Sodium in PDB 1vr5: Crystal Structure of Oligopeptide Abc Transporter, Periplasmic Oligopeptide-Binding (TM1223) From Thermotoga Maritima at 1.73 A Resolution

The structure of Crystal Structure of Oligopeptide Abc Transporter, Periplasmic Oligopeptide-Binding (TM1223) From Thermotoga Maritima at 1.73 A Resolution, PDB code: 1vr5 was solved by Joint Center For Structural Genomics (Jcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.61 / 1.73
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	140.030, 96.640, 115.780, 90.00, 90.00, 90.00
R / Rfree (%)	15.2 / 18.2

The structure of Crystal Structure of Oligopeptide Abc Transporter, Periplasmic Oligopeptide-Binding (TM1223) From Thermotoga Maritima at 1.73 A Resolution also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Sodium atom in the Crystal Structure of Oligopeptide Abc Transporter, Periplasmic Oligopeptide-Binding (TM1223) From Thermotoga Maritima at 1.73 A Resolution (pdb code 1vr5). 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 Oligopeptide Abc Transporter, Periplasmic Oligopeptide-Binding (TM1223) From Thermotoga Maritima at 1.73 A Resolution, PDB code: 1vr5:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Oligopeptide Abc Transporter, Periplasmic Oligopeptide-Binding (TM1223) From Thermotoga Maritima at 1.73 A Resolution


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 Oligopeptide Abc Transporter, Periplasmic Oligopeptide-Binding (TM1223) From Thermotoga Maritima at 1.73 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1 b:40.0 occ:1.00 OD1 A:ASP366 2.0 36.1 1.0 OD1 A:ASP362 2.1 25.7 1.0 OE2 A:GLU370 2.1 39.6 1.0 O A:PHE368 2.2 24.2 1.0 CD A:GLU370 2.8 28.8 1.0 OE1 A:GLU370 2.8 40.0 1.0 CG A:ASP366 3.0 34.5 1.0 CG A:ASP362 3.1 32.6 1.0 O A:HOH1076 3.3 56.2 1.0 C A:PHE368 3.3 26.6 1.0 N A:ASP366 3.6 38.2 1.0 OD2 A:ASP366 3.6 44.5 1.0 CA A:ASP362 3.7 26.2 1.0 N A:PHE368 3.8 28.4 1.0 CB A:ASN364 3.8 44.1 1.0 CB A:ASP362 3.8 25.2 1.0 OD2 A:ASP362 3.9 32.4 1.0 N A:ASN364 3.9 39.8 1.0 N A:LYS365 3.9 42.5 1.0 CA A:PHE368 4.0 27.7 1.0 CB A:ASP366 4.1 37.0 1.0 N A:VAL363 4.2 33.7 1.0 CA A:ASN364 4.2 40.8 1.0 C A:ASP362 4.2 31.2 1.0 C A:ASN364 4.2 42.3 1.0 CA A:ASP366 4.2 34.7 1.0 CG A:GLU370 4.3 28.8 1.0 N A:GLY367 4.4 33.4 1.0 N A:ARG369 4.4 24.0 1.0 CB A:PHE368 4.4 26.1 1.0 C A:ASP366 4.5 35.3 1.0 N A:GLU370 4.6 21.6 1.0 C A:LYS365 4.6 41.9 1.0 CG A:ASN364 4.6 49.2 1.0 CA A:LYS365 4.6 40.8 1.0 CA A:ARG369 4.7 23.0 1.0 C A:ARG369 4.7 21.3 1.0 C A:GLY367 4.8 30.3 1.0 C A:VAL363 4.9 37.9 1.0 ND2 A:ASN364 4.9 49.0 1.0 O A:ASN364 5.0 43.0 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Oligopeptide Abc Transporter, Periplasmic Oligopeptide-Binding (TM1223) From Thermotoga Maritima at 1.73 A Resolution


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 Oligopeptide Abc Transporter, Periplasmic Oligopeptide-Binding (TM1223) From Thermotoga Maritima at 1.73 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Na2 b:51.7 occ:1.00 OE2 B:GLU370 1.9 41.7 1.0 OD1 B:ASP366 2.1 30.3 1.0 O B:PHE368 2.2 22.9 1.0 OD1 B:ASP362 2.4 30.0 1.0 OD1 B:ASN364 2.5 59.2 1.0 CD B:GLU370 2.8 28.2 1.0 OE1 B:GLU370 3.0 36.5 1.0 CG B:ASP366 3.0 34.5 1.0 O B:HOH841 3.2 46.5 1.0 CG B:ASP362 3.4 35.1 1.0 C B:PHE368 3.4 21.3 1.0 OD2 B:ASP366 3.5 43.8 1.0 CG B:ASN364 3.5 47.1 1.0 N B:ASP366 3.8 33.7 1.0 CA B:ASP362 3.9 27.8 1.0 N B:PHE368 3.9 25.8 1.0 N B:ASN364 3.9 37.2 1.0 CA B:PHE368 4.1 21.9 1.0 ND2 B:ASN364 4.1 53.3 1.0 CB B:ASP366 4.1 34.8 1.0 CB B:ASP362 4.1 26.6 1.0 N B:LYS365 4.1 37.7 1.0 CG B:GLU370 4.1 26.3 1.0 OD2 B:ASP362 4.2 32.4 1.0 C B:ASP362 4.2 30.7 1.0 N B:VAL363 4.3 32.3 1.0 C B:ASN364 4.3 38.2 1.0 CB B:PHE368 4.3 26.1 1.0 CA B:ASP366 4.4 33.6 1.0 CA B:ASN364 4.4 39.7 1.0 N B:ARG369 4.5 18.2 1.0 CB B:ASN364 4.5 41.8 1.0 N B:GLY367 4.6 31.1 1.0 N B:GLU370 4.6 21.2 1.0 C B:ASP366 4.7 32.2 1.0 C B:ARG369 4.7 21.6 1.0 CA B:ARG369 4.7 21.5 1.0 C B:LYS365 4.8 37.6 1.0 O B:ASN364 4.9 39.3 1.0 CA B:LYS365 4.9 38.7 1.0 O B:HOH705 4.9 35.3 1.0 O B:ASP362 4.9 31.5 1.0 C B:VAL363 4.9 37.2 1.0

Joint Center For Structural Genomics (Jcsg), Joint Center For Structural Genomics (Jcsg). N/A N/A.