Phe66, D: Glu219, D: Lys221, D: Asp254, D: His257, D: Asp289, D: Asp291, D: Asp327, D: Rns2004, D: Zn507, D: Hoh2358, conact list: Atom Atom Distance (A) Zn NH2 C:Arg65 4.58 Zn CZ C:Phe66 4.87 Zn OE2 D:Glu219 4.98 Zn CE D:Lys221 4.02 Zn CD D:Lys221 4.38 Zn NZ D:Lys221 3.78 Zn OD2 D:Asp254 3.87 Zn OD1 D:Asp254 4.65 Zn CG D:Asp254 4.40 Zn NE2 D:His257 2.05 Zn ND1 D:His257 4.05 Zn CD2 D:His257 3.13 Zn CE1 D:His257 2.90 Zn CG D:His257 4.19 Zn CB D:Asp289 4.30 Zn OD2 D:Asp289 2.20 Zn OD1 D:Asp289 3.03 Zn CG D:Asp289 2.91 Zn OD2 D:Asp291 4.14 Zn OD1 D:Asp291 3.89 Zn CG D:Asp291 4.45 Zn OD2 D:Asp327 4.33 Zn O2 D:Rns2004 2.31 Zn C4 D:Rns2004 4.73 Zn C1 D:Rns2004 2.82 Zn O1 D:Rns2004 2.15 Zn C3 D:Rns2004 4.38 Zn O3 D:Rns2004 4.98 Zn O4 D:Rns2004 4.07 Zn C2 D:Rns2004 3.00 Zn ZN D:Zn507 4.28 Zn O D:Hoh2358 1.98 interactive model: