Mercury in the structure of Crystal Structure of Translation Elongation Factor Selb From Methanococcus Maripaludis in Complex With Gdp (pdb 4ac9)

The binding sites of Mercury atom in the structure of Crystal Structure of Translation Elongation Factor Selb From Methanococcus Maripaludis in Complex With Gdp (pdb code 4ac9). This binding sites where shown with 5.0 Angstroms radius around Mercury atom. The 4ac9 structure was solved by M.LEIBUNDGUT, C.FRICK, M.THANBICHLER, A.BOECK, N.BAN, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 20.0-3.0 Space group P3112 a (A) 146.920 b (A) 146.920 c (A) 297.480 alpha (°) 90.00 beta (°) 90.00 gamma (°) 120.00 Rfactor (%) 18.99 Rfree (%) 22.21 Mercury Binding Sites: Mercury binding site 1 out of 16 in 4ac9 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Mercury in the PDB 4ac9. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Mercury atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Leu221, A: Pro222, A: Tyr261, A: Gly263, A: Cmh264, conact list: Atom Atom Distance (A) Hg O A:Leu221 3.82 Hg C A:Leu221 4.51 Hg N A:Pro222 4.39 Hg CD A:Pro222 3.28 Hg CG A:Pro222 4.14 Hg O A:Tyr261 4.21 Hg N A:Tyr261 4.58 Hg CE2 A:Tyr261 3.66 Hg CD1 A:Tyr261 4.09 Hg CD2 A:Tyr261 4.03 Hg CZ A:Tyr261 3.50 Hg C A:Tyr261 4.69 Hg CE1 A:Tyr261 3.73 Hg CG A:Tyr261 4.24 Hg OH A:Tyr261 3.88 Hg O A:Gly263 3.71 Hg N A:Gly263 4.08 Hg C A:Gly263 3.23 Hg CA A:Gly263 3.90 Hg HG A:Cmh264 0.00 Hg CM A:Cmh264 2.10 Hg N A:Cmh264 2.86 Hg CB A:Cmh264 3.15 Hg SG A:Cmh264 2.35 Hg C A:Cmh264 4.46 Hg CA A:Cmh264 2.99 interactive model: Mercury binding site 2 out of 16 in 4ac9 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Mercury in the PDB 4ac9. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Mercury atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Ile283, A: Ile285, A: Ile333, A: Gly335, A: Asn336, A: Glu337, A: Cmh338, conact list: Atom Atom Distance (A) Hg O A:Ile283 4.09 Hg CD1 A:Ile285 3.71 Hg CG1 A:Ile285 4.31 Hg O A:Ile333 4.78 Hg CB A:Ile333 4.67 Hg CG2 A:Ile333 3.29 Hg CA A:Ile333 4.90 Hg O A:Gly335 4.47 Hg O A:Asn336 3.64 Hg C A:Asn336 3.96 Hg CA A:Asn336 4.55 Hg O A:Glu337 3.90 Hg N A:Glu337 4.41 Hg C A:Glu337 3.92 Hg CA A:Glu337 4.73 Hg HG A:Cmh338 0.00 Hg CM A:Cmh338 2.10 Hg N A:Cmh338 3.89 Hg CB A:Cmh338 3.13 Hg SG A:Cmh338 2.35 Hg CA A:Cmh338 4.01 interactive model: Mercury binding site 3 out of 16 in 4ac9 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Mercury in the PDB 4ac9. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Mercury atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Ile283, A: Tyr291, A: Pro314, A: Cmh338, A: Tyr339, A: Cmh340, conact list: Atom Atom Distance (A) Hg CB A:Ile283 4.37 Hg CD1 A:Ile283 3.50 Hg CG2 A:Ile283 4.45 Hg CG1 A:Ile283 4.45 Hg CZ A:Tyr291 4.86 Hg CE1 A:Tyr291 4.82 Hg OH A:Tyr291 3.94 Hg N A:Pro314 4.51 Hg CB A:Pro314 3.91 Hg CD A:Pro314 4.74 Hg CG A:Pro314 3.91 Hg CA A:Pro314 4.06 Hg O A:Cmh338 4.22 Hg CB A:Cmh338 4.53 Hg SG A:Cmh338 4.97 Hg C A:Cmh338 4.84 Hg O A:Tyr339 4.82 Hg C A:Tyr339 4.89 Hg HG A:Cmh340 0.00 Hg CM A:Cmh340 2.10 Hg N A:Cmh340 4.56 Hg CB A:Cmh340 3.20 Hg SG A:Cmh340 2.35 Hg CA A:Cmh340 4.10 interactive model: Mercury binding site 4 out of 16 in 4ac9 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Mercury in the PDB 4ac9. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Mercury atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Arg360, A: Leu368, A: Arg369, A: Ile370, A: Cmh371, conact list: Atom Atom Distance (A) Hg N A:Arg360 4.72 Hg CB A:Arg360 4.33 Hg O A:Leu368 4.90 Hg O A:Arg369 4.14 Hg C A:Arg369 4.32 Hg O A:Ile370 3.57 Hg N A:Ile370 4.43 Hg C A:Ile370 3.57 Hg CA A:Ile370 4.55 Hg HG A:Cmh371 0.00 Hg CM A:Cmh371 2.09 Hg N A:Cmh371 3.41 Hg CB A:Cmh371 3.15 Hg SG A:Cmh371 2.35 Hg C A:Cmh371 4.71 Hg CA A:Cmh371 3.25 interactive model: Mercury binding site 5 out of 16 in 4ac9 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Mercury in the PDB 4ac9. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Mercury atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: B: Leu221, B: Pro222, B: Ile223, B: Tyr261, B: Arg262, B: Gly263, B: Cmh264, conact list: Atom Atom Distance (A) Hg O B:Leu221 4.77 Hg N B:Pro222 4.66 Hg CD B:Pro222 3.53 Hg CG B:Pro222 3.79 Hg CD1 B:Ile223 4.83 Hg CG1 B:Ile223 4.64 Hg O B:Tyr261 3.76 Hg N B:Tyr261 4.50 Hg CB B:Tyr261 4.72 Hg CE2 B:Tyr261 3.29 Hg CD1 B:Tyr261 3.51 Hg CD2 B:Tyr261 3.56 Hg CZ B:Tyr261 3.10 Hg C B:Tyr261 4.13 Hg CE1 B:Tyr261 3.23 Hg CG B:Tyr261 3.68 Hg OH B:Tyr261 3.66 Hg CA B:Tyr261 4.64 Hg N B:Arg262 4.69 Hg C B:Arg262 4.65 Hg O B:Gly263 3.71 Hg N B:Gly263 3.74 Hg C B:Gly263 3.23 Hg CA B:Gly263 3.84 Hg HG B:Cmh264 0.00 Hg CM B:Cmh264 2.10 Hg N B:Cmh264 2.92 Hg CB B:Cmh264 3.23 Hg SG B:Cmh264 2.35 Hg C B:Cmh264 4.68 Hg CA B:Cmh264 3.17 interactive model: Mercury binding site 6 out of 16 in 4ac9 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Mercury in the PDB 4ac9. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Mercury atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: B: Ile283, B: Ile285, B: Leu329, B: Ser334, B: Asn336, B: Glu337, B: Cmh338, B: Cmh340, conact list: Atom Atom Distance (A) Hg O B:Ile283 4.08 Hg N B:Ile285 4.89 Hg CB B:Ile285 4.53 Hg CG2 B:Ile285 3.46 Hg CD2 B:Leu329 4.85 Hg O B:Ser334 4.85 Hg CB B:Ser334 4.93 Hg O B:Asn336 4.93 Hg C B:Asn336 4.90 Hg O B:Glu337 3.07 Hg N B:Glu337 4.38 Hg C B:Glu337 3.12 Hg CA B:Glu337 3.84 Hg HG B:Cmh338 0.00 Hg CM B:Cmh338 2.10 Hg N B:Cmh338 3.35 Hg CB B:Cmh338 3.14 Hg SG B:Cmh338 2.35 Hg C B:Cmh338 4.80 Hg CA B:Cmh338 3.84 Hg CM B:Cmh340 4.87 interactive model: Mercury binding site 7 out of 16 in 4ac9 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Mercury in the PDB 4ac9. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Mercury atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: B: Ile283, B: Met297, B: Val313, B: Pro314, B: Cmh338, B: Tyr339, B: Cmh340, B: Phe342, B: Ile358, B: Cmh371, conact list: Atom Atom Distance (A) Hg CB B:Ile283 4.50 Hg CG2 B:Ile283 4.50 Hg CG1 B:Ile283 4.00 Hg CE B:Met297 3.79 Hg O B:Val313 4.77 Hg C B:Val313 4.67 Hg N B:Pro314 4.22 Hg CB B:Pro314 3.95 Hg CD B:Pro314 4.46 Hg CG B:Pro314 4.70 Hg CA B:Pro314 4.01 Hg SG B:Cmh338 4.62 Hg O B:Tyr339 3.91 Hg C B:Tyr339 4.43 Hg HG B:Cmh340 0.00 Hg CM B:Cmh340 2.10 Hg N B:Cmh340 4.49 Hg CB B:Cmh340 3.21 Hg SG B:Cmh340 2.35 Hg CA B:Cmh340 3.98 Hg CZ B:Phe342 4.96 Hg CD1 B:Ile358 4.48 Hg CM B:Cmh371 3.67 interactive model: Mercury binding site 8 out of 16 in 4ac9 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Mercury in the PDB 4ac9. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Mercury atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: B: Ile285, B: Met297, B: Cmh340, B: Ile358, B: Arg360, B: Cmh371, B: Gly372, conact list: Atom Atom Distance (A) Hg CD1 B:Ile285 4.12 Hg CG1 B:Ile285 4.69 Hg CE B:Met297 4.44 Hg CM B:Cmh340 4.90 Hg CB B:Ile358 3.99 Hg CD1 B:Ile358 3.71 Hg CG2 B:Ile358 3.89 Hg CG1 B:Ile358 4.46 Hg NH1 B:Arg360 4.99 Hg O B:Cmh371 3.53 Hg HG B:Cmh371 0.00 Hg CM B:Cmh371 2.09 Hg N B:Cmh371 4.74 Hg CB B:Cmh371 3.16 Hg SG B:Cmh371 2.35 Hg C B:Cmh371 3.50 Hg CA B:Cmh371 3.90 Hg N B:Gly372 3.87 Hg CA B:Gly372 4.38 interactive model: Mercury binding site 9 out of 16 in 4ac9 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 9 of Mercury in the PDB 4ac9. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Mercury atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: C: Leu221, C: Pro222, C: Tyr261, C: Arg262, C: Gly263, C: Cmh264, conact list: Atom Atom Distance (A) Hg O C:Leu221 4.62 Hg N C:Pro222 4.62 Hg CD C:Pro222 3.43 Hg CG C:Pro222 3.81 Hg O C:Tyr261 3.65 Hg N C:Tyr261 4.44 Hg CB C:Tyr261 4.67 Hg CE2 C:Tyr261 3.71 Hg CD1 C:Tyr261 3.38 Hg CD2 C:Tyr261 3.86 Hg CZ C:Tyr261 3.37 Hg C C:Tyr261 4.08 Hg CE1 C:Tyr261 3.20 Hg CG C:Tyr261 3.71 Hg OH C:Tyr261 3.98 Hg CA C:Tyr261 4.58 Hg N C:Arg262 4.70 Hg C C:Arg262 4.59 Hg O C:Gly263 4.02 Hg N C:Gly263 3.72 Hg C C:Gly263 3.34 Hg CA C:Gly263 3.79 Hg HG C:Cmh264 0.00 Hg CM C:Cmh264 2.10 Hg N C:Cmh264 2.89 Hg CB C:Cmh264 3.24 Hg SG C:Cmh264 2.35 Hg C C:Cmh264 4.73 Hg CA C:Cmh264 3.21 interactive model: Mercury binding site 10 out of 16 in 4ac9 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 10 of Mercury in the PDB 4ac9. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Mercury atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: C: Lys316, C: Leu329, C: Asn336, C: Glu337, C: Cmh338, conact list: Atom Atom Distance (A) Hg CB C:Lys316 4.34 Hg CD1 C:Leu329 4.15 Hg CB C:Asn336 4.88 Hg O C:Glu337 2.98 Hg N C:Glu337 4.38 Hg C C:Glu337 3.60 Hg CA C:Glu337 4.66 Hg HG C:Cmh338 0.00 Hg CM C:Cmh338 2.10 Hg N C:Cmh338 3.94 Hg CB C:Cmh338 3.20 Hg SG C:Cmh338 2.35 Hg CA C:Cmh338 3.63 interactive model: Mercury binding site 11 out of 16 in 4ac9 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 11 of Mercury in the PDB 4ac9. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Mercury atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: C: Ile283, C: Leu293, C: Pro314, C: Val332, C: Cmh338, C: Tyr339, C: Cmh340, C: Cmh371, conact list: Atom Atom Distance (A) Hg O C:Ile283 4.99 Hg CB C:Ile283 3.93 Hg CD1 C:Ile283 4.76 Hg CG2 C:Ile283 3.95 Hg CG1 C:Ile283 4.69 Hg CD2 C:Leu293 4.61 Hg CB C:Pro314 4.61 Hg CA C:Pro314 4.59 Hg CG2 C:Val332 4.66 Hg CB C:Cmh338 4.75 Hg C C:Cmh338 4.81 Hg O C:Tyr339 3.64 Hg N C:Tyr339 4.66 Hg C C:Tyr339 3.82 Hg CA C:Tyr339 4.73 Hg HG C:Cmh340 0.00 Hg CM C:Cmh340 2.10 Hg N C:Cmh340 3.85 Hg CB C:Cmh340 3.20 Hg SG C:Cmh340 2.35 Hg CA C:Cmh340 3.82 Hg CM C:Cmh371 3.94 interactive model: Mercury binding site 12 out of 16 in 4ac9 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 12 of Mercury in the PDB 4ac9. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Mercury atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: C: Ile285, C: Leu293, C: Ile358, C: Cmh371, C: Gly372, conact list: Atom Atom Distance (A) Hg CD1 C:Ile285 4.93 Hg CG1 C:Ile285 4.61 Hg CB C:Leu293 4.82 Hg CD1 C:Leu293 3.26 Hg CD2 C:Leu293 3.74 Hg CG C:Leu293 4.07 Hg O C:Ile358 4.92 Hg CB C:Ile358 3.92 Hg CD1 C:Ile358 3.84 Hg CG2 C:Ile358 4.13 Hg CG1 C:Ile358 4.40 Hg O C:Cmh371 4.62 Hg HG C:Cmh371 0.00 Hg CM C:Cmh371 2.10 Hg N C:Cmh371 4.63 Hg CB C:Cmh371 3.18 Hg SG C:Cmh371 2.35 Hg C C:Cmh371 3.70 Hg CA C:Cmh371 4.00 Hg N C:Gly372 2.90 Hg C C:Gly372 4.66 Hg CA C:Gly372 3.43 interactive model: Mercury binding site 13 out of 16 in 4ac9 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 13 of Mercury in the PDB 4ac9. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Mercury atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: D: Leu221, D: Pro222, D: Tyr261, D: Gly263, D: Cmh264, conact list: Atom Atom Distance (A) Hg O D:Leu221 4.75 Hg CD D:Pro222 3.71 Hg CG D:Pro222 4.37 Hg O D:Tyr261 4.46 Hg N D:Tyr261 4.86 Hg CE2 D:Tyr261 3.08 Hg CD1 D:Tyr261 3.99 Hg CD2 D:Tyr261 3.52 Hg CZ D:Tyr261 3.13 Hg C D:Tyr261 4.73 Hg CE1 D:Tyr261 3.61 Hg CG D:Tyr261 3.96 Hg OH D:Tyr261 3.55 Hg O D:Gly263 3.55 Hg N D:Gly263 3.99 Hg C D:Gly263 3.13 Hg CA D:Gly263 3.75 Hg HG D:Cmh264 0.00 Hg CM D:Cmh264 2.10 Hg N D:Cmh264 2.93 Hg CB D:Cmh264 3.23 Hg SG D:Cmh264 2.35 Hg C D:Cmh264 4.60 Hg CA D:Cmh264 3.10 interactive model: Mercury binding site 14 out of 16 in 4ac9 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 14 of Mercury in the PDB 4ac9. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Mercury atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: D: Ile283, D: Ile285, D: Asn336, D: Glu337, D: Cmh338, D: Tyr339, D: Cmh340, conact list: Atom Atom Distance (A) Hg O D:Ile283 3.93 Hg CB D:Ile283 4.71 Hg CG2 D:Ile283 4.47 Hg C D:Ile283 4.79 Hg CG2 D:Ile285 4.92 Hg C D:Asn336 4.99 Hg N D:Glu337 4.87 Hg C D:Glu337 4.63 Hg O D:Cmh338 3.28 Hg HG D:Cmh338 0.00 Hg CM D:Cmh338 2.09 Hg N D:Cmh338 3.54 Hg CB D:Cmh338 3.18 Hg SG D:Cmh338 2.35 Hg C D:Cmh338 3.30 Hg CA D:Cmh338 3.45 Hg O D:Tyr339 4.52 Hg N D:Tyr339 3.95 Hg C D:Tyr339 4.79 Hg CA D:Tyr339 4.72 Hg SG D:Cmh340 4.38 interactive model: Mercury binding site 15 out of 16 in 4ac9 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 15 of Mercury in the PDB 4ac9. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Mercury atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: D: Leu293, D: Ala312, D: Pro314, D: Cmh340, D: Phe342, D: Ile358, D: Cmh371, conact list: Atom Atom Distance (A) Hg CD1 D:Leu293 4.62 Hg CD2 D:Leu293 3.17 Hg CG D:Leu293 4.39 Hg CB D:Ala312 4.08 Hg N D:Pro314 4.72 Hg CB D:Pro314 4.58 Hg CD D:Pro314 4.67 Hg CA D:Pro314 4.76 Hg HG D:Cmh340 0.00 Hg CM D:Cmh340 2.10 Hg CB D:Cmh340 3.16 Hg SG D:Cmh340 2.35 Hg CA D:Cmh340 4.34 Hg CZ D:Phe342 4.05 Hg CE1 D:Phe342 3.98 Hg CD1 D:Ile358 3.72 Hg CG1 D:Ile358 4.98 Hg CM D:Cmh371 4.02 interactive model: Mercury binding site 16 out of 16 in 4ac9 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 16 of Mercury in the PDB 4ac9. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Mercury atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: D: Ile285, D: Tyr291, D: Ile358, D: Cmh371, D: Gly372, conact list: Atom Atom Distance (A) Hg CD1 D:Ile285 4.70 Hg CB D:Tyr291 4.53 Hg CD1 D:Tyr291 4.99 Hg CD2 D:Tyr291 4.99 Hg CG D:Tyr291 4.63 Hg CB D:Ile358 4.43 Hg CD1 D:Ile358 4.39 Hg CG2 D:Ile358 3.61 Hg O D:Cmh371 3.65 Hg HG D:Cmh371 0.00 Hg CM D:Cmh371 2.09 Hg CB D:Cmh371 3.21 Hg SG D:Cmh371 2.35 Hg C D:Cmh371 3.92 Hg CA D:Cmh371 4.15 Hg N D:Gly372 4.64 interactive model: