Sodium in PDB 3dc7: Crystal Structure of the Protein Q88SR8 From Lactobacillus Plantarum. Northeast Structural Genomics Consortium Target LPR109.

The structure of Crystal Structure of the Protein Q88SR8 From Lactobacillus Plantarum. Northeast Structural Genomics Consortium Target LPR109., PDB code: 3dc7 was solved by A.P.Kuzin, M.Abashidze, S.M.Vorobiev, J.Seetharaman, L.Zhao, L.Mao, C.Ciccosanti, R.Xiao, R.Nair, M.C.Baran, T.B.Acton, B.Rost, G.T.Montelione, J.F.Hunt, L.Tong, Northeast Structural Genomicsconsortium (Nesg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.74 / 2.12
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	48.610, 101.440, 125.550, 90.00, 90.00, 90.00
R / Rfree (%)	18.4 / 22.4

The structure of Crystal Structure of the Protein Q88SR8 From Lactobacillus Plantarum. Northeast Structural Genomics Consortium Target LPR109. also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Sodium atom in the Crystal Structure of the Protein Q88SR8 From Lactobacillus Plantarum. Northeast Structural Genomics Consortium Target LPR109. (pdb code 3dc7). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of the Protein Q88SR8 From Lactobacillus Plantarum. Northeast Structural Genomics Consortium Target LPR109., PDB code: 3dc7:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of the Protein Q88SR8 From Lactobacillus Plantarum. Northeast Structural Genomics Consortium Target LPR109.


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 the Protein Q88SR8 From Lactobacillus Plantarum. Northeast Structural Genomics Consortium Target LPR109. within 5.0Å range: probe atom residue distance (Å) B Occ B:Na233 b:33.3 occ:1.00 OD1 B:ASP29 2.2 35.4 1.0 O B:PHE89 2.3 31.1 1.0 N B:ASP29 2.4 32.3 1.0 CG B:ASP29 2.8 35.7 1.0 CA B:GLY28 3.3 30.4 1.0 OG1 B:THR32 3.3 33.1 1.0 C B:GLY28 3.3 31.2 1.0 CA B:ASP29 3.3 33.1 1.0 C B:PHE89 3.5 29.7 1.0 OD2 B:ASP29 3.5 40.3 1.0 CB B:ASP29 3.6 33.6 1.0 CB B:PHE89 3.8 28.9 1.0 C B:ASP29 3.8 33.2 1.0 CG B:PHE89 3.9 30.1 1.0 N B:THR32 3.9 33.3 1.0 CB B:THR32 3.9 34.3 1.0 O B:ASP29 4.0 32.9 1.0 CD1 B:PHE89 4.1 31.2 1.0 N B:ILE31 4.2 33.9 1.0 CB B:ILE31 4.2 33.1 1.0 CA B:PHE89 4.2 28.5 1.0 O B:GLY28 4.5 30.9 1.0 CA B:ILE31 4.5 33.3 1.0 C B:ILE31 4.5 33.0 1.0 N B:GLY90 4.5 30.5 1.0 N B:SER30 4.5 33.6 1.0 CD2 B:PHE89 4.5 30.2 1.0 CA B:THR32 4.6 34.0 1.0 N B:GLY28 4.6 29.1 1.0 CA B:GLY90 4.7 31.5 1.0 CE1 B:PHE89 4.8 32.7 1.0 N B:PHE89 5.0 26.6 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of the Protein Q88SR8 From Lactobacillus Plantarum. Northeast Structural Genomics Consortium Target LPR109.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of the Protein Q88SR8 From Lactobacillus Plantarum. Northeast Structural Genomics Consortium Target LPR109. within 5.0Å range: probe atom residue distance (Å) B Occ C:Na233 b:29.6 occ:1.00 O A:HOH289 2.3 31.6 1.0 OD1 A:ASP183 2.3 33.3 1.0 N C:HIS177 2.4 22.7 1.0 CA C:PRO176 3.1 20.8 1.0 C C:PRO176 3.2 21.2 1.0 O C:HOH250 3.3 25.3 1.0 CG A:ASP183 3.4 32.9 1.0 CA C:HIS177 3.5 21.4 1.0 O C:HIS177 3.6 19.9 1.0 CB C:HIS177 3.8 21.9 1.0 CB C:PRO176 3.9 21.0 1.0 OD2 A:ASP183 3.9 36.0 1.0 C C:HIS177 3.9 20.8 1.0 CZ C:PHE219 4.1 24.4 1.0 O C:VAL175 4.3 21.3 1.0 N C:PRO176 4.3 20.5 1.0 O C:PRO176 4.4 20.1 1.0 O A:ARG182 4.5 30.0 1.0 O C:HOH289 4.5 28.7 1.0 CB A:ASP183 4.7 30.7 1.0 C C:VAL175 4.7 20.8 1.0 CE1 C:PHE219 4.9 23.2 1.0 CG C:PRO176 5.0 19.9 1.0 CE2 C:PHE219 5.0 25.4 1.0

A.P.Kuzin, M.Abashidze, S.M.Vorobiev, J.Seetharaman, L.Zhao, L.Mao, C.Ciccosanti, R.Xiao, R.Nair, M.C.Baran, T.B.Acton, B.Rost, G.T.Montelione, J.F.Hunt, L.Tong. Crystal Structure of the Protein Q88SR8 From Lactobacillus Plantarum. Northeast Structural Genomics Consortium Target LPR109. (Casp Target) To Be Published.