Sodium in the structure of E. Coli Methionine Aminopeptidase in Complex With Nlep, 1: 1, Di-Metalated (pdb 2gu5)

The binding sites of Sodium atom in the structure of E. Coli Methionine Aminopeptidase in Complex With Nlep, 1: 1, Di-Metalated (pdb code 2gu5). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 2gu5 structure was solved by Q.Z.YE, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 14.2-1.6 Space group P1211 a (A) 49.790 b (A) 64.606 c (A) 76.354 alpha (°) 90.00 beta (°) 107.77 gamma (°) 90.00 Rfactor (%) 21.1 Rfree (%) 23.3 Sodium Binding Sites: Sodium binding site 1 out of 2 in 2gu5 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 2gu5. 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: Ser72, A: Ile73, A: Asn74, A: Glu75, A: Val76, A: Val77, A: Ile93, A: Met112, A: Ser231, A: Ala232, A: Hoh3809, A: Hoh3810, A: Hoh3829, conact list: Atom Atom Distance (A) Na O A:Ser72 4.37 Na CB A:Ser72 4.78 Na C A:Ser72 4.58 Na O A:Ile73 4.22 Na N A:Ile73 4.66 Na C A:Ile73 3.92 Na CA A:Ile73 4.61 Na O A:Asn74 2.24 Na N A:Asn74 3.65 Na C A:Asn74 3.21 Na CA A:Asn74 3.76 Na O A:Glu75 4.97 Na N A:Glu75 4.28 Na C A:Glu75 4.33 Na CA A:Glu75 4.66 Na O A:Val76 2.30 Na N A:Val76 3.90 Na CB A:Val76 4.74 Na C A:Val76 3.45 Na CA A:Val76 4.25 Na N A:Val77 4.42 Na CA A:Val77 4.60 Na O A:Ile93 4.87 Na CD1 A:Ile93 4.42 Na CG1 A:Ile93 4.55 Na CE A:Met112 4.89 Na O A:Ser231 2.25 Na N A:Ser231 3.82 Na CB A:Ser231 3.88 Na OG A:Ser231 4.65 Na C A:Ser231 3.30 Na CA A:Ser231 3.88 Na N A:Ala232 4.40 Na CA A:Ala232 4.74 Na O A:Hoh3809 3.45 Na O A:Hoh3810 4.36 Na O A:Hoh3829 2.30 interactive model: Sodium binding site 2 out of 2 in 2gu5 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 2gu5. 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: Ser72, B: Ile73, B: Asn74, B: Glu75, B: Val76, B: Val77, B: Ile93, B: Met112, B: Ser231, B: Ala232, B: Hoh3809, B: Hoh3810, B: Hoh3817, conact list: Atom Atom Distance (A) Na O B:Ser72 4.41 Na CB B:Ser72 4.75 Na C B:Ser72 4.60 Na O B:Ile73 4.18 Na N B:Ile73 4.68 Na C B:Ile73 3.94 Na CA B:Ile73 4.64 Na O B:Asn74 2.25 Na N B:Asn74 3.68 Na C B:Asn74 3.20 Na CA B:Asn74 3.78 Na O B:Glu75 4.86 Na N B:Glu75 4.25 Na C B:Glu75 4.26 Na CA B:Glu75 4.59 Na O B:Val76 2.33 Na N B:Val76 3.89 Na CB B:Val76 4.74 Na C B:Val76 3.47 Na CA B:Val76 4.25 Na N B:Val77 4.45 Na CA B:Val77 4.64 Na O B:Ile93 4.94 Na CD1 B:Ile93 4.39 Na CG1 B:Ile93 4.56 Na CE B:Met112 4.88 Na O B:Ser231 2.27 Na N B:Ser231 3.84 Na CB B:Ser231 3.88 Na OG B:Ser231 4.66 Na C B:Ser231 3.30 Na CA B:Ser231 3.88 Na N B:Ala232 4.39 Na CA B:Ala232 4.74 Na O B:Hoh3809 3.42 Na O B:Hoh3810 4.36 Na O B:Hoh3817 2.25 interactive model: