Sodium in the structure of Crystal Structure of the Aminoglycoside Phosphotransferase Aph(3')-Ia, With Substrate Kanamycin and Small Molecule Inhibitor Pyrazolopyrimidine PP2 (pdb 4few)

The binding sites of Sodium atom in the structure of Crystal Structure of the Aminoglycoside Phosphotransferase Aph(3')-Ia, With Substrate Kanamycin and Small Molecule Inhibitor Pyrazolopyrimidine PP2 (pdb code 4few). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 4few structure was solved by P.J.STOGIOS, E.EVDOKIMOVA, Z.WAWRZAK, G.MINASOV, O.EGOROVA, R.DI LEO, T.SHAKYA, P.SPANOGIANNOPOULOS, G.D.WRIGHT, A.SAVCHENKO, W.F.ANDERSON, CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS DISEASES (CSGID), with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 23.9-2.0 Space group P1 a (A) 57.280 b (A) 93.579 c (A) 96.399 alpha (°) 61.22 beta (°) 73.18 gamma (°) 87.35 Rfactor (%) 15.7 Rfree (%) 21.6 Sodium Binding Sites: Sodium binding site 1 out of 7 in 4few Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 4few. 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: Thr76, A: Ala77, A: Mse79, A: Pro80, A: Leu81, A: Act305, A: Hoh486, A: Hoh510, A: Hoh630, conact list: Atom Atom Distance (A) Na O A:Thr76 2.38 Na N A:Thr76 4.93 Na CB A:Thr76 3.52 Na CG2 A:Thr76 4.44 Na OG1 A:Thr76 2.44 Na C A:Thr76 3.27 Na CA A:Thr76 3.50 Na N A:Ala77 4.53 Na O A:Mse79 2.51 Na N A:Mse79 4.45 Na C A:Mse79 3.55 Na CA A:Mse79 4.65 Na N A:Pro80 4.17 Na C A:Pro80 4.45 Na CA A:Pro80 3.89 Na O A:Leu81 4.90 Na N A:Leu81 3.97 Na CB A:Leu81 4.92 Na O A:Act305 2.36 Na CH3 A:Act305 3.64 Na C A:Act305 3.19 Na OXT A:Act305 4.16 Na O A:Hoh486 2.52 Na O A:Hoh510 2.32 Na O A:Hoh630 4.18 interactive model: Sodium binding site 2 out of 7 in 4few Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 4few. 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: Thr76, B: Ala77, B: Mse79, B: Pro80, B: Leu81, B: Act304, conact list: Atom Atom Distance (A) Na O B:Thr76 2.51 Na N B:Thr76 4.87 Na CB B:Thr76 3.58 Na CG2 B:Thr76 4.68 Na OG1 B:Thr76 2.57 Na C B:Thr76 3.34 Na CA B:Thr76 3.47 Na N B:Ala77 4.62 Na O B:Mse79 2.60 Na N B:Mse79 4.69 Na C B:Mse79 3.57 Na CA B:Mse79 4.77 Na N B:Pro80 4.06 Na CB B:Pro80 4.88 Na C B:Pro80 4.27 Na CA B:Pro80 3.69 Na O B:Leu81 4.78 Na N B:Leu81 3.78 Na CB B:Leu81 4.82 Na CA B:Leu81 4.85 Na O B:Act304 2.60 Na CH3 B:Act304 4.33 Na C B:Act304 3.22 Na OXT B:Act304 3.43 interactive model: Sodium binding site 3 out of 7 in 4few Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Sodium in the PDB 4few. 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: Asp167, D: Glu169, D: Trp233, D: Asn234, D: Gln244, D: Kan301, D: Hoh418, D: Hoh469, D: Hoh522, D: Hoh583, D: Hoh584, D: Hoh612, conact list: Atom Atom Distance (A) Na CB D:Asp167 4.77 Na OD2 D:Asp167 4.67 Na OD1 D:Asp167 4.69 Na CG D:Asp167 4.51 Na OE1 D:Glu169 4.44 Na OE2 D:Glu169 4.49 Na CD D:Glu169 4.92 Na CE3 D:Trp233 4.59 Na CZ3 D:Trp233 3.91 Na CH2 D:Trp233 4.67 Na O D:Asn234 4.29 Na CB D:Asn234 4.40 Na ND2 D:Asn234 4.39 Na C D:Asn234 4.71 Na OD1 D:Asn234 2.26 Na CG D:Asn234 3.48 Na CA D:Asn234 4.18 Na NE2 D:Gln244 4.57 Na N4 D:Kan301 4.29 Na O D:Hoh418 4.25 Na O D:Hoh469 2.43 Na O D:Hoh522 2.49 Na O D:Hoh583 2.45 Na O D:Hoh584 4.32 Na O D:Hoh612 2.50 interactive model: Sodium binding site 4 out of 7 in 4few Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Sodium in the PDB 4few. 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: Thr76, D: Ala77, D: Mse79, D: Pro80, D: Leu81, D: Act306, D: Hoh524, conact list: Atom Atom Distance (A) Na O D:Thr76 2.46 Na N D:Thr76 4.86 Na CB D:Thr76 3.46 Na CG2 D:Thr76 4.29 Na OG1 D:Thr76 2.43 Na C D:Thr76 3.29 Na CA D:Thr76 3.43 Na N D:Ala77 4.56 Na O D:Mse79 2.57 Na N D:Mse79 4.55 Na C D:Mse79 3.59 Na CA D:Mse79 4.69 Na N D:Pro80 4.21 Na C D:Pro80 4.38 Na CA D:Pro80 3.93 Na O D:Leu81 4.69 Na N D:Leu81 3.81 Na CB D:Leu81 4.70 Na CG D:Leu81 4.99 Na CA D:Leu81 4.80 Na O D:Act306 2.57 Na CH3 D:Act306 4.18 Na C D:Act306 3.57 Na OXT D:Act306 4.45 Na O D:Hoh524 2.39 interactive model: Sodium binding site 5 out of 7 in 4few Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Sodium in the PDB 4few. 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: E: Thr76, E: Ala77, E: Mse79, E: Pro80, E: Leu81, E: Act304, E: Hoh521, E: Hoh581, conact list: Atom Atom Distance (A) Na O E:Thr76 2.38 Na N E:Thr76 4.92 Na CB E:Thr76 3.57 Na CG2 E:Thr76 4.52 Na OG1 E:Thr76 2.53 Na C E:Thr76 3.27 Na CA E:Thr76 3.50 Na N E:Ala77 4.52 Na O E:Mse79 2.53 Na N E:Mse79 4.44 Na C E:Mse79 3.53 Na CA E:Mse79 4.63 Na N E:Pro80 4.13 Na C E:Pro80 4.43 Na CA E:Pro80 3.88 Na O E:Leu81 4.94 Na N E:Leu81 3.95 Na CB E:Leu81 4.98 Na CG E:Leu81 4.99 Na O E:Act304 2.41 Na CH3 E:Act304 4.69 Na C E:Act304 3.40 Na OXT E:Act304 3.65 Na O E:Hoh521 2.38 Na O E:Hoh581 2.51 Na O E:Hoh581 3.81 interactive model: Sodium binding site 6 out of 7 in 4few Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Sodium in the PDB 4few. 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: F: Asp167, F: Glu169, F: Trp233, F: Asn234, F: Gln244, F: Kan301, F: Hoh478, F: Hoh513, F: Hoh515, F: Hoh525, F: Hoh600, conact list: Atom Atom Distance (A) Na CB F:Asp167 4.76 Na OD2 F:Asp167 4.74 Na OD1 F:Asp167 4.82 Na CG F:Asp167 4.58 Na OE1 F:Glu169 4.57 Na OE2 F:Glu169 4.40 Na CD F:Glu169 4.95 Na CE3 F:Trp233 4.61 Na CZ3 F:Trp233 3.86 Na CH2 F:Trp233 4.57 Na O F:Asn234 4.41 Na CB F:Asn234 4.50 Na ND2 F:Asn234 4.44 Na C F:Asn234 4.85 Na OD1 F:Asn234 2.34 Na CG F:Asn234 3.56 Na CA F:Asn234 4.32 Na NE2 F:Gln244 4.59 Na N4 F:Kan301 4.41 Na O F:Hoh478 4.09 Na O F:Hoh513 2.48 Na O F:Hoh515 2.38 Na O F:Hoh525 2.50 Na O F:Hoh600 2.44 interactive model: Sodium binding site 7 out of 7 in 4few Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Sodium in the PDB 4few. 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: F: Thr76, F: Ala77, F: Mse79, F: Pro80, F: Leu81, F: Act305, F: Hoh595, F: Hoh602, conact list: Atom Atom Distance (A) Na O F:Thr76 2.35 Na N F:Thr76 4.88 Na CB F:Thr76 3.46 Na CG2 F:Thr76 4.37 Na OG1 F:Thr76 2.40 Na C F:Thr76 3.22 Na CA F:Thr76 3.44 Na N F:Ala77 4.48 Na O F:Mse79 2.49 Na N F:Mse79 4.49 Na C F:Mse79 3.51 Na CA F:Mse79 4.64 Na N F:Pro80 4.11 Na C F:Pro80 4.46 Na CA F:Pro80 3.87 Na O F:Leu81 4.88 Na N F:Leu81 4.00 Na O F:Act305 3.99 Na CH3 F:Act305 4.45 Na C F:Act305 3.38 Na OXT F:Act305 2.15 Na O F:Hoh595 2.40 Na O F:Hoh602 2.34 interactive model: