Sodium in PDB 5l26: Structure of Cntnw in An Inward-Facing Substrate-Bound State

The structure of Structure of Cntnw in An Inward-Facing Substrate-Bound State, PDB code: 5l26 was solved by M.Hirschi, Z.L.Johnson, S.-Y.Lee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	55.05 / 3.40
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	115.220, 115.220, 264.028, 90.00, 90.00, 120.00
R / Rfree (%)	24.2 / 26.6

The binding sites of Sodium atom in the Structure of Cntnw in An Inward-Facing Substrate-Bound State (pdb code 5l26). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Structure of Cntnw in An Inward-Facing Substrate-Bound State, PDB code: 5l26:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Structure of Cntnw in An Inward-Facing Substrate-Bound State


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Cntnw in An Inward-Facing Substrate-Bound State within 5.0Å range: probe atom residue distance (Å) B Occ A:Na506 b:68.0 occ:1.00 O A:HOH601 2.4 67.3 1.0 O A:VAL184 2.4 88.0 1.0 O A:VAL152 2.4 68.3 1.0 OD1 A:ASN149 2.4 77.0 1.0 OG A:SER183 2.5 76.7 1.0 O A:ASN149 2.5 77.0 1.0 CA A:ASN149 3.2 71.6 1.0 CG A:ASN149 3.2 74.9 1.0 C A:ASN149 3.2 78.0 1.0 CB A:SER183 3.2 74.0 1.0 CB A:ASN149 3.3 71.0 1.0 C A:VAL184 3.5 73.8 1.0 C A:VAL152 3.6 72.3 1.0 C A:GLY153 3.6 71.1 1.0 N A:VAL184 3.7 73.4 1.0 O A:GLY153 3.9 73.8 1.0 CA A:GLY153 3.9 75.9 1.0 N A:GLN154 3.9 67.7 1.0 C A:SER183 4.1 71.9 1.0 N A:GLY153 4.2 76.3 1.0 CA A:VAL184 4.2 68.2 1.0 CA A:SER183 4.3 68.2 1.0 CA A:GLN154 4.4 70.0 1.0 ND2 A:ASN149 4.5 78.1 1.0 N A:ILE150 4.5 72.5 1.0 O A:GLY180 4.5 70.2 1.0 N A:ALA185 4.6 69.2 1.0 N A:ASN149 4.6 72.5 1.0 O A:SER183 4.7 74.4 1.0 CA A:VAL152 4.8 70.9 1.0 N A:VAL152 4.8 70.7 1.0 O A:GLY179 4.8 66.6 1.0 CA A:ALA185 4.8 70.7 1.0 CA A:GLY180 4.9 65.3 1.0 CB A:GLN154 5.0 65.7 1.0

Sodium binding site 2 out of 3 in the Structure of Cntnw in An Inward-Facing Substrate-Bound State


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of Cntnw in An Inward-Facing Substrate-Bound State within 5.0Å range: probe atom residue distance (Å) B Occ B:Na505 b:81.0 occ:1.00 O B:ASN149 2.1 86.4 1.0 O B:HOH601 2.3 83.2 1.0 O B:VAL184 2.5 78.9 1.0 OG B:SER183 2.5 75.0 1.0 O B:VAL152 2.5 77.6 1.0 OD1 B:ASN149 2.5 84.4 1.0 C B:ASN149 2.9 79.1 1.0 CA B:ASN149 3.0 81.9 1.0 CG B:ASN149 3.3 83.9 1.0 CB B:ASN149 3.3 80.2 1.0 CB B:SER183 3.5 75.7 1.0 C B:VAL184 3.6 77.3 1.0 C B:VAL152 3.6 80.6 1.0 O B:SER183 3.7 79.4 1.0 C B:SER183 3.8 75.0 1.0 C B:GLY153 3.9 85.5 1.0 CA B:GLY153 4.1 83.8 1.0 N B:GLN154 4.1 86.6 1.0 N B:ILE150 4.2 73.6 1.0 CA B:SER183 4.3 75.0 1.0 N B:VAL184 4.3 76.6 1.0 O B:GLY153 4.3 89.2 1.0 N B:GLY153 4.3 88.4 1.0 N B:ASN149 4.4 86.5 1.0 N B:ALA185 4.5 78.9 1.0 CA B:VAL184 4.5 75.8 1.0 ND2 B:ASN149 4.6 86.3 1.0 O B:GLY180 4.6 80.2 1.0 O B:ALA148 4.7 87.3 1.0 CA B:GLN154 4.7 82.5 1.0 CA B:ALA185 4.7 75.2 1.0 N B:VAL152 4.7 76.4 1.0 CA B:VAL152 4.8 74.3 1.0 O B:GLY179 4.9 91.1 1.0 CA B:ILE150 4.9 78.4 1.0 C B:ALA148 5.0 86.6 1.0 C B:ILE150 5.0 76.7 1.0

Sodium binding site 3 out of 3 in the Structure of Cntnw in An Inward-Facing Substrate-Bound State


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of Cntnw in An Inward-Facing Substrate-Bound State within 5.0Å range: probe atom residue distance (Å) B Occ C:Na504 b:69.7 occ:1.00 O C:ASN149 2.3 83.2 1.0 O C:HOH601 2.3 72.4 1.0 O C:VAL184 2.4 91.2 1.0 OG C:SER183 2.4 78.8 1.0 O C:VAL152 2.4 72.1 1.0 OD1 C:ASN149 2.5 73.8 1.0 C C:ASN149 3.0 77.6 1.0 CA C:ASN149 3.1 70.3 1.0 CG C:ASN149 3.2 71.6 1.0 CB C:ASN149 3.2 71.7 1.0 CB C:SER183 3.2 72.5 1.0 C C:VAL184 3.5 77.9 1.0 C C:VAL152 3.6 73.6 1.0 C C:GLY153 3.7 72.5 1.0 O C:GLY153 3.8 71.9 1.0 N C:VAL184 3.8 80.1 1.0 C C:SER183 3.9 77.1 1.0 CA C:GLY153 3.9 75.4 1.0 N C:GLN154 4.2 72.1 1.0 CA C:SER183 4.2 76.9 1.0 N C:GLY153 4.2 78.0 1.0 CA C:VAL184 4.2 73.4 1.0 N C:ILE150 4.3 77.9 1.0 O C:SER183 4.4 70.9 1.0 O C:GLY180 4.4 76.5 1.0 ND2 C:ASN149 4.4 73.6 1.0 N C:ALA185 4.6 75.9 1.0 N C:ASN149 4.6 71.5 1.0 O C:GLY179 4.6 77.9 1.0 CA C:GLN154 4.6 71.8 1.0 CA C:GLY180 4.7 70.3 1.0 N C:VAL152 4.8 71.4 1.0 CA C:VAL152 4.8 71.6 1.0 CA C:ALA185 4.9 80.0 1.0

M.Hirschi, Z.L.Johnson, S.Y.Lee. Visualizing Multistep Elevator-Like Transitions of A Nucleoside Transporter. Nature V. 545 66 2017.
ISSN: ISSN 0028-0836
PubMed: 28424521
DOI: 10.1038/NATURE22057