Sodium in the structure of Crystal Structure of Uronate Isomerase From Bacillus Halodurans Complexed With Zinc and D-Arabinarate, Monoclinic Crystal Form (pdb 3hk7)

The binding sites of Sodium atom in the structure of Crystal Structure of Uronate Isomerase From Bacillus Halodurans Complexed With Zinc and D-Arabinarate, Monoclinic Crystal Form (pdb code 3hk7). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 3hk7 structure was solved by A.A.FEDOROV, E.V.FEDOROV, T.T.NGUYEN, F.M.RAUSHEL, S.C.ALMO, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 25.0-2.2 Space group C121 a (A) 274.823 b (A) 156.516 c (A) 185.959 alpha (°) 90.00 beta (°) 116.20 gamma (°) 90.00 Rfactor (%) 21.3 Rfree (%) 24.5 Sodium Binding Sites: Sodium binding site 1 out of 4 in 3hk7 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 3hk7. 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: Glu332, A: Glu336, B: Glu332, B: Glu336, C: Glu332, C: Glu336, A: Hoh433, A: Hoh441, A: Hoh881, B: Hoh433, B: Hoh443, B: Hoh1378, C: Hoh466, C: Hoh467, C: Hoh1634, conact list: Atom Atom Distance (A) Na OE2 A:Glu332 3.78 Na CD A:Glu332 4.92 Na OE2 A:Glu336 4.54 Na OE2 B:Glu332 4.10 Na OE2 B:Glu336 4.43 Na OE2 C:Glu332 4.00 Na OE2 C:Glu336 4.67 Na O A:Hoh433 2.37 Na O A:Hoh441 3.94 Na O A:Hoh881 2.47 Na O B:Hoh433 2.53 Na O B:Hoh443 4.12 Na O B:Hoh1378 2.34 Na O C:Hoh466 2.43 Na O C:Hoh467 4.21 Na O C:Hoh1634 2.34 interactive model: Sodium binding site 2 out of 4 in 3hk7 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 3hk7. 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: Glu332, D: Glu336, E: Glu332, E: Glu336, F: Glu332, F: Glu336, D: Hoh441, D: Hoh823, D: Hoh1832, E: Hoh441, E: Hoh651, E: Hoh1613, F: Hoh450, F: Hoh461, F: Hoh683, conact list: Atom Atom Distance (A) Na OE2 D:Glu332 3.90 Na OE2 D:Glu336 4.53 Na OE2 E:Glu332 4.07 Na OE2 E:Glu336 4.53 Na OE2 F:Glu332 4.02 Na OE2 F:Glu336 4.65 Na O D:Hoh441 4.02 Na O D:Hoh823 2.46 Na O D:Hoh1832 2.41 Na O E:Hoh441 4.13 Na O E:Hoh651 2.47 Na O E:Hoh1613 2.60 Na O F:Hoh450 2.35 Na O F:Hoh461 4.11 Na O F:Hoh683 2.35 interactive model: Sodium binding site 3 out of 4 in 3hk7 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Sodium in the PDB 3hk7. 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: G: Glu332, G: Glu336, H: Glu332, H: Glu336, I: Glu332, I: Glu336, G: Hoh522, G: Hoh754, G: Hoh1011, H: Hoh432, H: Hoh443, H: Hoh1213, I: Hoh438, I: Hoh463, I: Hoh714, conact list: Atom Atom Distance (A) Na OE2 G:Glu332 3.94 Na OE2 G:Glu336 4.58 Na OE2 H:Glu332 3.85 Na CD H:Glu332 4.96 Na CB H:Glu336 4.96 Na OE2 H:Glu336 4.39 Na OE2 I:Glu332 4.08 Na OE2 I:Glu336 4.49 Na O G:Hoh522 2.28 Na O G:Hoh754 4.04 Na O G:Hoh1011 2.58 Na O H:Hoh432 2.51 Na O H:Hoh443 4.05 Na O H:Hoh1213 2.35 Na O I:Hoh438 2.38 Na O I:Hoh463 4.17 Na O I:Hoh714 2.41 interactive model: Sodium binding site 4 out of 4 in 3hk7 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Sodium in the PDB 3hk7. 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: J: Glu332, J: Glu336, K: Glu332, K: Glu336, L: Glu332, L: Glu336, J: Hoh476, J: Hoh585, J: Hoh1661, K: Hoh439, K: Hoh462, K: Hoh1264, L: Hoh431, L: Hoh452, L: Hoh577, conact list: Atom Atom Distance (A) Na OE2 J:Glu332 4.13 Na OE2 J:Glu336 4.45 Na OE2 K:Glu332 3.98 Na OE2 K:Glu336 4.51 Na OE2 L:Glu332 3.90 Na CD L:Glu332 4.93 Na OE2 L:Glu336 4.43 Na O J:Hoh476 4.15 Na O J:Hoh585 2.39 Na O J:Hoh1661 2.56 Na O K:Hoh439 4.07 Na O K:Hoh462 2.38 Na O K:Hoh1264 2.45 Na O L:Hoh431 2.38 Na O L:Hoh452 3.95 Na O L:Hoh577 2.36 interactive model: