Sodium in PDB 5vu0: Crystal Structure of the Complex Between Afucosylated/Galactosylated Human IGG1 Fc and Fc Gamma Receptor Iiia (CD16A) with MAN5 N-Glycans

The structure of Crystal Structure of the Complex Between Afucosylated/Galactosylated Human IGG1 Fc and Fc Gamma Receptor Iiia (CD16A) with MAN5 N-Glycans, PDB code: 5vu0 was solved by G.S.Subedi, A.M.Marcella, A.W.Barb, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.00 / 2.26
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	124.069, 48.846, 134.927, 90.00, 103.77, 90.00
R / Rfree (%)	19.2 / 23.7

The binding sites of Sodium atom in the Crystal Structure of the Complex Between Afucosylated/Galactosylated Human IGG1 Fc and Fc Gamma Receptor Iiia (CD16A) with MAN5 N-Glycans (pdb code 5vu0). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 9 binding sites of Sodium where determined in the Crystal Structure of the Complex Between Afucosylated/Galactosylated Human IGG1 Fc and Fc Gamma Receptor Iiia (CD16A) with MAN5 N-Glycans, PDB code: 5vu0:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Sodium binding site 1 out of 9 in the Crystal Structure of the Complex Between Afucosylated/Galactosylated Human IGG1 Fc and Fc Gamma Receptor Iiia (CD16A) with MAN5 N-Glycans


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of the Complex Between Afucosylated/Galactosylated Human IGG1 Fc and Fc Gamma Receptor Iiia (CD16A) with MAN5 N-Glycans within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1014 b:44.0 occ:1.00 OE1 A:GLU357 2.8 43.2 1.0 N A:SER354 3.2 42.5 1.0 NA A:NA1018 3.3 41.0 1.0 CD A:GLU357 3.6 45.6 1.0 CA A:PRO353 3.6 41.7 1.0 CD2 B:LEU368 3.7 29.9 1.0 CB A:SER354 3.8 47.2 1.0 CD2 B:LEU351 3.9 40.5 1.0 O A:SER364 3.9 31.4 1.0 C A:PRO353 3.9 42.0 1.0 CB A:SER364 4.0 32.1 1.0 CB B:TYR349 4.0 32.8 1.0 CA A:SER354 4.1 45.0 1.0 OE2 A:GLU357 4.2 43.6 1.0 CG B:TYR349 4.2 33.6 1.0 CB A:PRO353 4.3 42.5 1.0 CB A:GLU357 4.3 48.9 1.0 CD2 B:TYR349 4.4 33.5 1.0 CG A:GLU357 4.5 47.6 1.0 OG A:SER364 4.6 32.5 1.0 O A:PRO352 4.6 35.4 1.0 C A:SER364 4.7 31.7 1.0 CA A:SER364 4.7 32.8 1.0 N A:PRO353 4.8 40.3 1.0 N A:SER364 4.8 34.5 1.0 CG B:LEU351 4.9 39.4 1.0 CD1 B:TYR349 4.9 34.4 1.0 CG B:LEU368 4.9 28.9 1.0 CD1 B:LEU351 4.9 39.3 1.0

Sodium binding site 2 out of 9 in the Crystal Structure of the Complex Between Afucosylated/Galactosylated Human IGG1 Fc and Fc Gamma Receptor Iiia (CD16A) with MAN5 N-Glycans


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of the Complex Between Afucosylated/Galactosylated Human IGG1 Fc and Fc Gamma Receptor Iiia (CD16A) with MAN5 N-Glycans within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1015 b:38.8 occ:1.00 O A:TRP313 2.7 29.6 1.0 O A:LYS317 2.7 32.8 1.0 N A:LYS338 3.1 35.2 1.0 CA A:GLY316 3.4 37.6 1.0 N A:LYS317 3.4 37.2 1.0 C A:GLY316 3.4 37.2 1.0 CB A:LYS338 3.5 40.0 1.0 C A:TRP313 3.6 31.5 1.0 CA A:SER337 3.7 36.1 1.0 CE3 A:TRP313 3.7 29.9 1.0 CD2 A:TRP313 3.7 29.3 1.0 CB A:SER337 3.8 37.2 1.0 CA A:TRP313 3.8 30.6 1.0 C A:LYS317 3.8 36.2 1.0 N A:GLY316 3.8 37.1 1.0 C A:SER337 3.9 34.8 1.0 CA A:LYS338 3.9 36.0 1.0 O A:GLY316 4.0 39.5 1.0 CG A:TRP313 4.1 29.3 1.0 CZ3 A:TRP313 4.2 30.2 1.0 CA A:LYS317 4.2 36.4 1.0 CE2 A:TRP313 4.2 29.5 1.0 O A:ASP312 4.2 35.3 1.0 CE1 A:TYR319 4.5 34.8 1.0 CB A:TRP313 4.5 29.1 1.0 CH2 A:TRP313 4.6 29.3 1.0 CZ2 A:TRP313 4.7 29.2 1.0 CD1 A:TRP313 4.7 29.9 1.0 CD1 A:TYR319 4.8 33.0 1.0 NE1 A:TRP313 4.8 29.0 1.0 N A:TRP313 4.8 31.5 1.0 N A:LEU314 4.8 32.4 1.0 CG A:LYS338 4.9 45.4 1.0 C A:ASP312 4.9 34.4 1.0 N A:GLU318 4.9 37.4 1.0 OG A:SER337 5.0 37.5 1.0 CB A:LYS317 5.0 37.2 1.0

Sodium binding site 3 out of 9 in the Crystal Structure of the Complex Between Afucosylated/Galactosylated Human IGG1 Fc and Fc Gamma Receptor Iiia (CD16A) with MAN5 N-Glycans


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of the Complex Between Afucosylated/Galactosylated Human IGG1 Fc and Fc Gamma Receptor Iiia (CD16A) with MAN5 N-Glycans within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1016 b:36.3 occ:1.00 OD1 A:ASN325 2.8 33.3 1.0 NE2 C:HIS134 2.9 41.6 1.0 O A:ASP270 3.0 42.3 1.0 OG A:SER267 3.1 35.2 1.0 N A:SER267 3.4 32.0 1.0 CE1 C:HIS134 3.6 41.1 1.0 CG A:ASN325 3.6 34.5 1.0 CB A:ALA327 3.7 44.8 1.0 ND2 A:ASN325 3.7 33.8 1.0 CB A:ASP270 3.8 46.4 1.0 C A:ASP270 3.9 43.8 1.0 CG A:PRO238 3.9 43.7 1.0 CB A:SER267 4.0 34.7 1.0 CA A:VAL266 4.0 31.1 1.0 O A:HOH1104 4.1 36.6 1.0 CD2 C:HIS134 4.1 41.2 1.0 CG1 A:VAL266 4.1 31.5 1.0 C A:VAL266 4.2 31.7 1.0 CA A:SER267 4.2 33.0 1.0 CD A:PRO238 4.3 44.3 1.0 CA A:ASP270 4.3 45.3 1.0 O A:SER267 4.4 33.0 1.0 N A:ASP270 4.6 46.2 1.0 CB A:VAL266 4.6 31.2 1.0 N A:ALA327 4.6 45.3 1.0 O A:ASP265 4.6 29.5 1.0 C A:SER267 4.8 33.8 1.0 CA A:ALA327 4.8 45.8 1.0 ND1 C:HIS134 4.9 41.0 1.0 CG A:ASP270 5.0 48.1 1.0 N A:PRO271 5.0 43.7 1.0

Sodium binding site 4 out of 9 in the Crystal Structure of the Complex Between Afucosylated/Galactosylated Human IGG1 Fc and Fc Gamma Receptor Iiia (CD16A) with MAN5 N-Glycans


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of the Complex Between Afucosylated/Galactosylated Human IGG1 Fc and Fc Gamma Receptor Iiia (CD16A) with MAN5 N-Glycans within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1017 b:34.6 occ:1.00 O A:ASN421 2.6 40.4 1.0 O A:TRP417 2.8 47.4 1.0 N A:ASN421 3.1 47.7 1.0 C A:GLY420 3.2 49.2 1.0 N A:LEU443 3.2 50.3 1.0 CA A:GLY420 3.3 50.6 1.0 C A:ASN421 3.5 42.0 1.0 N A:GLY420 3.6 52.3 1.0 CE3 A:TRP417 3.7 39.8 1.0 CB A:LEU443 3.7 57.0 1.0 C A:TRP417 3.7 48.1 1.0 O A:GLY420 3.8 48.0 1.0 CA A:ASN421 3.8 45.9 1.0 CA A:SER442 3.9 47.8 1.0 C A:SER442 4.0 48.5 1.0 CA A:TRP417 4.0 43.6 1.0 CB A:SER442 4.0 48.9 1.0 CA A:LEU443 4.0 54.4 1.0 CZ3 A:TRP417 4.1 38.4 1.0 CD2 A:TRP417 4.1 39.9 1.0 O A:ARG416 4.2 45.5 1.0 CE2 A:PHE423 4.6 34.1 1.0 CG A:TRP417 4.6 40.6 1.0 CB A:ASN421 4.7 45.2 1.0 N A:VAL422 4.7 40.7 1.0 CE2 A:TRP417 4.7 39.3 1.0 CH2 A:TRP417 4.8 38.0 1.0 CD2 A:PHE423 4.8 33.0 1.0 C A:GLN419 4.8 56.2 1.0 CB A:TRP417 4.9 41.2 1.0 O A:HOH1196 4.9 50.8 1.0 N A:GLN418 5.0 51.1 1.0

Sodium binding site 5 out of 9 in the Crystal Structure of the Complex Between Afucosylated/Galactosylated Human IGG1 Fc and Fc Gamma Receptor Iiia (CD16A) with MAN5 N-Glycans


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of the Complex Between Afucosylated/Galactosylated Human IGG1 Fc and Fc Gamma Receptor Iiia (CD16A) with MAN5 N-Glycans within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1018 b:41.0 occ:1.00 OG1 A:THR366 2.6 23.1 1.0 O A:SER364 2.7 31.4 1.0 O A:PRO352 3.2 35.4 1.0 NA A:NA1014 3.3 44.0 1.0 CB A:THR366 3.4 24.3 1.0 O A:LEU351 3.5 34.3 1.0 C A:SER364 3.5 31.7 1.0 C A:PRO352 3.6 38.1 1.0 N A:THR366 3.6 26.5 1.0 CD1 B:LEU351 3.7 39.3 1.0 CA A:PRO353 3.8 41.7 1.0 N A:PRO353 3.8 40.3 1.0 C A:LEU365 4.0 27.4 1.0 CA A:LEU365 4.0 29.4 1.0 N A:LEU365 4.1 30.3 1.0 CA A:THR366 4.1 25.0 1.0 CD2 B:LEU351 4.1 40.5 1.0 CB A:SER364 4.3 32.1 1.0 C A:LEU351 4.3 35.9 1.0 CA A:SER364 4.5 32.8 1.0 CG B:LEU351 4.6 39.4 1.0 CA A:PRO352 4.6 38.5 1.0 CB A:LEU351 4.7 35.8 1.0 C A:PRO353 4.7 42.0 1.0 N A:SER354 4.7 42.5 1.0 CG2 A:THR366 4.8 23.7 1.0 O A:LEU365 4.8 25.9 1.0 CD2 B:LEU368 4.8 29.9 1.0 OH B:TYR407 4.9 23.6 1.0 CB A:PRO353 4.9 42.5 1.0 N A:PRO352 4.9 38.2 1.0 CD A:PRO353 4.9 41.9 1.0 OE1 A:GLU357 5.0 43.2 1.0

Sodium binding site 6 out of 9 in the Crystal Structure of the Complex Between Afucosylated/Galactosylated Human IGG1 Fc and Fc Gamma Receptor Iiia (CD16A) with MAN5 N-Glycans


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Crystal Structure of the Complex Between Afucosylated/Galactosylated Human IGG1 Fc and Fc Gamma Receptor Iiia (CD16A) with MAN5 N-Glycans within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1011 b:40.3 occ:1.00 O B:SER364 2.6 36.9 1.0 OG1 B:THR366 2.8 30.9 1.0 O B:PRO352 3.1 36.5 1.0 NA B:NA1014 3.3 39.9 1.0 CB B:THR366 3.5 31.1 1.0 C B:SER364 3.5 36.1 1.0 O B:LEU351 3.5 40.1 1.0 C B:PRO352 3.5 39.2 1.0 N B:THR366 3.6 32.4 1.0 CD1 A:LEU351 3.7 35.1 1.0 CA B:PRO353 3.8 41.6 1.0 N B:PRO353 3.8 40.7 1.0 CD2 A:LEU351 3.9 35.6 1.0 C B:LEU365 4.1 32.6 1.0 CA B:LEU365 4.1 35.1 1.0 CA B:THR366 4.2 32.0 1.0 N B:LEU365 4.2 34.0 1.0 CB B:SER364 4.3 36.8 1.0 C B:LEU351 4.4 38.5 1.0 CG A:LEU351 4.5 34.9 1.0 CA B:SER364 4.5 36.8 1.0 CA B:PRO352 4.6 39.8 1.0 N B:SER354 4.6 45.2 1.0 C B:PRO353 4.6 42.7 1.0 CD B:PRO353 4.7 42.1 1.0 CG2 B:THR366 4.8 29.7 1.0 CD2 A:LEU368 4.8 28.5 1.0 N B:PRO352 4.9 39.7 1.0 CB B:LEU351 4.9 39.0 1.0 CB B:PRO353 4.9 42.3 1.0 O B:LEU365 4.9 31.5 1.0 OE1 B:GLU357 4.9 45.5 1.0 OH A:TYR407 5.0 24.8 1.0

Sodium binding site 7 out of 9 in the Crystal Structure of the Complex Between Afucosylated/Galactosylated Human IGG1 Fc and Fc Gamma Receptor Iiia (CD16A) with MAN5 N-Glycans


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Crystal Structure of the Complex Between Afucosylated/Galactosylated Human IGG1 Fc and Fc Gamma Receptor Iiia (CD16A) with MAN5 N-Glycans within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1012 b:33.5 occ:1.00 O B:TRP313 2.7 28.5 1.0 O B:LYS317 2.8 33.2 1.0 N B:LYS338 3.0 31.7 1.0 CA B:GLY316 3.3 36.6 1.0 C B:GLY316 3.3 37.7 1.0 N B:LYS317 3.4 38.6 1.0 CA B:SER337 3.5 30.3 1.0 C B:TRP313 3.6 30.3 1.0 CB B:SER337 3.6 30.8 1.0 N B:GLY316 3.6 36.7 1.0 C B:SER337 3.7 31.3 1.0 CE3 B:TRP313 3.8 29.3 1.0 CA B:TRP313 3.8 30.2 1.0 C B:LYS317 3.8 35.6 1.0 CD2 B:TRP313 3.9 27.9 1.0 CB B:LYS338 3.9 34.2 1.0 CG B:LYS338 3.9 38.7 1.0 CA B:LYS338 4.0 32.2 1.0 O B:GLY316 4.0 37.0 1.0 CA B:LYS317 4.2 38.2 1.0 O B:ASP312 4.2 36.1 1.0 CZ3 B:TRP313 4.2 28.7 1.0 CG B:TRP313 4.2 28.8 1.0 CE2 B:TRP313 4.3 27.7 1.0 CE1 B:TYR319 4.5 30.8 1.0 CH2 B:TRP313 4.6 28.0 1.0 CB B:TRP313 4.6 29.5 1.0 CZ2 B:TRP313 4.7 27.8 1.0 OG B:SER337 4.7 30.7 1.0 N B:LEU314 4.8 30.6 1.0 N B:TRP313 4.9 31.9 1.0 CD1 B:TRP313 4.9 29.0 1.0 NE1 B:TRP313 4.9 29.1 1.0 N B:SER337 4.9 30.4 1.0 O B:SER337 4.9 31.8 1.0 CD1 B:TYR319 4.9 30.4 1.0 C B:ASN315 4.9 36.8 1.0 C B:ASP312 4.9 35.5 1.0 O B:LYS338 5.0 29.9 1.0 N B:GLU318 5.0 34.5 1.0 C B:LYS338 5.0 29.9 1.0

Sodium binding site 8 out of 9 in the Crystal Structure of the Complex Between Afucosylated/Galactosylated Human IGG1 Fc and Fc Gamma Receptor Iiia (CD16A) with MAN5 N-Glycans


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Crystal Structure of the Complex Between Afucosylated/Galactosylated Human IGG1 Fc and Fc Gamma Receptor Iiia (CD16A) with MAN5 N-Glycans within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1013 b:46.7 occ:1.00 O B:ASN421 2.6 53.7 1.0 O B:TRP417 2.7 52.5 1.0 N B:LEU443 3.3 66.3 1.0 C B:GLY420 3.3 63.6 1.0 N B:ASN421 3.4 62.2 1.0 CA B:GLY420 3.4 66.5 1.0 C B:ASN421 3.6 57.2 1.0 CB B:SER442 3.6 53.3 1.0 CE3 B:TRP417 3.6 45.9 1.0 CA B:SER442 3.7 53.5 1.0 C B:TRP417 3.7 55.6 1.0 N B:GLY420 3.7 66.9 1.0 CB B:LEU443 3.9 76.7 1.0 O B:GLY420 3.9 60.3 1.0 CZ3 B:TRP417 3.9 45.2 1.0 C B:SER442 4.0 57.4 1.0 CA B:ASN421 4.0 60.0 1.0 CA B:TRP417 4.0 53.0 1.0 CD2 B:TRP417 4.1 46.8 1.0 CE2 B:PHE423 4.2 41.5 1.0 O B:ARG416 4.2 55.1 1.0 CA B:LEU443 4.3 75.1 1.0 CD2 B:PHE423 4.5 41.5 1.0 CH2 B:TRP417 4.5 44.9 1.0 CG B:TRP417 4.6 48.0 1.0 OG B:SER442 4.7 51.2 1.0 CE2 B:TRP417 4.7 45.9 1.0 CB B:ASN421 4.8 60.2 1.0 N B:VAL422 4.8 53.2 1.0 CZ2 B:TRP417 4.9 44.8 1.0 CB B:TRP417 4.9 50.6 1.0 C B:GLN419 4.9 69.4 1.0 N B:GLN418 5.0 60.6 1.0

Sodium binding site 9 out of 9 in the Crystal Structure of the Complex Between Afucosylated/Galactosylated Human IGG1 Fc and Fc Gamma Receptor Iiia (CD16A) with MAN5 N-Glycans


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Crystal Structure of the Complex Between Afucosylated/Galactosylated Human IGG1 Fc and Fc Gamma Receptor Iiia (CD16A) with MAN5 N-Glycans within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1014 b:39.9 occ:1.00 OE1 B:GLU357 2.6 45.5 1.0 N B:SER354 3.2 45.2 1.0 NA B:NA1011 3.3 40.3 1.0 CA B:PRO353 3.5 41.6 1.0 CD B:GLU357 3.7 50.0 1.0 CD2 A:LEU368 3.7 28.5 1.0 O B:SER364 3.9 36.9 1.0 C B:PRO353 3.9 42.7 1.0 CB B:SER354 3.9 49.0 1.0 CD2 A:LEU351 3.9 35.6 1.0 CB B:SER364 4.1 36.8 1.0 CD2 A:TYR349 4.1 35.7 1.0 CB B:GLU357 4.1 51.1 1.0 CB A:TYR349 4.1 33.4 1.0 CA B:SER354 4.1 47.1 1.0 CB B:PRO353 4.2 42.3 1.0 CG A:TYR349 4.2 35.0 1.0 OE2 B:GLU357 4.5 50.9 1.0 CG B:GLU357 4.5 50.5 1.0 O B:PRO352 4.6 36.5 1.0 N B:PRO353 4.6 40.7 1.0 C B:SER364 4.7 36.1 1.0 OG B:SER364 4.7 37.5 1.0 O B:SER354 4.7 49.0 1.0 CA B:SER364 4.8 36.8 1.0 N B:SER364 4.8 38.6 1.0 CE2 A:TYR349 4.8 38.1 1.0 C B:SER354 5.0 49.9 1.0

D.J.Falconer, G.P.Subedi, A.M.Marcella, A.W.Barb. Antibody Fucosylation Lowers the Fc Gamma Riiia/CD16A Affinity By Limiting the Conformations Sampled By the N162-Glycan. Acs Chem. Biol. V. 13 2179 2018.
ISSN: ESSN 1554-8937
PubMed: 30016589
DOI: 10.1021/ACSCHEMBIO.8B00342