Sodium in the structure of E. Coli (Lacz) Beta-Galactosidase (N460S) (pdb 3vd5)

The binding sites of Sodium atom in the structure of E. Coli (Lacz) Beta-Galactosidase (N460S) (pdb code 3vd5). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 3vd5 structure was solved by R.W.WHEATLEY, J.C.KAPPELHOFF, J.N.HAHN, M.L.DUGDALE, M.J.DUTKOSKI, S.D.TAMMAN, M.E.FRASER, R.E.HUBER, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 54.6-2.7 Space group P1211 a (A) 126.299 b (A) 150.745 c (A) 131.086 alpha (°) 90.00 beta (°) 104.06 gamma (°) 90.00 Rfactor (%) 20.3 Rfree (%) 27.6 Sodium Binding Sites: Sodium binding site 1 out of 11 in 3vd5 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 3vd5. 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: Tyr100, A: Asn102, A: Asp201, A: His540, A: Trp568, A: Phe601, A: Cys602, A: Asn604, A: Hoh4014, A: Hoh4266, A: Hoh4267, conact list: Atom Atom Distance (A) Na CZ A:Tyr100 4.93 Na OH A:Tyr100 3.77 Na ND2 A:Asn102 4.41 Na O A:Asp201 4.92 Na CB A:Asp201 4.69 Na OD2 A:Asp201 2.40 Na OD1 A:Asp201 3.60 Na CG A:Asp201 3.34 Na NE2 A:His540 4.32 Na CE1 A:His540 4.70 Na CZ2 A:Trp568 4.94 Na CE2 A:Trp568 4.87 Na NE1 A:Trp568 4.16 Na O A:Phe601 2.38 Na CB A:Phe601 4.46 Na CD2 A:Phe601 4.91 Na C A:Phe601 3.57 Na CA A:Phe601 4.47 Na N A:Cys602 4.48 Na CA A:Cys602 4.53 Na CB A:Asn604 4.69 Na ND2 A:Asn604 3.57 Na OD1 A:Asn604 2.38 Na CG A:Asn604 3.30 Na O A:Hoh4014 4.80 Na O A:Hoh4266 2.07 Na O A:Hoh4267 2.47 interactive model: Sodium binding site 2 out of 11 in 3vd5 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 3vd5. 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: Leu350, A: Ala555, A: Phe556, A: Arg557, A: Tyr559, A: Pro560, A: Arg561, A: Leu562, A: Gln563, A: Hoh4112, A: Hoh4268, A: Hoh4269, conact list: Atom Atom Distance (A) Na CD1 A:Leu350 4.74 Na O A:Ala555 4.95 Na O A:Phe556 2.38 Na CB A:Phe556 4.80 Na C A:Phe556 3.49 Na CA A:Phe556 4.18 Na N A:Arg557 4.53 Na C A:Arg557 4.89 Na CA A:Arg557 4.77 Na O A:Tyr559 2.38 Na N A:Tyr559 4.69 Na C A:Tyr559 3.46 Na CA A:Tyr559 4.62 Na O A:Pro560 3.16 Na N A:Pro560 4.07 Na C A:Pro560 3.64 Na CA A:Pro560 3.78 Na N A:Arg561 4.59 Na C A:Arg561 4.93 Na O A:Leu562 2.37 Na N A:Leu562 4.20 Na CB A:Leu562 4.54 Na C A:Leu562 3.39 Na CA A:Leu562 4.28 Na N A:Gln563 4.20 Na CB A:Gln563 4.93 Na CG A:Gln563 4.52 Na CA A:Gln563 4.16 Na O A:Hoh4112 2.54 Na O A:Hoh4268 2.08 Na O A:Hoh4269 3.93 interactive model: Sodium binding site 3 out of 11 in 3vd5 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Sodium in the PDB 3vd5. 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: Phe931, A: Pro932, A: Ser933, A: Leu967, A: Met968, A: Glu969, A: Thr970, A: Ser971, A: Hoh4191, A: Hoh4270, conact list: Atom Atom Distance (A) Na CE2 A:Phe931 3.97 Na CD1 A:Phe931 4.54 Na CD2 A:Phe931 4.47 Na CZ A:Phe931 3.72 Na C A:Phe931 4.92 Na CE1 A:Phe931 4.04 Na CG A:Phe931 4.74 Na O A:Pro932 2.73 Na N A:Pro932 4.27 Na CB A:Pro932 4.04 Na CD A:Pro932 4.18 Na C A:Pro932 3.74 Na CG A:Pro932 4.50 Na CA A:Pro932 4.28 Na N A:Ser933 4.82 Na O A:Leu967 2.38 Na C A:Leu967 3.52 Na CA A:Leu967 4.65 Na O A:Met968 4.01 Na N A:Met968 4.17 Na C A:Met968 3.90 Na CA A:Met968 3.91 Na N A:Glu969 4.40 Na C A:Glu969 4.77 Na O A:Thr970 2.38 Na N A:Thr970 3.84 Na CB A:Thr970 4.90 Na C A:Thr970 3.45 Na CA A:Thr970 4.19 Na N A:Ser971 4.46 Na CA A:Ser971 4.71 Na O A:Hoh4191 4.35 Na O A:Hoh4270 3.17 interactive model: Sodium binding site 4 out of 11 in 3vd5 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Sodium in the PDB 3vd5. 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: Tyr100, C: Asn102, C: Asp201, C: His540, C: Trp568, C: Phe601, C: Cys602, C: Asn604, C: Hoh4173, conact list: Atom Atom Distance (A) Na CZ C:Tyr100 4.61 Na CE1 C:Tyr100 4.99 Na OH C:Tyr100 3.50 Na ND2 C:Asn102 4.63 Na O C:Asp201 4.41 Na CB C:Asp201 4.36 Na OD2 C:Asp201 2.41 Na OD1 C:Asp201 3.61 Na CG C:Asp201 3.22 Na NE2 C:His540 4.57 Na CZ2 C:Trp568 4.58 Na CE2 C:Trp568 4.64 Na NE1 C:Trp568 3.98 Na O C:Phe601 2.38 Na CB C:Phe601 4.64 Na C C:Phe601 3.57 Na CA C:Phe601 4.61 Na O C:Cys602 4.88 Na N C:Cys602 4.34 Na C C:Cys602 4.67 Na CA C:Cys602 4.26 Na CB C:Asn604 4.74 Na ND2 C:Asn604 3.76 Na OD1 C:Asn604 2.37 Na CG C:Asn604 3.39 Na O C:Hoh4173 2.40 interactive model: Sodium binding site 5 out of 11 in 3vd5 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Sodium in the PDB 3vd5. 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: Leu350, C: Phe556, C: Arg557, C: Tyr559, C: Pro560, C: Arg561, C: Leu562, C: Gln563, C: Hoh4074, conact list: Atom Atom Distance (A) Na CD1 C:Leu350 4.32 Na O C:Phe556 2.37 Na CB C:Phe556 4.76 Na C C:Phe556 3.53 Na CA C:Phe556 4.21 Na N C:Arg557 4.60 Na CA C:Arg557 4.86 Na O C:Tyr559 2.38 Na N C:Tyr559 4.76 Na C C:Tyr559 3.43 Na CA C:Tyr559 4.64 Na O C:Pro560 3.29 Na N C:Pro560 3.98 Na C C:Pro560 3.61 Na CA C:Pro560 3.69 Na N C:Arg561 4.48 Na C C:Arg561 4.89 Na O C:Leu562 2.38 Na N C:Leu562 4.13 Na CB C:Leu562 4.54 Na C C:Leu562 3.31 Na CA C:Leu562 4.21 Na N C:Gln563 4.05 Na CB C:Gln563 4.83 Na CG C:Gln563 4.53 Na CA C:Gln563 4.04 Na O C:Hoh4074 2.71 interactive model: Sodium binding site 6 out of 11 in 3vd5 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Sodium in the PDB 3vd5. 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: Phe931, C: Pro932, C: Leu967, C: Met968, C: Glu969, C: Thr970, C: Ser971, C: Hoh4178, conact list: Atom Atom Distance (A) Na CE2 C:Phe931 4.06 Na CD1 C:Phe931 4.60 Na CD2 C:Phe931 4.71 Na CZ C:Phe931 3.62 Na CE1 C:Phe931 3.92 Na CG C:Phe931 4.97 Na O C:Pro932 2.99 Na N C:Pro932 4.52 Na CB C:Pro932 4.19 Na CD C:Pro932 4.32 Na C C:Pro932 4.01 Na CG C:Pro932 4.63 Na CA C:Pro932 4.49 Na O C:Leu967 2.63 Na C C:Leu967 3.80 Na O C:Met968 3.93 Na N C:Met968 4.40 Na C C:Met968 3.91 Na CA C:Met968 4.02 Na N C:Glu969 4.43 Na C C:Glu969 4.63 Na O C:Thr970 2.38 Na N C:Thr970 3.80 Na CB C:Thr970 4.90 Na C C:Thr970 3.33 Na CA C:Thr970 4.14 Na N C:Ser971 4.19 Na C C:Ser971 4.99 Na CA C:Ser971 4.27 Na O C:Hoh4178 3.29 interactive model: Sodium binding site 7 out of 11 in 3vd5 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Sodium in the PDB 3vd5. 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: Tyr100, D: Asp201, D: Trp568, D: Phe601, D: Cys602, D: Met603, D: Asn604, D: Hoh4233, D: Hoh4234, conact list: Atom Atom Distance (A) Na CZ D:Tyr100 4.65 Na OH D:Tyr100 3.53 Na O D:Asp201 4.42 Na CB D:Asp201 4.42 Na OD2 D:Asp201 2.41 Na OD1 D:Asp201 3.33 Na CG D:Asp201 3.13 Na CZ2 D:Trp568 4.60 Na CE2 D:Trp568 4.72 Na NE1 D:Trp568 4.10 Na O D:Phe601 2.38 Na CB D:Phe601 4.78 Na C D:Phe601 3.52 Na CA D:Phe601 4.64 Na O D:Cys602 4.59 Na N D:Cys602 4.18 Na C D:Cys602 4.37 Na CA D:Cys602 3.99 Na N D:Met603 5.00 Na CB D:Asn604 4.75 Na ND2 D:Asn604 3.93 Na OD1 D:Asn604 2.38 Na CG D:Asn604 3.46 Na O D:Hoh4233 2.47 Na O D:Hoh4234 3.61 interactive model: Sodium binding site 8 out of 11 in 3vd5 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Sodium in the PDB 3vd5. 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: Leu350, D: Phe556, D: Arg557, D: Tyr559, D: Pro560, D: Arg561, D: Leu562, D: Gln563, D: Hoh4237, conact list: Atom Atom Distance (A) Na CD1 D:Leu350 4.88 Na O D:Phe556 2.37 Na CB D:Phe556 4.99 Na C D:Phe556 3.57 Na CA D:Phe556 4.37 Na O D:Arg557 4.73 Na N D:Arg557 4.56 Na C D:Arg557 4.74 Na CA D:Arg557 4.68 Na O D:Tyr559 2.38 Na N D:Tyr559 4.48 Na C D:Tyr559 3.32 Na CA D:Tyr559 4.44 Na O D:Pro560 3.02 Na N D:Pro560 3.88 Na C D:Pro560 3.53 Na CA D:Pro560 3.68 Na N D:Arg561 4.52 Na C D:Arg561 4.89 Na O D:Leu562 2.37 Na N D:Leu562 4.02 Na CB D:Leu562 4.55 Na C D:Leu562 3.40 Na CA D:Leu562 4.19 Na N D:Gln563 4.31 Na CG D:Gln563 4.64 Na CA D:Gln563 4.39 Na O D:Hoh4237 3.82 interactive model: Sodium binding site 9 out of 11 in 3vd5 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 9 of Sodium in the PDB 3vd5. 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: Tyr100, B: Asn102, B: Asp201, B: His540, B: Trp568, B: Phe601, B: Cys602, B: Asn604, B: Hoh4160, B: Hoh4244, B: Hoh4245, conact list: Atom Atom Distance (A) Na CZ B:Tyr100 4.49 Na CE1 B:Tyr100 4.90 Na OH B:Tyr100 3.32 Na ND2 B:Asn102 4.49 Na O B:Asp201 4.22 Na CB B:Asp201 4.20 Na OD2 B:Asp201 2.41 Na OD1 B:Asp201 3.28 Na CG B:Asp201 3.02 Na NE2 B:His540 4.56 Na CZ2 B:Trp568 4.65 Na CE2 B:Trp568 4.72 Na NE1 B:Trp568 4.07 Na O B:Phe601 2.38 Na CB B:Phe601 4.65 Na C B:Phe601 3.51 Na CA B:Phe601 4.61 Na O B:Cys602 4.99 Na N B:Cys602 4.22 Na C B:Cys602 4.63 Na CA B:Cys602 4.15 Na CB B:Asn604 4.72 Na ND2 B:Asn604 3.85 Na OD1 B:Asn604 2.38 Na CG B:Asn604 3.42 Na O B:Hoh4160 4.76 Na O B:Hoh4244 2.30 Na O B:Hoh4245 2.64 interactive model: Sodium binding site 10 out of 11 in 3vd5 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 10 of Sodium in the PDB 3vd5. 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: Leu350, B: Phe556, B: Arg557, B: Tyr559, B: Pro560, B: Arg561, B: Leu562, B: Gln563, B: Hoh4129, B: Hoh4217, B: Hoh4241, conact list: Atom Atom Distance (A) Na CD1 B:Leu350 4.70 Na O B:Phe556 2.37 Na CB B:Phe556 4.86 Na C B:Phe556 3.53 Na CA B:Phe556 4.26 Na O B:Arg557 4.75 Na N B:Arg557 4.56 Na C B:Arg557 4.75 Na CA B:Arg557 4.71 Na O B:Tyr559 2.38 Na N B:Tyr559 4.59 Na C B:Tyr559 3.35 Na CA B:Tyr559 4.52 Na O B:Pro560 3.19 Na N B:Pro560 3.90 Na C B:Pro560 3.55 Na CA B:Pro560 3.63 Na N B:Arg561 4.47 Na C B:Arg561 4.94 Na O B:Leu562 2.38 Na N B:Leu562 4.11 Na CB B:Leu562 4.62 Na C B:Leu562 3.43 Na CA B:Leu562 4.28 Na N B:Gln563 4.28 Na CG B:Gln563 4.57 Na CA B:Gln563 4.34 Na O B:Hoh4129 4.04 Na O B:Hoh4217 2.42 Na O B:Hoh4241 3.13 interactive model: Sodium binding site 11 out of 11 in 3vd5 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 11 of Sodium in the PDB 3vd5. 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: Ser647, B: Asp648, B: Asn649, B: Glu650, B: Leu651, B: Pro669, B: Leu670, B: Asp671, B: Hoh4013, B: Hoh4155, conact list: Atom Atom Distance (A) Na O B:Ser647 2.72 Na CB B:Ser647 4.86 Na OG B:Ser647 4.42 Na C B:Ser647 3.76 Na CA B:Ser647 4.95 Na O B:Asp648 4.51 Na N B:Asp648 4.32 Na C B:Asp648 4.10 Na CA B:Asp648 4.01 Na N B:Asn649 4.38 Na C B:Asn649 4.81 Na CA B:Asn649 4.91 Na O B:Glu650 2.75 Na N B:Glu650 3.73 Na CB B:Glu650 4.72 Na C B:Glu650 3.81 Na CA B:Glu650 4.24 Na N B:Leu651 4.99 Na C B:Pro669 4.88 Na O B:Leu670 2.38 Na N B:Leu670 3.84 Na CB B:Leu670 4.38 Na C B:Leu670 3.47 Na CA B:Leu670 4.05 Na N B:Asp671 4.59 Na CA B:Asp671 4.99 Na O B:Hoh4013 2.94 Na O B:Hoh4155 2.90 interactive model: