Sodium in PDB 8vui: Structure of FABS1CE-Epr-1, An Elbow-Locked Fab, in Complex with the Erythropoeitin Receptor

The structure of Structure of FABS1CE-Epr-1, An Elbow-Locked Fab, in Complex with the Erythropoeitin Receptor, PDB code: 8vui was solved by A.U.Singer, H.A.Bruce, L.Blazer, J.J.Adams, S.S.Sidhu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	98.51 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	56.39, 71.93, 197.02, 90, 90, 90
R / Rfree (%)	19.7 / 24

The structure of Structure of FABS1CE-Epr-1, An Elbow-Locked Fab, in Complex with the Erythropoeitin Receptor also contains other interesting chemical elements:

Chlorine

(Cl)

6 atoms

The binding sites of Sodium atom in the Structure of FABS1CE-Epr-1, An Elbow-Locked Fab, in Complex with the Erythropoeitin Receptor (pdb code 8vui). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Structure of FABS1CE-Epr-1, An Elbow-Locked Fab, in Complex with the Erythropoeitin Receptor, PDB code: 8vui:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Structure of FABS1CE-Epr-1, An Elbow-Locked Fab, in Complex with the Erythropoeitin Receptor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of FABS1CE-Epr-1, An Elbow-Locked Fab, in Complex with the Erythropoeitin Receptor within 5.0Å range: probe atom residue distance (Å) B Occ A:Na302 b:59.1 occ:1.00 OG A:SER7 2.3 59.9 1.0 O A:VAL5 3.0 52.4 1.0 CB A:SER7 3.4 48.7 1.0 C A:GLU6 3.6 48.6 1.0 N A:SER7 3.7 49.8 1.0 CB A:SER22 3.8 47.7 1.0 C A:VAL5 3.9 51.5 1.0 O A:GLU6 4.0 52.5 1.0 CA A:GLU6 4.0 46.5 1.0 N A:ALA24 4.1 53.3 1.0 CB A:ALA24 4.1 57.5 1.0 O A:SER22 4.1 51.0 1.0 C A:SER22 4.1 51.5 1.0 CA A:SER7 4.2 46.8 1.0 N A:GLU6 4.3 48.0 1.0 N A:CYS23 4.4 46.1 1.0 CA A:SER22 4.6 52.5 1.0 CA A:CYS23 4.7 50.5 1.0 CA A:ALA24 4.7 57.1 1.0 CG1 A:VAL5 4.8 55.8 1.0 C A:CYS23 4.8 54.0 1.0 OG A:SER22 4.9 59.4 1.0 CB A:VAL5 4.9 56.8 1.0

Sodium binding site 2 out of 4 in the Structure of FABS1CE-Epr-1, An Elbow-Locked Fab, in Complex with the Erythropoeitin Receptor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of FABS1CE-Epr-1, An Elbow-Locked Fab, in Complex with the Erythropoeitin Receptor within 5.0Å range: probe atom residue distance (Å) B Occ A:Na303 b:54.7 occ:1.00 O A:GLN206 2.6 50.0 1.0 O A:LEU203 2.7 57.0 1.0 O A:HOH422 3.0 36.8 1.0 C A:LEU203 3.6 61.4 1.0 CD2 A:TYR208 3.6 43.0 1.0 CA A:LEU203 3.7 54.5 1.0 C A:GLN206 3.8 48.7 1.0 CE2 A:TYR208 3.9 41.8 1.0 CD A:PRO227 4.2 49.6 1.0 O A:SER202 4.3 60.0 1.0 CL A:CL305 4.3 76.4 1.0 O A:VAL225 4.4 35.6 1.0 CD2 A:LEU203 4.5 47.1 1.0 CA A:THR207 4.5 43.6 1.0 CB A:LEU203 4.6 52.8 1.0 N A:THR207 4.6 48.7 1.0 N A:TYR208 4.6 38.1 1.0 CG A:PRO227 4.7 55.2 1.0 N A:GLN206 4.7 60.6 1.0 CG A:TYR208 4.7 40.0 1.0 N A:GLY204 4.8 64.8 1.0 CA A:GLN206 4.8 56.2 1.0 N A:LEU203 4.9 54.9 1.0 C A:THR207 4.9 38.5 1.0 C A:SER202 5.0 57.1 1.0

Sodium binding site 3 out of 4 in the Structure of FABS1CE-Epr-1, An Elbow-Locked Fab, in Complex with the Erythropoeitin Receptor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of FABS1CE-Epr-1, An Elbow-Locked Fab, in Complex with the Erythropoeitin Receptor within 5.0Å range: probe atom residue distance (Å) B Occ G:Na303 b:42.7 occ:1.00 O G:HOH481 2.6 37.5 1.0 OG1 G:THR184 2.7 33.7 1.0 O G:GLU185 2.7 36.6 1.0 O G:THR192 3.3 37.1 1.0 CB G:THR184 3.5 32.0 1.0 N G:ASP187 3.6 45.7 1.0 CE1 A:HIS178 3.8 39.7 1.0 CB G:ASP187 3.9 46.7 1.0 C G:GLU185 3.9 42.2 1.0 ND1 A:HIS178 3.9 34.9 1.0 N G:SER194 4.0 35.6 1.0 CA G:ASP187 4.0 45.4 1.0 CA G:TYR193 4.1 36.3 1.0 C G:GLN186 4.1 41.6 1.0 O A:HOH441 4.1 40.6 1.0 C G:THR192 4.2 39.3 1.0 C G:TYR193 4.2 37.4 1.0 CG2 G:THR184 4.4 33.9 1.0 OG G:SER194 4.5 35.0 1.0 CA G:GLN186 4.5 38.5 1.0 N G:TYR193 4.5 34.5 1.0 C G:THR184 4.6 41.1 1.0 N G:GLN186 4.7 39.6 1.0 CA G:THR184 4.7 31.3 1.0 N G:GLU185 4.7 38.5 1.0 NE2 A:HIS178 4.7 37.4 1.0 OD1 G:ASP187 4.7 56.1 1.0 CB G:SER194 4.7 32.7 1.0 O G:GLN186 4.8 45.3 1.0 CG G:ASP187 4.9 51.7 1.0 O G:THR184 4.9 36.6 1.0 CA G:SER194 5.0 33.8 1.0 CA G:GLU185 5.0 41.0 1.0

Sodium binding site 4 out of 4 in the Structure of FABS1CE-Epr-1, An Elbow-Locked Fab, in Complex with the Erythropoeitin Receptor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structure of FABS1CE-Epr-1, An Elbow-Locked Fab, in Complex with the Erythropoeitin Receptor within 5.0Å range: probe atom residue distance (Å) B Occ G:Na304 b:54.1 occ:1.00 OE1 G:GLN218 2.3 41.7 1.0 O G:TYR160 3.0 43.1 1.0 O G:ALA131 3.1 37.5 1.0 CD G:GLN218 3.1 46.3 1.0 C G:ALA131 3.5 44.0 1.0 CG1 G:VAL130 3.6 45.8 1.0 NE2 G:GLN218 3.7 41.8 1.0 CA G:ALA132 3.8 36.3 1.0 N G:ALA132 3.9 35.5 1.0 C G:TYR160 3.9 39.7 1.0 CB G:GLN218 3.9 39.6 1.0 N G:ALA131 4.0 40.7 1.0 CD G:PRO161 4.1 42.1 1.0 CG G:GLN218 4.1 40.9 1.0 N G:PRO161 4.4 41.2 1.0 CA G:ALA131 4.5 40.9 1.0 CD G:PRO133 4.5 40.0 1.0 N G:TYR160 4.7 35.3 1.0 CB G:ALA132 4.8 37.5 1.0 C G:ALA132 4.8 37.5 1.0 CB G:VAL130 4.9 53.4 1.0 C G:VAL130 4.9 42.6 1.0 N G:PRO133 5.0 34.5 1.0

H.A.Bruce, A.U.Singer, L.L.Blazer, K.Luu, L.Ploder, A.Pavlenco, I.Kurinov, J.J.Adams, S.S.Sidhu. Antigen-Binding Fragments with Improved Crystal Lattice Packing and Enhanced Conformational Flexibility at the Elbow Region As Crystallization Chaperones. Protein Sci. V. 33 E5081 2024.
ISSN: ESSN 1469-896X
PubMed: 38924648
DOI: 10.1002/PRO.5081