Sodium in PDB 6bhy: Mouse Immunoglobulin G 2C Fc Fragment with Single Glcnac

The structure of Mouse Immunoglobulin G 2C Fc Fragment with Single Glcnac, PDB code: 6bhy was solved by D.Falconer, A.Barb, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.61 / 2.04
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	103.233, 89.215, 69.851, 90.00, 132.20, 90.00
R / Rfree (%)	21.1 / 25.4

The binding sites of Sodium atom in the Mouse Immunoglobulin G 2C Fc Fragment with Single Glcnac (pdb code 6bhy). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the Mouse Immunoglobulin G 2C Fc Fragment with Single Glcnac, PDB code: 6bhy:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in the Mouse Immunoglobulin G 2C Fc Fragment with Single Glcnac


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Mouse Immunoglobulin G 2C Fc Fragment with Single Glcnac within 5.0Å range: probe atom residue distance (Å) B Occ A:Na502 b:39.6 occ:1.00 OE2 A:GLU430 2.9 42.4 1.0 N A:GLU430 2.9 40.2 1.0 O A:GLU376 2.9 35.3 1.0 CG A:GLU430 3.4 40.8 1.0 CD2 A:HIS429 3.4 25.0 1.0 CB A:GLU430 3.5 40.1 1.0 CD A:GLU430 3.6 41.5 1.0 NE2 A:HIS429 3.6 25.0 1.0 CG1 A:ILE247 3.6 30.3 1.0 CG A:HIS429 3.7 24.9 1.0 CA A:HIS429 3.7 24.3 1.0 CA A:GLU430 3.7 40.0 1.0 C A:HIS429 3.8 24.0 1.0 CD1 A:ILE247 3.8 30.0 1.0 ND1 A:HIS429 3.9 24.8 1.0 CE1 A:HIS429 4.0 24.8 1.0 C A:GLU376 4.0 35.6 1.0 CD1 A:LEU251 4.0 42.8 1.0 CB A:HIS429 4.3 24.9 1.0 CB A:GLU376 4.4 35.8 1.0 CG A:PRO374 4.6 32.5 1.0 CA A:GLU376 4.7 35.9 1.0 OE1 A:GLU430 4.8 41.2 1.0 CD A:PRO374 4.9 32.6 1.0 C A:GLU430 4.9 39.9 1.0 N A:ILE377 4.9 27.7 1.0 O A:PRO374 4.9 33.9 1.0 CB A:ILE247 4.9 30.1 1.0 O A:HIS429 4.9 23.7 1.0 N A:HIS429 4.9 24.2 1.0 N A:GLU376 5.0 36.2 1.0 N A:GLY431 5.0 31.4 1.0

Sodium binding site 2 out of 6 in the Mouse Immunoglobulin G 2C Fc Fragment with Single Glcnac


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Mouse Immunoglobulin G 2C Fc Fragment with Single Glcnac within 5.0Å range: probe atom residue distance (Å) B Occ A:Na503 b:34.3 occ:1.00 OE2 A:GLU318 2.5 39.1 1.0 N A:ASN281 2.9 34.9 1.0 O A:GLU318 3.1 35.2 1.0 N A:ASN280 3.3 32.7 1.0 O A:PHE278 3.4 23.8 1.0 CD A:GLU318 3.5 39.6 1.0 C A:PHE278 3.5 24.0 1.0 CB A:PHE278 3.6 24.8 1.0 CA A:ASN280 3.6 32.9 1.0 CB A:LYS320 3.7 24.6 1.0 C A:ASN280 3.7 33.5 1.0 N A:VAL279 3.8 24.2 1.0 C A:VAL279 3.8 24.0 1.0 CA A:ASN281 3.9 35.7 1.0 CG A:GLU318 3.9 38.1 1.0 C A:GLU318 3.9 35.3 1.0 CA A:VAL279 4.0 23.7 1.0 OD1 A:ASN281 4.0 37.9 1.0 CE A:LYS320 4.1 26.4 1.0 CB A:GLU318 4.2 36.5 1.0 N A:LYS320 4.2 23.6 1.0 CA A:PHE278 4.2 24.4 1.0 CG A:ASN281 4.4 36.7 1.0 NZ A:LYS320 4.5 26.7 1.0 C A:PHE319 4.6 24.6 1.0 CA A:LYS320 4.6 24.0 1.0 O A:VAL279 4.6 24.4 1.0 N A:PHE319 4.6 24.0 1.0 CA A:GLU318 4.6 35.4 1.0 CA A:PHE319 4.7 24.0 1.0 OE1 A:GLU318 4.7 41.1 1.0 CD A:LYS320 4.7 26.1 1.0 CB A:ASN281 4.7 36.2 1.0 CG A:LYS320 4.8 25.5 1.0 CG A:PHE278 4.9 25.2 1.0 O A:ASN280 4.9 33.3 1.0 C A:ASN281 4.9 35.4 1.0 ND2 A:ASN281 5.0 36.4 1.0

Sodium binding site 3 out of 6 in the Mouse Immunoglobulin G 2C Fc Fragment with Single Glcnac


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Mouse Immunoglobulin G 2C Fc Fragment with Single Glcnac within 5.0Å range: probe atom residue distance (Å) B Occ A:Na504 b:38.2 occ:1.00 O A:TRP313 2.7 26.2 1.0 O A:LYS317 2.8 31.7 1.0 N A:LYS338 3.1 32.5 1.0 N A:LYS317 3.3 30.8 1.0 CA A:GLY316 3.3 28.8 1.0 C A:GLY316 3.3 28.9 1.0 C A:TRP313 3.5 26.1 1.0 O A:ASP312 3.5 32.7 1.0 CA A:TRP313 3.5 26.2 1.0 N A:GLY316 3.6 28.5 1.0 CE3 A:TRP313 3.6 26.9 1.0 CB A:LYS338 3.7 32.5 1.0 CA A:SER337 3.7 28.8 1.0 CB A:SER337 3.8 28.8 1.0 C A:LYS317 3.8 32.1 1.0 C A:SER337 3.9 28.8 1.0 CD2 A:TRP313 3.9 26.7 1.0 CA A:LYS338 4.0 32.8 1.0 CE1 A:PHE319 4.0 22.3 1.0 O A:GLY316 4.0 29.4 1.0 CA A:LYS317 4.1 31.6 1.0 CZ3 A:TRP313 4.1 27.2 1.0 CG A:TRP313 4.3 26.4 1.0 C A:ASP312 4.4 32.8 1.0 N A:TRP313 4.4 26.1 1.0 CD1 A:PHE319 4.5 22.6 1.0 CB A:TRP313 4.5 26.2 1.0 CE2 A:TRP313 4.5 26.9 1.0 O A:LYS338 4.7 32.9 1.0 CH2 A:TRP313 4.8 27.4 1.0 N A:MET314 4.8 32.1 1.0 CB A:LYS317 4.8 31.8 1.0 C A:LYS338 4.9 33.1 1.0 C A:SER315 4.9 36.1 1.0 CZ2 A:TRP313 5.0 27.3 1.0

Sodium binding site 4 out of 6 in the Mouse Immunoglobulin G 2C Fc Fragment with Single Glcnac


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Mouse Immunoglobulin G 2C Fc Fragment with Single Glcnac within 5.0Å range: probe atom residue distance (Å) B Occ B:Na502 b:37.2 occ:1.00 N B:LYS338 2.7 31.1 1.0 O B:LYS317 2.7 27.4 1.0 O B:TRP313 2.9 22.5 1.0 C B:GLY316 3.4 32.2 1.0 CA B:SER337 3.4 31.2 1.0 C B:SER337 3.5 30.8 1.0 N B:LYS317 3.5 26.6 1.0 CA B:GLY316 3.5 31.7 1.0 CB B:LYS338 3.6 30.9 1.0 CE3 B:TRP313 3.6 23.5 1.0 CB B:SER337 3.7 31.2 1.0 CA B:LYS338 3.7 31.3 1.0 C B:TRP313 3.8 22.3 1.0 C B:LYS317 3.8 27.8 1.0 CA B:TRP313 3.8 22.7 1.0 CD2 B:TRP313 3.8 23.1 1.0 N B:GLY316 3.9 31.3 1.0 O B:GLY316 3.9 33.0 1.0 O B:ASP312 4.0 27.8 1.0 CZ3 B:TRP313 4.1 23.8 1.0 CE1 B:PHE319 4.1 22.7 1.0 CA B:LYS317 4.2 27.3 1.0 CG B:TRP313 4.3 22.7 1.0 CE2 B:TRP313 4.4 23.1 1.0 CD1 B:PHE319 4.5 22.7 1.0 O B:LYS338 4.5 31.2 1.0 CH2 B:TRP313 4.6 23.6 1.0 CB B:TRP313 4.6 22.7 1.0 C B:LYS338 4.6 31.5 1.0 O B:SER337 4.7 30.8 1.0 CZ2 B:TRP313 4.8 23.3 1.0 N B:SER337 4.8 31.5 1.0 OG B:SER337 4.8 31.2 1.0 N B:TRP313 4.8 22.7 1.0 C B:ASP312 4.9 27.8 1.0 CD1 B:TRP313 5.0 22.6 1.0 N B:GLU318 5.0 33.7 1.0 CG B:LYS338 5.0 31.1 1.0

Sodium binding site 5 out of 6 in the Mouse Immunoglobulin G 2C Fc Fragment with Single Glcnac


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Mouse Immunoglobulin G 2C Fc Fragment with Single Glcnac within 5.0Å range: probe atom residue distance (Å) B Occ B:Na503 b:40.6 occ:1.00 O B:SER364 2.6 37.5 1.0 O B:PRO352 3.0 37.5 1.0 OG1 B:THR366 3.1 26.7 1.0 N B:THR366 3.6 25.8 1.0 C B:SER364 3.6 37.0 1.0 C B:PRO352 3.6 37.0 1.0 O B:LEU351 3.7 31.7 1.0 CB B:THR366 3.7 26.3 1.0 CA B:PRO353 3.7 43.0 1.0 CA B:LEU365 3.8 32.1 1.0 N B:PRO353 3.9 42.4 1.0 C B:LEU365 3.9 32.2 1.0 CD B:PRO354 4.0 45.8 1.0 N B:LEU365 4.1 32.1 1.0 CA B:THR366 4.2 25.7 1.0 C B:LEU351 4.4 32.3 1.0 C B:PRO353 4.5 43.9 1.0 N B:PRO354 4.6 45.5 1.0 CB B:SER364 4.6 37.8 1.0 CA B:SER364 4.7 37.2 1.0 CA B:PRO352 4.7 36.4 1.0 CB B:LEU351 4.8 33.6 1.0 CB B:PRO353 4.8 42.6 1.0 O B:LEU365 4.8 31.9 1.0 N B:PRO352 4.9 36.4 1.0

Sodium binding site 6 out of 6 in the Mouse Immunoglobulin G 2C Fc Fragment with Single Glcnac


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Mouse Immunoglobulin G 2C Fc Fragment with Single Glcnac within 5.0Å range: probe atom residue distance (Å) B Occ B:Na504 b:48.8 occ:1.00 O B:TRP417 2.6 39.1 1.0 O B:SER421 2.8 44.5 1.0 N B:ARG443 3.1 54.6 1.0 N B:SER421 3.3 44.2 1.0 C B:GLY420 3.3 48.2 1.0 C B:TRP417 3.5 39.5 1.0 CB B:ARG443 3.6 55.8 1.0 CA B:GLY420 3.6 48.7 1.0 CB B:SER442 3.7 40.0 1.0 C B:SER421 3.8 44.2 1.0 CA B:TRP417 3.8 39.6 1.0 CA B:SER442 3.8 40.8 1.0 O B:GLY420 3.9 47.5 1.0 CE3 B:TRP417 3.9 41.2 1.0 N B:GLY420 3.9 48.9 1.0 C B:SER442 4.0 41.5 1.0 CA B:ARG443 4.0 55.5 1.0 CD2 B:TRP417 4.0 41.5 1.0 CA B:SER421 4.1 44.0 1.0 CE2 B:PHE423 4.2 33.9 1.0 CG B:TRP417 4.3 41.0 1.0 O B:THR416 4.3 49.2 1.0 CZ3 B:TRP417 4.4 41.8 1.0 CE2 B:TRP417 4.6 42.1 1.0 CB B:TRP417 4.6 40.4 1.0 N B:GLU418 4.8 50.9 1.0 CB B:SER421 4.8 43.9 1.0 CD2 B:PHE423 4.8 33.7 1.0 CG B:ARG443 4.9 57.3 1.0 OG B:SER442 4.9 40.1 1.0 CH2 B:TRP417 4.9 42.4 1.0 CD1 B:TRP417 4.9 41.7 1.0 N B:TRP417 4.9 39.0 1.0

D.J.Falconer, A.W.Barb. Mouse IGG2C Fc Loop Residues Promote Greater Receptor-Binding Affinity Than Mouse IGG2B or Human IGG1. Plos One V. 13 92123 2018.
ISSN: ESSN 1932-6203
PubMed: 29408873
DOI: 10.1371/JOURNAL.PONE.0192123