Sodium in PDB 8dir: The Complex Structure Between Human IGG1 Fc and Its High Affinity Receptor Fcgri H174R Variant

The structure of The Complex Structure Between Human IGG1 Fc and Its High Affinity Receptor Fcgri H174R Variant, PDB code: 8dir was solved by J.Lu, P.D.Sun, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.87 / 2.30
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	204.286, 89.276, 56.032, 90, 97.72, 90
R / Rfree (%)	19.6 / 23.3

The binding sites of Sodium atom in the The Complex Structure Between Human IGG1 Fc and Its High Affinity Receptor Fcgri H174R Variant (pdb code 8dir). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the The Complex Structure Between Human IGG1 Fc and Its High Affinity Receptor Fcgri H174R Variant, PDB code: 8dir:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the The Complex Structure Between Human IGG1 Fc and Its High Affinity Receptor Fcgri H174R Variant


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of The Complex Structure Between Human IGG1 Fc and Its High Affinity Receptor Fcgri H174R Variant within 5.0Å range: probe atom residue distance (Å) B Occ A:Na601 b:46.5 occ:1.00 ND1 C:HIS148 2.5 41.1 1.0 OG A:SER267 2.7 37.3 1.0 OD2 A:ASP270 2.8 43.3 1.0 CE1 C:HIS148 3.2 31.2 1.0 CB A:SER267 3.5 32.2 1.0 CG C:HIS148 3.6 37.9 1.0 CG A:ASP270 3.7 41.3 1.0 CB A:ASP270 3.9 31.1 1.0 CZ3 C:TRP149 3.9 63.7 1.0 CB A:ALA327 4.0 35.1 1.0 CB A:GLU269 4.1 34.6 1.0 CB C:HIS148 4.1 25.6 1.0 N A:ASP270 4.2 35.0 1.0 NE2 C:HIS148 4.3 44.9 1.0 CH2 C:TRP149 4.5 59.0 1.0 O A:HOH753 4.5 28.4 1.0 OE1 A:GLU269 4.5 49.5 1.0 CD2 C:HIS148 4.6 29.9 1.0 CA A:ASP270 4.7 38.0 1.0 C A:GLU269 4.7 41.9 1.0 CE3 C:TRP149 4.8 66.8 1.0 OD1 A:ASP270 4.8 39.7 1.0 O C:HOH467 4.8 38.0 1.0 CA A:GLU269 4.9 33.1 1.0 CA A:SER267 4.9 34.2 1.0

Sodium binding site 2 out of 3 in the The Complex Structure Between Human IGG1 Fc and Its High Affinity Receptor Fcgri H174R Variant


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of The Complex Structure Between Human IGG1 Fc and Its High Affinity Receptor Fcgri H174R Variant within 5.0Å range: probe atom residue distance (Å) B Occ A:Na602 b:55.3 occ:1.00 O A:TYR296 2.5 36.5 1.0 N C:ALA143 2.7 29.6 1.0 CA A:ASN297 3.1 23.4 1.0 C A:TYR296 3.2 39.8 1.0 CB C:ALA143 3.4 21.6 1.0 N A:ASN297 3.4 32.3 1.0 CA C:ALA143 3.5 29.5 1.0 CG C:LYS142 3.5 37.8 1.0 O C:ALA143 3.5 35.1 1.0 C C:LYS142 3.6 38.6 1.0 CB A:ASN297 3.7 26.3 1.0 CA C:LYS142 3.7 43.7 1.0 CD2 A:TYR296 3.8 33.9 1.0 C C:ALA143 4.0 31.6 1.0 CB C:LYS142 4.2 35.0 1.0 C A:ASN297 4.3 22.4 1.0 CG A:TYR296 4.3 33.8 1.0 CE2 A:TYR296 4.4 44.6 1.0 CA A:TYR296 4.4 36.3 1.0 NZ C:LYS142 4.5 34.7 1.0 CB A:TYR296 4.5 38.2 1.0 O C:GLY141 4.7 44.6 1.0 CE2 C:TYR138 4.8 39.0 1.0 O C:LYS142 4.8 26.6 1.0 CD C:LYS142 4.8 37.3 1.0 O A:ASN297 4.9 30.4 1.0 CE C:LYS142 4.9 41.6 1.0 N A:SER298 4.9 24.7 1.0 N C:LYS142 5.0 32.0 1.0 C6 E:FUC9 5.0 43.5 1.0

Sodium binding site 3 out of 3 in the The Complex Structure Between Human IGG1 Fc and Its High Affinity Receptor Fcgri H174R Variant


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of The Complex Structure Between Human IGG1 Fc and Its High Affinity Receptor Fcgri H174R Variant within 5.0Å range: probe atom residue distance (Å) B Occ C:Na301 b:53.4 occ:1.00 O C:HOH443 2.8 31.2 1.0 O C:HOH458 3.1 33.5 1.0 NE C:ARG123 3.4 27.6 1.0 ND2 C:ASN150 3.5 28.6 1.0 O C:CYS124 3.6 29.0 1.0 NH2 C:ARG123 3.8 34.9 1.0 CG C:ASN150 4.0 41.8 1.0 CG C:ARG123 4.0 29.9 1.0 CZ C:ARG123 4.0 42.5 1.0 OD1 C:ASN152 4.1 32.9 1.0 CD C:ARG123 4.3 25.7 1.0 OD1 C:ASN150 4.3 29.7 1.0 C C:CYS124 4.5 28.3 1.0 CA C:HIS125 4.6 34.9 1.0 ND1 C:HIS125 4.8 29.5 1.0 CB C:ASN150 4.9 29.3 1.0 O C:HOH449 4.9 35.2 1.0 N C:HIS125 5.0 32.8 1.0

J.Lu, M.Spencer, Z.Zou, M.Traver, J.Brzostowski, P.D.Sun. Fc Gamma Ri Fg-Loop Functions As A pH Sensitive Switch For Igg Binding and Release. Front Immunol V. 14 00499 2023.
ISSN: ESSN 1664-3224
PubMed: 36814926
DOI: 10.3389/FIMMU.2023.1100499