Cadmium in the structure of Crystal Structure Hp-Nap From Strain YS29 Cadmium Loaded (Cocrystallization 50MM) (pdb 4evd)

The binding sites of Cadmium atom in the structure of Crystal Structure Hp-Nap From Strain YS29 Cadmium Loaded (Cocrystallization 50MM) (pdb code 4evd). This binding sites where shown with 5.0 Angstroms radius around Cadmium atom. The 4evd structure was solved by H.YOKOYAMA, O.TSURUTA, N.AKAO, S.FUJII, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 19.6-2.2 Space group F432 a (A) 187.412 b (A) 187.412 c (A) 187.412 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 21.3 Rfree (%) 23.7 Cadmium Binding Sites: Cadmium binding site 1 out of 16 in 4evd Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Cadmium in the PDB 4evd. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Cadmium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: His25, A: Trp26, A: His37, A: Glu41, A: Tyr44, A: Cd202, A: Hoh301, A: Hoh302, A: Hoh303, A: Hoh305, A: Hoh381, conact list: Atom Atom Distance (A) Cd NE2 A:His25 2.31 Cd ND1 A:His25 4.43 Cd CD2 A:His25 3.19 Cd CE1 A:His25 3.35 Cd CG A:His25 4.39 Cd CD1 A:Trp26 4.77 Cd NE1 A:Trp26 4.69 Cd NE2 A:His37 4.05 Cd CE1 A:His37 4.17 Cd OE1 A:Glu41 4.79 Cd OH A:Tyr44 4.22 Cd CD A:Cd202 4.29 Cd O A:Hoh301 2.69 Cd O A:Hoh302 2.49 Cd O A:Hoh303 3.87 Cd O A:Hoh305 4.46 Cd O A:Hoh381 3.41 interactive model: Cadmium binding site 2 out of 16 in 4evd Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Cadmium in the PDB 4evd. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Cadmium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: His25, A: His37, A: Glu41, A: Cd201, A: Hoh301, A: Hoh303, A: Hoh304, A: Hoh305, A: Hoh381, conact list: Atom Atom Distance (A) Cd NE2 A:His25 4.89 Cd CE1 A:His25 4.82 Cd NE2 A:His37 2.51 Cd ND1 A:His37 4.63 Cd CD2 A:His37 3.03 Cd CE1 A:His37 3.73 Cd CG A:His37 4.33 Cd OE1 A:Glu41 4.87 Cd CD A:Cd201 4.29 Cd O A:Hoh301 2.19 Cd O A:Hoh303 2.18 Cd O A:Hoh304 2.59 Cd O A:Hoh305 2.45 Cd O A:Hoh381 4.29 interactive model: Cadmium binding site 3 out of 16 in 4evd Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Cadmium in the PDB 4evd. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Cadmium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: His101, A: Glu105, A: Hoh306, A: Hoh307, A: Hoh308, A: Hoh309, conact list: Atom Atom Distance (A) Cd O A:His101 4.36 Cd NE2 A:His101 4.52 Cd CB A:His101 3.78 Cd ND1 A:His101 2.46 Cd CD2 A:His101 4.61 Cd C A:His101 4.64 Cd CE1 A:His101 3.36 Cd CG A:His101 3.49 Cd CA A:His101 4.11 Cd OE1 A:Glu105 4.37 Cd O A:Hoh306 1.98 Cd O A:Hoh307 2.40 Cd O A:Hoh308 1.97 Cd O A:Hoh309 2.26 interactive model: Cadmium binding site 4 out of 16 in 4evd Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Cadmium in the PDB 4evd. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Cadmium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Lys93, A: Glu94, A: Glu97, A: Cd215, A: Hoh310, A: Hoh311, A: Hoh312, A: Hoh335, A: Hoh336, A: Hoh337, A: Hoh376, A: Hoh384, conact list: Atom Atom Distance (A) Cd CG A:Lys93 4.66 Cd OE1 A:Glu94 2.42 Cd OE2 A:Glu94 2.98 Cd CD A:Glu94 3.05 Cd CG A:Glu94 4.51 Cd CA A:Glu94 4.89 Cd OE1 A:Glu97 2.56 Cd OE2 A:Glu97 2.48 Cd CD A:Glu97 2.86 Cd CG A:Glu97 4.37 Cd CD A:Cd215 3.11 Cd O A:Hoh310 1.99 Cd O A:Hoh311 2.46 Cd O A:Hoh312 2.70 Cd O A:Hoh335 4.95 Cd O A:Hoh336 4.74 Cd O A:Hoh337 4.92 Cd O A:Hoh376 4.91 Cd O A:Hoh384 4.43 interactive model: Cadmium binding site 5 out of 16 in 4evd Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Cadmium in the PDB 4evd. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Cadmium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Asp49, A: Asp53, A: Hoh313, A: Hoh314, A: Hoh315, A: Hoh356, A: Hoh373, A: Hoh383, conact list: Atom Atom Distance (A) Cd O A:Asp49 4.45 Cd CB A:Asp49 4.32 Cd OD2 A:Asp49 2.37 Cd C A:Asp49 4.86 Cd OD1 A:Asp49 2.55 Cd CG A:Asp49 2.80 Cd CB A:Asp53 4.60 Cd OD2 A:Asp53 2.35 Cd OD1 A:Asp53 3.30 Cd CG A:Asp53 3.18 Cd O A:Hoh313 1.79 Cd O A:Hoh314 2.54 Cd O A:Hoh315 1.78 Cd O A:Hoh356 4.21 Cd O A:Hoh373 3.89 Cd O A:Hoh383 3.98 interactive model: Cadmium binding site 6 out of 16 in 4evd Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Cadmium in the PDB 4evd. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Cadmium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Glu5, A: His9, A: Hoh316, A: Hoh317, A: Hoh318, conact list: Atom Atom Distance (A) Cd CB A:Glu5 4.86 Cd OE2 A:Glu5 3.47 Cd CD A:Glu5 4.53 Cd NE2 A:His9 2.36 Cd ND1 A:His9 4.39 Cd CD2 A:His9 3.40 Cd CE1 A:His9 3.23 Cd CG A:His9 4.50 Cd O A:Hoh316 1.98 Cd O A:Hoh317 2.01 Cd O A:Hoh318 2.65 interactive model: Cadmium binding site 7 out of 16 in 4evd Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Cadmium in the PDB 4evd. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Cadmium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Ala144, A: Hoh319, A: Hoh320, A: Hoh359, conact list: Atom Atom Distance (A) Cd O A:Ala144 2.38 Cd C A:Ala144 2.82 Cd CA A:Ala144 4.31 Cd OXT A:Ala144 2.48 Cd O A:Hoh319 2.07 Cd O A:Hoh320 2.15 Cd O A:Hoh359 3.99 interactive model: Cadmium binding site 8 out of 16 in 4evd Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Cadmium in the PDB 4evd. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Cadmium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Glu41, A: Glu42, A: Glu45, A: Hoh321, A: Hoh322, A: Hoh368, conact list: Atom Atom Distance (A) Cd OE2 A:Glu41 2.89 Cd CD A:Glu41 3.87 Cd CG A:Glu41 4.07 Cd OE1 A:Glu42 3.59 Cd OE2 A:Glu42 2.57 Cd CD A:Glu42 3.44 Cd CG A:Glu42 4.83 Cd OE1 A:Glu45 2.51 Cd OE2 A:Glu45 2.47 Cd CD A:Glu45 2.83 Cd CG A:Glu45 4.34 Cd O A:Hoh321 1.96 Cd O A:Hoh322 1.75 Cd O A:Hoh368 4.82 interactive model: Cadmium binding site 9 out of 16 in 4evd Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 9 of Cadmium in the PDB 4evd. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Cadmium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Arg77, A: Glu105, A: Glu108, A: Hoh323, A: Hoh324, A: Hoh325, A: Hoh385, conact list: Atom Atom Distance (A) Cd NH2 A:Arg77 4.89 Cd NH1 A:Arg77 4.26 Cd OE1 A:Glu105 2.51 Cd OE2 A:Glu105 2.68 Cd CD A:Glu105 2.94 Cd CG A:Glu105 4.44 Cd CA A:Glu105 4.95 Cd OE1 A:Glu108 2.10 Cd CB A:Glu108 4.68 Cd OE2 A:Glu108 3.14 Cd CD A:Glu108 2.94 Cd CG A:Glu108 4.33 Cd O A:Hoh323 1.76 Cd O A:Hoh324 1.90 Cd O A:Hoh325 2.15 Cd O A:Hoh385 4.79 interactive model: Cadmium binding site 10 out of 16 in 4evd Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 10 of Cadmium in the PDB 4evd. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Cadmium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Phe86, A: His87, A: Asp90, A: Hoh326, A: Hoh327, A: Hoh328, conact list: Atom Atom Distance (A) Cd C A:Phe86 4.66 Cd CA A:Phe86 4.92 Cd NE2 A:His87 4.92 Cd N A:His87 3.77 Cd CB A:His87 3.64 Cd ND1 A:His87 2.91 Cd CD2 A:His87 4.80 Cd CE1 A:His87 3.91 Cd CG A:His87 3.63 Cd CA A:His87 4.32 Cd CB A:Asp90 4.77 Cd OD2 A:Asp90 2.47 Cd OD1 A:Asp90 3.53 Cd CG A:Asp90 3.37 Cd O A:Hoh326 2.34 Cd O A:Hoh327 2.15 Cd O A:Hoh328 2.15 interactive model: Cadmium binding site 11 out of 16 in 4evd Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 11 of Cadmium in the PDB 4evd. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Cadmium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Phe4, A: Gly62, A: His63, A: His64, A: Hoh329, conact list: Atom Atom Distance (A) Cd CZ A:Phe4 4.76 Cd CE1 A:Phe4 4.71 Cd O A:Gly62 4.92 Cd NE2 A:His63 4.29 Cd CB A:His63 3.89 Cd ND1 A:His63 2.31 Cd CD2 A:His63 4.48 Cd CE1 A:His63 3.08 Cd CG A:His63 3.45 Cd CA A:His63 4.23 Cd N A:His64 4.83 Cd O A:Hoh329 2.46 interactive model: Cadmium binding site 12 out of 16 in 4evd Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 12 of Cadmium in the PDB 4evd. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Cadmium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Lys2, A: Leu61, A: His63, A: Hoh330, A: Hoh331, A: Hoh380, conact list: Atom Atom Distance (A) Cd CE A:Lys2 4.30 Cd NZ A:Lys2 4.78 Cd O A:Leu61 4.48 Cd NE2 A:His63 2.46 Cd ND1 A:His63 4.26 Cd CD2 A:His63 3.64 Cd CE1 A:His63 3.04 Cd CG A:His63 4.58 Cd O A:Hoh330 2.00 Cd O A:Hoh331 1.81 Cd O A:Hoh380 4.23 interactive model: Cadmium binding site 13 out of 16 in 4evd Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 13 of Cadmium in the PDB 4evd. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Cadmium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: His64, A: Cd214, A: Hoh332, A: Hoh333, A: Hoh334, conact list: Atom Atom Distance (A) Cd NE2 A:His64 2.67 Cd ND1 A:His64 4.79 Cd CD2 A:His64 3.51 Cd CE1 A:His64 3.71 Cd CG A:His64 4.73 Cd CD A:Cd214 4.60 Cd O A:Hoh332 2.22 Cd O A:Hoh333 2.29 Cd O A:Hoh334 1.95 interactive model: Cadmium binding site 14 out of 16 in 4evd Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 14 of Cadmium in the PDB 4evd. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Cadmium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: His64, A: Cd213, A: Hoh332, A: Hoh333, conact list: Atom Atom Distance (A) Cd NE2 A:His64 3.64 Cd ND1 A:His64 3.79 Cd CD2 A:His64 4.87 Cd CE1 A:His64 2.80 Cd CG A:His64 4.95 Cd CD A:Cd213 4.60 Cd O A:Hoh332 2.60 Cd O A:Hoh333 4.49 interactive model: Cadmium binding site 15 out of 16 in 4evd Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 15 of Cadmium in the PDB 4evd. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Cadmium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Lys20, A: Glu94, A: Glu97, A: Asp98, A: Cd204, A: Hoh310, A: Hoh311, A: Hoh335, A: Hoh336, A: Hoh337, A: Hoh343, conact list: Atom Atom Distance (A) Cd NZ A:Lys20 4.68 Cd O A:Glu94 4.95 Cd OE1 A:Glu94 4.10 Cd CB A:Glu94 4.96 Cd OE2 A:Glu94 2.52 Cd CD A:Glu94 3.61 Cd CG A:Glu94 4.81 Cd CA A:Glu94 4.84 Cd OE1 A:Glu97 4.35 Cd CB A:Glu97 4.35 Cd OE2 A:Glu97 2.35 Cd CD A:Glu97 3.60 Cd CG A:Glu97 4.59 Cd OD1 A:Asp98 4.97 Cd CD A:Cd204 3.11 Cd O A:Hoh310 2.02 Cd O A:Hoh311 3.98 Cd O A:Hoh335 2.40 Cd O A:Hoh336 2.33 Cd O A:Hoh337 2.20 Cd O A:Hoh343 3.91 interactive model: Cadmium binding site 16 out of 16 in 4evd Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 16 of Cadmium in the PDB 4evd. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Cadmium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Ile43, A: Glu46, A: Ser135, A: Hoh338, A: Hoh365, A: Hoh367, A: Hoh379, conact list: Atom Atom Distance (A) Cd CG1 A:Ile43 4.77 Cd OE1 A:Glu46 2.44 Cd OE2 A:Glu46 2.56 Cd CD A:Glu46 2.85 Cd CG A:Glu46 4.36 Cd OG A:Ser135 4.26 Cd O A:Hoh338 2.08 Cd O A:Hoh365 3.30 Cd O A:Hoh367 4.46 Cd O A:Hoh379 4.59 interactive model: