Sodium in PDB 8oyg: Crystal Structure of Asbtnm in Complex with Pantoate

The structure of Crystal Structure of Asbtnm in Complex with Pantoate, PDB code: 8oyg was solved by P.Becker, A.D.Cameron, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.00 / 2.30
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	84.963, 89.364, 53.052, 90, 124.4, 90
R / Rfree (%)	22.6 / 26.6

The structure of Crystal Structure of Asbtnm in Complex with Pantoate also contains other interesting chemical elements:

Cadmium

(Cd)

2 atoms

The binding sites of Sodium atom in the Crystal Structure of Asbtnm in Complex with Pantoate (pdb code 8oyg). 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 Asbtnm in Complex with Pantoate, PDB code: 8oyg:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Asbtnm in Complex with Pantoate


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 Asbtnm in Complex with Pantoate within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1001 b:37.6 occ:1.00 O A:VAL261 2.2 44.2 1.0 O A:MET263 2.3 40.1 1.0 OE1 A:GLN77 2.3 37.7 1.0 OE1 A:GLN264 2.3 33.8 1.0 O A:GLU260 2.4 41.8 1.0 HA A:VAL261 2.7 48.5 1.0 HE22 A:GLN77 2.7 50.4 1.0 C A:VAL261 2.9 39.2 1.0 HA2 A:GLY110 3.0 37.7 1.0 CD A:GLN77 3.1 39.7 1.0 CA A:VAL261 3.2 40.4 1.0 NE2 A:GLN77 3.2 42.0 1.0 HG3 A:MET81 3.3 54.2 1.0 C A:GLU260 3.4 38.3 1.0 C A:MET263 3.4 31.3 1.0 CD A:GLN264 3.5 34.3 1.0 HA A:GLN264 3.6 39.7 1.0 N A:VAL261 3.7 35.5 1.0 CA A:GLY110 3.8 31.4 1.0 HG2 A:GLN264 3.9 44.8 1.0 H A:MET263 3.9 45.0 1.0 HA3 A:GLY110 3.9 37.7 1.0 N A:MET263 3.9 37.5 1.0 N A:GLY262 3.9 43.8 1.0 O A:HOH1111 4.0 37.0 1.0 HE21 A:GLN77 4.0 50.4 1.0 CG A:MET81 4.1 45.2 1.0 C A:GLY262 4.2 33.5 1.0 HG2 A:MET81 4.2 54.2 1.0 HE2 A:MET81 4.2 44.3 1.0 CG A:GLN264 4.2 37.4 1.0 N A:GLN264 4.3 39.8 1.0 CA A:MET263 4.3 37.6 1.0 HG13 A:VAL261 4.3 51.6 1.0 CA A:GLN264 4.4 33.1 1.0 H A:GLY111 4.4 35.9 1.0 N A:GLY110 4.4 32.8 1.0 HG3 A:GLU260 4.5 48.2 1.0 HA A:GLN77 4.5 40.9 1.0 NE2 A:GLN264 4.5 39.3 1.0 CG A:GLN77 4.6 38.0 1.0 CB A:VAL261 4.6 42.4 1.0 CA A:GLY262 4.6 39.2 1.0 H A:GLY262 4.6 52.5 1.0 HE22 A:GLN264 4.6 47.2 1.0 H A:VAL261 4.6 42.6 1.0 O A:HOH1105 4.6 39.0 1.0 H A:GLY110 4.7 39.4 1.0 O A:GLY262 4.7 42.3 1.0 HB2 A:GLN77 4.7 40.2 1.0 CA A:GLU260 4.7 45.3 1.0 HA2 A:GLY262 4.8 47.1 1.0 HA A:GLU260 4.8 54.4 1.0 HB2 A:MET263 4.8 46.5 1.0 CG1 A:VAL261 4.8 43.0 1.0 HG12 A:VAL261 4.9 51.6 1.0 O A:PRO109 4.9 41.0 1.0 CB A:GLN264 4.9 32.4 1.0 C A:PRO109 4.9 42.6 1.0 C A:GLY110 4.9 32.4 1.0 N A:GLY111 4.9 29.9 1.0 HG2 A:GLN77 4.9 45.6 1.0 HB2 A:MET81 5.0 49.9 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Asbtnm in Complex with Pantoate


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 Asbtnm in Complex with Pantoate within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1002 b:42.1 occ:1.00 OG1 A:THR132 2.3 36.0 1.0 OG A:SER128 2.3 38.6 1.0 OG A:SER114 2.4 41.4 1.0 OD1 A:ASN115 2.4 41.2 1.0 OE1 A:GLU260 2.4 33.2 1.0 O A:SER128 2.5 41.3 1.0 C A:SER128 3.0 41.7 1.0 HB A:THR132 3.2 42.8 1.0 CB A:THR132 3.3 35.6 1.0 HA A:SER128 3.4 51.3 1.0 CB A:SER128 3.4 45.3 1.0 CD A:GLU260 3.4 38.9 1.0 CA A:SER128 3.5 42.8 1.0 CB A:SER114 3.5 41.4 1.0 HB2 A:SER114 3.5 49.7 1.0 CG A:ASN115 3.5 45.0 1.0 HA A:ASN115 3.6 47.7 1.0 N A:ASN115 3.7 41.9 1.0 H A:ASN115 3.7 50.3 1.0 O A:HOH1110 3.7 41.2 1.0 H A:THR132 3.7 44.8 1.0 OE2 A:GLU260 3.8 38.6 1.0 HB3 A:SER128 3.9 54.3 1.0 HA A:VAL129 3.9 49.5 1.0 C A:SER114 3.9 49.1 1.0 HG21 A:THR132 3.9 47.0 1.0 N A:VAL129 4.0 41.3 1.0 CA A:ASN115 4.1 39.7 1.0 HB2 A:SER128 4.1 54.3 1.0 HB3 A:SER114 4.2 49.7 1.0 CG2 A:THR132 4.2 39.1 1.0 CA A:SER114 4.3 39.2 1.0 HD21 A:ASN115 4.3 50.4 1.0 N A:THR132 4.4 37.3 1.0 O A:GLY111 4.4 34.2 1.0 O A:SER114 4.4 43.2 1.0 ND2 A:ASN115 4.4 42.0 1.0 CA A:THR132 4.4 37.7 1.0 CB A:ASN115 4.4 45.6 1.0 CA A:VAL129 4.4 41.2 1.0 H A:VAL129 4.6 49.6 1.0 HA A:GLU260 4.6 54.4 1.0 HB2 A:GLU260 4.6 45.0 1.0 O A:HOH1111 4.7 37.0 1.0 H A:SER114 4.7 49.2 1.0 HG1 A:THR118 4.7 68.1 1.0 HA A:THR132 4.7 45.2 1.0 CG A:GLU260 4.8 40.1 1.0 HG23 A:THR132 4.8 47.0 1.0 HG22 A:THR132 4.9 47.0 1.0 N A:SER114 4.9 41.0 1.0 HB A:VAL131 4.9 46.7 1.0 N A:SER128 4.9 47.8 1.0 HB3 A:ASN115 5.0 54.8 1.0

P.Becker, F.B.Naughton, D.H.Brotherton, R.Pacheco-Gomez, O.Beckstein, A.D.Cameron. Mechanism of Substrate Binding and Transport in Bass Transporters. To Be Published.