Sodium in the structure of Structure Of The SH2 Domain of the Candida Glabrata Transcription Elongation Factor SPT6, Crystal Form A (pdb 3gxw)

The binding sites of Sodium atom in the structure of Structure Of The SH2 Domain of the Candida Glabrata Transcription Elongation Factor SPT6, Crystal Form A (pdb code 3gxw). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 3gxw structure was solved by S.DENGL, A.MAYER, M.SUN, P.CRAMER, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 20.0-1.9 Space group P65 a (A) 54.499 b (A) 54.499 c (A) 253.434 alpha (°) 90.00 beta (°) 90.00 gamma (°) 120.00 Rfactor (%) 19.6 Rfree (%) 24.1 Sodium Binding Sites: Sodium binding site 1 out of 4 in 3gxw Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 3gxw. 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: Gln37, A: Ser38, A: Ser39, A: Gly41, A: Asp42, A: His44, A: Hoh105, A: Hoh115, A: Hoh1027, conact list: Atom Atom Distance (A) Na OE1 A:Gln37 4.24 Na O A:Ser38 2.51 Na N A:Ser38 4.00 Na C A:Ser38 3.48 Na CA A:Ser38 4.32 Na N A:Ser39 4.34 Na C A:Ser39 4.89 Na CA A:Ser39 4.45 Na O A:Gly41 2.70 Na N A:Gly41 4.30 Na C A:Gly41 3.42 Na CA A:Gly41 4.36 Na O A:Asp42 4.85 Na N A:Asp42 3.97 Na C A:Asp42 4.61 Na OD1 A:Asp42 4.41 Na CA A:Asp42 3.96 Na O A:His44 4.37 Na O A:Hoh105 2.62 Na O A:Hoh115 2.62 Na O A:Hoh1027 2.58 interactive model: Sodium binding site 2 out of 4 in 3gxw Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 3gxw. 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: Gln37, B: Ser38, B: Ser39, B: Gly41, B: Asp42, B: His44, B: Hoh112, B: Hoh1286, conact list: Atom Atom Distance (A) Na OE1 B:Gln37 4.48 Na O B:Ser38 2.61 Na N B:Ser38 4.19 Na C B:Ser38 3.59 Na CA B:Ser38 4.49 Na N B:Ser39 4.38 Na C B:Ser39 4.85 Na CA B:Ser39 4.41 Na O B:Gly41 2.70 Na N B:Gly41 4.25 Na C B:Gly41 3.43 Na CA B:Gly41 4.27 Na N B:Asp42 4.10 Na C B:Asp42 4.85 Na OD1 B:Asp42 4.54 Na CA B:Asp42 4.20 Na O B:His44 4.48 Na O B:Hoh112 2.68 Na O B:Hoh1286 2.69 interactive model: Sodium binding site 3 out of 4 in 3gxw Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Sodium in the PDB 3gxw. 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: C: Gln37, C: Ser38, C: Ser39, C: Gly41, C: Asp42, C: His44, C: Hoh1018, C: Hoh1031, C: Hoh1112, C: Hoh1449, conact list: Atom Atom Distance (A) Na OE1 C:Gln37 4.47 Na CB C:Gln37 4.95 Na O C:Ser38 2.58 Na N C:Ser38 4.01 Na C C:Ser38 3.64 Na CA C:Ser38 4.40 Na N C:Ser39 4.56 Na C C:Ser39 4.96 Na CA C:Ser39 4.68 Na O C:Gly41 2.75 Na N C:Gly41 4.15 Na C C:Gly41 3.37 Na CA C:Gly41 4.19 Na N C:Asp42 3.96 Na C C:Asp42 4.86 Na OD1 C:Asp42 4.15 Na CA C:Asp42 4.06 Na O C:His44 4.47 Na O C:Hoh1018 2.70 Na O C:Hoh1031 2.71 Na O C:Hoh1112 2.66 Na O C:Hoh1449 4.21 interactive model: Sodium binding site 4 out of 4 in 3gxw Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Sodium in the PDB 3gxw. 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: D: Mse4, D: Gln37, D: Ser38, D: Ser39, D: Gly41, D: Asp42, D: His44, D: Hoh105, D: Hoh117, D: Hoh136, D: Hoh1022, D: Hoh1376, conact list: Atom Atom Distance (A) Na CE D:Mse4 4.20 Na OE1 D:Gln37 4.54 Na O D:Ser38 2.52 Na N D:Ser38 4.01 Na C D:Ser38 3.58 Na CA D:Ser38 4.35 Na N D:Ser39 4.51 Na C D:Ser39 4.97 Na CA D:Ser39 4.63 Na O D:Gly41 2.69 Na N D:Gly41 4.20 Na C D:Gly41 3.40 Na CA D:Gly41 4.27 Na N D:Asp42 4.03 Na C D:Asp42 4.74 Na OD1 D:Asp42 4.50 Na CA D:Asp42 4.07 Na O D:His44 4.39 Na O D:Hoh105 2.61 Na O D:Hoh117 2.66 Na O D:Hoh136 2.73 Na O D:Hoh1022 2.70 Na O D:Hoh1376 4.33 interactive model: