Sodium in the structure of 2.27 Angstrom Crystal Structure of Beta-Phosphoglucomutase (Pgmb) From Clostridium Difficile (pdb 4gib)

The binding sites of Sodium atom in the structure of 2.27 Angstrom Crystal Structure of Beta-Phosphoglucomutase (Pgmb) From Clostridium Difficile (pdb code 4gib). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 4gib structure was solved by G.MINASOV, A.HALAVATY, L.SHUVALOVA, I.DUBROVSKA, J.WINSOR, S.GRIMSHAW, L.PAPAZISI, W.F.ANDERSON, CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUSDISEASES (CSGID), with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 29.9-2.3 Space group P1211 a (A) 61.807 b (A) 51.364 c (A) 79.442 alpha (°) 90.00 beta (°) 112.04 gamma (°) 90.00 Rfactor (%) 19.3 Rfree (%) 25.9 Sodium Binding Sites: Sodium binding site 1 out of 4 in 4gib Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 4gib. 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: Asn180, A: Met184, A: Phe185, A: Ser186, A: Asn199, A: Tyr220, A: Hoh402, A: Hoh463, A: Hoh470, conact list: Atom Atom Distance (A) Na O A:Asn180 4.75 Na N A:Asn180 4.75 Na CB A:Asn180 3.93 Na ND2 A:Asn180 4.55 Na C A:Asn180 4.85 Na OD1 A:Asn180 2.59 Na CG A:Asn180 3.48 Na CA A:Asn180 3.87 Na O A:Met184 2.47 Na N A:Met184 4.50 Na C A:Met184 3.61 Na CA A:Met184 4.69 Na N A:Phe185 4.33 Na C A:Phe185 4.61 Na CA A:Phe185 4.20 Na N A:Ser186 4.15 Na CB A:Ser186 4.72 Na OG A:Ser186 4.38 Na CB A:Asn199 4.81 Na ND2 A:Asn199 3.56 Na OD1 A:Asn199 2.48 Na CG A:Asn199 3.38 Na CE2 A:Tyr220 4.91 Na CZ A:Tyr220 3.80 Na CE1 A:Tyr220 3.91 Na OH A:Tyr220 3.08 Na O A:Hoh402 2.38 Na O A:Hoh463 4.74 Na O A:Hoh470 2.33 interactive model: Sodium binding site 2 out of 4 in 4gib Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 4gib. 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: Asp8, A: Asp10, A: Gly11, A: Val12, A: Lys44, A: Lys146, A: Glu170, A: Asp171, A: Ala172, A: Po4303, A: Hoh427, conact list: Atom Atom Distance (A) Na CB A:Asp8 3.86 Na OD2 A:Asp8 2.20 Na OD1 A:Asp8 4.33 Na CG A:Asp8 3.29 Na O A:Asp10 2.47 Na N A:Asp10 4.56 Na CB A:Asp10 4.28 Na OD2 A:Asp10 4.87 Na C A:Asp10 3.61 Na CG A:Asp10 4.80 Na CA A:Asp10 4.36 Na N A:Gly11 4.62 Na CA A:Gly11 4.79 Na CG2 A:Val12 4.56 Na CE A:Lys44 4.46 Na NZ A:Lys44 4.52 Na NZ A:Lys146 4.67 Na OE1 A:Glu170 2.23 Na OE2 A:Glu170 3.57 Na CD A:Glu170 3.20 Na C A:Glu170 4.88 Na CG A:Glu170 4.46 Na CA A:Glu170 4.88 Na N A:Asp171 3.90 Na CB A:Asp171 4.35 Na OD2 A:Asp171 4.03 Na C A:Asp171 4.80 Na OD1 A:Asp171 2.32 Na CG A:Asp171 3.36 Na CA A:Asp171 4.53 Na N A:Ala172 4.54 Na CB A:Ala172 4.87 Na O1 A:Po4303 3.80 Na O A:Hoh427 2.16 interactive model: Sodium binding site 3 out of 4 in 4gib Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Sodium in the PDB 4gib. 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: Asn180, B: Asn183, B: Met184, B: Phe185, B: Ser186, B: Asn199, B: Tyr220, B: Hoh432, B: Hoh449, B: Hoh450, conact list: Atom Atom Distance (A) Na O B:Asn180 4.60 Na N B:Asn180 4.85 Na CB B:Asn180 4.00 Na ND2 B:Asn180 4.69 Na C B:Asn180 4.80 Na OD1 B:Asn180 2.66 Na CG B:Asn180 3.58 Na CA B:Asn180 3.93 Na C B:Asn183 4.83 Na O B:Met184 2.44 Na N B:Met184 4.39 Na C B:Met184 3.57 Na CA B:Met184 4.63 Na N B:Phe185 4.28 Na C B:Phe185 4.69 Na CA B:Phe185 4.17 Na N B:Ser186 4.33 Na OG B:Ser186 4.35 Na CB B:Asn199 4.97 Na ND2 B:Asn199 3.78 Na OD1 B:Asn199 2.65 Na CG B:Asn199 3.56 Na CE2 B:Tyr220 4.92 Na CZ B:Tyr220 3.90 Na CE1 B:Tyr220 4.22 Na OH B:Tyr220 3.07 Na O B:Hoh432 2.30 Na O B:Hoh449 4.07 Na O B:Hoh450 2.37 interactive model: Sodium binding site 4 out of 4 in 4gib Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Sodium in the PDB 4gib. 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: Asp8, B: Asp10, B: Gly11, B: Val12, B: Lys44, B: Glu170, B: Asp171, B: Ala172, B: Po4304, conact list: Atom Atom Distance (A) Na CB B:Asp8 4.00 Na OD2 B:Asp8 2.42 Na OD1 B:Asp8 4.57 Na CG B:Asp8 3.51 Na O B:Asp10 2.31 Na N B:Asp10 4.48 Na CB B:Asp10 4.12 Na OD2 B:Asp10 4.14 Na C B:Asp10 3.46 Na CG B:Asp10 4.46 Na CA B:Asp10 4.23 Na N B:Gly11 4.46 Na CA B:Gly11 4.67 Na CG2 B:Val12 4.66 Na CE B:Lys44 4.13 Na NZ B:Lys44 4.77 Na OE1 B:Glu170 4.05 Na OE2 B:Glu170 2.11 Na CD B:Glu170 3.34 Na C B:Glu170 4.94 Na CG B:Glu170 4.39 Na CA B:Glu170 4.95 Na N B:Asp171 3.97 Na CB B:Asp171 4.36 Na OD2 B:Asp171 3.89 Na C B:Asp171 4.66 Na OD1 B:Asp171 2.25 Na CG B:Asp171 3.29 Na CA B:Asp171 4.57 Na N B:Ala172 4.55 Na CB B:Ala172 4.41 Na O1 B:Po4304 3.47 Na P B:Po4304 4.90 interactive model: