Sodium in PDB 7r63: NB82, A Nanobody Against Voltage Gated Sodium Channels NAV1.4 and NAV1.5

The structure of NB82, A Nanobody Against Voltage Gated Sodium Channels NAV1.4 and NAV1.5, PDB code: 7r63 was solved by L.Srinivasan, S.B.Gabelli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.65 / 2.00
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	77.745, 82.474, 170.7, 90, 90, 90
R / Rfree (%)	18.4 / 24.4

The structure of NB82, A Nanobody Against Voltage Gated Sodium Channels NAV1.4 and NAV1.5 also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the NB82, A Nanobody Against Voltage Gated Sodium Channels NAV1.4 and NAV1.5 (pdb code 7r63). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the NB82, A Nanobody Against Voltage Gated Sodium Channels NAV1.4 and NAV1.5, PDB code: 7r63:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the NB82, A Nanobody Against Voltage Gated Sodium Channels NAV1.4 and NAV1.5


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of NB82, A Nanobody Against Voltage Gated Sodium Channels NAV1.4 and NAV1.5 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na201 b:36.4 occ:1.00 OG B:SER61 2.6 23.9 1.0 O B:PHE47 2.6 24.0 1.0 OE1 B:GLU46 2.8 40.2 1.0 CB B:SER61 3.3 24.0 1.0 CD B:GLU46 3.5 43.0 1.0 C B:PHE47 3.7 23.3 1.0 CG B:GLU46 3.7 34.3 1.0 CB B:GLU46 3.9 29.6 1.0 N B:PHE47 3.9 26.2 1.0 O B:HOH334 4.1 44.9 1.0 CA B:PHE47 4.2 25.2 1.0 C B:GLU46 4.4 28.0 1.0 OG B:SER63 4.4 29.0 1.0 CA B:SER61 4.4 21.8 1.0 O B:HOH355 4.5 27.9 1.0 CB B:PHE47 4.5 25.7 1.0 OE2 B:GLU46 4.5 38.6 1.0 CA B:GLU46 4.7 29.8 1.0 N B:VAL48 4.8 20.6 1.0 CB B:SER63 5.0 30.0 1.0

Sodium binding site 2 out of 4 in the NB82, A Nanobody Against Voltage Gated Sodium Channels NAV1.4 and NAV1.5


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of NB82, A Nanobody Against Voltage Gated Sodium Channels NAV1.4 and NAV1.5 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na202 b:37.2 occ:1.00 OG B:SER37 2.6 24.9 1.0 O B:ALA35 3.1 25.6 1.0 CB B:SER37 3.2 22.6 1.0 N B:SER37 3.3 21.8 1.0 O B:TYR95 3.5 23.2 1.0 CH2 B:TRP114 3.5 27.0 1.0 CZ3 B:TRP114 3.5 27.2 1.0 CB B:ALA97 3.6 26.0 1.0 C B:TRP36 3.7 24.0 1.0 C B:ALA35 3.8 26.5 1.0 CA B:SER37 3.8 21.3 1.0 N B:ALA97 3.9 23.7 1.0 C B:TYR95 4.0 25.4 1.0 CA B:TRP36 4.0 24.3 1.0 C B:CYS96 4.1 23.8 1.0 CE3 B:TRP114 4.1 26.2 1.0 CB B:TYR95 4.2 22.3 1.0 CZ2 B:TRP114 4.2 25.6 1.0 N B:TRP36 4.3 23.8 1.0 CA B:CYS96 4.3 25.0 1.0 CA B:ALA97 4.4 25.9 1.0 N B:CYS96 4.4 24.8 1.0 O B:TRP36 4.4 22.1 1.0 CB B:ALA35 4.5 26.5 1.0 O B:CYS96 4.7 23.7 1.0 CD2 B:TRP114 4.7 25.9 1.0 CA B:ALA35 4.8 25.5 1.0 CE2 B:TRP114 4.8 24.4 1.0 CA B:TYR95 4.8 21.0 1.0 C B:SER37 4.9 23.7 1.0 O B:SER37 5.0 23.6 1.0

Sodium binding site 3 out of 4 in the NB82, A Nanobody Against Voltage Gated Sodium Channels NAV1.4 and NAV1.5


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of NB82, A Nanobody Against Voltage Gated Sodium Channels NAV1.4 and NAV1.5 within 5.0Å range: probe atom residue distance (Å) B Occ C:Na201 b:43.9 occ:1.00 OG C:SER37 2.7 36.9 1.0 O C:ALA35 3.0 26.7 1.0 N C:SER37 3.1 25.7 1.0 O C:TYR95 3.2 24.0 1.0 CZ3 C:TRP114 3.4 35.6 1.0 CB C:SER37 3.4 31.4 1.0 CH2 C:TRP114 3.5 36.3 1.0 C C:TRP36 3.5 22.8 1.0 C C:ALA35 3.6 26.1 1.0 CB C:ALA97 3.6 23.8 1.0 N C:ALA97 3.7 25.7 1.0 CA C:TRP36 3.8 22.9 1.0 CA C:SER37 3.9 25.8 1.0 C C:TYR95 3.9 24.5 1.0 C C:CYS96 3.9 28.5 1.0 N C:TRP36 4.0 21.4 1.0 CA C:CYS96 4.1 29.0 1.0 CE3 C:TRP114 4.1 36.2 1.0 CG1 C:ILE108 4.2 52.8 1.0 CD1 C:ILE108 4.2 54.6 1.0 O C:TRP36 4.2 23.6 1.0 CZ2 C:TRP114 4.3 34.3 1.0 CA C:ALA97 4.3 27.9 1.0 CB C:ALA35 4.3 26.6 1.0 CB C:TYR95 4.3 26.3 1.0 N C:CYS96 4.4 26.9 1.0 O C:CYS96 4.5 25.7 1.0 CA C:ALA35 4.5 26.1 1.0 CA C:TYR95 4.8 25.2 1.0 CD2 C:TRP114 4.9 38.0 1.0 C C:SER37 4.9 25.1 1.0 CE2 C:TRP114 4.9 35.7 1.0 O C:SER37 4.9 23.9 1.0

Sodium binding site 4 out of 4 in the NB82, A Nanobody Against Voltage Gated Sodium Channels NAV1.4 and NAV1.5


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of NB82, A Nanobody Against Voltage Gated Sodium Channels NAV1.4 and NAV1.5 within 5.0Å range: probe atom residue distance (Å) B Occ D:Na201 b:32.5 occ:1.00 O D:GLY8 2.7 27.2 1.0 N D:ARG19 3.1 22.0 1.0 O D:ARG19 3.1 26.7 1.0 CD2 D:LEU18 3.5 27.2 1.0 CB D:LEU18 3.6 25.7 1.0 C D:GLY8 3.6 26.8 1.0 CA D:LEU18 3.6 23.0 1.0 C D:ARG19 3.7 25.6 1.0 CA D:GLY8 3.8 25.9 1.0 C D:LEU18 3.8 23.1 1.0 CA D:ARG19 4.0 22.7 1.0 CG D:LEU18 4.1 26.7 1.0 CB D:ARG19 4.7 24.0 1.0 N D:LEU20 4.7 23.6 1.0 N D:GLY9 4.9 26.2 1.0 CD1 D:LEU18 4.9 25.9 1.0 O D:HOH321 4.9 34.4 1.0 CD2 D:LEU20 4.9 27.6 1.0

L.Srinivasan, V.Alzogaray, D.Selvakumar, S.Nathan, J.B.Yoder, K.M.Wright, S.Klinke, J.N.Nwafor, M.S.Labanda, F.A.Goldbaum, A.Schon, E.Freire, G.F.Tomaselli, L.M.Amzel, M.Ben-Johny, S.B.Gabelli. Development of High-Affinity Nanobodies Specific For Na V 1.4 and Na V 1.5 Voltage-Gated Sodium Channel Isoforms. J.Biol.Chem. V. 298 01763 2022.
ISSN: ESSN 1083-351X
PubMed: 35202650
DOI: 10.1016/J.JBC.2022.101763