Sodium in PDB 5i1t: 2.6 Angstrom Resolution Crystal Structure of Stage II Sporulation Protein D (Spoiid) From Clostridium Difficile in Complex with Triacetylchitotriose

The structure of 2.6 Angstrom Resolution Crystal Structure of Stage II Sporulation Protein D (Spoiid) From Clostridium Difficile in Complex with Triacetylchitotriose, PDB code: 5i1t was solved by S.Nocadello, G.Minasov, L.Shuvalova, I.Dubrovska, S.Grimshaw, K.Kwon, W.F.Anderson, Center For 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)	29.08 / 2.60
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	98.082, 98.082, 108.327, 90.00, 90.00, 120.00
R / Rfree (%)	15.5 / 19.6

The structure of 2.6 Angstrom Resolution Crystal Structure of Stage II Sporulation Protein D (Spoiid) From Clostridium Difficile in Complex with Triacetylchitotriose also contains other interesting chemical elements:

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

The binding sites of Sodium atom in the 2.6 Angstrom Resolution Crystal Structure of Stage II Sporulation Protein D (Spoiid) From Clostridium Difficile in Complex with Triacetylchitotriose (pdb code 5i1t). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the 2.6 Angstrom Resolution Crystal Structure of Stage II Sporulation Protein D (Spoiid) From Clostridium Difficile in Complex with Triacetylchitotriose, PDB code: 5i1t:

Sodium binding site 1 out of 1 in the 2.6 Angstrom Resolution Crystal Structure of Stage II Sporulation Protein D (Spoiid) From Clostridium Difficile in Complex with Triacetylchitotriose


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of 2.6 Angstrom Resolution Crystal Structure of Stage II Sporulation Protein D (Spoiid) From Clostridium Difficile in Complex with Triacetylchitotriose within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:56.9 occ:1.00 O A:LYS179 2.2 64.1 1.0 O A:TYR354 2.3 65.8 1.0 OD2 A:ASP352 2.3 60.7 1.0 C A:LYS179 3.3 60.2 1.0 CG A:ASP352 3.3 62.5 1.0 C A:TYR354 3.4 64.9 1.0 CB A:ASP352 3.7 63.6 1.0 OXT A:TYR354 3.8 70.5 1.0 O A:HOH588 3.8 72.4 1.0 CA A:GLY180 4.0 58.8 1.0 N A:GLY180 4.0 61.7 1.0 C A:GLY180 4.2 57.8 1.0 CB A:LYS179 4.4 63.9 1.0 CA A:LYS179 4.4 60.6 1.0 CA A:ASP352 4.4 64.3 1.0 OD1 A:ASP352 4.5 60.9 1.0 CG A:LYS179 4.5 66.7 1.0 O A:GLY180 4.6 56.2 1.0 N A:TYR354 4.6 65.5 1.0 CG A:GLN181 4.6 57.9 1.0 CA A:TYR354 4.6 65.4 1.0 N A:GLN181 4.7 55.7 1.0 CD A:LYS179 4.8 70.3 1.0 N A:LYS179 4.9 58.4 1.0 C A:ASP352 5.0 63.9 1.0

S.Nocadello, G.Minasov, L.S.Shuvalova, I.Dubrovska, E.Sabini, W.F.Anderson. Crystal Structures of the Spoiid Lytic Transglycosylases Essential For Bacterial Sporulation. J.Biol.Chem. V. 291 14915 2016.
ISSN: ESSN 1083-351X
PubMed: 27226615
DOI: 10.1074/JBC.M116.729749