Sodium in PDB 7pgi: NAVAB1P (Bicelles)

The structure of NAVAB1P (Bicelles), PDB code: 7pgi was solved by M.Lolicato, C.Arrigoni, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	14.99 / 3.64
Space group	I 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	178.18, 191.8, 192.32, 90, 90, 90
R / Rfree (%)	28.7 / 30.4

The structure of NAVAB1P (Bicelles) also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Sodium atom in the NAVAB1P (Bicelles) (pdb code 7pgi). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the NAVAB1P (Bicelles), PDB code: 7pgi:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the NAVAB1P (Bicelles)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of NAVAB1P (Bicelles) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na502 b:113.5 occ:1.00 OXT D:ACT401 2.8 92.7 1.0 O C:ACT301 3.0 123.7 1.0 O A:ACT501 3.1 119.6 1.0 C D:ACT401 3.1 114.8 1.0 C C:ACT301 3.2 125.7 1.0 OXT C:ACT301 3.2 95.3 1.0 O D:ACT401 3.2 122.7 1.0 OXT A:ACT501 3.8 95.4 1.0 C A:ACT501 3.8 109.9 1.0 CG1 A:VAL158 3.9 88.7 1.0 CH3 C:ACT301 4.3 101.9 1.0 CH3 D:ACT401 4.4 90.0 1.0 NA A:NA503 4.4 68.6 1.0 OH B:TYR154 4.7 97.1 1.0 CG2 A:VAL158 4.7 96.7 1.0 CB A:VAL158 4.9 90.3 1.0

Sodium binding site 2 out of 4 in the NAVAB1P (Bicelles)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of NAVAB1P (Bicelles) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na503 b:68.6 occ:1.00 OH C:TYR154 2.7 111.7 1.0 OH B:TYR154 2.8 97.1 1.0 OH D:TYR154 2.8 98.9 1.0 O D:ACT401 3.0 122.7 1.0 OH A:TYR154 3.0 102.0 1.0 O C:ACT301 3.3 123.7 1.0 CZ C:TYR154 3.7 94.0 1.0 CE2 C:TYR154 3.7 77.5 1.0 CZ B:TYR154 3.8 89.5 1.0 CZ D:TYR154 3.9 88.3 1.0 CE2 B:TYR154 4.0 86.8 1.0 CE2 D:TYR154 4.0 80.9 1.0 CZ A:TYR154 4.0 94.5 1.0 C D:ACT401 4.0 114.8 1.0 CE2 A:TYR154 4.1 87.2 1.0 NA A:NA502 4.4 113.5 1.0 OXT D:ACT401 4.5 92.7 1.0 C C:ACT301 4.6 125.7 1.0 CE1 C:TYR154 4.9 88.9 1.0

Sodium binding site 3 out of 4 in the NAVAB1P (Bicelles)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of NAVAB1P (Bicelles) within 5.0Å range: probe atom residue distance (Å) B Occ F:Na301 b:106.6 occ:1.00 OXT E:ACT302 2.6 98.6 1.0 O G:ACT302 3.3 94.7 1.0 O H:ACT401 3.4 117.5 1.0 C E:ACT302 3.9 108.6 1.0 C H:ACT401 3.9 139.9 1.0 OXT H:ACT401 4.1 155.5 1.0 C G:ACT302 4.4 103.2 1.0 CH3 E:ACT302 4.5 68.9 1.0 OXT G:ACT302 4.8 100.4 1.0 O E:ACT302 4.9 127.2 1.0 CH3 H:ACT401 4.9 89.7 1.0

Sodium binding site 4 out of 4 in the NAVAB1P (Bicelles)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of NAVAB1P (Bicelles) within 5.0Å range: probe atom residue distance (Å) B Occ G:Na301 b:68.8 occ:1.00 OH G:TYR154 2.6 98.7 1.0 OH F:TYR154 2.9 102.0 1.0 OH E:TYR154 3.0 110.9 1.0 OH H:TYR154 3.1 107.3 1.0 CE2 F:TYR154 3.4 83.5 1.0 CE2 G:TYR154 3.4 87.3 1.0 CZ G:TYR154 3.4 90.9 1.0 CE2 E:TYR154 3.5 87.3 1.0 CE2 H:TYR154 3.5 83.8 1.0 CZ F:TYR154 3.6 91.7 1.0 O E:ACT302 3.6 127.2 1.0 CZ E:TYR154 3.7 95.3 1.0 CZ H:TYR154 3.8 92.4 1.0 C E:ACT302 4.6 108.6 1.0 CD2 F:TYR154 4.7 89.4 1.0 CD2 H:TYR154 4.7 91.9 1.0 CD2 G:TYR154 4.7 90.1 1.0 CD2 E:TYR154 4.7 88.7 1.0 CE1 G:TYR154 4.7 83.0 1.0 CE1 F:TYR154 4.9 82.4 1.0

C.Arrigoni, M.Lolicato, D.Shaya, A.Rohaim, F.Findeisen, L.K.Fong, C.M.Colleran, P.Dominik, S.S.Kim, J.P.Schuermann, W.F.Degrado, M.Grabe, A.A.Kossiakoff, D.L.Minor Jr.. Quaternary Structure Independent Folding of Voltage-Gated Ion Channel Pore Domain Subunits. Nat.Struct.Mol.Biol. V. 29 537 2022.
ISSN: ESSN 1545-9985
PubMed: 35655098
DOI: 10.1038/S41594-022-00775-X