Sodium in PDB 8oyf: Crystal Structure of Asbtnm in Lipidic Cubic Phase Without Substrate Bound

The structure of Crystal Structure of Asbtnm in Lipidic Cubic Phase Without Substrate Bound, PDB code: 8oyf 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)	58.96 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	49.479, 80.609, 86.453, 90, 90, 90
R / Rfree (%)	21.1 / 23.9

The structure of Crystal Structure of Asbtnm in Lipidic Cubic Phase Without Substrate Bound also contains other interesting chemical elements:

Nickel

(Ni)

1 atom

The binding sites of Sodium atom in the Crystal Structure of Asbtnm in Lipidic Cubic Phase Without Substrate Bound (pdb code 8oyf). 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 Lipidic Cubic Phase Without Substrate Bound, PDB code: 8oyf:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Asbtnm in Lipidic Cubic Phase Without Substrate Bound


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 Lipidic Cubic Phase Without Substrate Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1001 b:28.1 occ:1.00 OD1 A:ASN115 2.3 28.2 1.0 OG1 A:THR132 2.3 26.0 1.0 OG A:SER114 2.3 26.4 1.0 OE1 A:GLU260 2.4 33.9 1.0 OG A:SER128 2.4 26.0 1.0 O A:SER128 2.4 25.3 1.0 C A:SER128 3.0 29.6 1.0 HB A:THR132 3.2 39.1 1.0 CB A:THR132 3.3 32.5 1.0 HA A:SER128 3.4 35.3 1.0 CB A:SER128 3.4 28.7 1.0 CD A:GLU260 3.4 33.9 1.0 CG A:ASN115 3.4 31.0 1.0 CA A:SER128 3.5 29.4 1.0 CB A:SER114 3.6 28.0 1.0 H A:THR132 3.6 35.8 1.0 O A:HOH1103 3.6 29.1 1.0 H A:ASN115 3.7 31.6 1.0 N A:ASN115 3.7 26.3 1.0 HB2 A:SER114 3.7 33.7 1.0 HA A:ASN115 3.7 35.1 1.0 OE2 A:GLU260 3.7 38.4 1.0 HA A:VAL129 3.8 37.1 1.0 HB3 A:SER128 3.8 34.5 1.0 N A:VAL129 3.9 27.0 1.0 C A:SER114 3.9 29.6 1.0 HG21 A:THR132 4.1 40.6 1.0 CA A:ASN115 4.1 29.2 1.0 HB2 A:SER128 4.2 34.5 1.0 N A:THR132 4.2 29.8 1.0 HB3 A:SER114 4.2 33.7 1.0 HD21 A:ASN115 4.3 37.2 1.0 CG2 A:THR132 4.3 33.8 1.0 CA A:VAL129 4.3 30.9 1.0 CA A:SER114 4.3 29.6 1.0 ND2 A:ASN115 4.3 30.9 1.0 CA A:THR132 4.3 27.7 1.0 CB A:ASN115 4.4 27.2 1.0 O A:SER114 4.4 28.4 1.0 HA A:THR112 4.4 43.8 1.0 O A:GLY111 4.5 32.7 1.0 O A:HOH1124 4.5 29.6 1.0 H A:VAL129 4.5 32.5 1.0 HA A:GLU260 4.6 32.7 1.0 HA A:THR132 4.7 33.3 1.0 HB2 A:GLU260 4.7 32.5 1.0 H A:SER114 4.7 35.0 1.0 CG A:GLU260 4.8 33.1 1.0 HB A:VAL131 4.8 32.1 1.0 HG23 A:THR132 4.9 40.6 1.0 N A:SER114 4.9 29.1 1.0 N A:SER128 4.9 26.9 1.0 C A:VAL129 4.9 32.9 1.0 HB3 A:ASN115 5.0 32.7 1.0 HG22 A:THR132 5.0 40.6 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Asbtnm in Lipidic Cubic Phase Without Substrate Bound


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 Lipidic Cubic Phase Without Substrate Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1002 b:27.2 occ:1.00 O A:VAL261 2.3 23.0 1.0 OE1 A:GLN264 2.3 24.3 1.0 O A:GLU260 2.4 25.7 1.0 O A:MET263 2.4 27.9 1.0 OE1 A:GLN77 2.4 29.4 1.0 HA A:VAL261 2.8 30.9 1.0 C A:VAL261 2.9 25.9 1.0 HE22 A:GLN77 2.9 33.1 1.0 HA2 A:GLY110 3.3 33.1 1.0 CD A:GLN77 3.3 30.7 1.0 CA A:VAL261 3.3 25.6 1.0 C A:MET263 3.3 24.9 1.0 C A:GLU260 3.4 27.7 1.0 NE2 A:GLN77 3.4 27.5 1.0 CD A:GLN264 3.5 25.9 1.0 HG3 A:MET81 3.5 34.7 1.0 HA A:GLN264 3.6 32.4 1.0 H A:MET263 3.6 30.4 1.0 N A:MET263 3.7 25.2 1.0 HG2 A:GLN264 3.8 36.3 1.0 N A:GLY262 3.8 28.6 1.0 N A:VAL261 3.8 25.0 1.0 HA3 A:GLY110 3.9 33.1 1.0 CA A:GLY110 4.0 27.6 1.0 O A:HOH1124 4.0 29.6 1.0 C A:GLY262 4.0 26.5 1.0 CA A:MET263 4.1 25.9 1.0 CG A:GLN264 4.2 30.2 1.0 N A:GLN264 4.2 28.9 1.0 HE21 A:GLN77 4.3 33.1 1.0 HE2 A:MET81 4.3 28.9 1.0 CA A:GLN264 4.3 26.9 1.0 H A:GLY262 4.4 34.4 1.0 CA A:GLY262 4.4 28.5 1.0 CG A:MET81 4.4 28.8 1.0 HG2 A:MET81 4.4 34.7 1.0 HG13 A:VAL261 4.5 31.8 1.0 N A:GLY110 4.5 30.1 1.0 HG3 A:GLU260 4.5 39.9 1.0 HA2 A:GLY262 4.5 34.3 1.0 NE2 A:GLN264 4.6 23.7 1.0 HE22 A:GLN264 4.6 28.5 1.0 H A:VAL261 4.6 30.1 1.0 O A:GLY262 4.7 26.0 1.0 CB A:VAL261 4.7 25.5 1.0 CG A:GLN77 4.7 28.6 1.0 HB2 A:MET263 4.7 29.7 1.0 HA A:GLN77 4.7 28.4 1.0 CA A:GLU260 4.7 27.2 1.0 O A:HOH1109 4.7 26.2 1.0 HA A:GLU260 4.7 32.7 1.0 H A:GLY111 4.8 39.2 1.0 H A:GLY110 4.8 36.1 1.0 CB A:GLN264 4.8 26.1 1.0 HA A:MET263 4.8 31.1 1.0 HB2 A:GLN77 4.8 31.3 1.0 O A:ILE259 4.9 24.7 1.0 H A:GLN264 5.0 34.7 1.0 CG1 A:VAL261 5.0 26.4 1.0 HG3 A:GLN264 5.0 36.3 1.0 HG12 A:VAL261 5.0 31.8 1.0 O A:PRO109 5.0 26.4 1.0 C A:PRO109 5.0 26.9 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.