Sodium in the structure of Homoserine Dehydrogenase in Complex With Suicide Inhibitor Complex Nad-5-Hydroxy-4-Oxonorvaline (pdb 1q7g)

The binding sites of Sodium atom in the structure of Homoserine Dehydrogenase in Complex With Suicide Inhibitor Complex Nad-5-Hydroxy-4-Oxonorvaline (pdb code 1q7g). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 1q7g structure was solved by S.L.JACQUES, I.A.MIRZA, L.EJIM, K.KOTEVA, D.W.HUGHES, K.GREEN, R.KINACH, J.F.HONEK, H.K.LAI, A.M.BERGHUIS, G.D.WRIGHT, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 40.4-2.6 Space group P43212 a (A) 80.863 b (A) 80.863 c (A) 248.986 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 24.7 Rfree (%) 30.6 Sodium Binding Sites: Sodium binding site 1 out of 2 in 1q7g Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 1q7g. 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: Glu143, A: Ala144, A: Val146, A: Gly147, A: Ala148, A: Gly149, A: Leu150, A: Pro151, A: Ile152, A: Ile153, conact list: Atom Atom Distance (A) Na O A:Glu143 2.84 Na OE1 A:Glu143 4.82 Na CB A:Glu143 4.87 Na OE2 A:Glu143 2.71 Na CD A:Glu143 3.66 Na C A:Glu143 3.96 Na CG A:Glu143 3.86 Na CA A:Glu143 4.74 Na N A:Ala144 4.88 Na CA A:Ala144 4.92 Na O A:Val146 2.73 Na N A:Val146 4.94 Na C A:Val146 3.68 Na CA A:Val146 4.87 Na O A:Gly147 3.28 Na N A:Gly147 4.16 Na C A:Gly147 3.42 Na CA A:Gly147 3.79 Na O A:Ala148 3.07 Na N A:Ala148 4.00 Na C A:Ala148 3.69 Na CA A:Ala148 4.48 Na N A:Gly149 4.25 Na C A:Gly149 4.11 Na CA A:Gly149 4.30 Na O A:Leu150 2.68 Na N A:Leu150 3.31 Na CB A:Leu150 4.16 Na C A:Leu150 3.62 Na CA A:Leu150 3.88 Na N A:Pro151 4.85 Na N A:Ile152 4.46 Na CB A:Ile152 4.71 Na CD1 A:Ile152 4.93 Na CG2 A:Ile152 3.94 Na CG1 A:Ile152 4.45 Na N A:Ile153 4.99 interactive model: Sodium binding site 2 out of 2 in 1q7g Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 1q7g. 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: Glu143, B: Ala144, B: Val146, B: Gly147, B: Ala148, B: Gly149, B: Leu150, B: Ile152, conact list: Atom Atom Distance (A) Na O B:Glu143 2.78 Na OE1 B:Glu143 4.85 Na CB B:Glu143 4.30 Na OE2 B:Glu143 3.00 Na CD B:Glu143 3.61 Na C B:Glu143 3.50 Na CG B:Glu143 3.36 Na CA B:Glu143 4.21 Na N B:Ala144 4.26 Na C B:Ala144 4.91 Na CA B:Ala144 4.45 Na O B:Val146 3.01 Na N B:Val146 4.54 Na C B:Val146 3.72 Na CA B:Val146 4.69 Na O B:Gly147 3.33 Na N B:Gly147 4.21 Na C B:Gly147 3.52 Na CA B:Gly147 4.04 Na O B:Ala148 3.09 Na N B:Ala148 4.00 Na C B:Ala148 3.59 Na CA B:Ala148 4.38 Na O B:Gly149 4.86 Na N B:Gly149 4.10 Na C B:Gly149 4.09 Na CA B:Gly149 4.19 Na O B:Leu150 2.95 Na N B:Leu150 3.71 Na CB B:Leu150 4.57 Na C B:Leu150 3.97 Na CA B:Leu150 4.30 Na N B:Ile152 4.62 Na CB B:Ile152 4.48 Na CD1 B:Ile152 4.77 interactive model: