Sodium in the structure of Crystal Structure Of the C-Terminal Domain of Wzt (pdb 2r5o)

The binding sites of Sodium atom in the structure of Crystal Structure Of the C-Terminal Domain of Wzt (pdb code 2r5o). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 2r5o structure was solved by M.S.KIMBER, L.CUTHBERTSON, C.WHITFIELD, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 20.0-1.3 Space group P42212 a (A) 106.081 b (A) 106.081 c (A) 70.351 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 16.6 Rfree (%) 18.2 Sodium Binding Sites: Sodium binding site 1 out of 5 in 2r5o Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 2r5o. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Tyr284, A: Arg285, A: Trp286, A: Hoh491, conact list: Atom Atom Distance (A) Na CE2 A:Tyr284 4.65 Na CD1 A:Tyr284 4.67 Na CZ A:Tyr284 3.35 Na CE1 A:Tyr284 3.35 Na OH A:Tyr284 2.54 Na O A:Arg285 4.87 Na CB A:Trp286 3.90 Na CG A:Trp286 4.96 Na CA A:Trp286 4.83 Na O A:Hoh491 4.49 interactive model: Sodium binding site 2 out of 5 in 2r5o Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 2r5o. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Tyr345, A: Thr347, A: Ala352, B: Asp416, B: Phe417, B: Asp422, B: Leu423, B: Lys424, B: Ser425, A: Hoh434, B: Hoh447, B: Hoh548, B: Hoh591, conact list: Atom Atom Distance (A) Na CE2 A:Tyr345 4.86 Na CD1 A:Tyr345 4.90 Na CZ A:Tyr345 3.53 Na CE1 A:Tyr345 3.58 Na OH A:Tyr345 2.66 Na CB A:Thr347 4.69 Na OG1 A:Thr347 4.44 Na CA A:Ala352 4.82 Na O B:Asp416 4.47 Na CB B:Phe417 4.01 Na CG B:Phe417 4.92 Na CB B:Asp422 4.96 Na OD2 B:Asp422 4.12 Na OD1 B:Asp422 2.67 Na CG B:Asp422 3.72 Na N B:Leu423 4.96 Na C B:Leu423 4.90 Na N B:Lys424 3.69 Na CB B:Lys424 4.94 Na C B:Lys424 4.22 Na CA B:Lys424 3.69 Na O B:Ser425 4.73 Na N B:Ser425 3.90 Na CA B:Ser425 4.97 Na O A:Hoh434 2.74 Na O B:Hoh447 2.70 Na O B:Hoh548 4.61 Na O B:Hoh591 3.32 interactive model: Sodium binding site 3 out of 5 in 2r5o Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Sodium in the PDB 2r5o. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: B: Leu335, B: Ile336, B: Lys337, B: Leu383, B: Leu384, B: Ser385, B: Tyr404, B: Asp405, conact list: Atom Atom Distance (A) Na O B:Leu335 3.26 Na CB B:Leu335 4.24 Na CB B:Leu335 4.16 Na CD1 B:Leu335 4.95 Na CD2 B:Leu335 4.04 Na C B:Leu335 3.88 Na CG B:Leu335 3.92 Na CA B:Leu335 4.70 Na N B:Ile336 4.36 Na C B:Ile336 4.40 Na CA B:Ile336 4.33 Na N B:Lys337 3.94 Na CB B:Lys337 4.05 Na CB B:Lys337 4.02 Na CE B:Lys337 3.82 Na CE B:Lys337 4.90 Na CD B:Lys337 3.76 Na CD B:Lys337 3.58 Na CG B:Lys337 3.48 Na CG B:Lys337 3.72 Na CA B:Lys337 4.64 Na NZ B:Lys337 4.79 Na O B:Leu383 2.89 Na CB B:Leu383 4.04 Na C B:Leu383 3.47 Na CA B:Leu383 4.42 Na O B:Leu384 4.20 Na N B:Leu384 3.88 Na C B:Leu384 3.63 Na CA B:Leu384 3.85 Na N B:Ser385 3.47 Na CB B:Ser385 3.60 Na OG B:Ser385 2.65 Na CA B:Ser385 4.13 Na CD1 B:Tyr404 4.70 Na CE1 B:Tyr404 4.65 Na N B:Asp405 4.12 Na CB B:Asp405 4.74 Na OD2 B:Asp405 4.87 Na OD1 B:Asp405 2.77 Na CG B:Asp405 3.97 Na CA B:Asp405 4.25 interactive model: Sodium binding site 4 out of 5 in 2r5o Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Sodium in the PDB 2r5o. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: B: Tyr284, B: Arg285, B: Trp286, B: Hoh446, conact list: Atom Atom Distance (A) Na CE2 B:Tyr284 4.62 Na CD1 B:Tyr284 4.76 Na CZ B:Tyr284 3.34 Na CE1 B:Tyr284 3.43 Na OH B:Tyr284 2.53 Na O B:Arg285 4.71 Na CB B:Trp286 3.83 Na CG B:Trp286 4.79 Na CA B:Trp286 4.82 Na O B:Hoh446 2.63 interactive model: Sodium binding site 5 out of 5 in 2r5o Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Sodium in the PDB 2r5o. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Phe417, A: Asp422, A: Lys424, A: Ser425, B: Tyr345, B: Thr347, A: Hoh551, A: Hoh585, B: Hoh599, conact list: Atom Atom Distance (A) Na CE2 A:Phe417 4.64 Na CD2 A:Phe417 4.89 Na CD2 A:Phe417 4.23 Na CG A:Phe417 4.83 Na CB A:Asp422 4.99 Na OD2 A:Asp422 3.92 Na OD1 A:Asp422 2.69 Na CG A:Asp422 3.66 Na N A:Lys424 3.80 Na CB A:Lys424 4.96 Na C A:Lys424 4.29 Na CA A:Lys424 3.74 Na O A:Ser425 4.78 Na N A:Ser425 3.99 Na CE2 B:Tyr345 4.79 Na CD1 B:Tyr345 4.72 Na CZ B:Tyr345 3.45 Na CE1 B:Tyr345 3.43 Na OH B:Tyr345 2.64 Na CB B:Thr347 4.60 Na OG1 B:Thr347 4.37 Na O A:Hoh551 2.85 Na O A:Hoh585 2.96 Na O B:Hoh599 2.74 interactive model: