Sodium in the structure of Crystal Structure of Putative Alpha-L-Fucosidase (NP_812709.1) From Bacteroides Thetaiotaomicron Vpi-5482 At 1.60 A Resolution (pdb 3gza)

The binding sites of Sodium atom in the structure of Crystal Structure of Putative Alpha-L-Fucosidase (NP_812709.1) From Bacteroides Thetaiotaomicron Vpi-5482 At 1.60 A Resolution (pdb code 3gza). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 3gza structure was solved by JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG), with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 28.1-1.6 Space group C121 a (A) 117.052 b (A) 81.532 c (A) 111.572 alpha (°) 90.00 beta (°) 103.55 gamma (°) 90.00 Rfactor (%) 13.9 Rfree (%) 16.8 Sodium Binding Sites: Sodium binding site 1 out of 2 in 3gza Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 3gza. 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: His48, A: Val49, A: Phe50, A: Asp51, A: Gly52, A: Ile53, A: Arg54, A: Tyr55, A: Trp302, A: Glu303, A: Pro304, A: Hoh578, A: Hoh629, A: Hoh668, conact list: Atom Atom Distance (A) Na O A:His48 2.38 Na CB A:His48 4.39 Na ND1 A:His48 4.45 Na C A:His48 3.48 Na CG A:His48 4.91 Na CA A:His48 4.46 Na O A:Val49 4.37 Na N A:Val49 4.22 Na C A:Val49 4.32 Na CA A:Val49 4.15 Na N A:Phe50 4.93 Na N A:Asp51 4.47 Na CB A:Asp51 4.51 Na OD2 A:Asp51 3.56 Na C A:Asp51 4.91 Na OD1 A:Asp51 2.43 Na CG A:Asp51 3.27 Na CA A:Asp51 4.80 Na N A:Gly52 4.67 Na O A:Ile53 2.33 Na N A:Ile53 4.06 Na C A:Ile53 3.53 Na CG1 A:Ile53 4.63 Na CA A:Ile53 4.37 Na O A:Arg54 4.23 Na N A:Arg54 4.49 Na C A:Arg54 4.14 Na CA A:Arg54 4.55 Na N A:Tyr55 4.33 Na CA A:Tyr55 4.73 Na O A:Trp302 4.51 Na CG A:Glu303 4.83 Na CD A:Pro304 4.91 Na O A:Hoh578 2.57 Na O A:Hoh629 2.40 Na O A:Hoh668 2.46 interactive model: Sodium binding site 2 out of 2 in 3gza Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 3gza. 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: His48, B: Val49, B: Phe50, B: Asp51, B: Gly52, B: Ile53, B: Arg54, B: Tyr55, B: Trp302, B: Glu303, B: Pro304, B: Hoh687, B: Hoh912, B: Hoh1016, B: Hoh1017, conact list: Atom Atom Distance (A) Na O B:His48 2.43 Na CB B:His48 4.48 Na ND1 B:His48 4.43 Na C B:His48 3.49 Na CG B:His48 4.96 Na CA B:His48 4.50 Na O B:Val49 4.21 Na N B:Val49 4.19 Na C B:Val49 4.21 Na CA B:Val49 4.09 Na N B:Phe50 4.89 Na N B:Asp51 4.40 Na CB B:Asp51 4.56 Na OD2 B:Asp51 3.68 Na C B:Asp51 4.86 Na OD1 B:Asp51 2.44 Na CG B:Asp51 3.33 Na CA B:Asp51 4.77 Na N B:Gly52 4.59 Na O B:Ile53 2.30 Na N B:Ile53 3.96 Na C B:Ile53 3.47 Na CG1 B:Ile53 4.67 Na CA B:Ile53 4.29 Na O B:Arg54 4.35 Na N B:Arg54 4.43 Na C B:Arg54 4.27 Na CA B:Arg54 4.55 Na N B:Tyr55 4.43 Na CA B:Tyr55 4.82 Na O B:Trp302 4.48 Na CG B:Glu303 4.70 Na CD B:Pro304 4.95 Na O B:Hoh687 2.33 Na O B:Hoh912 3.00 Na O B:Hoh1016 2.51 Na O B:Hoh1017 2.13 interactive model: