Sodium in PDB 5kis: Yenb/RHS2 Complex

The structure of Yenb/RHS2 Complex, PDB code: 5kis was solved by J.N.Busby, M.R.H.Hurst, J.S.Lott, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	32.51 / 2.40
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	148.607, 132.765, 155.361, 90.00, 103.85, 90.00
R / Rfree (%)	21.6 / 26

The structure of Yenb/RHS2 Complex also contains other interesting chemical elements:

Chlorine	(Cl)	4 atoms
Calcium	(Ca)	2 atoms

The binding sites of Sodium atom in the Yenb/RHS2 Complex (pdb code 5kis). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Yenb/RHS2 Complex, PDB code: 5kis:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Yenb/RHS2 Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Yenb/RHS2 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1502 b:28.1 occ:1.00 OD1 B:ASN166 2.4 29.8 1.0 O B:LYS163 2.4 33.3 1.0 OD1 A:ASN1203 2.4 28.3 1.0 OG1 A:THR1223 2.4 30.4 1.0 O A:THR1223 2.5 32.6 1.0 CG A:ASN1203 3.3 28.1 1.0 C A:THR1223 3.3 33.0 1.0 O A:ASN1201 3.4 32.9 1.0 CG B:ASN166 3.4 31.3 1.0 ND2 A:ASN1203 3.4 27.7 1.0 C B:LYS163 3.5 33.0 1.0 CB A:THR1223 3.6 30.2 1.0 N A:THR1223 3.6 29.1 1.0 CA A:THR1223 3.7 31.0 1.0 O A:HOH1677 3.7 35.3 1.0 CB A:ASN1201 3.8 31.3 1.0 ND2 B:ASN166 4.0 31.8 1.0 CA B:THR164 4.1 32.1 1.0 N B:THR164 4.1 33.0 1.0 C B:THR164 4.3 31.9 1.0 N B:ASN166 4.3 32.6 1.0 C A:ASN1201 4.3 31.1 1.0 O B:THR164 4.4 28.9 1.0 N A:GLU1224 4.4 36.7 1.0 CA B:ASN166 4.5 33.1 1.0 CA B:LYS163 4.5 32.7 1.0 CB B:ASN166 4.5 32.5 1.0 CG2 A:THR1223 4.6 30.7 1.0 CA A:ASN1201 4.7 30.3 1.0 CB A:ASN1203 4.7 28.1 1.0 CG A:ASN1201 4.8 33.6 1.0 CD2 B:LEU188 4.8 33.1 1.0 N A:ASN1203 4.9 29.0 1.0 N B:LEU165 4.9 32.1 1.0 CB B:LYS163 4.9 32.2 1.0 C A:GLY1222 4.9 27.4 1.0

Sodium binding site 2 out of 2 in the Yenb/RHS2 Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Yenb/RHS2 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1503 b:66.0 occ:1.00 OD1 A:ASN466 2.2 63.9 1.0 OD1 A:ASP472 2.4 51.5 1.0 OD1 A:ASP464 2.5 68.0 1.0 O A:ARG470 2.6 58.0 1.0 OD1 A:ASP468 2.9 56.9 1.0 OD2 A:ASP468 3.2 59.2 1.0 CG A:ASP472 3.2 54.3 1.0 CG A:ASP468 3.3 61.8 1.0 OD2 A:ASP472 3.3 55.7 1.0 CG A:ASN466 3.3 64.8 1.0 CG A:ASP464 3.5 69.7 1.0 CA A:ASP464 3.8 69.9 1.0 C A:ARG470 3.8 64.0 1.0 ND2 A:ASN466 3.9 62.0 1.0 CB A:ASP464 4.0 69.5 1.0 C A:ASP464 4.1 76.0 1.0 N A:ILE465 4.1 73.2 1.0 N A:ASN466 4.2 67.0 1.0 CD1 A:TRP473 4.2 37.5 1.0 N A:ARG470 4.2 70.4 1.0 N A:ASP472 4.3 58.0 1.0 N A:ASP468 4.3 65.8 1.0 OD2 A:ASP464 4.4 68.3 1.0 CA A:ARG470 4.5 69.5 1.0 CB A:ASP472 4.5 54.5 1.0 CB A:ASP468 4.5 63.4 1.0 CB A:ASN466 4.6 67.0 1.0 N A:GLY467 4.6 64.0 1.0 O A:MET463 4.7 66.9 1.0 CB A:ARG470 4.7 73.3 1.0 CA A:ASN466 4.8 64.7 1.0 NE1 A:TRP473 4.8 38.0 1.0 CA A:ASP468 4.8 64.8 1.0 CA A:ASP472 4.8 54.7 1.0 N A:LEU471 4.9 65.6 1.0 O A:ASP464 4.9 86.8 1.0 N A:GLY469 4.9 67.5 1.0 C A:ASN466 4.9 63.1 1.0 N A:ASP464 5.0 67.6 1.0

J.N.Busby, M.R.H.Hurst, J.S.Lott. Structure of A New Bc Complex From Yersinia Entomophaga To Be Published.