Sodium in the structure of Pantothenate Kinase From Mycobacterium Tuberculosis (Mtpank) in Complex With Adp and Phosphopantothenate (pdb 2zsa)

The binding sites of Sodium atom in the structure of Pantothenate Kinase From Mycobacterium Tuberculosis (Mtpank) in Complex With Adp and Phosphopantothenate (pdb code 2zsa). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 2zsa structure was solved by B.CHETNANI, S.DAS, P.KUMAR, A.SUROLIA, M.VIJAYAN, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 34.1-2.5 Space group P3121 a (A) 104.092 b (A) 104.092 c (A) 90.440 alpha (°) 90.00 beta (°) 90.00 gamma (°) 120.00 Rfactor (%) 19.8 Rfree (%) 23.6 Sodium Binding Sites: Sodium binding site 1 out of 4 in 2zsa Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 2zsa. 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: Arg122, A: Asp124, A: Val191, A: Val192, A: Arg193, conact list: Atom Atom Distance (A) Na CD A:Arg122 4.12 Na CZ A:Arg122 4.77 Na CG A:Arg122 4.70 Na NE A:Arg122 4.44 Na NH1 A:Arg122 4.81 Na OD2 A:Asp124 3.14 Na OD1 A:Asp124 3.35 Na CG A:Asp124 3.63 Na O A:Val191 3.80 Na C A:Val191 4.70 Na N A:Val192 4.87 Na C A:Val192 4.29 Na CA A:Val192 4.07 Na O A:Arg193 4.58 Na N A:Arg193 3.50 Na CB A:Arg193 4.30 Na CD A:Arg193 4.97 Na C A:Arg193 4.91 Na CG A:Arg193 4.61 Na CA A:Arg193 4.40 interactive model: Sodium binding site 2 out of 4 in 2zsa Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 2zsa. 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: Leu40, A: Gly41, A: Glu42, A: Ala100, A: Val101, A: Gly102, A: Trp234, A: Arg238, A: His302, A: Adp800, A: Hoh330, A: Hoh391, A: Hoh392, A: Hoh418, conact list: Atom Atom Distance (A) Na O A:Leu40 4.62 Na O A:Gly41 4.78 Na C A:Gly41 4.76 Na N A:Glu42 4.94 Na OE1 A:Glu42 4.58 Na OE2 A:Glu42 2.40 Na CD A:Glu42 3.49 Na CG A:Glu42 3.95 Na O A:Ala100 2.93 Na C A:Ala100 3.60 Na CB A:Ala100 4.97 Na CA A:Ala100 4.32 Na O A:Val101 4.32 Na N A:Val101 4.25 Na C A:Val101 3.91 Na CA A:Val101 4.35 Na N A:Gly102 3.72 Na CA A:Gly102 4.05 Na CB A:Trp234 4.81 Na CD2 A:Trp234 4.90 Na CE3 A:Trp234 4.38 Na CZ3 A:Trp234 5.00 Na NH1 A:Arg238 4.79 Na NE2 A:His302 3.78 Na CD2 A:His302 3.88 Na O1B A:Adp800 4.52 Na O A:Hoh330 4.60 Na O A:Hoh391 2.72 Na O A:Hoh392 4.95 Na O A:Hoh418 2.84 interactive model: Sodium binding site 3 out of 4 in 2zsa Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Sodium in the PDB 2zsa. 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: Tyr223, A: Val224, A: Asp225, A: Ala226, A: Ile231, A: Leu281, A: Leu286, A: Arg289, A: Hoh337, A: Hoh474, A: Hoh475, A: Hoh515, conact list: Atom Atom Distance (A) Na CE2 A:Tyr223 4.77 Na CD1 A:Tyr223 4.51 Na CZ A:Tyr223 3.40 Na CE1 A:Tyr223 3.21 Na OH A:Tyr223 2.71 Na O A:Val224 4.47 Na CB A:Asp225 4.19 Na OD2 A:Asp225 4.52 Na C A:Asp225 4.71 Na OD1 A:Asp225 2.38 Na CG A:Asp225 3.54 Na CA A:Asp225 4.07 Na O A:Ala226 4.08 Na N A:Ala226 4.21 Na CD1 A:Ile231 4.41 Na CD1 A:Leu281 3.93 Na CD2 A:Leu281 4.94 Na CG A:Leu281 4.92 Na CD1 A:Leu286 4.87 Na CD2 A:Leu286 3.47 Na CG A:Leu286 4.11 Na NH1 A:Arg289 4.74 Na O A:Hoh337 2.92 Na O A:Hoh474 2.89 Na O A:Hoh475 4.76 Na O A:Hoh515 4.54 interactive model: Sodium binding site 4 out of 4 in 2zsa Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Sodium in the PDB 2zsa. 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: Arg146, A: Phe149, A: Glu151, A: Glu283, A: Asn284, A: Hoh380, A: Hoh482, A: Hoh510, conact list: Atom Atom Distance (A) Na CZ A:Arg146 4.75 Na NH2 A:Arg146 3.74 Na CE2 A:Phe149 3.97 Na CD2 A:Phe149 3.85 Na OE1 A:Glu151 4.84 Na OE2 A:Glu151 4.82 Na OE1 A:Glu283 3.06 Na CB A:Glu283 4.09 Na CD A:Glu283 4.21 Na CG A:Glu283 4.71 Na ND2 A:Asn284 3.27 Na OD1 A:Asn284 3.50 Na CG A:Asn284 3.80 Na O A:Hoh380 4.08 Na O A:Hoh482 3.28 Na O A:Hoh510 4.10 interactive model: