Sodium in the structure of Structure Of The Structure Of the H13A Mutant of YKR043C in Complex With Sedoheptulose-1,7-Bisphosphate (pdb 3oi7)

The binding sites of Sodium atom in the structure of Structure Of The Structure Of the H13A Mutant of YKR043C in Complex With Sedoheptulose-1,7-Bisphosphate (pdb code 3oi7). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 3oi7 structure was solved by A.U.SINGER, X.XU, A.DONG, H.CUI, M.F.CLASQUIN, A.A.CAUDY, A.M.EDWARDS, A.SAVCHENKO, A.JOACHIMIAK, A.F.YAKUNIN, MIDWEST CENTER FOR STRUCTURALGENOMICS (MCSG), with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 27.5-2.4 Space group P1 a (A) 58.559 b (A) 74.945 c (A) 83.615 alpha (°) 90.04 beta (°) 89.92 gamma (°) 77.22 Rfactor (%) 22.8 Rfree (%) 26 Sodium Binding Sites: Sodium binding site 1 out of 5 in 3oi7 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 3oi7. 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: Ala153, A: Arg154, A: Ile155, A: Asn157, A: Leu158, A: Val213, A: Pro214, A: Val216, conact list: Atom Atom Distance (A) Na O A:Ala153 4.71 Na O A:Arg154 2.82 Na N A:Arg154 4.88 Na CB A:Arg154 4.05 Na C A:Arg154 3.60 Na CG A:Arg154 4.45 Na CA A:Arg154 3.61 Na N A:Ile155 4.89 Na N A:Asn157 4.97 Na CB A:Asn157 3.49 Na ND2 A:Asn157 3.02 Na C A:Asn157 4.38 Na OD1 A:Asn157 4.93 Na CG A:Asn157 3.72 Na CA A:Asn157 4.48 Na N A:Leu158 3.83 Na CB A:Leu158 4.47 Na CD1 A:Leu158 4.44 Na CD2 A:Leu158 4.53 Na CG A:Leu158 3.74 Na CA A:Leu158 4.50 Na CB A:Val213 4.99 Na C A:Val213 4.33 Na CG1 A:Val213 3.99 Na CA A:Val213 4.67 Na O A:Pro214 2.89 Na N A:Pro214 3.70 Na CB A:Pro214 3.78 Na CD A:Pro214 3.50 Na C A:Pro214 3.83 Na CG A:Pro214 3.98 Na CA A:Pro214 4.02 Na CG2 A:Val216 4.37 interactive model: Sodium binding site 2 out of 5 in 3oi7 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 3oi7. 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: Arg12, B: Ala13, B: Gly14, B: Gln15, B: Thr16, B: Ser19, B: Ala234, B: Oi7301, B: Mg311, B: Hoh281, conact list: Atom Atom Distance (A) Na CD B:Arg12 4.73 Na CZ B:Arg12 4.35 Na CG B:Arg12 4.54 Na NE B:Arg12 3.83 Na NH2 B:Arg12 4.07 Na O B:Ala13 3.25 Na N B:Ala13 4.98 Na C B:Ala13 3.93 Na CB B:Ala13 4.15 Na CA B:Ala13 4.58 Na O B:Gly14 3.05 Na N B:Gly14 4.68 Na C B:Gly14 3.93 Na CA B:Gly14 4.80 Na N B:Gln15 4.62 Na C B:Gln15 4.79 Na CA B:Gln15 4.58 Na N B:Thr16 4.58 Na CG2 B:Thr16 4.55 Na OG1 B:Thr16 4.59 Na CB B:Ser19 3.43 Na OG B:Ser19 3.47 Na CA B:Ser19 4.95 Na CB B:Ala234 4.11 Na CA B:Ala234 4.51 Na P1 B:Oi7301 3.29 Na C1 B:Oi7301 4.72 Na O1 B:Oi7301 4.47 Na O3P B:Oi7301 4.28 Na O1P B:Oi7301 2.24 Na O2P B:Oi7301 3.19 Na MG B:Mg311 4.25 Na O B:Hoh281 4.89 interactive model: Sodium binding site 3 out of 5 in 3oi7 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Sodium in the PDB 3oi7. 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: Arg12, C: Ala13, C: Gly14, C: Gln15, C: Thr16, C: Ser19, C: Ala234, C: Oi7301, C: Mg311, conact list: Atom Atom Distance (A) Na CD C:Arg12 4.85 Na CZ C:Arg12 4.42 Na CG C:Arg12 4.64 Na NE C:Arg12 3.94 Na NH2 C:Arg12 4.12 Na O C:Ala13 3.27 Na N C:Ala13 5.00 Na C C:Ala13 3.94 Na CB C:Ala13 4.17 Na CA C:Ala13 4.59 Na O C:Gly14 3.00 Na N C:Gly14 4.66 Na C C:Gly14 3.89 Na CA C:Gly14 4.77 Na N C:Gln15 4.58 Na C C:Gln15 4.71 Na CA C:Gln15 4.52 Na N C:Thr16 4.51 Na CG2 C:Thr16 4.46 Na OG1 C:Thr16 4.55 Na CB C:Ser19 3.41 Na OG C:Ser19 3.45 Na CA C:Ser19 4.93 Na CB C:Ala234 4.11 Na CA C:Ala234 4.51 Na P1 C:Oi7301 3.35 Na C1 C:Oi7301 4.78 Na O1 C:Oi7301 4.52 Na O3P C:Oi7301 4.34 Na O1P C:Oi7301 2.25 Na O2P C:Oi7301 3.26 Na MG C:Mg311 4.04 interactive model: Sodium binding site 4 out of 5 in 3oi7 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Sodium in the PDB 3oi7. 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: Thr16, C: Glu17, C: Leu30, C: Pro31, C: Leu32, C: Thr33, conact list: Atom Atom Distance (A) Na O C:Thr16 4.96 Na CB C:Thr16 3.77 Na CG2 C:Thr16 4.52 Na OG1 C:Thr16 4.84 Na C C:Thr16 3.79 Na CA C:Thr16 3.76 Na N C:Glu17 2.91 Na CB C:Glu17 3.52 Na OE2 C:Glu17 4.39 Na CD C:Glu17 4.13 Na CG C:Glu17 2.83 Na CA C:Glu17 3.78 Na CB C:Leu30 4.38 Na CD1 C:Leu30 4.70 Na CD2 C:Leu30 4.97 Na C C:Leu30 4.90 Na CG C:Leu30 4.95 Na O C:Pro31 2.73 Na N C:Pro31 4.29 Na CB C:Pro31 4.94 Na CD C:Pro31 3.96 Na C C:Pro31 3.79 Na CG C:Pro31 4.16 Na CA C:Pro31 4.59 Na O C:Leu32 4.55 Na N C:Leu32 4.70 Na C C:Leu32 4.22 Na CA C:Leu32 4.75 Na N C:Thr33 3.98 Na CB C:Thr33 4.87 Na CG2 C:Thr33 4.00 Na CA C:Thr33 4.45 interactive model: Sodium binding site 5 out of 5 in 3oi7 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Sodium in the PDB 3oi7. 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: Arg12, D: Ala13, D: Gly14, D: Gln15, D: Thr16, D: Ser19, D: Ala234, D: Oi7301, D: Mg311, D: Hoh336, conact list: Atom Atom Distance (A) Na CD D:Arg12 4.80 Na CZ D:Arg12 4.39 Na CG D:Arg12 4.61 Na NE D:Arg12 3.89 Na NH2 D:Arg12 4.09 Na O D:Ala13 3.25 Na N D:Ala13 5.00 Na C D:Ala13 3.95 Na CB D:Ala13 4.21 Na CA D:Ala13 4.61 Na O D:Gly14 2.99 Na N D:Gly14 4.67 Na C D:Gly14 3.88 Na CA D:Gly14 4.78 Na N D:Gln15 4.57 Na C D:Gln15 4.71 Na CA D:Gln15 4.51 Na N D:Thr16 4.49 Na CG2 D:Thr16 4.51 Na OG1 D:Thr16 4.53 Na CB D:Ser19 3.38 Na OG D:Ser19 3.41 Na CA D:Ser19 4.90 Na CB D:Ala234 4.06 Na CA D:Ala234 4.54 Na P1 D:Oi7301 3.36 Na C1 D:Oi7301 4.77 Na O1 D:Oi7301 4.52 Na O3P D:Oi7301 4.35 Na O1P D:Oi7301 2.24 Na O2P D:Oi7301 3.30 Na MG D:Mg311 4.00 Na O D:Hoh336 4.88 interactive model: