Sodium in the structure of Crystal Structure of A Putative Kdpg (2-Keto-3-Deoxy-6- Phosphogluconate) Aldolase From Oleispira Antarctica (pdb 3lab)

The binding sites of Sodium atom in the structure of Crystal Structure of A Putative Kdpg (2-Keto-3-Deoxy-6- Phosphogluconate) Aldolase From Oleispira Antarctica (pdb code 3lab). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 3lab structure was solved by P.J.STOGIOS, V.YIM, R.DI LEO, O.KAGAN, A.JOACHIMIAK, A.M.EDWARDS, A.SAVCHENKO, MIDWEST CENTER FOR STRUCTURAL GENOMICS (MCSG), ONTARIO CENTRE FOR STRUCTURAL PROTEOMICS (OCSP), with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 50.0-1.8 Space group H3 a (A) 76.020 b (A) 76.020 c (A) 241.121 alpha (°) 90.00 beta (°) 90.00 gamma (°) 120.00 Rfactor (%) 17.1 Rfree (%) 21.5 Sodium Binding Sites: Sodium binding site 1 out of 20 in 3lab Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 3lab. 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: Lys58, A: Val61, A: Pro62, A: Glu63, A: Ala64, A: Ile65, A: Val66, A: Gln86, A: Hoh278, A: Hoh290, A: Hoh445, A: Hoh807, A: Hoh816, A: Hoh818, conact list: Atom Atom Distance (A) Na CE A:Lys58 4.34 Na CD A:Lys58 4.13 Na O A:Val61 4.37 Na O A:Pro62 3.19 Na C A:Pro62 3.95 Na CA A:Pro62 4.28 Na N A:Glu63 4.97 Na C A:Glu63 4.80 Na O A:Ala64 2.31 Na N A:Ala64 4.42 Na C A:Ala64 3.52 Na CA A:Ala64 4.62 Na N A:Ile65 4.21 Na CD1 A:Ile65 4.63 Na C A:Ile65 4.79 Na CA A:Ile65 3.97 Na N A:Val66 4.43 Na NE2 A:Gln86 3.49 Na OE1 A:Gln86 2.37 Na CD A:Gln86 3.25 Na CG A:Gln86 4.64 Na O A:Hoh278 4.76 Na O A:Hoh290 2.53 Na O A:Hoh445 2.51 Na O A:Hoh807 4.14 Na O A:Hoh816 2.21 Na O A:Hoh818 4.51 interactive model: Sodium binding site 2 out of 20 in 3lab Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 3lab. 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: Tyr175, A: Leu176, A: Gly177, A: Leu178, A: Pro179, A: Val181, A: Ile182, A: Leu213, A: Hoh515, A: Hoh737, A: Hoh740, A: Hoh747, conact list: Atom Atom Distance (A) Na O A:Tyr175 4.81 Na O A:Leu176 2.19 Na C A:Leu176 3.39 Na CA A:Leu176 4.29 Na O A:Gly177 4.39 Na N A:Gly177 4.34 Na C A:Gly177 4.10 Na CA A:Gly177 4.38 Na O A:Leu178 2.45 Na N A:Leu178 4.02 Na C A:Leu178 3.52 Na CA A:Leu178 4.40 Na O A:Pro179 4.48 Na N A:Pro179 4.38 Na C A:Pro179 4.46 Na CA A:Pro179 4.34 Na O A:Val181 2.29 Na N A:Val181 4.03 Na CB A:Val181 4.24 Na C A:Val181 3.44 Na CG1 A:Val181 4.67 Na CA A:Val181 4.10 Na N A:Ile182 4.53 Na CA A:Ile182 4.76 Na CD1 A:Leu213 4.65 Na CD2 A:Leu213 4.76 Na O A:Hoh515 2.51 Na O A:Hoh737 4.46 Na O A:Hoh740 4.16 Na O A:Hoh747 2.39 interactive model: Sodium binding site 3 out of 20 in 3lab Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Sodium in the PDB 3lab. 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: Glu202, A: Arg206, A: Hoh342, A: Hoh397, conact list: Atom Atom Distance (A) Na OE1 A:Glu202 4.19 Na OE2 A:Glu202 3.31 Na CD A:Glu202 3.81 Na CG A:Glu202 4.59 Na CZ A:Arg206 3.91 Na NE A:Arg206 4.28 Na NH2 A:Arg206 2.78 Na O A:Hoh342 4.21 Na O A:Hoh397 3.90 interactive model: Sodium binding site 4 out of 20 in 3lab Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Sodium in the PDB 3lab. 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: Glu123, A: Hoh237, A: Hoh730, conact list: Atom Atom Distance (A) Na OE2 A:Glu123 3.12 Na CD A:Glu123 3.87 Na CG A:Glu123 3.72 Na O A:Hoh237 2.34 Na O A:Hoh730 2.77 interactive model: Sodium binding site 5 out of 20 in 3lab Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Sodium in the PDB 3lab. 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: Asn201, A: Arg205, A: Hoh531, A: Hoh669, conact list: Atom Atom Distance (A) Na O A:Asn201 3.91 Na CB A:Asn201 4.72 Na C A:Asn201 4.58 Na CB A:Arg205 3.78 Na CD A:Arg205 4.09 Na CG A:Arg205 4.36 Na NH1 A:Arg205 4.93 Na CA A:Arg205 4.82 Na O A:Hoh531 3.88 Na O A:Hoh669 4.98 interactive model: Sodium binding site 6 out of 20 in 3lab Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Sodium in the PDB 3lab. 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: Ile20, A: Asp21, A: Asp22, A: His25, A: Leu195, A: Ile196, A: Cl224, A: Hoh651, conact list: Atom Atom Distance (A) Na CB A:Ile20 4.83 Na CD1 A:Ile20 4.75 Na C A:Ile20 4.33 Na CG1 A:Ile20 3.79 Na CA A:Ile20 4.55 Na N A:Asp21 3.51 Na CB A:Asp21 4.22 Na C A:Asp21 4.01 Na CA A:Asp21 4.06 Na O A:Asp22 4.00 Na N A:Asp22 3.05 Na CB A:Asp22 3.86 Na OD2 A:Asp22 3.79 Na C A:Asp22 4.41 Na OD1 A:Asp22 4.78 Na CG A:Asp22 3.98 Na CA A:Asp22 3.87 Na NE2 A:His25 4.66 Na CB A:His25 3.81 Na ND1 A:His25 2.60 Na CD2 A:His25 4.72 Na CE1 A:His25 3.52 Na CG A:His25 3.58 Na O A:Leu195 4.65 Na CB A:Leu195 4.07 Na CD1 A:Leu195 4.78 Na C A:Leu195 4.55 Na CA A:Leu195 4.96 Na N A:Ile196 4.60 Na CA A:Ile196 4.97 Na CL A:Cl224 1.87 Na O A:Hoh651 4.86 interactive model: Sodium binding site 7 out of 20 in 3lab Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Sodium in the PDB 3lab. 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: Tyr175, B: Leu176, B: Gly177, B: Leu178, B: Pro179, B: Asn180, B: Val181, B: Ile182, B: Leu213, B: Hoh446, B: Hoh518, B: Hoh736, conact list: Atom Atom Distance (A) Na O B:Tyr175 4.71 Na O B:Leu176 2.28 Na C B:Leu176 3.43 Na CA B:Leu176 4.30 Na O B:Gly177 4.28 Na N B:Gly177 4.38 Na C B:Gly177 4.00 Na CA B:Gly177 4.43 Na O B:Leu178 2.36 Na N B:Leu178 3.89 Na C B:Leu178 3.47 Na CA B:Leu178 4.34 Na O B:Pro179 4.51 Na N B:Pro179 4.31 Na C B:Pro179 4.39 Na CA B:Pro179 4.24 Na N B:Asn180 4.90 Na O B:Val181 2.30 Na N B:Val181 4.00 Na CB B:Val181 4.28 Na C B:Val181 3.42 Na CG1 B:Val181 4.78 Na CA B:Val181 4.06 Na N B:Ile182 4.48 Na CA B:Ile182 4.70 Na CD1 B:Leu213 4.62 Na O B:Hoh446 2.46 Na O B:Hoh518 2.37 Na O B:Hoh736 4.50 interactive model: Sodium binding site 8 out of 20 in 3lab Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Sodium in the PDB 3lab. 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: Lys58, B: Val61, B: Pro62, B: Glu63, B: Ala64, B: Ile65, B: Val66, B: Gln86, B: Hoh296, B: Hoh325, B: Hoh340, B: Hoh433, B: Hoh561, conact list: Atom Atom Distance (A) Na CE B:Lys58 4.51 Na CD B:Lys58 4.36 Na O B:Val61 4.36 Na O B:Pro62 2.97 Na C B:Pro62 3.77 Na CA B:Pro62 4.19 Na N B:Glu63 4.75 Na C B:Glu63 4.73 Na O B:Ala64 2.22 Na N B:Ala64 4.37 Na C B:Ala64 3.40 Na CA B:Ala64 4.52 Na N B:Ile65 4.08 Na CB B:Ile65 4.92 Na C B:Ile65 4.81 Na CG1 B:Ile65 4.66 Na CA B:Ile65 3.95 Na N B:Val66 4.45 Na NE2 B:Gln86 3.56 Na OE1 B:Gln86 2.49 Na CD B:Gln86 3.33 Na CG B:Gln86 4.74 Na O B:Hoh296 4.60 Na O B:Hoh325 2.45 Na O B:Hoh340 4.74 Na O B:Hoh433 2.43 Na O B:Hoh561 3.67 interactive model: Sodium binding site 9 out of 20 in 3lab Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 9 of Sodium in the PDB 3lab. 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: Glu48, B: Ala49, B: Gly50, B: Leu51, B: Ala52, B: Hoh266, B: Hoh670, B: Hoh679, conact list: Atom Atom Distance (A) Na O B:Glu48 2.88 Na OE2 B:Glu48 4.17 Na CD B:Glu48 4.73 Na C B:Glu48 4.01 Na O B:Ala49 4.02 Na N B:Ala49 4.57 Na C B:Ala49 3.99 Na CA B:Ala49 4.13 Na N B:Gly50 4.52 Na C B:Gly50 4.78 Na N B:Leu51 3.83 Na CB B:Leu51 3.70 Na CD1 B:Leu51 4.99 Na C B:Leu51 3.94 Na CG B:Leu51 4.82 Na CA B:Leu51 3.97 Na N B:Ala52 3.06 Na CB B:Ala52 3.37 Na CA B:Ala52 3.77 Na O B:Hoh266 4.15 Na O B:Hoh670 3.90 Na O B:Hoh679 3.12 interactive model: Sodium binding site 10 out of 20 in 3lab Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 10 of Sodium in the PDB 3lab. 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: Ala142, B: Ile143, B: Gly144, B: Hoh408, B: Hoh649, conact list: Atom Atom Distance (A) Na O B:Ala142 4.67 Na O B:Ile143 3.40 Na CB B:Ile143 4.13 Na CG2 B:Ile143 4.72 Na C B:Ile143 3.78 Na CA B:Ile143 3.75 Na N B:Gly144 4.77 Na O B:Hoh408 4.51 Na O B:Hoh649 2.99 interactive model: Sodium binding site 11 out of 20 in 3lab Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 11 of Sodium in the PDB 3lab. 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: Na223, B: Hoh840, B: Hoh841, B: Hoh849, conact list: Atom Atom Distance (A) Na NA B:Na223 2.79 Na O B:Hoh840 2.97 Na O B:Hoh841 4.83 Na O B:Hoh849 3.47 interactive model: Sodium binding site 12 out of 20 in 3lab Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 12 of Sodium in the PDB 3lab. 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: Na222, B: Na224, B: Na225, B: Hoh840, conact list: Atom Atom Distance (A) Na NA B:Na222 2.79 Na NA B:Na224 4.06 Na NA B:Na225 4.47 Na O B:Hoh840 4.21 interactive model: Sodium binding site 13 out of 20 in 3lab Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 13 of Sodium in the PDB 3lab. 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: Na223, B: Na225, conact list: Atom Atom Distance (A) Na NA B:Na223 4.06 Na NA B:Na225 2.85 interactive model: Sodium binding site 14 out of 20 in 3lab Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 14 of Sodium in the PDB 3lab. 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: Na223, B: Na224, conact list: Atom Atom Distance (A) Na NA B:Na223 4.47 Na NA B:Na224 2.85 interactive model: Sodium binding site 15 out of 20 in 3lab Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 15 of Sodium in the PDB 3lab. 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: Asn201, B: Arg205, B: Ipa235, B: Hoh269, B: Hoh319, B: Hoh370, B: Hoh848, conact list: Atom Atom Distance (A) Na O B:Asn201 3.95 Na CB B:Asn201 4.37 Na C B:Asn201 4.58 Na CB B:Arg205 4.05 Na CB B:Arg205 4.04 Na CD B:Arg205 4.31 Na CG B:Arg205 4.59 Na CG B:Arg205 4.73 Na CA B:Arg205 4.95 Na CA B:Arg205 4.95 Na C3 B:Ipa235 3.89 Na O2 B:Ipa235 2.19 Na C2 B:Ipa235 3.62 Na C1 B:Ipa235 4.67 Na O B:Hoh269 4.57 Na O B:Hoh319 4.22 Na O B:Hoh370 2.84 Na O B:Hoh848 2.45 interactive model: Sodium binding site 16 out of 20 in 3lab Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 16 of Sodium in the PDB 3lab. 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: Glu202, B: Arg205, B: Arg206, B: Na228, B: Hoh812, conact list: Atom Atom Distance (A) Na OE1 B:Glu202 4.16 Na OE2 B:Glu202 3.36 Na CD B:Glu202 3.84 Na CG B:Glu202 4.67 Na CZ B:Arg205 4.84 Na NH1 B:Arg205 3.81 Na CZ B:Arg206 4.14 Na NE B:Arg206 4.37 Na NH2 B:Arg206 3.08 Na NA B:Na228 2.48 Na O B:Hoh812 4.84 interactive model: Sodium binding site 17 out of 20 in 3lab Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 17 of Sodium in the PDB 3lab. 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: Leu194, B: Asp199, B: Glu202, B: Arg206, B: Na227, conact list: Atom Atom Distance (A) Na CD2 B:Leu194 4.36 Na OD2 B:Asp199 4.53 Na OE1 B:Glu202 3.67 Na CB B:Glu202 4.56 Na OE2 B:Glu202 3.75 Na CD B:Glu202 3.44 Na CG B:Glu202 3.64 Na CZ B:Arg206 4.76 Na NH2 B:Arg206 3.70 Na NA B:Na227 2.48 interactive model: Sodium binding site 18 out of 20 in 3lab Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 18 of Sodium in the PDB 3lab. 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: Pro95, B: Ile98, B: Hoh302, B: Hoh483, conact list: Atom Atom Distance (A) Na O B:Pro95 4.80 Na CB B:Pro95 4.07 Na C B:Pro95 4.99 Na CG B:Pro95 4.34 Na CA B:Pro95 4.10 Na CB B:Ile98 4.76 Na CD1 B:Ile98 4.07 Na CG2 B:Ile98 4.76 Na O B:Hoh302 2.86 Na O B:Hoh483 4.55 interactive model: Sodium binding site 19 out of 20 in 3lab Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 19 of Sodium in the PDB 3lab. 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: Val19, B: Ile20, B: Asp21, B: Asp22, B: His25, B: Ser192, B: Leu195, B: Ile196, B: Cl232, B: Hoh322, B: Hoh545, conact list: Atom Atom Distance (A) Na O B:Val19 4.30 Na N B:Ile20 4.90 Na CB B:Ile20 4.85 Na C B:Ile20 4.00 Na CG1 B:Ile20 4.40 Na CA B:Ile20 4.02 Na N B:Asp21 3.07 Na CB B:Asp21 3.74 Na OD2 B:Asp21 3.98 Na C B:Asp21 4.53 Na OD1 B:Asp21 4.80 Na CG B:Asp21 4.01 Na CA B:Asp21 3.89 Na N B:Asp22 4.08 Na ND1 B:His25 4.44 Na O B:Ser192 4.72 Na CB B:Leu195 3.76 Na CD1 B:Leu195 4.06 Na C B:Leu195 4.78 Na CG B:Leu195 4.56 Na CA B:Leu195 4.91 Na N B:Ile196 4.47 Na CD1 B:Ile196 4.68 Na CG1 B:Ile196 4.08 Na CL B:Cl232 1.92 Na O B:Hoh322 2.54 Na O B:Hoh545 4.80 interactive model: Sodium binding site 20 out of 20 in 3lab Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 20 of Sodium in the PDB 3lab. 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: Ser122, B: Glu123, B: Ile126, B: Cl233, B: Cl234, B: Hoh840, B: Hoh849, B: Hoh851, conact list: Atom Atom Distance (A) Na O B:Ser122 3.77 Na CB B:Ser122 3.85 Na CB B:Ser122 3.81 Na OG B:Ser122 3.75 Na C B:Ser122 3.73 Na CA B:Ser122 4.41 Na CA B:Ser122 4.42 Na N B:Glu123 3.91 Na CB B:Glu123 4.74 Na CG B:Glu123 3.99 Na CA B:Glu123 4.11 Na CB B:Ile126 4.52 Na CB B:Ile126 4.54 Na CD1 B:Ile126 2.95 Na CD1 B:Ile126 4.35 Na CG1 B:Ile126 3.87 Na CG1 B:Ile126 3.48 Na CL B:Cl233 2.20 Na CL B:Cl234 3.04 Na O B:Hoh840 4.61 Na O B:Hoh849 2.69 Na O B:Hoh851 4.84 interactive model: