Sodium in the structure of E. Coli (Lacz) Beta-Galactosidase (M542A) (pdb 3i3e)

The binding sites of Sodium atom in the structure of E. Coli (Lacz) Beta-Galactosidase (M542A) (pdb code 3i3e). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 3i3e structure was solved by M.L.DUGDALE, D.DYMIANIW, B.MINHAS, R.E.HUBER, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 17.7-2.1 Space group P212121 a (A) 149.701 b (A) 168.417 c (A) 200.709 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 18.2 Rfree (%) 22.1 Sodium Binding Sites: Sodium binding site 1 out of 16 in 3i3e Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 3i3e. 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: Asp201, A: His540, A: Trp568, A: Phe601, A: Cys602, A: Met603, A: Asn604, A: Hoh4052, A: Hoh4170, A: Hoh4278, A: Hoh4300, A: Hoh7309, A: Hoh7338, A: Hoh7434, A: Hoh7435, conact list: Atom Atom Distance (A) Na OH A:Tyr100 4.32 Na OD2 A:Asp201 3.50 Na OD1 A:Asp201 4.94 Na CG A:Asp201 4.59 Na NE2 A:His540 3.82 Na CE1 A:His540 4.24 Na NE1 A:Trp568 4.24 Na O A:Phe601 2.24 Na CB A:Phe601 4.37 Na C A:Phe601 3.44 Na CA A:Phe601 4.23 Na N A:Cys602 4.44 Na C A:Cys602 4.86 Na CA A:Cys602 4.57 Na N A:Met603 5.00 Na CB A:Asn604 4.53 Na ND2 A:Asn604 3.72 Na OD1 A:Asn604 2.22 Na CG A:Asn604 3.25 Na O A:Hoh4052 4.66 Na O A:Hoh4170 2.36 Na O A:Hoh4278 2.38 Na O A:Hoh4300 4.98 Na O A:Hoh7309 4.54 Na O A:Hoh7338 2.53 Na O A:Hoh7434 2.52 Na O A:Hoh7435 4.57 interactive model: Sodium binding site 2 out of 16 in 3i3e Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 3i3e. 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: Hoh4286, A: Hoh4410, A: Hoh4652, A: Hoh5118, conact list: Atom Atom Distance (A) Na CD1 A:Leu350 4.93 Na O A:Ala555 4.92 Na O A:Phe556 2.21 Na CB A:Phe556 4.78 Na C A:Phe556 3.38 Na CA A:Phe556 4.13 Na O A:Arg557 4.87 Na N A:Arg557 4.42 Na C A:Arg557 4.75 Na CA A:Arg557 4.63 Na O A:Tyr559 2.27 Na N A:Tyr559 4.51 Na C A:Tyr559 3.33 Na CA A:Tyr559 4.44 Na O A:Pro560 3.35 Na N A:Pro560 3.99 Na C A:Pro560 3.69 Na CA A:Pro560 3.78 Na N A:Arg561 4.57 Na C A:Arg561 4.86 Na O A:Leu562 2.27 Na N A:Leu562 3.97 Na CB A:Leu562 4.35 Na C A:Leu562 3.36 Na CA A:Leu562 4.18 Na N A:Gln563 4.27 Na CG A:Gln563 4.58 Na CA A:Gln563 4.32 Na O A:Hoh4286 4.08 Na O A:Hoh4410 2.61 Na O A:Hoh4652 2.41 Na O A:Hoh5118 3.99 interactive model: Sodium binding site 3 out of 16 in 3i3e Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Sodium in the PDB 3i3e. 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: Hoh4207, A: Hoh7324, conact list: Atom Atom Distance (A) Na CE2 A:Phe931 3.90 Na CD1 A:Phe931 4.31 Na CD2 A:Phe931 4.41 Na CZ A:Phe931 3.57 Na C A:Phe931 4.75 Na CE1 A:Phe931 3.80 Na CG A:Phe931 4.60 Na O A:Pro932 2.73 Na N A:Pro932 4.11 Na CB A:Pro932 3.84 Na CD A:Pro932 4.06 Na C A:Pro932 3.64 Na CG A:Pro932 4.49 Na CA A:Pro932 4.06 Na N A:Ser933 4.75 Na O A:Leu967 2.88 Na C A:Leu967 4.07 Na O A:Met968 3.95 Na N A:Met968 4.70 Na C A:Met968 4.22 Na CA A:Met968 4.37 Na N A:Glu969 4.93 Na O A:Thr970 2.79 Na N A:Thr970 4.54 Na C A:Thr970 3.86 Na CA A:Thr970 4.78 Na N A:Ser971 4.68 Na CA A:Ser971 4.66 Na O A:Hoh4207 3.17 Na O A:Hoh7324 3.82 interactive model: Sodium binding site 4 out of 16 in 3i3e Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Sodium in the PDB 3i3e. 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: Ser647, A: Asp648, A: Asn649, A: Glu650, A: Leu651, A: Pro669, A: Leu670, A: Asp671, A: Dms8425, A: Hoh6122, conact list: Atom Atom Distance (A) Na O A:Ser647 2.58 Na CB A:Ser647 4.75 Na OG A:Ser647 4.34 Na C A:Ser647 3.79 Na CA A:Ser647 4.92 Na O A:Asp648 4.69 Na N A:Asp648 4.49 Na C A:Asp648 4.18 Na CA A:Asp648 4.26 Na N A:Asn649 4.16 Na C A:Asn649 4.62 Na CA A:Asn649 4.74 Na O A:Glu650 2.47 Na N A:Glu650 3.52 Na OE1 A:Glu650 4.97 Na CB A:Glu650 4.44 Na C A:Glu650 3.53 Na CA A:Glu650 3.99 Na N A:Leu651 4.71 Na C A:Pro669 4.74 Na O A:Leu670 2.38 Na N A:Leu670 3.78 Na CB A:Leu670 4.22 Na C A:Leu670 3.48 Na CA A:Leu670 4.04 Na N A:Asp671 4.61 Na CA A:Asp671 4.95 Na S A:Dms8425 3.45 Na O A:Dms8425 2.27 Na C2 A:Dms8425 4.93 Na C1 A:Dms8425 4.05 Na O A:Hoh6122 2.87 interactive model: Sodium binding site 5 out of 16 in 3i3e Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Sodium in the PDB 3i3e. 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: Met603, B: Asn604, B: Hoh4052, B: Hoh4170, B: Hoh4278, B: Hoh7191, B: Hoh7211, B: Hoh7216, B: Hoh7279, conact list: Atom Atom Distance (A) Na OH B:Tyr100 4.18 Na OD2 B:Asp201 3.57 Na OD1 B:Asp201 4.83 Na CG B:Asp201 4.60 Na NE2 B:His540 3.82 Na CE1 B:His540 4.17 Na NE1 B:Trp568 4.46 Na O B:Phe601 2.09 Na CB B:Phe601 4.10 Na C B:Phe601 3.26 Na CA B:Phe601 4.02 Na N B:Cys602 4.29 Na C B:Cys602 4.80 Na CA B:Cys602 4.47 Na N B:Met603 4.93 Na CB B:Asn604 4.51 Na ND2 B:Asn604 3.65 Na OD1 B:Asn604 2.28 Na CG B:Asn604 3.24 Na O B:Hoh4052 4.75 Na O B:Hoh4170 2.30 Na O B:Hoh4278 2.37 Na O B:Hoh7191 4.63 Na O B:Hoh7211 2.38 Na O B:Hoh7216 2.40 Na O B:Hoh7279 4.36 interactive model: Sodium binding site 6 out of 16 in 3i3e Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Sodium in the PDB 3i3e. 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: Ala555, B: Phe556, B: Arg557, B: Tyr559, B: Pro560, B: Arg561, B: Leu562, B: Gln563, B: Hoh4286, B: Hoh4410, B: Hoh4652, B: Hoh5118, conact list: Atom Atom Distance (A) Na CD1 B:Leu350 4.69 Na O B:Ala555 4.91 Na O B:Phe556 2.20 Na CB B:Phe556 4.73 Na C B:Phe556 3.38 Na CA B:Phe556 4.09 Na O B:Arg557 4.85 Na N B:Arg557 4.44 Na C B:Arg557 4.78 Na CA B:Arg557 4.66 Na O B:Tyr559 2.22 Na N B:Tyr559 4.52 Na CB B:Tyr559 4.98 Na C B:Tyr559 3.26 Na CA B:Tyr559 4.41 Na O B:Pro560 3.32 Na N B:Pro560 3.87 Na C B:Pro560 3.60 Na CA B:Pro560 3.65 Na N B:Arg561 4.50 Na C B:Arg561 4.80 Na O B:Leu562 2.28 Na N B:Leu562 3.88 Na CB B:Leu562 4.28 Na C B:Leu562 3.30 Na CA B:Leu562 4.10 Na N B:Gln563 4.19 Na CG B:Gln563 4.70 Na CA B:Gln563 4.30 Na O B:Hoh4286 3.93 Na O B:Hoh4410 2.64 Na O B:Hoh4652 2.44 Na O B:Hoh5118 4.27 interactive model: Sodium binding site 7 out of 16 in 3i3e Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Sodium in the PDB 3i3e. 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: Phe931, B: Pro932, B: Ser933, B: Leu967, B: Met968, B: Glu969, B: Thr970, B: Ser971, B: Hoh4207, B: Hoh4558, B: Hoh4763, conact list: Atom Atom Distance (A) Na CE2 B:Phe931 3.96 Na CD1 B:Phe931 4.49 Na CD2 B:Phe931 4.45 Na CZ B:Phe931 3.70 Na C B:Phe931 4.79 Na CE1 B:Phe931 4.00 Na CG B:Phe931 4.71 Na O B:Pro932 2.71 Na N B:Pro932 4.12 Na CB B:Pro932 3.85 Na CD B:Pro932 4.07 Na C B:Pro932 3.61 Na CG B:Pro932 4.51 Na CA B:Pro932 4.05 Na N B:Ser933 4.70 Na O B:Leu967 2.58 Na C B:Leu967 3.76 Na CA B:Leu967 4.95 Na O B:Met968 3.83 Na N B:Met968 4.40 Na C B:Met968 4.05 Na CA B:Met968 4.14 Na N B:Glu969 4.79 Na O B:Thr970 2.50 Na N B:Thr970 4.24 Na C B:Thr970 3.66 Na CA B:Thr970 4.52 Na N B:Ser971 4.57 Na CA B:Ser971 4.63 Na O B:Hoh4207 3.20 Na O B:Hoh4558 3.09 Na O B:Hoh4763 3.28 interactive model: Sodium binding site 8 out of 16 in 3i3e Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Sodium in the PDB 3i3e. 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: Leu670, B: Dms8425, B: Hoh5010, B: Hoh5124, B: Hoh7217, conact list: Atom Atom Distance (A) Na O B:Ser647 2.38 Na CB B:Ser647 4.73 Na OG B:Ser647 4.51 Na C B:Ser647 3.44 Na CA B:Ser647 4.69 Na O B:Asp648 4.12 Na N B:Asp648 3.94 Na C B:Asp648 3.49 Na CA B:Asp648 3.61 Na N B:Asn649 3.40 Na C B:Asn649 4.05 Na CA B:Asn649 4.08 Na O B:Glu650 2.77 Na N B:Glu650 3.06 Na OE1 B:Glu650 4.45 Na CB B:Glu650 4.25 Na C B:Glu650 3.62 Na CA B:Glu650 3.77 Na N B:Leu651 4.87 Na O B:Leu670 2.87 Na N B:Leu670 4.36 Na CB B:Leu670 4.71 Na C B:Leu670 4.02 Na CA B:Leu670 4.62 Na S B:Dms8425 3.44 Na O B:Dms8425 2.18 Na C2 B:Dms8425 4.64 Na C1 B:Dms8425 3.70 Na O B:Hoh5010 3.29 Na O B:Hoh5124 4.57 Na O B:Hoh7217 2.64 interactive model: Sodium binding site 9 out of 16 in 3i3e Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 9 of Sodium in the PDB 3i3e. 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: Asp201, C: His540, C: Trp568, C: Phe601, C: Cys602, C: Met603, C: Asn604, C: Hoh4052, C: Hoh4170, C: Hoh4278, C: Hoh7252, C: Hoh7262, C: Hoh7263, C: Hoh7268, conact list: Atom Atom Distance (A) Na OH C:Tyr100 4.28 Na OD2 C:Asp201 3.53 Na OD1 C:Asp201 4.87 Na CG C:Asp201 4.57 Na NE2 C:His540 3.80 Na CE1 C:His540 4.19 Na CD1 C:Trp568 4.99 Na NE1 C:Trp568 4.20 Na O C:Phe601 2.19 Na CB C:Phe601 4.24 Na C C:Phe601 3.38 Na CA C:Phe601 4.15 Na N C:Cys602 4.39 Na C C:Cys602 4.86 Na CA C:Cys602 4.54 Na N C:Met603 4.97 Na CB C:Asn604 4.38 Na ND2 C:Asn604 3.30 Na OD1 C:Asn604 2.24 Na CG C:Asn604 3.04 Na O C:Hoh4052 4.57 Na O C:Hoh4170 2.31 Na O C:Hoh4278 2.28 Na O C:Hoh7252 4.39 Na O C:Hoh7262 2.48 Na O C:Hoh7263 4.55 Na O C:Hoh7268 2.38 interactive model: Sodium binding site 10 out of 16 in 3i3e Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 10 of Sodium in the PDB 3i3e. 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: Hoh4286, C: Hoh4410, C: Hoh4580, C: Hoh4652, conact list: Atom Atom Distance (A) Na CD1 C:Leu350 4.88 Na O C:Ala555 4.93 Na O C:Phe556 2.28 Na CB C:Phe556 4.81 Na C C:Phe556 3.45 Na CA C:Phe556 4.18 Na O C:Arg557 4.92 Na N C:Arg557 4.50 Na C C:Arg557 4.80 Na CA C:Arg557 4.69 Na O C:Tyr559 2.26 Na N C:Tyr559 4.53 Na CB C:Tyr559 4.99 Na C C:Tyr559 3.30 Na CA C:Tyr559 4.43 Na O C:Pro560 3.23 Na N C:Pro560 3.90 Na C C:Pro560 3.57 Na CA C:Pro560 3.66 Na N C:Arg561 4.49 Na C C:Arg561 4.81 Na O C:Leu562 2.33 Na N C:Leu562 3.92 Na CB C:Leu562 4.34 Na C C:Leu562 3.34 Na CA C:Leu562 4.16 Na N C:Gln563 4.20 Na CG C:Gln563 4.55 Na CA C:Gln563 4.28 Na O C:Hoh4286 4.05 Na O C:Hoh4410 2.55 Na O C:Hoh4580 4.25 Na O C:Hoh4652 2.72 interactive model: Sodium binding site 11 out of 16 in 3i3e Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 11 of Sodium in the PDB 3i3e. 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: Ser933, C: Leu967, C: Met968, C: Glu969, C: Thr970, C: Ser971, C: Hoh4207, C: Hoh4558, C: Hoh4763, conact list: Atom Atom Distance (A) Na CE2 C:Phe931 3.88 Na CD1 C:Phe931 4.60 Na CD2 C:Phe931 4.47 Na CZ C:Phe931 3.64 Na CE1 C:Phe931 4.04 Na CG C:Phe931 4.81 Na O C:Pro932 2.94 Na N C:Pro932 4.42 Na CB C:Pro932 4.12 Na CD C:Pro932 4.34 Na C C:Pro932 3.89 Na CG C:Pro932 4.76 Na CA C:Pro932 4.37 Na N C:Ser933 4.96 Na O C:Leu967 2.70 Na C C:Leu967 3.82 Na O C:Met968 3.64 Na N C:Met968 4.34 Na C C:Met968 3.83 Na CA C:Met968 3.94 Na N C:Glu969 4.57 Na C C:Glu969 4.91 Na O C:Thr970 2.69 Na N C:Thr970 4.18 Na C C:Thr970 3.74 Na CA C:Thr970 4.55 Na N C:Ser971 4.64 Na CA C:Ser971 4.75 Na O C:Hoh4207 3.12 Na O C:Hoh4558 3.21 Na O C:Hoh4763 3.13 interactive model: Sodium binding site 12 out of 16 in 3i3e Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 12 of Sodium in the PDB 3i3e. 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: Ser647, C: Asp648, C: Asn649, C: Glu650, C: Leu651, C: Leu670, C: Asp671, C: Dms8425, C: Hoh5010, C: Hoh7269, conact list: Atom Atom Distance (A) Na O C:Ser647 2.38 Na CB C:Ser647 4.65 Na OG C:Ser647 4.26 Na C C:Ser647 3.52 Na CA C:Ser647 4.72 Na O C:Asp648 4.42 Na N C:Asp648 4.12 Na C C:Asp648 3.81 Na CA C:Asp648 3.85 Na N C:Asn649 3.76 Na C C:Asn649 4.40 Na CA C:Asn649 4.44 Na O C:Glu650 2.67 Na N C:Glu650 3.36 Na OE1 C:Glu650 4.77 Na CB C:Glu650 4.37 Na C C:Glu650 3.64 Na CA C:Glu650 3.95 Na N C:Leu651 4.85 Na O C:Leu670 2.47 Na N C:Leu670 4.05 Na CB C:Leu670 4.47 Na C C:Leu670 3.62 Na CA C:Leu670 4.27 Na N C:Asp671 4.71 Na CA C:Asp671 4.99 Na S C:Dms8425 3.30 Na O C:Dms8425 2.26 Na C2 C:Dms8425 4.86 Na C1 C:Dms8425 3.69 Na O C:Hoh5010 2.93 Na O C:Hoh7269 4.12 interactive model: Sodium binding site 13 out of 16 in 3i3e Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 13 of Sodium in the PDB 3i3e. 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: Met603, D: Asn604, D: Hoh4052, D: Hoh4278, D: Hoh7318, D: Hoh7319, D: Hoh7341, D: Hoh7342, D: Hoh7378, conact list: Atom Atom Distance (A) Na OH D:Tyr100 4.30 Na OD2 D:Asp201 3.54 Na OD1 D:Asp201 4.92 Na CG D:Asp201 4.60 Na NE2 D:His540 3.85 Na CE1 D:His540 4.26 Na NE1 D:Trp568 4.34 Na O D:Phe601 2.18 Na CB D:Phe601 4.19 Na C D:Phe601 3.37 Na CA D:Phe601 4.12 Na N D:Cys602 4.39 Na C D:Cys602 4.87 Na CA D:Cys602 4.57 Na N D:Met603 4.97 Na CB D:Asn604 4.57 Na ND2 D:Asn604 3.82 Na OD1 D:Asn604 2.30 Na CG D:Asn604 3.33 Na O D:Hoh4052 4.65 Na O D:Hoh4278 2.52 Na O D:Hoh7318 4.36 Na O D:Hoh7319 2.41 Na O D:Hoh7341 2.44 Na O D:Hoh7342 4.29 Na O D:Hoh7378 2.53 interactive model: Sodium binding site 14 out of 16 in 3i3e Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 14 of Sodium in the PDB 3i3e. 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: Ala555, D: Phe556, D: Arg557, D: Tyr559, D: Pro560, D: Arg561, D: Leu562, D: Gln563, D: Hoh4286, D: Hoh4410, D: Hoh4652, D: Hoh5118, conact list: Atom Atom Distance (A) Na CD1 D:Leu350 4.86 Na O D:Ala555 4.93 Na O D:Phe556 2.23 Na CB D:Phe556 4.82 Na C D:Phe556 3.42 Na CA D:Phe556 4.18 Na O D:Arg557 4.83 Na N D:Arg557 4.45 Na C D:Arg557 4.75 Na CA D:Arg557 4.63 Na O D:Tyr559 2.20 Na N D:Tyr559 4.51 Na CB D:Tyr559 4.95 Na C D:Tyr559 3.27 Na CA D:Tyr559 4.39 Na O D:Pro560 3.20 Na N D:Pro560 3.91 Na C D:Pro560 3.59 Na CA D:Pro560 3.71 Na N D:Arg561 4.53 Na C D:Arg561 4.82 Na O D:Leu562 2.32 Na N D:Leu562 3.95 Na CB D:Leu562 4.41 Na C D:Leu562 3.39 Na CA D:Leu562 4.20 Na N D:Gln563 4.28 Na CG D:Gln563 4.64 Na CA D:Gln563 4.34 Na O D:Hoh4286 3.83 Na O D:Hoh4410 2.52 Na O D:Hoh4652 2.49 Na O D:Hoh5118 3.98 interactive model: Sodium binding site 15 out of 16 in 3i3e Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 15 of Sodium in the PDB 3i3e. 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: Leu967, D: Met968, D: Glu969, D: Thr970, D: Ser971, D: Hoh4207, D: Hoh4558, D: Hoh4763, conact list: Atom Atom Distance (A) Na CE2 D:Phe931 3.80 Na CD1 D:Phe931 4.12 Na CD2 D:Phe931 4.36 Na CZ D:Phe931 3.34 Na C D:Phe931 4.89 Na CE1 D:Phe931 3.52 Na CG D:Phe931 4.51 Na O D:Pro932 3.01 Na N D:Pro932 4.33 Na CB D:Pro932 4.13 Na CD D:Pro932 4.27 Na C D:Pro932 3.95 Na CG D:Pro932 4.73 Na CA D:Pro932 4.35 Na O D:Leu967 3.06 Na C D:Leu967 4.20 Na O D:Met968 3.78 Na N D:Met968 4.74 Na C D:Met968 4.12 Na CA D:Met968 4.30 Na N D:Glu969 4.90 Na O D:Thr970 2.86 Na N D:Thr970 4.43 Na C D:Thr970 3.82 Na CA D:Thr970 4.74 Na N D:Ser971 4.56 Na CA D:Ser971 4.52 Na O D:Hoh4207 3.39 Na O D:Hoh4558 3.07 Na O D:Hoh4763 3.33 interactive model: Sodium binding site 16 out of 16 in 3i3e Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 16 of Sodium in the PDB 3i3e. 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: Ser647, D: Asp648, D: Asn649, D: Glu650, D: Leu651, D: Leu670, D: Dms8425, conact list: Atom Atom Distance (A) Na O D:Ser647 2.46 Na CB D:Ser647 4.76 Na OG D:Ser647 4.35 Na C D:Ser647 3.57 Na CA D:Ser647 4.80 Na O D:Asp648 4.20 Na N D:Asp648 4.11 Na C D:Asp648 3.63 Na CA D:Asp648 3.74 Na N D:Asn649 3.60 Na C D:Asn649 4.23 Na CA D:Asn649 4.25 Na O D:Glu650 2.76 Na N D:Glu650 3.23 Na OE1 D:Glu650 4.60 Na CB D:Glu650 4.37 Na C D:Glu650 3.67 Na CA D:Glu650 3.90 Na N D:Leu651 4.91 Na O D:Leu670 2.81 Na N D:Leu670 4.20 Na CB D:Leu670 4.62 Na C D:Leu670 3.94 Na CA D:Leu670 4.50 Na S D:Dms8425 3.20 Na O D:Dms8425 2.28 Na C2 D:Dms8425 4.73 Na C1 D:Dms8425 4.10 interactive model: