Sodium in the structure of Crystal Structure of Beta-Galactosidase From Bacteroides Thetaiotaomicron Vpi-5482 (pdb 3bga)

The binding sites of Sodium atom in the structure of Crystal Structure of Beta-Galactosidase From Bacteroides Thetaiotaomicron Vpi-5482 (pdb code 3bga). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 3bga structure was solved by D.KUMARAN, S.K.BURLEY, S.SWAMINATHAN, NEW YORK SGX RESEARCHCENTER FOR STRUCTURAL GENOMICS (NYSGXRC), with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 49.8-2.1 Space group P1211 a (A) 88.335 b (A) 138.864 c (A) 102.818 alpha (°) 90.00 beta (°) 109.73 gamma (°) 90.00 Rfactor (%) 20 Rfree (%) 23.4 Sodium Binding Sites: Sodium binding site 1 out of 4 in 3bga Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 3bga. 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: Tyr119, A: Asp227, A: His551, A: Trp579, A: Phe614, A: Cys615, A: Asn617, A: Hoh1054, A: Hoh1333, A: Hoh1589, A: Hoh1591, A: Hoh1592, A: Hoh1593, conact list: Atom Atom Distance (A) Na CZ A:Tyr119 4.89 Na OH A:Tyr119 3.83 Na O A:Asp227 4.63 Na CB A:Asp227 4.39 Na OD2 A:Asp227 2.38 Na OD1 A:Asp227 3.65 Na CG A:Asp227 3.24 Na NE2 A:His551 4.47 Na CD1 A:Trp579 4.94 Na CZ2 A:Trp579 4.85 Na CE2 A:Trp579 4.76 Na NE1 A:Trp579 3.99 Na O A:Phe614 2.28 Na CB A:Phe614 4.43 Na C A:Phe614 3.46 Na CA A:Phe614 4.48 Na N A:Cys615 4.27 Na C A:Cys615 4.73 Na CA A:Cys615 4.20 Na CB A:Asn617 4.74 Na ND2 A:Asn617 2.33 Na OD1 A:Asn617 3.80 Na CG A:Asn617 3.45 Na O A:Hoh1054 2.35 Na O A:Hoh1333 3.17 Na O A:Hoh1589 2.31 Na O A:Hoh1591 4.23 Na O A:Hoh1592 4.44 Na O A:Hoh1593 3.92 interactive model: Sodium binding site 2 out of 4 in 3bga Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 3bga. 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: Ala790, A: Thr923, A: Pro924, A: Gln925, A: Leu966, A: Glu967, A: Lys968, A: Ala969, A: His970, A: Hoh1099, A: Hoh1163, A: Hoh1286, A: Hoh1346, A: Hoh1520, conact list: Atom Atom Distance (A) Na O A:Ala790 4.88 Na CG2 A:Thr923 4.65 Na O A:Pro924 2.39 Na N A:Pro924 4.65 Na CB A:Pro924 4.37 Na CD A:Pro924 4.95 Na C A:Pro924 3.54 Na CA A:Pro924 4.41 Na N A:Gln925 4.46 Na CA A:Gln925 4.55 Na O A:Leu966 2.64 Na C A:Leu966 3.73 Na O A:Glu967 2.83 Na N A:Glu967 4.18 Na OE1 A:Glu967 4.70 Na C A:Glu967 3.37 Na CA A:Glu967 3.71 Na O A:Lys968 4.83 Na N A:Lys968 4.31 Na C A:Lys968 4.39 Na CA A:Lys968 4.87 Na O A:Ala969 2.45 Na N A:Ala969 4.04 Na C A:Ala969 3.61 Na CB A:Ala969 4.78 Na CA A:Ala969 4.29 Na N A:His970 4.68 Na ND1 A:His970 4.25 Na CE1 A:His970 4.73 Na CA A:His970 4.92 Na O A:Hoh1099 2.47 Na O A:Hoh1163 4.38 Na O A:Hoh1286 4.19 Na O A:Hoh1346 4.69 Na O A:Hoh1520 2.35 interactive model: Sodium binding site 3 out of 4 in 3bga Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Sodium in the PDB 3bga. 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: Tyr119, B: Asp227, B: His551, B: Trp579, B: Phe614, B: Cys615, B: Asn617, B: Hoh1039, B: Hoh1136, B: Hoh1464, B: Hoh1560, B: Hoh1603, B: Hoh1604, conact list: Atom Atom Distance (A) Na CZ B:Tyr119 4.98 Na OH B:Tyr119 3.95 Na O B:Asp227 4.65 Na CB B:Asp227 4.26 Na OD2 B:Asp227 2.20 Na OD1 B:Asp227 3.67 Na CG B:Asp227 3.15 Na NE2 B:His551 4.55 Na CD1 B:Trp579 4.99 Na CE2 B:Trp579 4.89 Na NE1 B:Trp579 4.11 Na O B:Phe614 2.34 Na CB B:Phe614 4.42 Na C B:Phe614 3.54 Na CA B:Phe614 4.52 Na N B:Cys615 4.39 Na C B:Cys615 4.83 Na CA B:Cys615 4.32 Na CB B:Asn617 4.76 Na ND2 B:Asn617 2.36 Na OD1 B:Asn617 3.73 Na CG B:Asn617 3.44 Na O B:Hoh1039 2.43 Na O B:Hoh1136 3.58 Na O B:Hoh1464 4.45 Na O B:Hoh1560 3.30 Na O B:Hoh1603 2.45 Na O B:Hoh1604 4.58 interactive model: Sodium binding site 4 out of 4 in 3bga Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Sodium in the PDB 3bga. 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: Ala790, B: Thr923, B: Pro924, B: Gln925, B: Leu966, B: Glu967, B: Lys968, B: Ala969, B: His970, B: Hoh1054, B: Hoh1139, B: Hoh1470, B: Hoh1547, conact list: Atom Atom Distance (A) Na O B:Ala790 4.86 Na CG2 B:Thr923 4.67 Na O B:Pro924 2.39 Na N B:Pro924 4.59 Na CB B:Pro924 4.16 Na CD B:Pro924 4.82 Na C B:Pro924 3.50 Na CA B:Pro924 4.31 Na N B:Gln925 4.44 Na CA B:Gln925 4.56 Na O B:Leu966 2.41 Na C B:Leu966 3.51 Na CA B:Leu966 4.81 Na O B:Glu967 2.62 Na N B:Glu967 3.99 Na OE1 B:Glu967 4.73 Na CB B:Glu967 4.96 Na C B:Glu967 3.23 Na CA B:Glu967 3.55 Na O B:Lys968 4.79 Na N B:Lys968 4.24 Na C B:Lys968 4.33 Na CA B:Lys968 4.82 Na O B:Ala969 2.44 Na N B:Ala969 3.99 Na C B:Ala969 3.57 Na CB B:Ala969 4.63 Na CA B:Ala969 4.22 Na N B:His970 4.66 Na ND1 B:His970 4.57 Na CA B:His970 4.98 Na O B:Hoh1054 4.45 Na O B:Hoh1139 4.36 Na O B:Hoh1470 2.54 Na O B:Hoh1547 2.81 interactive model: