Sodium in PDB 4lp4: Crystal Structure of the Human Rage VC1 Fragment in Space Group P62

The structure of Crystal Structure of the Human Rage VC1 Fragment in Space Group P62, PDB code: 4lp4 was solved by L.Yatime, G.R.Andersen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.39 / 2.40
Space group	P 62
Cell size a, b, c (Å), α, β, γ (°)	102.000, 102.000, 103.400, 90.00, 90.00, 120.00
R / Rfree (%)	17.8 / 21.7

The binding sites of Sodium atom in the Crystal Structure of the Human Rage VC1 Fragment in Space Group P62 (pdb code 4lp4). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of the Human Rage VC1 Fragment in Space Group P62, PDB code: 4lp4:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Crystal Structure of the Human Rage VC1 Fragment in Space Group P62


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 Human Rage VC1 Fragment in Space Group P62 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na301 b:41.8 occ:1.00 O A:HOH401 3.1 26.0 1.0 N A:ALA21 3.3 37.5 1.0 CD1 A:ILE96 3.6 39.6 1.0 O A:ALA21 3.7 36.0 1.0 ND2 A:ASN112 3.7 38.3 1.0 NH2 A:ARG98 3.7 51.6 1.0 CA A:GLY20 3.9 35.5 1.0 CG2 A:ILE96 4.0 32.4 1.0 C A:GLY20 4.0 36.8 1.0 OD1 A:ASN112 4.2 35.1 1.0 CG1 A:ILE96 4.2 33.5 1.0 CA A:ALA21 4.2 41.3 1.0 C A:ALA21 4.3 38.9 1.0 CB A:ALA21 4.4 40.2 1.0 CG A:ASN112 4.4 34.6 1.0 CZ A:ARG98 4.7 45.0 1.0 NE A:ARG98 4.7 40.9 1.0 CB A:ILE96 4.7 33.3 1.0 CB A:ALA23 4.8 28.0 1.0

Sodium binding site 2 out of 4 in the Crystal Structure of the Human Rage VC1 Fragment in Space Group P62


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 Human Rage VC1 Fragment in Space Group P62 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na301 b:14.5 occ:1.00 O B:HOH489 3.0 43.3 1.0 N B:ARG179 3.3 25.6 1.0 CA B:ARG178 3.7 25.9 1.0 CB B:ARG178 3.9 26.7 1.0 C B:ARG178 4.0 23.9 1.0 O B:ARG179 4.1 28.4 1.0 CG B:ARG178 4.2 36.5 1.0 CB B:ARG179 4.3 34.1 1.0 CA B:ARG179 4.3 28.3 1.0 C B:ARG179 4.6 28.1 1.0 O B:THR177 4.7 27.2 1.0 O B:HOH477 4.9 45.2 1.0

Sodium binding site 3 out of 4 in the Crystal Structure of the Human Rage VC1 Fragment in Space Group P62


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 Human Rage VC1 Fragment in Space Group P62 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na302 b:16.8 occ:1.00 N B:GLU59 3.3 24.7 1.0 CA B:THR58 3.8 28.3 1.0 CB B:THR58 4.0 26.9 1.0 CB B:LYS62 4.1 23.1 1.0 C B:THR58 4.1 23.6 1.0 O B:GLU59 4.1 31.1 1.0 CB B:GLU59 4.2 30.8 1.0 CA B:GLU59 4.2 26.1 1.0 CD B:LYS62 4.5 26.1 1.0 C B:GLU59 4.5 30.7 1.0 CG B:LYS62 4.6 23.7 1.0 CG2 B:THR58 4.6 22.6 1.0 O B:ARG57 4.8 33.9 1.0 CA B:LYS62 4.9 24.0 1.0 O B:TRP61 5.0 26.1 1.0

Sodium binding site 4 out of 4 in the Crystal Structure of the Human Rage VC1 Fragment in Space Group P62


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 Human Rage VC1 Fragment in Space Group P62 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na303 b:48.4 occ:1.00 O B:HOH401 3.1 24.7 1.0 N B:ALA21 3.3 38.0 1.0 CD1 B:ILE96 3.6 41.6 1.0 O B:ALA21 3.7 36.3 1.0 ND2 B:ASN112 3.7 40.4 1.0 NH2 B:ARG98 3.7 50.6 1.0 CA B:GLY20 3.9 37.4 1.0 CG2 B:ILE96 4.0 31.5 1.0 C B:GLY20 4.0 37.5 1.0 OD1 B:ASN112 4.1 37.6 1.0 CG1 B:ILE96 4.2 34.6 1.0 CA B:ALA21 4.2 39.0 1.0 C B:ALA21 4.3 37.9 1.0 CB B:ALA21 4.4 36.4 1.0 CG B:ASN112 4.4 37.3 1.0 CZ B:ARG98 4.7 44.0 1.0 NE B:ARG98 4.7 42.4 1.0 CB B:ILE96 4.7 32.9 1.0 CB B:ALA23 4.8 26.3 1.0

L.Yatime, G.R.Andersen. Structural Insights Into the Oligomerization Mode of the Human Receptor For Advanced Glycation End-Products. Febs J. V. 280 6556 2013.
ISSN: ISSN 1742-464X
PubMed: 24119142
DOI: 10.1111/FEBS.12556