Sodium in the structure of Crystal Structure of Phosphoglycerate Kinase From Thermus Thermophilus HB8 (pdb 1v6s)

The binding sites of Sodium atom in the structure of Crystal Structure of Phosphoglycerate Kinase From Thermus Thermophilus HB8 (pdb code 1v6s). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 1v6s structure was solved by H.MIZUTANI, N.KUNISHIMA, RIKEN STRUCTURAL GENOMICS/PROTEOMICSINITIATIVE (RSGI), with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 30.0-1.5 Space group P65 a (A) 143.175 b (A) 143.175 c (A) 75.641 alpha (°) 90.00 beta (°) 90.00 gamma (°) 120.00 Rfactor (%) 20.1 Rfree (%) 21.5 Sodium Binding Sites: Sodium binding site 1 out of 3 in 1v6s Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 1v6s. 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: Ser204, A: Arg208, A: Leu377, A: Glu378, A: Lys379, A: Gly380, A: Hoh1480, A: Hoh1569, A: Hoh1606, A: Hoh1681, A: Hoh1755, A: Hoh1756, A: Hoh1757, conact list: Atom Atom Distance (A) Na O A:Ser204 4.80 Na CB A:Ser204 3.35 Na OG A:Ser204 2.67 Na C A:Ser204 4.85 Na CA A:Ser204 4.07 Na CZ A:Arg208 4.84 Na NH2 A:Arg208 4.93 Na NH1 A:Arg208 3.82 Na O A:Leu377 4.14 Na O A:Glu378 2.40 Na C A:Glu378 3.40 Na CA A:Glu378 4.31 Na O A:Lys379 4.51 Na N A:Lys379 4.19 Na C A:Lys379 4.28 Na CA A:Lys379 4.26 Na N A:Gly380 4.68 Na O A:Hoh1480 4.38 Na O A:Hoh1569 2.39 Na O A:Hoh1606 4.61 Na O A:Hoh1681 4.67 Na O A:Hoh1755 2.30 Na O A:Hoh1756 2.48 Na O A:Hoh1757 2.43 interactive model: Sodium binding site 2 out of 3 in 1v6s Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 1v6s. 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: Ser204, B: Arg208, B: Leu377, B: Glu378, B: Lys379, B: Gly380, B: Hoh1560, B: Hoh1595, B: Hoh1617, B: Hoh1664, B: Hoh1717, B: Hoh1718, B: Hoh1748, conact list: Atom Atom Distance (A) Na CB B:Ser204 3.42 Na OG B:Ser204 2.67 Na CA B:Ser204 4.21 Na CZ B:Arg208 4.97 Na NH2 B:Arg208 4.86 Na NH1 B:Arg208 4.12 Na O B:Leu377 3.91 Na C B:Leu377 4.82 Na O B:Glu378 2.20 Na N B:Glu378 4.97 Na C B:Glu378 3.30 Na CA B:Glu378 4.15 Na O B:Lys379 4.89 Na N B:Lys379 4.22 Na C B:Lys379 4.52 Na CA B:Lys379 4.36 Na N B:Gly380 4.82 Na O B:Hoh1560 4.50 Na O B:Hoh1595 2.57 Na O B:Hoh1617 4.80 Na O B:Hoh1664 4.86 Na O B:Hoh1717 2.34 Na O B:Hoh1718 2.36 Na O B:Hoh1748 2.48 interactive model: Sodium binding site 3 out of 3 in 1v6s Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Sodium in the PDB 1v6s. 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: Leu338, B: Glu339, B: Gly340, B: Ala341, B: Arg362, B: Hoh1428, B: Hoh1443, B: Hoh1445, B: Hoh1484, B: Hoh1496, B: Hoh1545, B: Hoh1547, B: Hoh1668, B: Hoh1733, B: Hoh1746, conact list: Atom Atom Distance (A) Na O B:Leu338 4.14 Na C B:Glu339 5.00 Na CA B:Glu339 4.96 Na N B:Gly340 4.13 Na CA B:Gly340 4.76 Na O B:Ala341 4.05 Na N B:Ala341 4.63 Na O B:Arg362 4.25 Na O B:Hoh1428 4.34 Na O B:Hoh1443 4.26 Na O B:Hoh1445 4.36 Na O B:Hoh1484 2.76 Na O B:Hoh1496 2.61 Na O B:Hoh1545 2.47 Na O B:Hoh1547 2.50 Na O B:Hoh1668 2.58 Na O B:Hoh1733 4.25 Na O B:Hoh1746 2.65 interactive model: