Sodium in PDB 8vvm: Structure of FABS1CE1-EPR1-1 in Complex with the Erythropoietin Receptor

The structure of Structure of FABS1CE1-EPR1-1 in Complex with the Erythropoietin Receptor, PDB code: 8vvm was solved by A.U.Singer, H.A.Bruce, A.Pavlenco, L.Ploder, G.Luu, 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)	84.38 / 2.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	73.165, 91.612, 216.735, 90, 90, 90
R / Rfree (%)	21.9 / 27.3

The structure of Structure of FABS1CE1-EPR1-1 in Complex with the Erythropoietin Receptor also contains other interesting chemical elements:

Chlorine

(Cl)

7 atoms

The binding sites of Sodium atom in the Structure of FABS1CE1-EPR1-1 in Complex with the Erythropoietin Receptor (pdb code 8vvm). 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 FABS1CE1-EPR1-1 in Complex with the Erythropoietin Receptor, PDB code: 8vvm:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Structure of FABS1CE1-EPR1-1 in Complex with the Erythropoietin 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 FABS1CE1-EPR1-1 in Complex with the Erythropoietin Receptor within 5.0Å range: probe atom residue distance (Å) B Occ A:Na302 b:72.6 occ:1.00 OG1 G:THR198 2.9 59.4 1.0 OG A:SER193 3.1 68.3 1.0 CB G:THR198 4.0 59.0 1.0 C A:LEU192 4.1 63.6 1.0 CA A:LEU192 4.1 62.9 1.0 N A:SER193 4.1 61.6 1.0 CD1 A:LEU155 4.2 64.5 1.0 OG G:SER196 4.3 61.5 1.0 CB A:SER193 4.4 65.8 1.0 CG2 G:THR198 4.4 60.4 1.0 CG1 A:VAL183 4.4 66.0 1.0 N A:LEU192 4.5 63.4 1.0 O A:LEU192 4.6 64.3 1.0 OG A:SER191 4.6 68.8 1.0 O A:SER191 4.6 63.4 1.0 C A:SER191 4.7 62.7 1.0 CA A:SER193 4.9 62.7 1.0 CB A:SER191 4.9 67.2 1.0

Sodium binding site 2 out of 4 in the Structure of FABS1CE1-EPR1-1 in Complex with the Erythropoietin 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 FABS1CE1-EPR1-1 in Complex with the Erythropoietin Receptor within 5.0Å range: probe atom residue distance (Å) B Occ A:Na303 b:68.5 occ:1.00 O4 A:PEG301 3.8 71.4 1.0 C4 A:PEG301 3.9 71.4 1.0 O A:GLY162 4.0 68.9 1.0 C A:GLY162 4.1 67.3 1.0 CA A:GLY162 4.3 65.2 1.0 CD2 A:LEU123 4.4 65.7 1.0 CG2 A:THR125 4.5 67.0 1.0 N A:GLY162 4.5 65.7 1.0 CG2 A:THR99 4.6 65.5 1.0 N A:PRO163 4.6 65.7 1.0 CG A:PRO46 4.8 63.2 1.0 CD1 A:LEU123 4.8 64.6 1.0 OG1 A:THR125 4.8 64.0 1.0 CD A:PRO163 4.9 68.8 1.0

Sodium binding site 3 out of 4 in the Structure of FABS1CE1-EPR1-1 in Complex with the Erythropoietin 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 FABS1CE1-EPR1-1 in Complex with the Erythropoietin Receptor within 5.0Å range: probe atom residue distance (Å) B Occ B:Na302 b:49.7 occ:1.00 OG B:SER191 3.2 60.4 1.0 OG1 C:THR198 3.3 49.4 1.0 OG B:SER193 3.7 57.6 1.0 CA B:LEU192 3.9 54.9 1.0 CD1 B:LEU155 3.9 60.2 1.0 C B:LEU192 3.9 53.9 1.0 N B:LEU192 4.0 56.5 1.0 C B:SER191 4.2 53.5 1.0 CB C:THR198 4.2 50.1 1.0 CB B:SER191 4.2 59.3 1.0 N B:SER193 4.3 54.5 1.0 O B:LEU192 4.3 54.6 1.0 O B:SER191 4.4 53.6 1.0 CG2 C:THR198 4.6 51.0 1.0 CB B:SER193 4.7 54.6 1.0 CG2 B:VAL183 4.8 58.2 1.0 CA B:SER191 4.8 55.5 1.0

Sodium binding site 4 out of 4 in the Structure of FABS1CE1-EPR1-1 in Complex with the Erythropoietin 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 FABS1CE1-EPR1-1 in Complex with the Erythropoietin Receptor within 5.0Å range: probe atom residue distance (Å) B Occ C:Na303 b:64.3 occ:1.00 OE1 C:GLN218 3.3 62.5 1.0 CD C:PRO133 3.6 61.5 1.0 O C:THR221 3.8 63.1 1.0 CB C:ALA132 3.9 64.2 1.0 CB C:GLN218 3.9 66.3 1.0 CG2 C:VAL216 4.1 58.8 1.0 CG2 C:THR221 4.3 64.7 1.0 CG C:PRO133 4.3 60.7 1.0 CD C:GLN218 4.3 61.6 1.0 CG2 C:VAL223 4.3 59.5 1.0 O C:VAL216 4.4 64.0 1.0 CB C:THR221 4.5 66.2 1.0 C C:THR221 4.6 64.2 1.0 CA C:ALA132 4.6 62.9 1.0 N C:PRO133 4.7 61.4 1.0 N C:GLN218 4.7 67.4 1.0 CG C:GLN218 4.7 63.1 1.0 CB C:VAL223 4.9 57.8 1.0 O C:GLN218 4.9 72.1 1.0 CA C:GLN218 4.9 67.3 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