Sodium in PDB 5e3e: Crystal Structure of Cdia-Ct/Cdii Complex From Y. Kristensenii 33638

The structure of Crystal Structure of Cdia-Ct/Cdii Complex From Y. Kristensenii 33638, PDB code: 5e3e was solved by K.Michalska, G.Joachimiak, R.Jedrzejczak, C.W.Goulding, A.Joachimiak, Structure-Function Analysis Of Polymorphic Cdi Toxin-Immunityprotein Complexes (Uc4Cdi), Midwest Center For Structural Genomics(Mcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 1.70
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	48.890, 57.146, 64.302, 78.25, 90.21, 79.11
R / Rfree (%)	17.4 / 20.2

The binding sites of Sodium atom in the Crystal Structure of Cdia-Ct/Cdii Complex From Y. Kristensenii 33638 (pdb code 5e3e). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Cdia-Ct/Cdii Complex From Y. Kristensenii 33638, PDB code: 5e3e:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Cdia-Ct/Cdii Complex From Y. Kristensenii 33638


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 Cdia-Ct/Cdii Complex From Y. Kristensenii 33638 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na301 b:32.5 occ:1.00 O B:HOH470 2.3 33.3 1.0 O B:HOH456 2.3 29.9 1.0 OG1 B:THR256 2.4 17.6 1.0 O B:SER237 2.4 21.0 1.0 O B:HOH459 2.4 29.8 1.0 OD1 B:ASN257 2.6 17.6 1.0 CG B:ASN257 3.3 17.6 1.0 CB B:THR256 3.5 17.3 1.0 ND2 B:ASN257 3.6 19.4 1.0 C B:SER237 3.6 21.9 1.0 N B:SER237 4.1 21.6 1.0 O B:HOH484 4.2 46.7 1.0 OD1 B:ASN238 4.3 28.7 1.0 C B:THR256 4.3 15.8 1.0 O B:HOH435 4.3 26.4 1.0 N B:ASN257 4.4 15.2 1.0 CA B:THR256 4.5 16.5 1.0 CA B:SER237 4.5 21.9 1.0 CG2 B:THR256 4.5 17.7 1.0 CB B:ASN257 4.6 16.0 1.0 N B:ASN238 4.6 22.1 1.0 O B:THR256 4.6 15.7 1.0 O B:HOH468 4.6 30.6 1.0 CA B:ASN238 4.7 23.1 1.0 CA B:ASN257 4.9 15.2 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Cdia-Ct/Cdii Complex From Y. Kristensenii 33638


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 Cdia-Ct/Cdii Complex From Y. Kristensenii 33638 within 5.0Å range: probe atom residue distance (Å) B Occ E:Na201 b:24.3 occ:1.00 O E:HOH362 2.3 19.0 1.0 O E:HOH310 2.4 32.9 1.0 OE1 E:GLU87 2.4 19.1 1.0 O E:HOH314 2.6 19.2 1.0 CD E:GLU87 3.6 18.9 1.0 O E:HOH320 3.8 14.8 1.0 O E:LEU60 4.0 16.9 1.0 O E:HOH368 4.2 19.2 1.0 CB E:GLU87 4.2 17.0 1.0 O E:HOH356 4.4 24.7 1.0 OE2 E:GLU87 4.5 20.4 1.0 CG E:GLU87 4.5 18.0 1.0 O E:HOH321 4.8 22.4 1.0 O E:HOH343 4.9 26.1 1.0

G.Batot, K.Michalska, G.Ekberg, E.M.Irimpan, G.Joachimiak, R.Jedrzejczak, G.Babnigg, C.S.Hayes, A.Joachimiak, C.W.Goulding. The Cdi Toxin of Yersinia Kristensenii Is A Novel Bacterial Member of the Rnase A Superfamily. Nucleic Acids Res. V. 45 5013 2017.
ISSN: ESSN 1362-4962
PubMed: 28398546
DOI: 10.1093/NAR/GKX230