Sodium in the structure of E. Coli (Lacz) Beta-Galactosidase (N460T) (pdb 3vda)

The binding sites of Sodium atom in the structure of E. Coli (Lacz) Beta-Galactosidase (N460T) (pdb code 3vda). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 3vda 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) 46.0-2.5 Space group P212121 a (A) 152.596 b (A) 164.691 c (A) 203.245 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 17.4 Rfree (%) 23.7 Sodium Binding Sites: Sodium binding site 1 out of 10 in 3vda Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 3vda. 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: Hoh4084, A: Hoh4286, A: Hoh4311, A: Hoh4397, conact list: Atom Atom Distance (A) Na OH A:Tyr100 3.85 Na ND2 A:Asn102 4.93 Na O A:Asp201 4.74 Na CB A:Asp201 4.40 Na OD2 A:Asp201 2.41 Na OD1 A:Asp201 3.63 Na CG A:Asp201 3.24 Na NE2 A:His540 4.66 Na CZ2 A:Trp568 4.72 Na CE2 A:Trp568 4.76 Na NE1 A:Trp568 4.11 Na O A:Phe601 2.38 Na CB A:Phe601 4.63 Na C A:Phe601 3.56 Na CA A:Phe601 4.60 Na N A:Cys602 4.35 Na C A:Cys602 4.86 Na CA A:Cys602 4.29 Na CB A:Asn604 4.78 Na ND2 A:Asn604 3.71 Na OD1 A:Asn604 2.40 Na CG A:Asn604 3.40 Na O A:Hoh4084 4.60 Na O A:Hoh4286 3.33 Na O A:Hoh4311 2.28 Na O A:Hoh4397 4.00 interactive model: Sodium binding site 2 out of 10 in 3vda Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 3vda. 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: Phe556, A: Arg557, A: Tyr559, A: Pro560, A: Arg561, A: Leu562, A: Gln563, A: Hoh4041, A: Hoh4312, conact list: Atom Atom Distance (A) Na CD1 A:Leu350 4.89 Na O A:Phe556 2.37 Na C A:Phe556 3.57 Na CA A:Phe556 4.35 Na O A:Arg557 4.61 Na N A:Arg557 4.58 Na C A:Arg557 4.73 Na CA A:Arg557 4.72 Na O A:Tyr559 2.38 Na N A:Tyr559 4.56 Na C A:Tyr559 3.37 Na CA A:Tyr559 4.51 Na O A:Pro560 3.20 Na N A:Pro560 3.95 Na C A:Pro560 3.58 Na CA A:Pro560 3.62 Na N A:Arg561 4.54 Na C A:Arg561 4.97 Na O A:Leu562 2.39 Na N A:Leu562 4.14 Na CB A:Leu562 4.57 Na C A:Leu562 3.51 Na CA A:Leu562 4.30 Na N A:Gln563 4.47 Na CG A:Gln563 4.87 Na CA A:Gln563 4.57 Na O A:Hoh4041 2.44 Na O A:Hoh4312 2.76 interactive model: Sodium binding site 3 out of 10 in 3vda Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Sodium in the PDB 3vda. 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: Hoh4014, A: Hoh4065, conact list: Atom Atom Distance (A) Na CE2 A:Phe931 3.88 Na CD1 A:Phe931 4.60 Na CD2 A:Phe931 4.45 Na CZ A:Phe931 3.66 Na C A:Phe931 4.99 Na CE1 A:Phe931 4.05 Na CG A:Phe931 4.79 Na O A:Pro932 2.39 Na N A:Pro932 4.14 Na CB A:Pro932 4.11 Na CD A:Pro932 4.13 Na C A:Pro932 3.45 Na CG A:Pro932 4.64 Na CA A:Pro932 4.09 Na N A:Ser933 4.51 Na CA A:Ser933 4.89 Na O A:Leu967 2.55 Na C A:Leu967 3.71 Na CA A:Leu967 4.93 Na O A:Met968 3.98 Na N A:Met968 4.28 Na C A:Met968 3.99 Na CA A:Met968 3.87 Na N A:Glu969 4.68 Na O A:Thr970 2.84 Na N A:Thr970 4.54 Na C A:Thr970 4.04 Na CA A:Thr970 4.91 Na N A:Ser971 4.94 Na CA A:Ser971 4.94 Na O A:Hoh4014 2.24 Na O A:Hoh4065 2.75 interactive model: Sodium binding site 4 out of 10 in 3vda Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Sodium in the PDB 3vda. 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: Asp201, B: His540, B: Trp568, B: Phe601, B: Cys602, B: Asn604, B: Hoh4274, B: Hoh4372, conact list: Atom Atom Distance (A) Na OH B:Tyr100 3.81 Na O B:Asp201 4.58 Na CB B:Asp201 4.47 Na OD2 B:Asp201 2.40 Na OD1 B:Asp201 3.66 Na CG B:Asp201 3.28 Na NE2 B:His540 4.70 Na CZ2 B:Trp568 4.68 Na CE2 B:Trp568 4.75 Na NE1 B:Trp568 4.10 Na O B:Phe601 2.71 Na CB B:Phe601 4.87 Na C B:Phe601 3.81 Na CA B:Phe601 4.86 Na N B:Cys602 4.53 Na C B:Cys602 4.89 Na CA B:Cys602 4.43 Na CB B:Asn604 4.76 Na ND2 B:Asn604 3.98 Na OD1 B:Asn604 2.40 Na CG B:Asn604 3.49 Na O B:Hoh4274 2.55 Na O B:Hoh4372 2.69 interactive model: Sodium binding site 5 out of 10 in 3vda Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Sodium in the PDB 3vda. 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: Hoh4079, B: Hoh4175, B: Hoh4275, conact list: Atom Atom Distance (A) Na CD1 B:Leu350 4.44 Na O B:Phe556 2.36 Na CB B:Phe556 4.84 Na C B:Phe556 3.52 Na CA B:Phe556 4.28 Na O B:Arg557 4.60 Na N B:Arg557 4.52 Na C B:Arg557 4.74 Na CA B:Arg557 4.67 Na O B:Tyr559 2.38 Na N B:Tyr559 4.63 Na C B:Tyr559 3.46 Na CA B:Tyr559 4.60 Na O B:Pro560 3.56 Na N B:Pro560 4.07 Na C B:Pro560 3.87 Na CA B:Pro560 3.87 Na N B:Arg561 4.76 Na O B:Leu562 2.39 Na N B:Leu562 4.33 Na CB B:Leu562 4.67 Na C B:Leu562 3.50 Na CA B:Leu562 4.37 Na N B:Gln563 4.40 Na CG B:Gln563 4.76 Na CA B:Gln563 4.43 Na O B:Hoh4079 2.58 Na O B:Hoh4175 3.90 Na O B:Hoh4275 3.09 interactive model: Sodium binding site 6 out of 10 in 3vda Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Sodium in the PDB 3vda. 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: Hoh4241, C: Hoh4279, C: Hoh4368, conact list: Atom Atom Distance (A) Na OH C:Tyr100 3.94 Na ND2 C:Asn102 4.74 Na CB C:Asp201 4.86 Na OD2 C:Asp201 2.62 Na OD1 C:Asp201 4.07 Na CG C:Asp201 3.66 Na NE2 C:His540 4.27 Na CE1 C:His540 4.48 Na NE1 C:Trp568 4.32 Na O C:Phe601 2.37 Na CB C:Phe601 4.40 Na CD1 C:Phe601 4.53 Na C C:Phe601 3.59 Na CA C:Phe601 4.45 Na N C:Cys602 4.54 Na CA C:Cys602 4.63 Na CB C:Asn604 4.71 Na ND2 C:Asn604 3.58 Na OD1 C:Asn604 2.41 Na CG C:Asn604 3.32 Na O C:Hoh4241 3.50 Na O C:Hoh4279 2.65 Na O C:Hoh4368 2.36 interactive model: Sodium binding site 7 out of 10 in 3vda Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Sodium in the PDB 3vda. 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: Ala555, C: Phe556, C: Arg557, C: Tyr559, C: Pro560, C: Arg561, C: Leu562, C: Gln563, C: Hoh4275, C: Hoh4280, C: Hoh4305, C: Hoh4336, conact list: Atom Atom Distance (A) Na CD1 C:Leu350 4.69 Na O C:Ala555 4.98 Na O C:Phe556 2.37 Na CB C:Phe556 4.85 Na C C:Phe556 3.54 Na CA C:Phe556 4.22 Na O C:Arg557 4.74 Na N C:Arg557 4.59 Na C C:Arg557 4.81 Na CA C:Arg557 4.75 Na O C:Tyr559 2.38 Na N C:Tyr559 4.61 Na C C:Tyr559 3.38 Na CA C:Tyr559 4.54 Na O C:Pro560 3.16 Na N C:Pro560 3.94 Na C C:Pro560 3.58 Na CA C:Pro560 3.66 Na N C:Arg561 4.53 Na C C:Arg561 4.88 Na O C:Leu562 2.38 Na N C:Leu562 4.10 Na CB C:Leu562 4.46 Na C C:Leu562 3.39 Na CA C:Leu562 4.18 Na N C:Gln563 4.28 Na CG C:Gln563 4.72 Na CA C:Gln563 4.33 Na O C:Hoh4275 2.61 Na O C:Hoh4280 2.33 Na O C:Hoh4305 4.10 Na O C:Hoh4336 4.90 interactive model: Sodium binding site 8 out of 10 in 3vda Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Sodium in the PDB 3vda. 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: His540, D: Trp568, D: Phe601, D: Cys602, D: Asn604, D: Hoh4049, D: Hoh4080, D: Hoh4212, D: Hoh4301, conact list: Atom Atom Distance (A) Na CZ D:Tyr100 4.97 Na OH D:Tyr100 3.79 Na O D:Asp201 5.00 Na CB D:Asp201 4.33 Na OD2 D:Asp201 2.40 Na OD1 D:Asp201 3.51 Na CG D:Asp201 3.17 Na NE2 D:His540 4.79 Na CZ2 D:Trp568 4.81 Na CE2 D:Trp568 4.83 Na NE1 D:Trp568 4.17 Na O D:Phe601 2.38 Na CB D:Phe601 4.66 Na C D:Phe601 3.58 Na CA D:Phe601 4.63 Na N D:Cys602 4.38 Na C D:Cys602 4.82 Na CA D:Cys602 4.33 Na CB D:Asn604 4.77 Na ND2 D:Asn604 3.82 Na OD1 D:Asn604 2.41 Na CG D:Asn604 3.44 Na O D:Hoh4049 2.38 Na O D:Hoh4080 4.43 Na O D:Hoh4212 2.52 Na O D:Hoh4301 3.63 interactive model: Sodium binding site 9 out of 10 in 3vda Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 9 of Sodium in the PDB 3vda. 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: Hoh4124, D: Hoh4244, conact list: Atom Atom Distance (A) Na CD1 D:Leu350 4.73 Na O D:Phe556 2.36 Na CB D:Phe556 4.91 Na C D:Phe556 3.54 Na CA D:Phe556 4.25 Na O D:Arg557 4.94 Na N D:Arg557 4.56 Na C D:Arg557 4.91 Na CA D:Arg557 4.75 Na O D:Tyr559 2.38 Na N D:Tyr559 4.67 Na C D:Tyr559 3.43 Na CA D:Tyr559 4.56 Na O D:Pro560 3.30 Na N D:Pro560 4.05 Na C D:Pro560 3.62 Na CA D:Pro560 3.73 Na N D:Arg561 4.47 Na C D:Arg561 4.87 Na O D:Leu562 2.38 Na N D:Leu562 4.06 Na CB D:Leu562 4.52 Na C D:Leu562 3.43 Na CA D:Leu562 4.24 Na N D:Gln563 4.32 Na CG D:Gln563 4.62 Na CA D:Gln563 4.38 Na O D:Hoh4124 2.56 Na O D:Hoh4244 2.58 interactive model: Sodium binding site 10 out of 10 in 3vda Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 10 of Sodium in the PDB 3vda. 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: Phe931, D: Pro932, D: Ser933, D: Leu967, D: Met968, D: Glu969, D: Thr970, D: Ser971, D: Hoh4134, D: Hoh4217, conact list: Atom Atom Distance (A) Na CE2 D:Phe931 4.07 Na CD1 D:Phe931 4.43 Na CD2 D:Phe931 4.72 Na CZ D:Phe931 3.54 Na CE1 D:Phe931 3.74 Na CG D:Phe931 4.89 Na O D:Pro932 2.84 Na N D:Pro932 4.49 Na CB D:Pro932 4.47 Na CD D:Pro932 4.33 Na C D:Pro932 3.88 Na CG D:Pro932 4.89 Na CA D:Pro932 4.52 Na N D:Ser933 4.87 Na O D:Leu967 2.61 Na C D:Leu967 3.74 Na O D:Met968 3.71 Na N D:Met968 4.24 Na CB D:Met968 4.98 Na C D:Met968 3.80 Na CA D:Met968 3.76 Na N D:Glu969 4.53 Na C D:Glu969 4.99 Na O D:Thr970 2.78 Na N D:Thr970 4.38 Na C D:Thr970 3.87 Na CA D:Thr970 4.75 Na N D:Ser971 4.73 Na CA D:Ser971 4.72 Na O D:Hoh4134 2.75 Na O D:Hoh4217 2.64 interactive model: