Sodium in the structure of Crystal Structure of Muconate Lactonizing Enzyme From Ruegeria Pomeroyi. (pdb 3i6e)

The binding sites of Sodium atom in the structure of Crystal Structure of Muconate Lactonizing Enzyme From Ruegeria Pomeroyi. (pdb code 3i6e). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 3i6e structure was solved by A.A.FEDOROV, E.V.FEDOROV, J.M.SAUDER, S.K.BURLEY, J.A.GERLT, S.C.ALMO, NEW YORK SGX RESEARCH CENTER FOR STRUCTURALGENOMICS (NYSGXRC), with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 24.9-1.7 Space group P1211 a (A) 109.135 b (A) 135.358 c (A) 113.024 alpha (°) 90.00 beta (°) 103.18 gamma (°) 90.00 Rfactor (%) 23.5 Rfree (%) 26.3 Sodium Binding Sites: Sodium binding site 1 out of 8 in 3i6e Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 3i6e. 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: Arg239, A: Gly240, A: Leu241, A: Thr242, A: Asp243, A: Val244, A: Asp268, A: Hoh401, A: Hoh406, A: Hoh419, A: Hoh427, A: Hoh559, A: Hoh579, conact list: Atom Atom Distance (A) Na O A:Arg239 2.39 Na CB A:Arg239 4.90 Na C A:Arg239 3.59 Na CG A:Arg239 4.04 Na NH1 A:Arg239 4.38 Na CA A:Arg239 4.50 Na N A:Gly240 4.47 Na C A:Gly240 4.72 Na CA A:Gly240 4.40 Na N A:Leu241 4.98 Na O A:Thr242 2.47 Na N A:Thr242 4.52 Na C A:Thr242 3.69 Na CA A:Thr242 4.76 Na N A:Asp243 4.43 Na C A:Asp243 4.80 Na OD1 A:Asp243 4.32 Na CA A:Asp243 4.21 Na O A:Val244 4.77 Na OD2 A:Asp268 4.34 Na OD1 A:Asp268 4.48 Na CG A:Asp268 4.83 Na O A:Hoh401 3.82 Na O A:Hoh406 2.67 Na O A:Hoh419 2.68 Na O A:Hoh427 2.65 Na O A:Hoh559 4.10 Na O A:Hoh579 2.54 interactive model: Sodium binding site 2 out of 8 in 3i6e Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 3i6e. 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: Arg239, B: Gly240, B: Leu241, B: Thr242, B: Asp243, B: Val244, B: Asp268, B: Hoh390, B: Hoh413, B: Hoh417, B: Hoh430, B: Hoh438, B: Hoh439, B: Hoh919, conact list: Atom Atom Distance (A) Na O B:Arg239 2.45 Na CB B:Arg239 4.98 Na C B:Arg239 3.63 Na CG B:Arg239 4.14 Na NH1 B:Arg239 4.42 Na CA B:Arg239 4.56 Na N B:Gly240 4.48 Na C B:Gly240 4.66 Na CA B:Gly240 4.38 Na N B:Leu241 4.99 Na O B:Thr242 2.46 Na N B:Thr242 4.48 Na C B:Thr242 3.66 Na CA B:Thr242 4.74 Na N B:Asp243 4.39 Na C B:Asp243 4.77 Na OD1 B:Asp243 4.29 Na CA B:Asp243 4.16 Na O B:Val244 4.84 Na OD2 B:Asp268 4.32 Na OD1 B:Asp268 4.48 Na CG B:Asp268 4.83 Na O B:Hoh390 2.69 Na O B:Hoh413 2.63 Na O B:Hoh417 2.55 Na O B:Hoh430 3.96 Na O B:Hoh438 4.09 Na O B:Hoh439 2.66 Na O B:Hoh919 4.04 interactive model: Sodium binding site 3 out of 8 in 3i6e Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Sodium in the PDB 3i6e. 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: C: Arg239, C: Gly240, C: Leu241, C: Thr242, C: Asp243, C: Val244, C: Asp268, C: Hoh394, C: Hoh395, C: Hoh400, C: Hoh412, C: Hoh464, C: Hoh932, conact list: Atom Atom Distance (A) Na O C:Arg239 2.45 Na CB C:Arg239 4.96 Na C C:Arg239 3.60 Na CG C:Arg239 4.15 Na NH1 C:Arg239 4.37 Na CA C:Arg239 4.56 Na N C:Gly240 4.42 Na C C:Gly240 4.66 Na CA C:Gly240 4.33 Na N C:Leu241 4.99 Na O C:Thr242 2.44 Na N C:Thr242 4.54 Na C C:Thr242 3.64 Na CA C:Thr242 4.74 Na N C:Asp243 4.35 Na C C:Asp243 4.74 Na OD1 C:Asp243 4.23 Na CA C:Asp243 4.10 Na O C:Val244 4.89 Na OD2 C:Asp268 4.38 Na OD1 C:Asp268 4.59 Na CG C:Asp268 4.92 Na O C:Hoh394 3.81 Na O C:Hoh395 4.06 Na O C:Hoh400 2.56 Na O C:Hoh412 2.66 Na O C:Hoh464 2.60 Na O C:Hoh932 2.66 interactive model: Sodium binding site 4 out of 8 in 3i6e Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Sodium in the PDB 3i6e. 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: Arg239, D: Gly240, D: Thr242, D: Asp243, D: Val244, D: Asp268, D: Hoh402, D: Hoh414, D: Hoh470, D: Hoh540, D: Hoh582, D: Hoh619, D: Hoh772, conact list: Atom Atom Distance (A) Na O D:Arg239 2.45 Na CB D:Arg239 4.99 Na C D:Arg239 3.64 Na CG D:Arg239 4.14 Na NH1 D:Arg239 4.51 Na CA D:Arg239 4.59 Na N D:Gly240 4.48 Na C D:Gly240 4.71 Na CA D:Gly240 4.40 Na O D:Thr242 2.48 Na N D:Thr242 4.54 Na C D:Thr242 3.68 Na CA D:Thr242 4.77 Na N D:Asp243 4.41 Na C D:Asp243 4.74 Na OD1 D:Asp243 4.31 Na CA D:Asp243 4.15 Na O D:Val244 4.81 Na OD2 D:Asp268 4.39 Na OD1 D:Asp268 4.51 Na CG D:Asp268 4.87 Na O D:Hoh402 2.57 Na O D:Hoh414 3.71 Na O D:Hoh470 4.14 Na O D:Hoh540 4.18 Na O D:Hoh582 2.69 Na O D:Hoh619 2.63 Na O D:Hoh772 2.61 interactive model: Sodium binding site 5 out of 8 in 3i6e Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Sodium in the PDB 3i6e. 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: Arg239, E: Gly240, E: Thr242, E: Asp243, E: Val244, E: Asp268, E: Hoh397, E: Hoh398, E: Hoh402, E: Hoh407, E: Hoh427, E: Hoh607, E: Hoh798, conact list: Atom Atom Distance (A) Na O E:Arg239 2.40 Na CB E:Arg239 4.95 Na C E:Arg239 3.57 Na CG E:Arg239 4.13 Na NH1 E:Arg239 4.44 Na CA E:Arg239 4.55 Na N E:Gly240 4.40 Na C E:Gly240 4.67 Na CA E:Gly240 4.30 Na O E:Thr242 2.46 Na N E:Thr242 4.54 Na C E:Thr242 3.66 Na CA E:Thr242 4.76 Na N E:Asp243 4.39 Na C E:Asp243 4.73 Na OD1 E:Asp243 4.34 Na CA E:Asp243 4.15 Na O E:Val244 4.81 Na OD2 E:Asp268 4.40 Na OD1 E:Asp268 4.48 Na CG E:Asp268 4.86 Na O E:Hoh397 2.65 Na O E:Hoh398 2.56 Na O E:Hoh402 2.60 Na O E:Hoh407 3.76 Na O E:Hoh427 3.95 Na O E:Hoh607 2.58 Na O E:Hoh798 4.01 interactive model: Sodium binding site 6 out of 8 in 3i6e Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Sodium in the PDB 3i6e. 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: F: Arg239, F: Gly240, F: Leu241, F: Thr242, F: Asp243, F: Val244, F: Asp268, F: Hoh396, F: Hoh404, F: Hoh415, F: Hoh428, F: Hoh566, F: Hoh628, F: Hoh664, conact list: Atom Atom Distance (A) Na O F:Arg239 2.39 Na CB F:Arg239 4.96 Na C F:Arg239 3.59 Na CG F:Arg239 4.12 Na NH1 F:Arg239 4.47 Na CA F:Arg239 4.54 Na N F:Gly240 4.43 Na C F:Gly240 4.62 Na CA F:Gly240 4.33 Na N F:Leu241 4.95 Na O F:Thr242 2.47 Na N F:Thr242 4.47 Na C F:Thr242 3.68 Na CA F:Thr242 4.74 Na N F:Asp243 4.44 Na C F:Asp243 4.83 Na OD1 F:Asp243 4.47 Na CA F:Asp243 4.25 Na O F:Val244 4.83 Na OD2 F:Asp268 4.35 Na OD1 F:Asp268 4.47 Na CG F:Asp268 4.84 Na O F:Hoh396 2.61 Na O F:Hoh404 2.70 Na O F:Hoh415 3.92 Na O F:Hoh428 2.53 Na O F:Hoh566 4.14 Na O F:Hoh628 4.00 Na O F:Hoh664 2.66 interactive model: Sodium binding site 7 out of 8 in 3i6e Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Sodium in the PDB 3i6e. 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: G: Arg239, G: Gly240, G: Leu241, G: Thr242, G: Asp243, G: Val244, G: Asp268, G: Hoh389, G: Hoh399, G: Hoh406, G: Hoh430, G: Hoh448, G: Hoh464, G: Hoh808, conact list: Atom Atom Distance (A) Na O G:Arg239 2.45 Na C G:Arg239 3.64 Na CG G:Arg239 4.24 Na NH1 G:Arg239 4.59 Na CA G:Arg239 4.61 Na N G:Gly240 4.46 Na C G:Gly240 4.64 Na CA G:Gly240 4.33 Na N G:Leu241 4.94 Na O G:Thr242 2.43 Na N G:Thr242 4.47 Na C G:Thr242 3.64 Na CA G:Thr242 4.72 Na N G:Asp243 4.37 Na C G:Asp243 4.79 Na OD1 G:Asp243 4.26 Na CA G:Asp243 4.15 Na O G:Val244 4.76 Na OD2 G:Asp268 4.33 Na OD1 G:Asp268 4.55 Na CG G:Asp268 4.86 Na O G:Hoh389 4.07 Na O G:Hoh399 2.59 Na O G:Hoh406 3.76 Na O G:Hoh430 2.52 Na O G:Hoh448 2.71 Na O G:Hoh464 4.04 Na O G:Hoh808 2.61 interactive model: Sodium binding site 8 out of 8 in 3i6e Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Sodium in the PDB 3i6e. 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: H: Arg239, H: Gly240, H: Thr242, H: Asp243, H: Val244, H: Asp268, H: Hoh392, H: Hoh396, H: Hoh496, H: Hoh643, H: Hoh644, H: Hoh736, conact list: Atom Atom Distance (A) Na O H:Arg239 2.45 Na CB H:Arg239 4.98 Na C H:Arg239 3.63 Na CG H:Arg239 4.15 Na NH1 H:Arg239 4.56 Na CA H:Arg239 4.56 Na O H:Gly240 5.00 Na N H:Gly240 4.47 Na C H:Gly240 4.66 Na CA H:Gly240 4.38 Na O H:Thr242 2.44 Na N H:Thr242 4.50 Na C H:Thr242 3.64 Na CA H:Thr242 4.73 Na N H:Asp243 4.36 Na C H:Asp243 4.75 Na OD1 H:Asp243 4.32 Na CA H:Asp243 4.14 Na O H:Val244 4.76 Na OD2 H:Asp268 4.38 Na OD1 H:Asp268 4.56 Na CG H:Asp268 4.90 Na O H:Hoh392 2.65 Na O H:Hoh396 2.55 Na O H:Hoh496 3.80 Na O H:Hoh643 2.72 Na O H:Hoh644 4.06 Na O H:Hoh736 2.64 interactive model: