Sodium in the structure of Crystal Structure of A Putative Sulfurtransferase Dsre (SWOL_2425) From Syntrophomonas Wolfei Str. Goettingen At 1.92 A Resolution (pdb 3pnx)

The binding sites of Sodium atom in the structure of Crystal Structure of A Putative Sulfurtransferase Dsre (SWOL_2425) From Syntrophomonas Wolfei Str. Goettingen At 1.92 A Resolution (pdb code 3pnx). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 3pnx 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) 29.4-1.9 Space group C121 a (A) 100.416 b (A) 76.504 c (A) 127.652 alpha (°) 90.00 beta (°) 93.08 gamma (°) 90.00 Rfactor (%) 19 Rfree (%) 21.5 Sodium Binding Sites: Sodium binding site 1 out of 10 in 3pnx Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 3pnx. 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: Glu62, A: Glu125, A: Ile126, A: Mse127, A: Gly128, C: Mse94, C: Glu97, C: Glu98, A: Hoh245, C: Hoh187, conact list: Atom Atom Distance (A) Na OE1 A:Glu62 4.48 Na OE2 A:Glu62 2.35 Na CD A:Glu62 3.34 Na CG A:Glu62 3.63 Na O A:Glu125 2.41 Na C A:Glu125 3.50 Na CA A:Glu125 4.81 Na O A:Ile126 2.59 Na N A:Ile126 3.96 Na CB A:Ile126 4.92 Na C A:Ile126 3.19 Na CA A:Ile126 3.51 Na N A:Mse127 4.20 Na C A:Mse127 4.49 Na CA A:Mse127 4.77 Na N A:Gly128 3.96 Na CA A:Gly128 4.23 Na O C:Mse94 4.34 Na OE1 C:Glu97 4.53 Na OE1 C:Glu98 2.71 Na CB C:Glu98 4.73 Na OE2 C:Glu98 4.62 Na CD C:Glu98 3.63 Na CG C:Glu98 4.07 Na O A:Hoh245 3.41 Na O C:Hoh187 2.12 interactive model: Sodium binding site 2 out of 10 in 3pnx Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 3pnx. 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: Gln156, A: Leu157, B: Gln156, B: Leu157, C: Gln156, C: Leu157, A: Cl161, conact list: Atom Atom Distance (A) Na O A:Gln156 2.20 Na N A:Gln156 4.27 Na OE1 A:Gln156 3.98 Na CB A:Gln156 4.26 Na CD A:Gln156 4.99 Na C A:Gln156 3.37 Na CA A:Gln156 4.17 Na N A:Leu157 4.37 Na CD2 A:Leu157 4.18 Na CA A:Leu157 4.55 Na O B:Gln156 2.18 Na N B:Gln156 4.30 Na OE1 B:Gln156 4.12 Na CB B:Gln156 4.15 Na C B:Gln156 3.36 Na CA B:Gln156 4.16 Na N B:Leu157 4.37 Na CD2 B:Leu157 4.41 Na CA B:Leu157 4.57 Na O C:Gln156 2.31 Na N C:Gln156 4.34 Na OE1 C:Gln156 4.05 Na CB C:Gln156 4.22 Na C C:Gln156 3.49 Na CA C:Gln156 4.26 Na N C:Leu157 4.49 Na CD2 C:Leu157 4.34 Na CA C:Leu157 4.63 Na CL A:Cl161 4.68 interactive model: Sodium binding site 3 out of 10 in 3pnx Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Sodium in the PDB 3pnx. 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: Phe158, A: Ile159, B: Phe158, B: Ile159, C: Phe158, C: Ile159, A: Cl161, B: Gol172, conact list: Atom Atom Distance (A) Na O A:Phe158 2.25 Na N A:Phe158 3.97 Na CB A:Phe158 3.81 Na CD1 A:Phe158 4.21 Na C A:Phe158 3.36 Na CG A:Phe158 4.50 Na CA A:Phe158 3.95 Na N A:Ile159 4.49 Na CA A:Ile159 4.88 Na O B:Phe158 2.22 Na N B:Phe158 4.03 Na CB B:Phe158 3.78 Na CD1 B:Phe158 4.21 Na C B:Phe158 3.35 Na CG B:Phe158 4.49 Na CA B:Phe158 3.96 Na N B:Ile159 4.48 Na CA B:Ile159 4.86 Na O C:Phe158 2.31 Na N C:Phe158 4.02 Na CB C:Phe158 3.86 Na CD1 C:Phe158 4.21 Na C C:Phe158 3.41 Na CG C:Phe158 4.53 Na CA C:Phe158 3.99 Na N C:Ile159 4.53 Na CA C:Ile159 4.92 Na CL A:Cl161 2.87 Na O2 B:Gol172 2.61 Na O2 B:Gol172 2.67 Na C1 B:Gol172 4.93 Na O1 B:Gol172 4.88 Na C3 B:Gol172 4.73 Na C3 B:Gol172 4.11 Na O3 B:Gol172 4.87 Na C2 B:Gol172 3.92 Na C2 B:Gol172 3.86 interactive model: Sodium binding site 4 out of 10 in 3pnx Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Sodium in the PDB 3pnx. 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: Mse94, A: Glu97, A: Glu98, B: Glu62, B: Glu125, B: Ile126, B: Mse127, B: Gly128, A: Hoh289, conact list: Atom Atom Distance (A) Na O A:Mse94 4.36 Na OE1 A:Glu97 4.52 Na OE1 A:Glu98 4.45 Na CB A:Glu98 4.96 Na OE2 A:Glu98 2.53 Na CD A:Glu98 3.34 Na CG A:Glu98 3.49 Na OE1 B:Glu62 4.40 Na OE2 B:Glu62 2.30 Na CD B:Glu62 3.33 Na CG B:Glu62 3.75 Na O B:Glu125 2.31 Na C B:Glu125 3.42 Na CA B:Glu125 4.69 Na O B:Ile126 2.66 Na N B:Ile126 3.92 Na CB B:Ile126 4.98 Na C B:Ile126 3.24 Na CA B:Ile126 3.55 Na N B:Mse127 4.23 Na C B:Mse127 4.49 Na CA B:Mse127 4.81 Na N B:Gly128 3.87 Na CA B:Gly128 4.14 Na O A:Hoh289 1.97 interactive model: Sodium binding site 5 out of 10 in 3pnx Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Sodium in the PDB 3pnx. 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: Mse94, B: Glu98, C: Glu62, C: Glu125, C: Ile126, C: Mse127, C: Gly128, B: Hoh277, C: Hoh357, conact list: Atom Atom Distance (A) Na O B:Mse94 4.15 Na C B:Mse94 4.98 Na OE1 B:Glu98 2.70 Na CB B:Glu98 4.40 Na OE2 B:Glu98 4.63 Na CD B:Glu98 3.68 Na CG B:Glu98 4.21 Na OE1 C:Glu62 4.42 Na OE2 C:Glu62 2.34 Na CD C:Glu62 3.32 Na CG C:Glu62 3.67 Na O C:Glu125 2.51 Na C C:Glu125 3.62 Na CA C:Glu125 4.89 Na O C:Ile126 2.66 Na N C:Ile126 4.11 Na C C:Ile126 3.32 Na CA C:Ile126 3.64 Na N C:Mse127 4.35 Na C C:Mse127 4.69 Na CA C:Mse127 4.96 Na N C:Gly128 4.15 Na CA C:Gly128 4.29 Na O B:Hoh277 2.07 Na O C:Hoh357 3.36 interactive model: Sodium binding site 6 out of 10 in 3pnx Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Sodium in the PDB 3pnx. 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: Glu62, D: Glu125, D: Ile126, D: Mse127, D: Gly128, E: Mse94, E: Glu97, E: Glu98, D: Hoh240, E: Hoh337, conact list: Atom Atom Distance (A) Na OE1 D:Glu62 4.32 Na OE2 D:Glu62 2.19 Na CD D:Glu62 3.18 Na CG D:Glu62 3.50 Na O D:Glu125 2.46 Na C D:Glu125 3.55 Na CA D:Glu125 4.86 Na O D:Ile126 2.38 Na N D:Ile126 4.00 Na CB D:Ile126 4.89 Na C D:Ile126 3.08 Na CA D:Ile126 3.51 Na N D:Mse127 4.09 Na C D:Mse127 4.35 Na CA D:Mse127 4.63 Na N D:Gly128 3.84 Na CA D:Gly128 4.09 Na O E:Mse94 4.31 Na OE1 E:Glu97 4.68 Na OE1 E:Glu98 4.50 Na CB E:Glu98 4.88 Na OE2 E:Glu98 2.52 Na CD E:Glu98 3.35 Na CG E:Glu98 3.45 Na O D:Hoh240 3.49 Na O E:Hoh337 2.20 interactive model: Sodium binding site 7 out of 10 in 3pnx Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Sodium in the PDB 3pnx. 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: Gln156, D: Leu157, E: Gln156, E: Leu157, F: Gln156, F: Leu157, D: Cl160, conact list: Atom Atom Distance (A) Na O D:Gln156 2.28 Na N D:Gln156 4.30 Na OE1 D:Gln156 4.17 Na CB D:Gln156 4.25 Na C D:Gln156 3.46 Na CA D:Gln156 4.23 Na N D:Leu157 4.47 Na CD2 D:Leu157 4.40 Na CA D:Leu157 4.64 Na O E:Gln156 2.22 Na N E:Gln156 4.35 Na OE1 E:Gln156 4.11 Na CB E:Gln156 4.18 Na C E:Gln156 3.39 Na CA E:Gln156 4.19 Na N E:Leu157 4.38 Na CD2 E:Leu157 4.23 Na CA E:Leu157 4.53 Na O F:Gln156 2.26 Na N F:Gln156 4.29 Na OE1 F:Gln156 4.08 Na CB F:Gln156 4.11 Na C F:Gln156 3.43 Na CA F:Gln156 4.18 Na N F:Leu157 4.44 Na CD2 F:Leu157 4.31 Na CA F:Leu157 4.60 Na CL D:Cl160 4.70 interactive model: Sodium binding site 8 out of 10 in 3pnx Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Sodium in the PDB 3pnx. 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: Phe158, D: Ile159, E: Phe158, E: Ile159, F: Phe158, F: Ile159, D: Cl160, D: Gol173, conact list: Atom Atom Distance (A) Na O D:Phe158 2.25 Na N D:Phe158 4.01 Na CB D:Phe158 3.83 Na CD1 D:Phe158 4.26 Na C D:Phe158 3.38 Na CG D:Phe158 4.54 Na CA D:Phe158 3.97 Na N D:Ile159 4.50 Na CA D:Ile159 4.87 Na O E:Phe158 2.26 Na N E:Phe158 4.05 Na CB E:Phe158 3.85 Na CD1 E:Phe158 4.21 Na C E:Phe158 3.36 Na CG E:Phe158 4.51 Na CA E:Phe158 3.97 Na N E:Ile159 4.47 Na CA E:Ile159 4.85 Na O F:Phe158 2.26 Na N F:Phe158 4.00 Na CB F:Phe158 3.77 Na CD1 F:Phe158 4.19 Na C F:Phe158 3.38 Na CG F:Phe158 4.47 Na CA F:Phe158 3.96 Na N F:Ile159 4.50 Na CA F:Ile159 4.88 Na CL D:Cl160 2.83 Na O2 D:Gol173 2.57 Na O2 D:Gol173 2.73 Na C1 D:Gol173 3.95 Na C1 D:Gol173 4.88 Na C3 D:Gol173 4.72 Na C3 D:Gol173 4.27 Na O3 D:Gol173 4.45 Na O3 D:Gol173 4.74 Na C2 D:Gol173 3.77 Na C2 D:Gol173 4.01 interactive model: Sodium binding site 9 out of 10 in 3pnx Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 9 of Sodium in the PDB 3pnx. 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: E: Glu62, E: Glu125, E: Ile126, E: Mse127, E: Gly128, F: Mse94, F: Glu97, F: Glu98, E: Hoh242, F: Hoh231, conact list: Atom Atom Distance (A) Na OE1 E:Glu62 4.36 Na OE2 E:Glu62 2.26 Na CD E:Glu62 3.23 Na CG E:Glu62 3.54 Na O E:Glu125 2.48 Na C E:Glu125 3.59 Na CA E:Glu125 4.89 Na O E:Ile126 2.46 Na N E:Ile126 4.06 Na CB E:Ile126 4.94 Na C E:Ile126 3.18 Na CA E:Ile126 3.57 Na N E:Mse127 4.20 Na C E:Mse127 4.46 Na CA E:Mse127 4.77 Na N E:Gly128 3.98 Na CA E:Gly128 4.22 Na O F:Mse94 4.27 Na CB F:Mse94 4.98 Na OE1 F:Glu97 4.66 Na OE1 F:Glu98 2.60 Na CB F:Glu98 4.37 Na OE2 F:Glu98 4.53 Na CD F:Glu98 3.62 Na CG F:Glu98 4.24 Na O E:Hoh242 3.53 Na O F:Hoh231 2.28 interactive model: Sodium binding site 10 out of 10 in 3pnx Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 10 of Sodium in the PDB 3pnx. 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: Mse94, D: Glu97, D: Glu98, F: Glu62, F: Glu125, F: Ile126, F: Mse127, F: Gly128, D: Hoh338, F: Hoh241, conact list: Atom Atom Distance (A) Na O D:Mse94 4.32 Na OE1 D:Glu97 4.79 Na OE1 D:Glu98 4.52 Na OE2 D:Glu98 4.05 Na OE2 D:Glu98 2.50 Na CD D:Glu98 4.41 Na CD D:Glu98 3.36 Na CG D:Glu98 3.75 Na CG D:Glu98 3.51 Na OE1 F:Glu62 4.13 Na OE2 F:Glu62 2.06 Na CD F:Glu62 3.07 Na CG F:Glu62 3.52 Na O F:Glu125 2.58 Na C F:Glu125 3.71 Na CA F:Glu125 4.97 Na O F:Ile126 2.69 Na N F:Ile126 4.23 Na C F:Ile126 3.37 Na CA F:Ile126 3.78 Na N F:Mse127 4.34 Na C F:Mse127 4.53 Na CA F:Mse127 4.86 Na N F:Gly128 3.97 Na CA F:Gly128 4.16 Na O D:Hoh338 2.08 Na O F:Hoh241 3.19 interactive model: