Sodium in the structure of The Crystal Structure of Human Haloacid Dehalogenase-Like Hydrolase Domain Containing 2 (HDHD2) (pdb 3hlt)

The binding sites of Sodium atom in the structure of The Crystal Structure of Human Haloacid Dehalogenase-Like Hydrolase Domain Containing 2 (HDHD2) (pdb code 3hlt). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 3hlt structure was solved by E.UGOCHUKWU, N.SHAFQAT, W.W.YUE, R.COCKING, J.E.BRAY, J.R.C.MUNIZ, T.KROJER, F.VON DELFT, C.BOUNTRA, C.H.ARROWSMITH, J.WEIGELT, A.EDWARDS, U.OPPERMANN, STRUCTURAL GENOMICS CONSORTIUM (SGC), with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 28.4-2.3 Space group P21221 a (A) 68.940 b (A) 77.680 c (A) 103.990 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 21.3 Rfree (%) 26.6 Sodium Binding Sites: Sodium binding site 1 out of 2 in 3hlt Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 3hlt. 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: Asp13, A: Ser15, A: Gly16, A: Thr17, A: Lys179, A: Asp204, A: Asp205, A: Asp209, A: Hoh288, A: Hoh307, A: Hoh314, conact list: Atom Atom Distance (A) Na CB A:Asp13 4.14 Na OD2 A:Asp13 2.04 Na OD1 A:Asp13 3.06 Na CG A:Asp13 2.82 Na O A:Ser15 2.39 Na N A:Ser15 4.61 Na CB A:Ser15 4.81 Na C A:Ser15 3.63 Na CA A:Ser15 4.56 Na N A:Gly16 4.55 Na CA A:Gly16 4.60 Na OG1 A:Thr17 4.95 Na NZ A:Lys179 4.50 Na N A:Asp204 4.52 Na CB A:Asp204 4.76 Na OD2 A:Asp204 3.89 Na OD1 A:Asp204 2.35 Na CG A:Asp204 3.47 Na N A:Asp205 4.98 Na CB A:Asp205 4.87 Na OD2 A:Asp209 3.65 Na OD1 A:Asp209 4.74 Na CG A:Asp209 4.62 Na O A:Hoh288 4.01 Na O A:Hoh307 1.98 Na O A:Hoh314 2.34 interactive model: Sodium binding site 2 out of 2 in 3hlt Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 3hlt. 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: Asp13, C: Leu14, C: Ser15, C: Gly16, C: Thr17, C: Asp204, C: Asp205, C: Asp209, conact list: Atom Atom Distance (A) Na CB C:Asp13 4.29 Na OD2 C:Asp13 2.09 Na OD1 C:Asp13 3.97 Na CG C:Asp13 3.26 Na C C:Leu14 5.00 Na O C:Ser15 2.31 Na N C:Ser15 4.56 Na C C:Ser15 3.54 Na CA C:Ser15 4.58 Na O C:Gly16 4.95 Na N C:Gly16 4.37 Na C C:Gly16 4.48 Na CA C:Gly16 4.30 Na N C:Thr17 4.69 Na OG1 C:Thr17 4.00 Na N C:Asp204 4.59 Na CB C:Asp204 4.80 Na OD2 C:Asp204 4.05 Na OD1 C:Asp204 2.44 Na CG C:Asp204 3.57 Na N C:Asp205 4.94 Na OD2 C:Asp209 4.12 Na CG C:Asp209 5.00 interactive model: