Sodium in PDB 3wmp: Crystal Structure of Sll-2

The structure of Crystal Structure of Sll-2, PDB code: 3wmp was solved by A.Kita, M.Jimbo, R.Sakai, Y.Morimoto, R.Takeuchi, H.Tanaka, T.Takahashi, K.Miki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	94.98 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	52.030, 189.950, 57.050, 90.00, 110.55, 90.00
R / Rfree (%)	25.1 / 27.1

The structure of Crystal Structure of Sll-2 also contains other interesting chemical elements:

Chlorine

(Cl)

12 atoms

The binding sites of Sodium atom in the Crystal Structure of Sll-2 (pdb code 3wmp). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the Crystal Structure of Sll-2, PDB code: 3wmp:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in the Crystal Structure of Sll-2


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 Sll-2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na106 b:65.7 occ:1.00 ND1 A:HIS15 3.6 46.2 1.0 SG A:CYS17 3.6 53.7 1.0 N A:ASP23 3.8 53.2 1.0 CB A:CYS22 4.2 51.8 1.0 CA A:CYS22 4.3 52.1 1.0 CB A:ASP23 4.3 56.7 1.0 CG A:ASP23 4.3 61.1 1.0 CE1 A:HIS15 4.5 44.9 1.0 CG A:HIS15 4.5 46.7 1.0 OD2 A:ASP23 4.5 62.3 1.0 C A:CYS22 4.5 51.6 1.0 CB A:HIS15 4.6 47.2 1.0 OH A:TYR86 4.6 44.8 1.0 CA A:ASP23 4.7 54.3 1.0 OD1 A:ASP23 4.7 63.1 1.0 SG A:CYS22 4.7 50.2 1.0 CB A:CYS17 4.8 50.2 1.0

Sodium binding site 2 out of 6 in the Crystal Structure of Sll-2


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 Sll-2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na105 b:56.8 occ:1.00 O B:HOH214 3.2 47.6 1.0 SG B:CYS17 3.6 50.3 1.0 ND1 B:HIS15 3.7 42.4 1.0 OD1 B:ASP23 3.8 50.7 1.0 N B:ASP23 3.9 45.2 1.0 CA B:CYS22 4.1 45.8 1.0 CG B:ASP23 4.2 50.9 1.0 CB B:CYS22 4.2 45.4 1.0 CB B:HIS15 4.4 43.8 1.0 CG B:HIS15 4.5 43.9 1.0 C B:CYS22 4.5 44.8 1.0 CB B:ASP23 4.6 49.0 1.0 CE1 B:HIS15 4.7 41.8 1.0 OH B:TYR86 4.7 40.1 1.0 OD2 B:ASP23 4.7 52.2 1.0 SG B:CYS22 4.7 45.3 1.0 CB B:CYS17 4.8 48.7 1.0 CA B:ASP23 4.9 47.2 1.0 CE2 B:TYR86 5.0 38.6 1.0

Sodium binding site 3 out of 6 in the Crystal Structure of Sll-2


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 Sll-2 within 5.0Å range: probe atom residue distance (Å) B Occ C:Na107 b:54.8 occ:1.00 O C:HOH220 3.0 42.7 1.0 N C:ASP23 3.5 50.1 1.0 ND1 C:HIS15 3.7 45.5 1.0 SG C:CYS17 3.7 54.3 1.0 CG C:ASP23 3.9 56.9 1.0 CA C:CYS22 4.0 49.2 1.0 CB C:CYS22 4.0 49.5 1.0 OD1 C:ASP23 4.1 59.2 1.0 OD2 C:ASP23 4.1 58.6 1.0 CB C:ASP23 4.2 53.0 1.0 C C:CYS22 4.3 49.9 1.0 CA C:ASP23 4.5 50.7 1.0 OH C:TYR86 4.5 46.9 1.0 CB C:HIS15 4.6 44.4 1.0 CG C:HIS15 4.6 45.1 1.0 CE1 C:HIS15 4.7 45.7 1.0 SG C:CYS22 4.7 50.7 1.0 CB C:CYS17 4.9 52.1 1.0 CE2 C:TYR86 4.9 42.8 1.0

Sodium binding site 4 out of 6 in the Crystal Structure of Sll-2


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 Sll-2 within 5.0Å range: probe atom residue distance (Å) B Occ D:Na106 b:59.7 occ:1.00 ND1 D:HIS15 3.1 45.4 1.0 O D:HOH217 3.5 56.9 1.0 SG D:CYS17 3.6 53.7 1.0 CG D:HIS15 4.0 44.9 1.0 CB D:HIS15 4.0 43.7 1.0 CE1 D:HIS15 4.0 45.7 1.0 N D:ASP23 4.3 51.7 1.0 OH D:TYR86 4.4 43.2 1.0 OD1 D:ASP23 4.5 57.4 1.0 CB D:CYS22 4.5 50.5 1.0 CA D:CYS22 4.6 51.5 1.0 CG D:ASP23 4.7 57.2 1.0 CE2 D:TYR86 4.8 40.4 1.0 SG D:CYS22 4.8 51.9 1.0 CB D:ASP23 4.8 55.1 1.0 CB D:CYS17 4.9 51.5 1.0 CZ D:TYR86 4.9 42.0 1.0 CA D:HIS15 5.0 45.8 1.0

Sodium binding site 5 out of 6 in the Crystal Structure of Sll-2


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 Sll-2 within 5.0Å range: probe atom residue distance (Å) B Occ E:Na105 b:56.3 occ:1.00 N E:ASP23 3.3 53.2 1.0 OD1 E:ASP23 3.6 59.7 1.0 SG E:CYS17 3.7 53.6 1.0 CG E:ASP23 3.7 58.2 1.0 CB E:CYS22 3.9 51.3 1.0 ND1 E:HIS15 3.9 46.9 1.0 CA E:CYS22 3.9 52.0 1.0 CB E:ASP23 4.0 56.0 1.0 C E:CYS22 4.1 52.1 1.0 OD2 E:ASP23 4.1 60.0 1.0 CA E:ASP23 4.3 53.6 1.0 SG E:CYS22 4.5 49.0 1.0 CB E:HIS15 4.6 46.8 1.0 OH E:TYR86 4.7 41.2 1.0 CG E:HIS15 4.7 46.9 1.0 CE1 E:HIS15 4.8 46.0 1.0 CB E:CYS17 5.0 52.7 1.0

Sodium binding site 6 out of 6 in the Crystal Structure of Sll-2


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 Sll-2 within 5.0Å range: probe atom residue distance (Å) B Occ F:Na106 b:59.6 occ:1.00 O F:HOH219 3.1 44.3 1.0 N F:ASP23 3.5 47.8 1.0 SG F:CYS17 3.6 49.5 1.0 ND1 F:HIS15 3.8 44.9 1.0 CG F:ASP23 3.9 55.2 1.0 OD1 F:ASP23 3.9 57.1 1.0 CA F:CYS22 4.0 46.1 1.0 CB F:CYS22 4.0 45.3 1.0 CB F:ASP23 4.2 52.5 1.0 OD2 F:ASP23 4.3 55.7 1.0 C F:CYS22 4.3 46.9 1.0 CA F:ASP23 4.5 49.5 1.0 SG F:CYS22 4.6 46.7 1.0 CB F:HIS15 4.6 44.4 1.0 CG F:HIS15 4.7 45.5 1.0 OH F:TYR86 4.7 38.2 1.0 CB F:CYS17 4.8 47.9 1.0 CE1 F:HIS15 4.8 46.4 1.0

A.Kita, M.Jimbo, R.Sakai, Y.Morimoto, R.Takeuchi, H.Tanaka, T.Takahashi, K.Miki. Crystal Structure of A Symbiosis Related Lectin: A Structural Implication of Cell Recognition Between the Symbiotic Algae and the Host Coral. To Be Published.