Copper in the structure of CU2+-Bound Form of Pseudomonas Stutzeri L-Rhamnose Isomerase (pdb 3iud)

The binding sites of Copper atom in the structure of CU2+-Bound Form of Pseudomonas Stutzeri L-Rhamnose Isomerase (pdb code 3iud). This binding sites where shown with 5.0 Angstroms radius around Copper atom. The 3iud structure was solved by H.YOSHIDA, M.YAMAJI, T.ISHII, K.IZUMORI, S.KAMITORI, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 42.0-2.4 Space group P1211 a (A) 74.687 b (A) 104.629 c (A) 114.979 alpha (°) 90.00 beta (°) 108.18 gamma (°) 90.00 Rfactor (%) 17.7 Rfree (%) 23.8 Copper Binding Sites: Copper binding site 1 out of 8 in 3iud Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Copper in the PDB 3iud. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Copper atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Glu219, A: Asp254, A: His257, A: His281, A: Asp327, A: Cu502, A: Hoh549, conact list: Atom Atom Distance (A) Cu OE1 A:Glu219 3.33 Cu OE2 A:Glu219 2.42 Cu CD A:Glu219 3.20 Cu CG A:Glu219 4.57 Cu CB A:Asp254 3.82 Cu OD2 A:Asp254 2.47 Cu OD1 A:Asp254 4.60 Cu CG A:Asp254 3.49 Cu NE2 A:His257 4.35 Cu ND1 A:His257 4.90 Cu CE1 A:His257 4.02 Cu NE2 A:His281 4.37 Cu CB A:His281 3.65 Cu ND1 A:His281 2.30 Cu CD2 A:His281 4.45 Cu CE1 A:His281 3.21 Cu CG A:His281 3.34 Cu CB A:Asp327 3.52 Cu OD2 A:Asp327 2.67 Cu OD1 A:Asp327 4.26 Cu CG A:Asp327 3.28 Cu CU A:Cu502 4.23 Cu O A:Hoh549 3.39 interactive model: Copper binding site 2 out of 8 in 3iud Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Copper in the PDB 3iud. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Copper atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Glu219, A: Lys221, A: Asp254, A: His257, A: Asn283, A: Asp289, A: Asp291, A: Asp327, B: Arg65, A: Cu501, A: Hoh454, A: Hoh524, A: Hoh549, A: Hoh572, conact list: Atom Atom Distance (A) Cu OE2 A:Glu219 4.80 Cu CE A:Lys221 4.70 Cu NZ A:Lys221 4.82 Cu OD2 A:Asp254 3.48 Cu OD1 A:Asp254 4.09 Cu CG A:Asp254 3.98 Cu NE2 A:His257 2.33 Cu ND1 A:His257 4.42 Cu CD2 A:His257 3.27 Cu CE1 A:His257 3.31 Cu CG A:His257 4.43 Cu ND2 A:Asn283 4.76 Cu CB A:Asp289 4.40 Cu OD2 A:Asp289 2.40 Cu OD1 A:Asp289 2.82 Cu CG A:Asp289 2.93 Cu OD2 A:Asp291 3.86 Cu OD1 A:Asp291 2.98 Cu CG A:Asp291 3.79 Cu OD2 A:Asp327 4.93 Cu OD1 A:Asp327 4.64 Cu CG A:Asp327 4.77 Cu NH2 B:Arg65 4.86 Cu CU A:Cu501 4.23 Cu O A:Hoh454 2.93 Cu O A:Hoh524 2.49 Cu O A:Hoh549 4.11 Cu O A:Hoh572 4.91 interactive model: Copper binding site 3 out of 8 in 3iud Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Copper in the PDB 3iud. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Copper 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: Cu504, B: Hoh539, B: Hoh675, conact list: Atom Atom Distance (A) Cu OE1 B:Glu219 3.11 Cu OE2 B:Glu219 2.75 Cu CD B:Glu219 3.18 Cu CG B:Glu219 4.50 Cu CB B:Asp254 3.86 Cu OD2 B:Asp254 2.42 Cu OD1 B:Asp254 4.60 Cu CG B:Asp254 3.49 Cu CA B:Asp254 4.95 Cu NE2 B:His257 4.65 Cu ND1 B:His257 4.93 Cu CE1 B:His257 4.14 Cu NE2 B:His281 4.57 Cu CB B:His281 3.55 Cu ND1 B:His281 2.47 Cu CD2 B:His281 4.55 Cu CE1 B:His281 3.47 Cu CG B:His281 3.38 Cu CB B:Asp327 3.60 Cu OD2 B:Asp327 2.32 Cu OD1 B:Asp327 4.39 Cu CG B:Asp327 3.28 Cu CU B:Cu504 4.83 Cu O B:Hoh539 3.41 Cu O B:Hoh675 3.86 interactive model: Copper binding site 4 out of 8 in 3iud Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Copper in the PDB 3iud. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Copper atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Arg65, B: Lys221, B: Asp254, B: His257, B: Asp289, B: Asp291, B: Asp327, B: Cu503, B: Hoh539, B: Hoh675, conact list: Atom Atom Distance (A) Cu NH2 A:Arg65 4.77 Cu CE B:Lys221 4.27 Cu CD B:Lys221 4.76 Cu NZ B:Lys221 4.35 Cu OD2 B:Asp254 3.81 Cu OD1 B:Asp254 4.29 Cu CG B:Asp254 4.25 Cu NE2 B:His257 2.13 Cu ND1 B:His257 4.20 Cu CD2 B:His257 3.17 Cu CE1 B:His257 3.05 Cu CG B:His257 4.28 Cu CB B:Asp289 4.32 Cu OD2 B:Asp289 2.30 Cu OD1 B:Asp289 2.82 Cu CG B:Asp289 2.87 Cu OD2 B:Asp291 3.78 Cu OD1 B:Asp291 3.15 Cu CG B:Asp291 3.86 Cu OD2 B:Asp327 4.88 Cu CU B:Cu503 4.83 Cu O B:Hoh539 3.42 Cu O B:Hoh675 2.12 interactive model: Copper binding site 5 out of 8 in 3iud Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Copper in the PDB 3iud. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Copper 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: Cu506, C: Hoh472, C: Hoh533, conact list: Atom Atom Distance (A) Cu OE1 C:Glu219 3.22 Cu OE2 C:Glu219 3.14 Cu CD C:Glu219 3.49 Cu CG C:Glu219 4.86 Cu CB C:Asp254 3.93 Cu OD2 C:Asp254 2.55 Cu OD1 C:Asp254 4.67 Cu CG C:Asp254 3.57 Cu NE2 C:His257 4.74 Cu CE1 C:His257 4.24 Cu NE2 C:His281 4.68 Cu CB C:His281 3.54 Cu ND1 C:His281 2.56 Cu CD2 C:His281 4.63 Cu CE1 C:His281 3.58 Cu CG C:His281 3.43 Cu CB C:Asp327 3.41 Cu OD2 C:Asp327 2.57 Cu OD1 C:Asp327 4.26 Cu CG C:Asp327 3.22 Cu CA C:Asp327 4.93 Cu CU C:Cu506 4.73 Cu O C:Hoh472 3.90 Cu O C:Hoh533 4.60 interactive model: Copper binding site 6 out of 8 in 3iud Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Copper in the PDB 3iud. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Copper atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: C: Lys221, C: Asp254, C: His257, C: Asp289, C: Asp291, D: Arg65, C: Cu505, C: Hoh472, conact list: Atom Atom Distance (A) Cu CE C:Lys221 4.44 Cu CD C:Lys221 4.76 Cu NZ C:Lys221 4.43 Cu OD2 C:Asp254 3.89 Cu OD1 C:Asp254 4.07 Cu CG C:Asp254 4.19 Cu NE2 C:His257 2.10 Cu ND1 C:His257 4.17 Cu CD2 C:His257 3.14 Cu CE1 C:His257 3.03 Cu CG C:His257 4.25 Cu CB C:Asp289 4.22 Cu OD2 C:Asp289 2.50 Cu OD1 C:Asp289 2.44 Cu CG C:Asp289 2.76 Cu OD2 C:Asp291 3.91 Cu OD1 C:Asp291 3.01 Cu CG C:Asp291 3.85 Cu NH1 D:Arg65 4.60 Cu CU C:Cu505 4.73 Cu O C:Hoh472 1.82 interactive model: Copper binding site 7 out of 8 in 3iud Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Copper in the PDB 3iud. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Copper atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: D: Glu219, D: Asp254, D: His257, D: His281, D: Asp327, D: Cu508, D: Hoh577, conact list: Atom Atom Distance (A) Cu OE1 D:Glu219 3.36 Cu OE2 D:Glu219 2.57 Cu CD D:Glu219 3.34 Cu CG D:Glu219 4.79 Cu CB D:Asp254 3.98 Cu OD2 D:Asp254 2.46 Cu OD1 D:Asp254 4.63 Cu CG D:Asp254 3.54 Cu NE2 D:His257 4.52 Cu ND1 D:His257 4.77 Cu CE1 D:His257 3.92 Cu NE2 D:His281 4.34 Cu CB D:His281 3.61 Cu ND1 D:His281 2.27 Cu CD2 D:His281 4.41 Cu CE1 D:His281 3.20 Cu CG D:His281 3.29 Cu CB D:Asp327 3.48 Cu OD2 D:Asp327 2.62 Cu OD1 D:Asp327 4.12 Cu CG D:Asp327 3.19 Cu CU D:Cu508 4.30 Cu O D:Hoh577 4.70 interactive model: Copper binding site 8 out of 8 in 3iud Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Copper in the PDB 3iud. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Copper atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: C: Arg65, D: Lys221, D: Asp254, D: His257, D: Asn283, D: Asp289, D: Asp291, D: Asp327, D: Cu507, D: Hoh487, D: Hoh500, conact list: Atom Atom Distance (A) Cu NH2 C:Arg65 4.93 Cu CE D:Lys221 4.90 Cu NZ D:Lys221 4.60 Cu CB D:Asp254 4.96 Cu OD2 D:Asp254 3.36 Cu OD1 D:Asp254 3.78 Cu CG D:Asp254 3.79 Cu NE2 D:His257 2.14 Cu ND1 D:His257 4.16 Cu CD2 D:His257 3.11 Cu CE1 D:His257 3.07 Cu CG D:His257 4.21 Cu ND2 D:Asn283 4.48 Cu CB D:Asp289 4.22 Cu OD2 D:Asp289 2.27 Cu OD1 D:Asp289 2.52 Cu CG D:Asp289 2.72 Cu OD2 D:Asp291 3.76 Cu OD1 D:Asp291 2.75 Cu CG D:Asp291 3.63 Cu OD1 D:Asp327 4.74 Cu CG D:Asp327 4.90 Cu CU D:Cu507 4.30 Cu O D:Hoh487 3.16 Cu O D:Hoh500 4.80 interactive model: