Sodium in PDB 5txu: 1.95 Angstrom Resolution Crystal Structure of Stage II Sporulation Protein D (Spoiid) From Clostridium Difficile in Apo Conformation

The structure of 1.95 Angstrom Resolution Crystal Structure of Stage II Sporulation Protein D (Spoiid) From Clostridium Difficile in Apo Conformation, PDB code: 5txu was solved by S.Nocadello, G.Minasov, O.Kiryukhina, L.Shuvalova, W.F.Anderson, Centerfor Structural Genomics Of Infectious Diseases (Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.06 / 1.95
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	98.043, 98.043, 108.241, 90.00, 90.00, 120.00
R / Rfree (%)	15.9 / 18.4

The structure of 1.95 Angstrom Resolution Crystal Structure of Stage II Sporulation Protein D (Spoiid) From Clostridium Difficile in Apo Conformation also contains other interesting chemical elements:

Chlorine	(Cl)	2 atoms
Zinc	(Zn)	1 atom

The binding sites of Sodium atom in the 1.95 Angstrom Resolution Crystal Structure of Stage II Sporulation Protein D (Spoiid) From Clostridium Difficile in Apo Conformation (pdb code 5txu). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the 1.95 Angstrom Resolution Crystal Structure of Stage II Sporulation Protein D (Spoiid) From Clostridium Difficile in Apo Conformation, PDB code: 5txu:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the 1.95 Angstrom Resolution Crystal Structure of Stage II Sporulation Protein D (Spoiid) From Clostridium Difficile in Apo Conformation


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of 1.95 Angstrom Resolution Crystal Structure of Stage II Sporulation Protein D (Spoiid) From Clostridium Difficile in Apo Conformation within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:35.6 occ:1.00 O A:LYS179 2.3 34.6 1.0 OD2 A:ASP352 2.3 38.8 1.0 O A:TYR354 2.4 42.7 1.0 CG A:ASP352 3.3 40.0 1.0 C A:TYR354 3.3 43.3 1.0 C A:LYS179 3.4 35.5 1.0 OXT A:TYR354 3.7 41.6 1.0 CB A:ASP352 3.7 40.6 1.0 CA A:GLY180 4.1 35.7 1.0 N A:GLY180 4.1 34.5 1.0 CB A:LYS179 4.2 38.4 1.0 CG A:LYS179 4.2 41.0 1.0 CA A:LYS179 4.3 35.1 1.0 C A:GLY180 4.4 34.3 1.0 OD1 A:ASP352 4.4 41.2 1.0 CA A:ASP352 4.5 40.3 1.0 CD A:LYS179 4.5 44.6 1.0 CA A:TYR354 4.6 44.2 1.0 N A:TYR354 4.6 42.7 1.0 CG A:GLN181 4.7 33.7 1.0 O A:GLY180 4.8 36.0 1.0 N A:GLN181 4.8 31.0 1.0 N A:LYS179 5.0 33.8 1.0 C A:ASP352 5.0 41.9 1.0

Sodium binding site 2 out of 2 in the 1.95 Angstrom Resolution Crystal Structure of Stage II Sporulation Protein D (Spoiid) From Clostridium Difficile in Apo Conformation


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of 1.95 Angstrom Resolution Crystal Structure of Stage II Sporulation Protein D (Spoiid) From Clostridium Difficile in Apo Conformation within 5.0Å range: probe atom residue distance (Å) B Occ A:Na403 b:47.5 occ:1.00 O A:HOH532 2.1 42.0 1.0 O A:HOH760 2.4 50.7 1.0 O A:HOH747 2.5 51.7 1.0 O A:LYS294 2.5 30.0 1.0 O A:HOH749 2.5 44.9 1.0 O A:HOH634 2.5 41.0 1.0 C A:LYS294 3.6 31.1 1.0 O A:HOH503 3.8 44.3 1.0 OD1 A:ASN296 3.8 27.6 1.0 O A:HOH699 3.8 42.6 1.0 CB A:LYS294 4.1 37.4 1.0 O A:HOH742 4.2 55.8 1.0 O A:HOH782 4.3 35.4 1.0 CA A:LYS294 4.4 33.1 1.0 C A:LEU295 4.4 27.8 1.0 O A:HOH588 4.4 42.0 1.0 O A:HOH660 4.5 46.1 1.0 N A:LEU295 4.5 28.7 1.0 O A:LEU295 4.5 27.9 1.0 C A:FMT419 4.6 54.9 1.0 CA A:LEU295 4.6 27.7 1.0 N A:ASN296 4.7 26.8 1.0 O1 A:FMT419 4.8 52.0 1.0 CG A:ASN296 5.0 28.0 1.0

S.Nocadello, G.Minasov, O.Kiryukhina, L.Shuvalova, W.F.Anderson, Center For Structural Genomics Of Infectious Diseases(Csgid). 1.95 Angstrom Resolution Crystal Structure of Stage II Sporulation Protein D (Spoiid) From Clostridium Difficile in Apo Conformation To Be Published.