Bromine in the structure of Sars Coronavirus Papain-Like Protease: Structure of A Viral Deubiquitinating Enzyme (pdb 2fe8)

The binding sites of Bromine atom in the structure of Sars Coronavirus Papain-Like Protease: Structure of A Viral Deubiquitinating Enzyme (pdb code 2fe8). This binding sites where shown with 5.0 Angstroms radius around Bromine atom. The 2fe8 structure was solved by K.RATIA, B.D.SANTARSIERO, A.D.MESECAR, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 20.0-1.9 Space group C121 a (A) 142.872 b (A) 103.065 c (A) 91.728 alpha (°) 90.00 beta (°) 111.15 gamma (°) 90.00 Rfactor (%) 20.1 Rfree (%) 22.9 Bromine Binding Sites: Bromine binding site 1 out of 9 in 2fe8 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Bromine in the PDB 2fe8. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Bromine atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Thr258, A: Phe259, A: Leu260, A: Phe305, A: Tyr306, A: Lys307, A: Hoh468, conact list: Atom Atom Distance (A) Br O A:Thr258 4.71 Br C A:Thr258 4.67 Br O A:Phe259 4.16 Br N A:Phe259 4.21 Br C A:Phe259 3.62 Br CA A:Phe259 3.74 Br N A:Leu260 3.63 Br CB A:Leu260 4.23 Br CA A:Leu260 4.25 Br O A:Phe305 4.90 Br CB A:Tyr306 4.18 Br CD1 A:Tyr306 4.37 Br C A:Tyr306 4.08 Br CG A:Tyr306 4.74 Br CA A:Tyr306 3.82 Br O A:Lys307 4.53 Br N A:Lys307 3.35 Br CB A:Lys307 4.25 Br C A:Lys307 4.95 Br CA A:Lys307 4.34 Br O A:Hoh468 3.35 interactive model: Bromine binding site 2 out of 9 in 2fe8 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Bromine in the PDB 2fe8. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Bromine atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Val126, A: Lys127, A: Phe128, A: Gln134, A: Tyr137, conact list: Atom Atom Distance (A) Br O A:Val126 4.72 Br N A:Lys127 4.92 Br CB A:Lys127 3.91 Br C A:Lys127 3.94 Br CG A:Lys127 4.93 Br CA A:Lys127 3.65 Br O A:Phe128 4.08 Br N A:Phe128 3.21 Br CB A:Phe128 4.28 Br CD2 A:Phe128 4.11 Br C A:Phe128 4.64 Br CG A:Phe128 4.67 Br CA A:Phe128 4.21 Br O A:Gln134 4.16 Br N A:Gln134 4.52 Br CB A:Gln134 3.55 Br CD A:Gln134 4.87 Br C A:Gln134 4.26 Br CG A:Gln134 4.06 Br CA A:Gln134 3.43 Br CB A:Tyr137 4.95 Br CD2 A:Tyr137 4.53 interactive model: Bromine binding site 3 out of 9 in 2fe8 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Bromine in the PDB 2fe8. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Bromine atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Arg83, A: Ser86, A: Ala87, A: His90, A: Thr159, A: Val160, A: Hoh362, A: Hoh413, conact list: Atom Atom Distance (A) Br O A:Arg83 4.95 Br O A:Ser86 4.03 Br CB A:Ser86 4.27 Br OG A:Ser86 3.46 Br C A:Ser86 3.97 Br CA A:Ser86 4.81 Br N A:Ala87 3.80 Br CB A:Ala87 4.09 Br CA A:Ala87 3.70 Br NE2 A:His90 4.68 Br CD2 A:His90 4.17 Br CB A:Thr159 3.84 Br CG2 A:Thr159 4.28 Br C A:Thr159 4.13 Br CA A:Thr159 3.90 Br O A:Val160 4.97 Br N A:Val160 3.34 Br CB A:Val160 3.93 Br CG2 A:Val160 3.83 Br CA A:Val160 4.26 Br O A:Hoh362 3.18 Br O A:Hoh413 4.39 interactive model: Bromine binding site 4 out of 9 in 2fe8 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Bromine in the PDB 2fe8. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Bromine atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: B: Thr258, B: Phe259, B: Leu260, B: Phe305, B: Tyr306, B: Lys307, conact list: Atom Atom Distance (A) Br O B:Thr258 4.47 Br C B:Thr258 4.44 Br O B:Phe259 4.13 Br N B:Phe259 4.11 Br C B:Phe259 3.63 Br CA B:Phe259 3.72 Br N B:Leu260 3.67 Br CB B:Leu260 4.41 Br CA B:Leu260 4.34 Br O B:Phe305 4.90 Br CB B:Tyr306 4.17 Br CD1 B:Tyr306 4.37 Br C B:Tyr306 4.09 Br CG B:Tyr306 4.73 Br CA B:Tyr306 3.88 Br O B:Lys307 4.44 Br N B:Lys307 3.29 Br CB B:Lys307 3.99 Br C B:Lys307 4.82 Br CA B:Lys307 4.21 interactive model: Bromine binding site 5 out of 9 in 2fe8 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Bromine in the PDB 2fe8. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Bromine atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: B: Val126, B: Lys127, B: Phe128, B: Gln134, B: Tyr137, B: Hoh373, B: Hoh486, conact list: Atom Atom Distance (A) Br O B:Val126 4.58 Br N B:Lys127 4.90 Br CB B:Lys127 3.81 Br C B:Lys127 3.97 Br CA B:Lys127 3.62 Br O B:Phe128 4.29 Br N B:Phe128 3.29 Br CB B:Phe128 4.34 Br CD2 B:Phe128 4.17 Br C B:Phe128 4.78 Br CG B:Phe128 4.74 Br CA B:Phe128 4.29 Br O B:Gln134 4.52 Br N B:Gln134 4.75 Br CB B:Gln134 3.96 Br CD B:Gln134 4.90 Br C B:Gln134 4.69 Br CG B:Gln134 3.97 Br CA B:Gln134 3.80 Br CB B:Tyr137 4.94 Br CD2 B:Tyr137 4.35 Br O B:Hoh373 3.01 Br O B:Hoh486 4.90 interactive model: Bromine binding site 6 out of 9 in 2fe8 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Bromine in the PDB 2fe8. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Bromine atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: B: Arg83, B: Ser86, B: Ala87, B: His90, B: Thr159, B: Val160, B: Hoh395, B: Hoh438, conact list: Atom Atom Distance (A) Br O B:Arg83 4.89 Br O B:Ser86 3.94 Br CB B:Ser86 4.28 Br OG B:Ser86 3.60 Br C B:Ser86 3.92 Br CA B:Ser86 4.79 Br N B:Ala87 3.75 Br C B:Ala87 4.99 Br CB B:Ala87 4.06 Br CA B:Ala87 3.64 Br NE2 B:His90 4.97 Br CD2 B:His90 4.40 Br CB B:Thr159 3.81 Br CG2 B:Thr159 4.20 Br C B:Thr159 4.19 Br CA B:Thr159 3.94 Br N B:Val160 3.40 Br CB B:Val160 3.92 Br CG2 B:Val160 3.77 Br CA B:Val160 4.28 Br O B:Hoh395 3.01 Br O B:Hoh438 4.19 interactive model: Bromine binding site 7 out of 9 in 2fe8 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Bromine in the PDB 2fe8. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Bromine atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: C: Thr258, C: Phe259, C: Leu260, C: Phe305, C: Tyr306, C: Lys307, C: Hoh403, conact list: Atom Atom Distance (A) Br O C:Thr258 4.35 Br C C:Thr258 4.42 Br O C:Phe259 4.22 Br N C:Phe259 4.14 Br C C:Phe259 3.67 Br CA C:Phe259 3.72 Br N C:Leu260 3.70 Br CB C:Leu260 4.54 Br CG C:Leu260 4.49 Br CA C:Leu260 4.42 Br O C:Phe305 4.88 Br CB C:Tyr306 4.18 Br CD1 C:Tyr306 4.37 Br C C:Tyr306 4.13 Br CG C:Tyr306 4.74 Br CA C:Tyr306 3.87 Br O C:Lys307 4.67 Br N C:Lys307 3.36 Br CB C:Lys307 4.16 Br CG C:Lys307 4.70 Br CA C:Lys307 4.34 Br O C:Hoh403 3.47 interactive model: Bromine binding site 8 out of 9 in 2fe8 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Bromine in the PDB 2fe8. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Bromine atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: C: Val126, C: Lys127, C: Phe128, C: Gln134, C: Tyr137, C: Hoh336, C: Hoh412, conact list: Atom Atom Distance (A) Br O C:Val126 4.42 Br N C:Lys127 4.91 Br CB C:Lys127 4.37 Br CD C:Lys127 4.10 Br C C:Lys127 4.11 Br CG C:Lys127 4.89 Br CA C:Lys127 3.79 Br O C:Phe128 4.55 Br N C:Phe128 3.39 Br CB C:Phe128 4.38 Br CD2 C:Phe128 4.14 Br C C:Phe128 4.99 Br CG C:Phe128 4.71 Br CA C:Phe128 4.41 Br O C:Gln134 4.61 Br N C:Gln134 4.79 Br CB C:Gln134 4.18 Br CD C:Gln134 4.96 Br C C:Gln134 4.79 Br CG C:Gln134 3.73 Br CA C:Gln134 3.92 Br CB C:Tyr137 4.88 Br CE2 C:Tyr137 4.95 Br CD2 C:Tyr137 4.16 Br O C:Hoh336 3.17 Br O C:Hoh412 3.15 interactive model: Bromine binding site 9 out of 9 in 2fe8 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 9 of Bromine in the PDB 2fe8. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Bromine atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: C: Arg83, C: Ser86, C: Ala87, C: His90, C: Thr159, C: Val160, C: Hoh328, C: Hoh383, C: Hoh452, conact list: Atom Atom Distance (A) Br O C:Arg83 4.95 Br O C:Ser86 4.08 Br CB C:Ser86 4.33 Br C C:Ser86 4.00 Br CA C:Ser86 4.86 Br N C:Ala87 3.73 Br C C:Ala87 4.95 Br CB C:Ala87 3.98 Br CA C:Ala87 3.60 Br ND1 C:His90 4.27 Br CE1 C:His90 4.60 Br CB C:Thr159 3.84 Br CG2 C:Thr159 4.22 Br C C:Thr159 4.07 Br CA C:Thr159 3.87 Br O C:Val160 4.82 Br N C:Val160 3.26 Br CB C:Val160 3.84 Br CG2 C:Val160 3.78 Br CA C:Val160 4.16 Br O C:Hoh328 3.12 Br O C:Hoh383 4.39 Br O C:Hoh452 3.79 interactive model: