Sodium in PDB 6yhn: Crystal Structure of Domains 4-5 of Cnfy From Yersinia Pseudotuberculosis

The structure of Crystal Structure of Domains 4-5 of Cnfy From Yersinia Pseudotuberculosis, PDB code: 6yhn was solved by P.Lukat, E.M.Gazdag, T.V.Heidler, W.Blankenfeldt, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.27 / 1.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	48.271, 90.531, 120.717, 90, 90, 90
R / Rfree (%)	15.8 / 19.1

The structure of Crystal Structure of Domains 4-5 of Cnfy From Yersinia Pseudotuberculosis also contains other interesting chemical elements:

Magnesium	(Mg)	4 atoms
Chlorine	(Cl)	1 atom

The binding sites of Sodium atom in the Crystal Structure of Domains 4-5 of Cnfy From Yersinia Pseudotuberculosis (pdb code 6yhn). 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 Domains 4-5 of Cnfy From Yersinia Pseudotuberculosis, PDB code: 6yhn:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Domains 4-5 of Cnfy From Yersinia Pseudotuberculosis


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 Domains 4-5 of Cnfy From Yersinia Pseudotuberculosis within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1206 b:65.6 occ:1.00 OD1 A:ASN611 2.4 22.1 1.0 HA A:ASN611 2.8 26.5 1.0 O A:HOH1474 2.8 37.8 1.0 O A:HOH1475 2.9 24.6 1.0 HD22 A:LEU533 2.9 30.1 1.0 HD23 A:LEU533 3.2 30.1 1.0 O A:ASN611 3.2 22.8 1.0 CG A:ASN611 3.4 22.6 1.0 CD2 A:LEU533 3.4 25.0 1.0 CA A:ASN611 3.5 22.1 1.0 HD21 A:LEU533 3.8 30.1 1.0 HA A:LEU533 3.8 28.2 1.0 C A:ASN611 3.8 20.6 1.0 CB A:ASN611 4.0 19.6 1.0 HB2 A:ASN611 4.3 23.6 1.0 ND2 A:ASN611 4.5 24.1 1.0 O A:ALA610 4.5 22.9 1.0 H A:ASP534 4.5 26.1 1.0 HD21 A:ASN611 4.6 28.9 1.0 CA A:LEU533 4.7 23.5 1.0 HB3 A:LEU533 4.7 31.6 1.0 N A:ASN611 4.7 20.8 1.0 CG A:LEU533 4.8 22.9 1.0 HB3 A:ASN611 4.8 23.6 1.0 HE3 A:LYS613 4.9 89.3 1.0 O A:GLY532 4.9 23.4 1.0 CB A:LEU533 5.0 26.3 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Domains 4-5 of Cnfy From Yersinia Pseudotuberculosis


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 Domains 4-5 of Cnfy From Yersinia Pseudotuberculosis within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1207 b:64.5 occ:1.00 OE2 A:GLU546 2.4 53.7 1.0 HG A:SER545 2.6 43.2 1.0 HG2 A:GLU546 2.8 53.7 1.0 OG A:SER545 2.9 36.0 1.0 O A:HOH1549 3.0 36.9 1.0 HD3 A:PRO700 3.1 138.8 1.0 HB2 A:SER545 3.1 38.5 1.0 CD A:GLU546 3.3 49.3 1.0 O A:PRO698 3.4 67.8 1.0 CG A:GLU546 3.5 44.8 1.0 CB A:SER545 3.5 32.1 1.0 HB3 A:PHE697 3.6 44.5 1.0 HB2 A:ASN557 3.6 38.3 1.0 HB3 A:PRO700 3.7 150.8 1.0 HB2 A:PHE697 3.7 44.5 1.0 HG3 A:GLU546 3.9 53.7 1.0 CD A:PRO700 3.9 115.7 1.0 HB3 A:ASN557 4.0 38.3 1.0 HG2 A:PRO543 4.0 39.0 1.0 O A:SER545 4.1 38.2 1.0 CB A:PHE697 4.1 37.0 1.0 C A:SER545 4.2 36.8 1.0 HG3 A:PRO700 4.2 140.1 1.0 HB3 A:SER545 4.2 38.5 1.0 CB A:ASN557 4.3 31.9 1.0 N A:PRO700 4.3 115.0 1.0 CB A:PRO700 4.4 125.7 1.0 O A:HOH1396 4.4 28.1 1.0 CG A:PRO700 4.4 116.7 1.0 OE1 A:GLU546 4.4 49.9 1.0 HA A:PRO700 4.5 150.2 1.0 N A:GLU546 4.5 32.3 1.0 CA A:SER545 4.5 32.3 1.0 HG3 A:PRO543 4.5 39.0 1.0 HA A:GLU699 4.6 109.0 1.0 HA A:GLU546 4.6 48.9 1.0 HA A:ASN557 4.6 33.5 1.0 C A:PRO698 4.6 62.6 1.0 HD2 A:PRO700 4.7 138.8 1.0 CA A:PRO700 4.7 125.2 1.0 HD22 A:ASN557 4.7 64.7 1.0 CB A:GLU546 4.7 37.3 1.0 CG A:PRO543 4.7 32.5 1.0 C A:GLU699 4.8 84.5 1.0 H A:GLU546 4.9 38.8 1.0 CA A:GLU546 4.9 40.7 1.0 CG A:PHE697 5.0 32.1 1.0

P.Chaoprasid, P.Lukat, S.Muhlen, T.Heidler, E.M.Gazdag, S.Dong, W.Bi, C.Ruter, M.Kirchenwitz, A.Steffen, L.Jansch, T.E.B.Stradal, P.Dersch, W.Blankenfeldt. Crystal Structure of Bacterial Cytotoxic Necrotizing Factor Cnf Y Reveals Molecular Building Blocks For Intoxication. Embo J. 05202 2021.
ISSN: ESSN 1460-2075
PubMed: 33410511
DOI: 10.15252/EMBJ.2020105202