Sodium in PDB 2vrp: Structure of Rhodocytin

The structure of Structure of Rhodocytin, PDB code: 2vrp was solved by A.A.Watson, C.A.O'callaghan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.76 / 2.41
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	61.933, 89.368, 120.996, 90.00, 90.00, 90.00
R / Rfree (%)	20.1 / 27.2

The structure of Structure of Rhodocytin also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Sodium atom in the Structure of Rhodocytin (pdb code 2vrp). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Structure of Rhodocytin, PDB code: 2vrp:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Structure of Rhodocytin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Rhodocytin within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1137 b:73.4 occ:1.00 CA A:SER91 3.7 29.7 1.0 N A:SER92 3.7 31.5 1.0 OG A:SER92 3.8 32.0 1.0 CB A:SER91 4.0 29.4 1.0 C A:SER91 4.2 30.6 1.0 O A:GLY90 4.5 27.7 1.0 CB A:SER92 4.7 32.4 1.0 N A:SER91 4.8 28.4 1.0 CA A:SER92 4.8 32.2 1.0

Sodium binding site 2 out of 4 in the Structure of Rhodocytin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of Rhodocytin within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1138 b:53.2 occ:1.00 OH A:TYR12 3.8 29.4 1.0 CE1 A:TYR12 4.0 25.9 1.0 CZ A:TYR12 4.4 25.6 1.0 CA A:GLY49 5.0 32.6 1.0

Sodium binding site 3 out of 4 in the Structure of Rhodocytin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of Rhodocytin within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1124 b:48.4 occ:1.00 OD2 B:ASP1 2.2 52.2 1.0 CG B:ASP1 3.3 52.9 1.0 O B:HOH2001 3.4 60.4 1.0 OG B:SER8 3.6 35.5 1.0 N B:SER8 3.7 35.8 1.0 OD1 B:ASP1 3.8 53.9 1.0 O B:TRP6 4.0 35.5 1.0 CA B:SER7 4.0 35.4 1.0 C B:SER7 4.4 35.3 1.0 CB B:SER8 4.5 35.5 1.0 CB B:ASP1 4.6 52.4 1.0 CB B:SER7 4.7 35.7 1.0 CA B:SER8 4.7 35.6 1.0 CB B:CYS2 4.8 48.3 1.0 C B:TRP6 4.9 35.8 1.0 N B:SER7 4.9 35.8 1.0 OG B:SER7 5.0 36.2 1.0

Sodium binding site 4 out of 4 in the Structure of Rhodocytin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structure of Rhodocytin within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1127 b:51.0 occ:1.00 N B:GLY5 3.5 41.3 1.0 CA B:SER4 4.1 43.8 1.0 C B:SER4 4.3 42.4 1.0 CA B:GLY5 4.3 39.4 1.0 OG B:SER4 4.6 45.7 1.0 CB B:SER4 4.7 44.3 1.0

A.A.Watson, J.A.Eble, C.A.O'callaghan. Crystal Structure of Rhodocytin, A Ligand For the Platelet-Activating Receptor Clec-2. Protein Sci. V. 17 1611 2008.
ISSN: ISSN 0961-8368
PubMed: 18583525
DOI: 10.1110/PS.035568.108