Sodium in PDB 4n01: The Crystal Structure of A Periplasmic Binding Protein From Veillonella Parvula Dsm 2008

The structure of The Crystal Structure of A Periplasmic Binding Protein From Veillonella Parvula Dsm 2008, PDB code: 4n01 was solved by R.Wu, M.Endres, A.Joachimiak, Midwest Center For Structural Genomics(Mcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.14 / 1.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	107.192, 46.330, 108.550, 90.00, 119.62, 90.00
R / Rfree (%)	17.1 / 20.4

The binding sites of Sodium atom in the The Crystal Structure of A Periplasmic Binding Protein From Veillonella Parvula Dsm 2008 (pdb code 4n01). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the The Crystal Structure of A Periplasmic Binding Protein From Veillonella Parvula Dsm 2008, PDB code: 4n01:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the The Crystal Structure of A Periplasmic Binding Protein From Veillonella Parvula Dsm 2008


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of The Crystal Structure of A Periplasmic Binding Protein From Veillonella Parvula Dsm 2008 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na401 b:48.9 occ:1.00 O A:HOH597 2.4 37.6 1.0 O A:HOH535 2.8 32.6 1.0 NE1 A:TRP248 3.9 18.8 1.0 CD2 A:LEU308 3.9 32.0 1.0 CD1 A:TRP248 4.0 17.9 1.0 CE2 A:TRP248 4.2 21.4 1.0 CG A:TRP248 4.2 24.6 1.0 CD2 A:TRP248 4.4 15.3 1.0 O A:HOH558 4.4 38.7 1.0 O A:HOH531 4.4 22.1 1.0 CD1 A:LEU308 4.6 24.4 1.0 CG A:LEU308 4.8 30.6 1.0 CZ2 A:TRP248 4.8 20.0 1.0

Sodium binding site 2 out of 2 in the The Crystal Structure of A Periplasmic Binding Protein From Veillonella Parvula Dsm 2008


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of The Crystal Structure of A Periplasmic Binding Protein From Veillonella Parvula Dsm 2008 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:63.4 occ:1.00 O A:HOH709 2.4 46.4 1.0 O A:HOH708 2.5 47.6 1.0 O A:HOH707 2.7 42.8 1.0 OG A:SER44 3.3 39.9 1.0 C A:TRP43 3.6 19.2 1.0 O A:HOH730 3.6 62.3 1.0 CA A:TRP43 3.7 21.5 1.0 O A:TRP43 3.8 20.8 1.0 N A:TRP43 3.9 18.2 1.0 N A:SER44 3.9 19.6 1.0 OG1 A:THR42 4.3 25.7 1.0 CB A:SER44 4.3 29.8 1.0 OD1 A:ASP53 4.3 32.2 1.0 C A:THR42 4.3 24.0 1.0 O A:HOH710 4.3 39.3 1.0 O A:HOH682 4.4 53.3 1.0 CB A:THR42 4.5 24.8 1.0 O A:HOH557 4.5 26.5 1.0 O A:THR42 4.6 21.7 1.0 CA A:SER44 4.6 19.9 1.0

R.Wu, M.Endres, A.Joachimiak, Midwest Center For Structural Genomics (Mcsg). The Crystal Structure of A Periplasmic Binding Protein From Veillonella Parvula Dsm 2008 To Be Published.