Sodium in PDB 3cym: Crystal Structure of Protein BAD_0989 From Bifidobacterium Adolescentis

The structure of Crystal Structure of Protein BAD_0989 From Bifidobacterium Adolescentis, PDB code: 3cym was solved by Y.Patskovsky, S.Ozyurt, J.Freeman, S.Chang, K.Bain, S.R.Wasserman, J.M.Sauder, S.K.Burley, S.C.Almo, New York Sgx Research Center Forstructural Genomics (Nysgxrc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	42.163, 94.422, 113.196, 90.00, 90.00, 90.00
R / Rfree (%)	22.2 / 29.4

The binding sites of Sodium atom in the Crystal Structure of Protein BAD_0989 From Bifidobacterium Adolescentis (pdb code 3cym). 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 Protein BAD_0989 From Bifidobacterium Adolescentis, PDB code: 3cym:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Protein BAD_0989 From Bifidobacterium Adolescentis


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 Protein BAD_0989 From Bifidobacterium Adolescentis within 5.0Å range: probe atom residue distance (Å) B Occ A:Na501 b:15.0 occ:1.00 O A:HOH605 2.4 47.1 1.0 O A:HOH637 2.4 15.8 1.0 OD2 A:ASP170 2.5 19.7 1.0 O A:HOH699 2.5 21.3 1.0 OD2 A:ASP42 2.7 25.7 1.0 OE2 A:GLU44 2.7 24.9 1.0 CD A:GLU44 3.5 21.4 1.0 CG A:ASP42 3.6 15.7 1.0 OE1 A:GLU44 3.6 26.4 1.0 CG A:ASP170 3.6 19.8 1.0 OD1 A:ASP42 3.8 17.2 1.0 O A:HOH725 3.9 25.6 1.0 NA A:NA502 3.9 27.8 1.0 OH A:TYR166 4.1 18.4 1.0 NZ A:LYS147 4.2 19.6 1.0 CB A:ASP170 4.2 18.8 1.0 O A:ALA43 4.3 15.7 1.0 CE2 A:TYR166 4.3 18.6 1.0 NE2 A:GLN59 4.5 18.3 1.0 CZ A:TYR166 4.6 21.7 1.0 OD1 A:ASP170 4.6 30.4 1.0 O A:HOH876 4.8 35.3 1.0 O A:HOH601 4.8 14.2 1.0 CB A:ASP42 4.8 14.9 1.0 CG A:GLU44 5.0 23.9 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Protein BAD_0989 From Bifidobacterium Adolescentis


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 Protein BAD_0989 From Bifidobacterium Adolescentis within 5.0Å range: probe atom residue distance (Å) B Occ A:Na502 b:27.8 occ:1.00 O A:HOH748 2.4 23.7 1.0 O A:HOH605 2.5 47.1 1.0 O A:HOH749 2.6 34.2 1.0 O A:HOH637 2.7 15.8 1.0 OD1 A:ASP42 2.8 17.2 1.0 OD2 A:ASP102 3.0 34.7 1.0 OD1 A:ASP102 3.4 28.0 1.0 CG A:ASP102 3.6 30.7 1.0 CG A:ASP42 3.8 15.7 1.0 NA A:NA501 3.9 15.0 1.0 O A:ALA43 4.0 15.7 1.0 OD2 A:ASP42 4.1 25.7 1.0 O A:HOH869 4.3 36.6 1.0 O A:HIS97 4.5 20.1 1.0 NH2 A:ARG45 4.6 23.3 1.0 O A:HOH725 4.7 25.6 1.0 N A:ALA43 4.7 13.6 1.0 CB A:GLN101 4.8 25.2 1.0 O A:HOH642 4.9 16.9 1.0

Y.Patskovsky, S.Ozyurt, J.Freeman, S.Chang, K.Bain, S.R.Wasserman, J.M.Sauder, S.K.Burley, S.C.Almo. Crystal Structure of Protein BAD_0989 From Bifidobacterium Adolescentis. To Be Published.