Sodium in PDB 5hkw: Crystal Structure of Apo C-Cbl Tkbd Refined to 2.25 A Resolution

The structure of Crystal Structure of Apo C-Cbl Tkbd Refined to 2.25 A Resolution, PDB code: 5hkw was solved by S.Lovell, K.P.Battaile, N.Mehzabeen, N.Zhang, A.Cooper, P.Gao, R.P.Perez, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.46 / 2.25
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	159.116, 106.523, 84.984, 90.00, 92.13, 90.00
R / Rfree (%)	18 / 23.4

The binding sites of Sodium atom in the Crystal Structure of Apo C-Cbl Tkbd Refined to 2.25 A Resolution (pdb code 5hkw). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of Apo C-Cbl Tkbd Refined to 2.25 A Resolution, PDB code: 5hkw:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of Apo C-Cbl Tkbd Refined to 2.25 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 Apo C-Cbl Tkbd Refined to 2.25 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Na401 b:35.8 occ:1.00 O A:TYR235 2.3 36.5 1.0 OD1 A:ASN233 2.4 35.6 1.0 OD1 A:ASP229 2.4 36.2 1.0 OE2 A:GLU240 2.5 39.2 1.0 OE1 A:GLU240 2.6 32.8 1.0 O A:HOH511 2.7 34.2 1.0 OG1 A:THR231 2.7 36.1 1.0 CD A:GLU240 2.9 38.4 1.0 CG A:ASN233 3.2 42.3 1.0 C A:TYR235 3.3 37.9 1.0 CG A:ASP229 3.4 30.4 1.0 ND2 A:ASN233 3.6 37.7 1.0 N A:TYR235 4.0 34.6 1.0 CB A:THR231 4.0 30.8 1.0 CA A:TYR235 4.1 37.3 1.0 N A:ASN233 4.1 33.5 1.0 CA A:ASP229 4.2 31.9 1.0 N A:THR231 4.2 28.9 1.0 OD2 A:ASP229 4.2 34.5 1.0 N A:ILE236 4.3 33.8 1.0 CB A:ASP229 4.3 30.5 1.0 C A:ASP229 4.4 39.1 1.0 CB A:TYR235 4.4 37.7 1.0 CG A:GLU240 4.4 33.6 1.0 CA A:ILE236 4.4 28.9 1.0 CB A:ASN233 4.5 32.5 1.0 CA A:THR231 4.5 32.8 1.0 N A:CYS232 4.5 33.7 1.0 N A:LEU230 4.6 34.4 1.0 C A:THR231 4.6 33.6 1.0 CA A:ASN233 4.7 35.6 1.0 N A:SER237 4.7 30.6 1.0 OE2 A:GLU164 4.7 34.2 1.0 N A:ASP234 4.7 35.9 1.0 CG2 A:THR231 4.8 33.8 1.0 O A:ASP229 4.8 30.9 1.0 C A:ASN233 4.8 37.3 1.0 CD1 A:ILE236 4.9 32.0 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of Apo C-Cbl Tkbd Refined to 2.25 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 Apo C-Cbl Tkbd Refined to 2.25 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Na401 b:34.5 occ:1.00 OD1 B:ASN233 2.3 42.1 1.0 O B:TYR235 2.3 38.9 1.0 OD1 B:ASP229 2.3 33.4 1.0 OE1 B:GLU240 2.5 32.6 1.0 OE2 B:GLU240 2.5 35.0 1.0 O B:HOH537 2.7 38.7 1.0 OG1 B:THR231 2.8 37.2 1.0 CD B:GLU240 2.8 36.7 1.0 CG B:ASN233 3.2 38.8 1.0 C B:TYR235 3.3 39.2 1.0 CG B:ASP229 3.3 35.6 1.0 ND2 B:ASN233 3.6 44.6 1.0 N B:TYR235 4.0 33.4 1.0 OD2 B:ASP229 4.1 34.5 1.0 CB B:THR231 4.1 37.3 1.0 CA B:ASP229 4.1 28.8 1.0 N B:THR231 4.1 31.6 1.0 CA B:TYR235 4.2 40.6 1.0 N B:ILE236 4.2 34.8 1.0 N B:ASN233 4.2 37.7 1.0 CB B:ASP229 4.2 28.4 1.0 CG B:GLU240 4.3 32.4 1.0 CA B:ILE236 4.3 34.0 1.0 C B:ASP229 4.4 39.8 1.0 CB B:ASN233 4.4 32.5 1.0 CA B:THR231 4.5 32.3 1.0 CB B:TYR235 4.5 39.6 1.0 N B:CYS232 4.5 35.3 1.0 C B:THR231 4.6 34.3 1.0 N B:LEU230 4.6 35.0 1.0 N B:SER237 4.6 32.0 1.0 CA B:ASN233 4.7 32.5 1.0 OE2 B:GLU164 4.8 34.2 1.0 N B:ASP234 4.8 30.5 1.0 CD1 B:ILE236 4.8 33.2 1.0 CG2 B:THR231 4.8 31.2 1.0 C B:ASN233 4.9 35.0 1.0 O B:ASP229 4.9 34.3 1.0 C B:ILE236 5.0 34.6 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of Apo C-Cbl Tkbd Refined to 2.25 A Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Apo C-Cbl Tkbd Refined to 2.25 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ C:Na401 b:41.9 occ:1.00 OD1 C:ASP229 2.3 43.9 1.0 OD1 C:ASN233 2.3 35.6 1.0 O C:TYR235 2.3 41.2 1.0 O C:HOH506 2.5 34.7 1.0 OE1 C:GLU240 2.5 38.1 1.0 OG1 C:THR231 2.6 35.5 1.0 OE2 C:GLU240 2.6 39.6 1.0 CD C:GLU240 2.9 43.3 1.0 CG C:ASN233 3.3 47.5 1.0 C C:TYR235 3.3 44.3 1.0 CG C:ASP229 3.4 47.1 1.0 ND2 C:ASN233 3.7 47.1 1.0 CB C:THR231 3.9 41.3 1.0 N C:TYR235 4.0 45.3 1.0 CA C:TYR235 4.1 44.3 1.0 OD2 C:ASP229 4.1 42.3 1.0 N C:ASN233 4.1 36.1 1.0 N C:THR231 4.2 31.8 1.0 CA C:ASP229 4.2 47.8 1.0 CB C:ASP229 4.2 50.2 1.0 N C:ILE236 4.3 42.5 1.0 N C:CYS232 4.3 42.6 1.0 CB C:TYR235 4.4 45.3 1.0 CA C:THR231 4.4 39.0 1.0 CA C:ILE236 4.4 39.2 1.0 CG C:GLU240 4.4 41.7 1.0 C C:ASP229 4.5 48.4 1.0 C C:THR231 4.5 47.4 1.0 CB C:ASN233 4.5 43.0 1.0 N C:LEU230 4.6 37.5 1.0 N C:SER237 4.7 37.2 1.0 OE2 C:GLU164 4.7 32.6 1.0 CA C:ASN233 4.7 41.2 1.0 CG2 C:THR231 4.8 41.2 1.0 N C:ASP234 4.8 38.6 1.0 CD1 C:ILE236 4.9 39.5 1.0 C C:ASN233 4.9 38.2 1.0

N.Zhang, D.Ferris, S.Lovell, A.Smalter-Hall, K.P.Battaile, A.Anbanandam, P.Gao, R.Hanzlik, R.P.Perez. Crystal Structure of Apo C-Cbl Tkbd Refined to 2.25 A Resolution To Be Published.