Sodium in PDB 5ns9: Crystal Structure of the GLUA2 Lbd (L483Y-N754S-L758V) in Complex with Glutamate

The structure of Crystal Structure of the GLUA2 Lbd (L483Y-N754S-L758V) in Complex with Glutamate, PDB code: 5ns9 was solved by C.Eibl, A.J.R.Plested, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.99 / 1.44
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	95.990, 121.297, 47.083, 90.00, 90.00, 90.00
R / Rfree (%)	14.7 / 20.5

The binding sites of Sodium atom in the Crystal Structure of the GLUA2 Lbd (L483Y-N754S-L758V) in Complex with Glutamate (pdb code 5ns9). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the Crystal Structure of the GLUA2 Lbd (L483Y-N754S-L758V) in Complex with Glutamate, PDB code: 5ns9:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in the Crystal Structure of the GLUA2 Lbd (L483Y-N754S-L758V) in Complex with Glutamate


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 GLUA2 Lbd (L483Y-N754S-L758V) in Complex with Glutamate within 5.0Å range: probe atom residue distance (Å) B Occ A:Na308 b:33.9 occ:1.00 OD1 A:ASP101 2.8 15.0 1.0 HA A:ASP101 3.0 11.4 1.0 HE3 A:LYS226 3.0 29.6 1.0 OE2 A:GLU97 3.0 14.2 1.0 O B:HOH415 3.0 35.9 1.0 O A:GLU97 3.1 12.0 1.0 O A:ILE100 3.1 13.2 1.0 HG3 A:LYS226 3.4 19.9 1.0 O A:HOH558 3.5 50.5 1.0 O A:HOH791 3.5 48.2 1.0 O A:HOH431 3.6 14.4 1.0 C A:ILE100 3.8 11.4 1.0 HG3 A:GLU97 3.8 12.4 1.0 CA A:ASP101 3.8 11.0 1.0 O A:HOH522 3.8 25.8 1.0 CG A:ASP101 3.9 14.3 1.0 CE A:LYS226 3.9 29.8 1.0 CD A:GLU97 4.0 13.1 1.0 N A:ASP101 4.1 10.6 1.0 C A:GLU97 4.2 10.4 1.0 CG A:LYS226 4.2 19.9 1.0 HD2 A:LYS226 4.3 23.7 1.0 HE2 A:LYS226 4.4 29.8 1.0 HA A:GLU97 4.4 11.1 1.0 CB A:ASP101 4.4 12.0 1.0 CG A:GLU97 4.4 12.6 1.0 CD A:LYS226 4.4 23.5 1.0 H A:PHE102 4.6 11.1 1.0 O A:HOH752 4.7 43.3 1.0 HB3 A:ASP101 4.7 11.5 1.0 HG2 A:LYS226 4.7 20.2 1.0 H A:ILE100 4.7 11.9 1.0 HA A:LYS226 4.7 14.3 1.0 CA A:GLU97 4.8 10.9 1.0 O B:HOH642 4.8 19.3 1.0 HZ1 A:LYS226 4.8 27.4 1.0 NZ A:LYS226 4.9 29.5 1.0 CA A:ILE100 4.9 11.0 1.0 H A:ASP101 4.9 11.2 1.0 OE1 A:GLU97 4.9 14.2 1.0 HZ2 A:LYS226 4.9 29.5 1.0 O B:HOH465 4.9 41.8 1.0 N A:ILE100 4.9 11.5 1.0 C A:ASP101 5.0 11.5 1.0 OD1 B:ASN232 5.0 47.9 0.5

Sodium binding site 2 out of 5 in the Crystal Structure of the GLUA2 Lbd (L483Y-N754S-L758V) in Complex with Glutamate


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 GLUA2 Lbd (L483Y-N754S-L758V) in Complex with Glutamate within 5.0Å range: probe atom residue distance (Å) B Occ A:Na309 b:34.6 occ:1.00 O B:HOH784 2.4 25.8 1.0 O A:HOH656 2.5 43.4 1.0 HA B:GLN244 2.7 16.3 1.0 O B:GLU243 2.9 14.7 1.0 O A:HOH472 3.1 20.4 1.0 O A:ARG149 3.1 16.2 1.0 HA A:SER150 3.3 13.1 1.0 HB3 A:ARG149 3.4 14.1 1.0 O A:HOH488 3.5 22.9 1.0 C B:GLU243 3.5 14.1 1.0 HG2 B:GLN244 3.5 15.8 1.0 CA B:GLN244 3.6 16.4 1.0 HB2 A:ARG149 3.7 13.9 1.0 C A:ARG149 3.7 15.1 1.0 N B:GLN244 3.8 14.9 1.0 HB3 B:GLU243 3.8 13.3 1.0 CB A:ARG149 3.9 14.0 1.0 CA A:SER150 4.1 13.3 1.0 HG3 B:GLN244 4.1 9.8 1.0 O A:HOH609 4.1 17.6 1.0 H A:LYS151 4.1 14.1 1.0 CG B:GLN244 4.1 16.7 1.0 N A:SER150 4.2 14.1 1.0 O B:HOH510 4.2 18.9 1.0 O B:HOH436 4.3 16.9 1.0 O A:HOH788 4.3 35.8 1.0 CB B:GLN244 4.4 16.7 1.0 CA A:ARG149 4.4 14.4 1.0 HG3 A:LYS151 4.5 21.8 1.0 O A:HOH524 4.5 26.4 1.0 CB B:GLU243 4.6 13.7 1.0 C B:GLN244 4.6 16.1 1.0 CA B:GLU243 4.6 13.5 1.0 H B:GLN244 4.6 14.0 1.0 HB3 B:GLN244 4.7 13.8 1.0 HB2 B:GLU243 4.7 14.2 1.0 N A:LYS151 4.7 14.6 1.0 C A:SER150 4.8 14.3 1.0 HE2 A:LYS151 4.9 38.8 1.0 HA A:ARG149 4.9 13.4 1.0 O B:HOH613 4.9 27.5 1.0 O B:GLN244 4.9 18.5 1.0 H A:SER150 5.0 13.5 1.0 O A:HOH744 5.0 20.5 1.0 HA B:GLU243 5.0 14.3 1.0

Sodium binding site 3 out of 5 in the Crystal Structure of the GLUA2 Lbd (L483Y-N754S-L758V) in Complex with Glutamate


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 GLUA2 Lbd (L483Y-N754S-L758V) in Complex with Glutamate within 5.0Å range: probe atom residue distance (Å) B Occ A:Na310 b:48.6 occ:1.00 OD2 B:ASP248 2.5 20.5 1.0 O B:HOH772 2.7 44.1 1.0 O B:HOH721 2.7 18.9 1.0 O A:HOH456 2.9 45.2 1.0 O A:LEU215 3.0 16.8 1.0 HE2 A:PHE155 3.5 14.0 1.0 CG B:ASP248 3.6 17.1 1.0 HD12 A:ILE152 3.6 17.6 1.0 HB2 B:ASP248 3.6 16.8 1.0 HA A:ASP216 3.7 14.6 1.0 HA2 B:GLY245 3.7 16.3 1.0 HD13 A:ILE152 3.7 18.0 1.0 HD11 A:ILE152 3.8 18.4 1.0 CD1 A:ILE152 3.9 18.2 1.0 CB B:ASP248 4.0 16.2 1.0 O B:HOH479 4.0 16.5 1.0 HB3 B:ASP248 4.0 16.4 1.0 HB3 A:ASP216 4.0 14.7 1.0 C A:LEU215 4.1 14.1 1.0 HA3 B:GLY245 4.1 14.3 1.0 O B:HOH592 4.3 33.0 1.0 O B:HOH563 4.3 14.4 1.0 HZ A:PHE146 4.3 17.5 1.0 CA B:GLY245 4.4 14.9 1.0 CE2 A:PHE155 4.4 14.7 1.0 HE2 A:PHE146 4.4 15.4 1.0 CA A:ASP216 4.4 14.2 1.0 CB A:ASP216 4.6 14.9 1.0 HB2 A:ASP216 4.6 15.5 1.0 OD1 B:ASP248 4.6 23.2 1.0 N A:ASP216 4.7 14.0 1.0 O B:HOH678 4.8 46.6 1.0 HZ A:PHE155 4.9 15.0 1.0 O B:HOH602 5.0 14.0 1.0 O A:HOH438 5.0 27.7 1.0

Sodium binding site 4 out of 5 in the Crystal Structure of the GLUA2 Lbd (L483Y-N754S-L758V) in Complex with Glutamate


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 GLUA2 Lbd (L483Y-N754S-L758V) in Complex with Glutamate within 5.0Å range: probe atom residue distance (Å) B Occ B:Na303 b:29.6 occ:1.00 OE1 B:GLU77 2.2 14.9 0.4 HA B:VAL56 2.7 15.1 1.0 OG1 B:THR54 2.8 12.6 0.3 OG1 B:THR9 2.8 14.9 1.0 O B:HOH582 2.8 28.7 1.0 HG1 B:THR54 2.8 13.8 0.0 HG1 B:THR9 3.0 15.8 0.0 HB B:THR9 3.0 13.3 1.0 HA B:THR9 3.1 12.2 1.0 O B:THR54 3.2 20.0 1.0 HG3 B:GLU77 3.2 15.6 0.6 HG21 B:THR54 3.2 19.3 0.7 CD B:GLU77 3.2 14.9 0.4 HB B:THR54 3.3 18.2 0.7 CB B:THR9 3.3 13.2 1.0 HG22 B:THR54 3.4 18.3 0.7 CA B:VAL56 3.5 14.9 1.0 N B:VAL56 3.5 13.7 1.0 OE2 B:GLU77 3.6 14.1 0.4 CG2 B:THR54 3.6 18.8 0.7 CA B:THR9 3.7 12.5 1.0 O B:ILE55 3.7 13.4 1.0 C B:ILE55 3.8 12.6 1.0 HB B:THR54 3.8 14.0 0.3 C B:THR54 3.8 13.5 1.0 CB B:THR54 3.8 14.4 0.3 CB B:THR54 3.8 17.3 0.7 H B:VAL56 3.9 13.3 1.0 H B:THR10 3.9 11.1 1.0 HB B:VAL56 4.0 14.7 1.0 H B:GLY57 4.0 16.3 1.0 CG B:GLU77 4.1 15.5 0.6 OE1 B:GLU77 4.1 18.4 0.6 HG23 B:VAL56 4.1 16.5 1.0 HB1 B:ALA83 4.2 17.4 1.0 CB B:VAL56 4.3 15.2 1.0 O B:HOH656 4.4 40.7 1.0 HB3 B:GLU77 4.4 12.2 0.4 HB3 B:GLU77 4.4 12.3 0.6 CA B:THR54 4.5 15.2 0.7 N B:ILE55 4.5 13.7 1.0 CD B:GLU77 4.5 16.4 0.6 CA B:THR54 4.5 14.9 0.3 CG B:GLU77 4.5 13.4 0.4 HG23 B:THR54 4.5 18.6 0.7 C B:VAL56 4.5 14.7 1.0 N B:GLY57 4.6 15.6 1.0 CA B:ILE55 4.6 11.8 1.0 N B:THR10 4.6 11.1 1.0 HB2 B:GLU77 4.6 11.4 0.4 N B:THR9 4.7 10.7 1.0 C B:THR9 4.7 12.2 1.0 HG2 B:GLU77 4.7 15.2 0.6 CG2 B:THR9 4.7 13.1 1.0 CG2 B:VAL56 4.7 16.7 1.0 HA B:ILE55 4.7 11.4 1.0 CB B:GLU77 4.8 11.8 0.6 CB B:GLU77 4.8 12.2 0.4 HG22 B:THR9 4.8 12.7 1.0 HB2 B:GLU77 4.9 10.9 0.6 O B:VAL8 4.9 15.1 1.0 HG22 B:THR54 5.0 14.3 0.3

Sodium binding site 5 out of 5 in the Crystal Structure of the GLUA2 Lbd (L483Y-N754S-L758V) in Complex with Glutamate


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 GLUA2 Lbd (L483Y-N754S-L758V) in Complex with Glutamate within 5.0Å range: probe atom residue distance (Å) B Occ B:Na304 b:48.9 occ:1.00 O B:HOH416 2.4 29.2 1.0 O B:GLY213 2.5 24.8 1.0 O B:VAL211 2.9 19.4 1.0 HG13 B:ILE113 2.9 16.4 1.0 HD11 B:LEU215 3.0 20.6 0.5 H B:ILE113 3.1 11.6 1.0 HD12 B:LEU215 3.1 20.2 0.5 O B:HOH591 3.2 29.7 1.0 HA3 B:GLY212 3.2 22.6 1.0 HA B:SER112 3.3 11.8 1.0 HD11 B:ILE113 3.3 17.0 1.0 HD12 B:ILE113 3.4 16.7 1.0 CD1 B:LEU215 3.4 20.2 0.5 HD13 B:LEU215 3.5 20.7 0.5 CG1 B:ILE113 3.5 16.8 1.0 HB B:ILE113 3.5 14.0 1.0 CD1 B:ILE113 3.6 16.8 1.0 C B:GLY212 3.6 24.2 1.0 HD22 B:LEU215 3.6 17.2 0.6 C B:GLY213 3.7 21.6 1.0 N B:ILE113 3.7 11.2 1.0 HD23 B:LEU215 3.7 16.1 0.6 N B:GLY213 3.8 24.9 1.0 CA B:GLY212 3.8 22.7 1.0 HG B:LEU215 3.9 18.8 0.6 C B:VAL211 3.9 17.9 1.0 CB B:ILE113 4.0 13.9 1.0 H B:GLY213 4.0 25.3 1.0 O B:GLY212 4.0 21.2 1.0 CD2 B:LEU215 4.1 16.4 0.6 CA B:SER112 4.1 11.7 1.0 HA B:ASN214 4.2 16.1 1.0 HA B:SER123 4.2 18.2 1.0 C B:SER112 4.3 12.3 1.0 HZ1 B:LYS210 4.3 31.1 1.0 HB2 B:SER112 4.3 13.4 1.0 N B:GLY212 4.4 21.1 1.0 HG12 B:ILE113 4.4 16.8 1.0 H B:ALA124 4.4 17.7 1.0 CA B:GLY213 4.4 25.7 1.0 CA B:ILE113 4.5 13.1 1.0 HD13 B:ILE113 4.5 16.5 1.0 CG B:LEU215 4.5 18.9 0.6 HA2 B:GLY212 4.6 22.5 1.0 HD12 B:LEU215 4.7 22.4 0.6 N B:ASN214 4.7 16.0 1.0 HZ3 B:LYS210 4.7 32.2 1.0 HG23 B:VAL211 4.7 21.8 1.0 CB B:SER112 4.8 13.7 1.0 CA B:ASN214 4.8 17.6 1.0 CG B:LEU215 4.9 20.0 0.5 HB1 B:ALA124 4.9 19.5 1.0 NZ B:LYS210 4.9 31.8 1.0 HD21 B:LEU215 4.9 16.7 0.6 H B:LEU215 4.9 17.1 1.0 O B:ILE111 5.0 16.3 1.0 N B:ALA124 5.0 19.2 1.0

W.Zhang, C.Eibl, A.M.Weeks, I.Riva, Y.J.Li, A.J.R.Plested, J.R.Howe. Unitary Properties of Ampa Receptors with Reduced Desensitization. Biophys. J. V. 113 2218 2017.
ISSN: ESSN 1542-0086
PubMed: 28863863
DOI: 10.1016/J.BPJ.2017.07.030