Sodium in PDB 3u13: Crystal Structure of De Novo Design of Cystein Esterase ECH13 at the Resolution 1.6A, Northeast Structural Genomics Consortium Target OR51

The structure of Crystal Structure of De Novo Design of Cystein Esterase ECH13 at the Resolution 1.6A, Northeast Structural Genomics Consortium Target OR51, PDB code: 3u13 was solved by A.Kuzin, M.Su, J.Seetharaman, S.Sahdev, R.Xiao, E.Kohan, F.Richter, J.K.Everett, T.B.Acton, D.Baker, G.T.Montelione, J.F.Hunt, L.Tong, Northeast Structural Genomics Consortium (Nesg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.04 / 1.60
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	73.436, 73.436, 105.083, 90.00, 90.00, 90.00
R / Rfree (%)	18 / 19.3

The structure of Crystal Structure of De Novo Design of Cystein Esterase ECH13 at the Resolution 1.6A, Northeast Structural Genomics Consortium Target OR51 also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Sodium atom in the Crystal Structure of De Novo Design of Cystein Esterase ECH13 at the Resolution 1.6A, Northeast Structural Genomics Consortium Target OR51 (pdb code 3u13). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Crystal Structure of De Novo Design of Cystein Esterase ECH13 at the Resolution 1.6A, Northeast Structural Genomics Consortium Target OR51, PDB code: 3u13:

Sodium binding site 1 out of 1 in the Crystal Structure of De Novo Design of Cystein Esterase ECH13 at the Resolution 1.6A, Northeast Structural Genomics Consortium Target OR51


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of De Novo Design of Cystein Esterase ECH13 at the Resolution 1.6A, Northeast Structural Genomics Consortium Target OR51 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na212 b:46.9 occ:1.00 O A:HOH259 3.1 17.6 1.0 N A:TYR108 3.2 16.6 1.0 CB A:MSE105 3.4 51.5 1.0 O4 A:PO4210 3.5 43.8 1.0 N A:CYS109 3.5 13.6 1.0 C A:MSE105 3.6 46.9 1.0 CD2 A:TYR108 3.6 21.7 1.0 N A:LYS107 3.7 23.9 1.0 CB A:TYR108 3.7 15.5 1.0 O A:MSE105 3.7 52.7 1.0 O3 A:PO4210 3.7 30.9 1.0 N A:PHE106 3.8 29.2 1.0 CA A:TYR108 3.8 13.7 1.0 CG A:TYR108 4.0 15.8 1.0 CA A:MSE105 4.0 49.5 1.0 P A:PO4210 4.0 46.4 1.0 O2 A:PO4210 4.0 21.4 1.0 O A:GLU67 4.1 20.0 1.0 C A:LYS107 4.2 20.1 1.0 C A:TYR108 4.2 14.4 1.0 CA A:LYS107 4.2 25.0 1.0 CB A:LYS107 4.2 26.6 1.0 CG A:MSE105 4.3 53.5 1.0 CB A:CYS109 4.3 14.7 1.0 C A:PHE106 4.4 21.7 1.0 CA A:PHE106 4.5 20.4 1.0 CE2 A:TYR108 4.5 20.3 1.0 CA A:CYS109 4.5 14.5 1.0 SE A:MSE105 4.7 70.9 1.0 C A:GLU67 4.8 19.2 1.0 CA A:GLU67 4.8 16.5 1.0

F.Richter, R.Blomberg, S.D.Khare, G.Kiss, A.P.Kuzin, A.J.Smith, J.Gallaher, Z.Pianowski, R.C.Helgeson, A.Grjasnow, R.Xiao, J.Seetharaman, M.Su, S.Vorobiev, S.Lew, F.Forouhar, G.J.Kornhaber, J.F.Hunt, G.T.Montelione, L.Tong, K.N.Houk, D.Hilvert, D.Baker. Computational Design of Catalytic Dyads and Oxyanion Holes For Ester Hydrolysis. J.Am.Chem.Soc. V. 134 16197 2012.
ISSN: ISSN 0002-7863
PubMed: 22871159
DOI: 10.1021/JA3037367