Sodium in PDB 6b2y: Apo Yiua Crystal Form 2

The structure of Apo Yiua Crystal Form 2, PDB code: 6b2y was solved by C.D.Radka, L.J.Delucas, S.G.Aller, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.57 / 1.77
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	46.371, 97.012, 74.284, 90.00, 100.69, 90.00
R / Rfree (%)	18.6 / 21.9

The binding sites of Sodium atom in the Apo Yiua Crystal Form 2 (pdb code 6b2y). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Apo Yiua Crystal Form 2, PDB code: 6b2y:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Apo Yiua Crystal Form 2


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Apo Yiua Crystal Form 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na401 b:34.0 occ:1.00 OH A:TYR61 2.6 25.1 1.0 O A:HOH617 2.9 30.1 1.0 OH A:TYR300 3.0 36.6 1.0 CE1 A:TYR61 3.2 24.4 1.0 CZ A:TYR61 3.3 28.2 1.0 CD1 A:LEU334 4.0 24.7 1.0 CZ A:TYR300 4.0 26.8 1.0 OG A:SER32 4.2 27.2 1.0 CE1 A:TYR300 4.2 24.2 1.0 CG2 A:THR57 4.3 21.4 1.0 CE2 A:PHE28 4.5 29.6 1.0 CD1 A:TYR61 4.5 28.1 1.0 O A:HOH794 4.6 35.9 1.0 CD2 A:LEU334 4.6 20.3 1.0 CB A:SER32 4.6 23.9 1.0 CE2 A:TYR61 4.6 26.1 1.0 OH A:TYR330 4.7 32.1 1.0 CG2 A:VAL336 4.7 28.7 1.0 CD1 A:TYR29 4.8 23.8 1.0 CG A:LEU334 4.9 22.7 1.0 O A:HOH536 4.9 28.7 1.0

Sodium binding site 2 out of 3 in the Apo Yiua Crystal Form 2


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Apo Yiua Crystal Form 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:35.6 occ:0.63 O A:HOH787 2.2 36.5 1.0 O B:HOH708 2.4 37.6 1.0 O A:HOH543 2.4 33.9 1.0 O A:HOH721 2.7 38.3 1.0 OD2 A:ASP206 3.7 28.7 1.0 CB A:ASP206 3.8 23.6 1.0 CD2 A:LEU131 4.0 32.4 1.0 CG A:ASP206 4.2 24.6 1.0 O A:HOH750 4.4 46.9 1.0 NZ A:LYS215 4.7 30.2 1.0 O A:HOH771 4.7 37.3 1.0 CD1 A:LEU131 4.8 28.7 1.0 CG A:LEU131 5.0 28.1 1.0

Sodium binding site 3 out of 3 in the Apo Yiua Crystal Form 2


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Apo Yiua Crystal Form 2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na401 b:32.0 occ:1.00 OH B:TYR61 2.7 18.7 1.0 O B:HOH532 2.8 27.2 1.0 OH B:TYR300 2.9 31.0 1.0 CE1 B:TYR61 3.4 19.4 1.0 CZ B:TYR61 3.4 23.0 1.0 CD1 B:LEU334 3.8 19.1 1.0 CZ B:TYR300 3.9 25.2 1.0 CE2 B:TYR300 4.1 26.9 1.0 OG B:SER32 4.2 22.4 1.0 CG2 B:THR57 4.3 19.1 1.0 CD2 B:LEU334 4.4 18.7 1.0 O B:HOH761 4.4 32.8 1.0 OH B:TYR330 4.4 21.3 1.0 CB B:SER32 4.6 18.2 1.0 CG2 B:VAL336 4.6 24.0 1.0 CG B:LEU334 4.7 16.8 1.0 CD1 B:TYR61 4.7 18.3 1.0 CE2 B:TYR330 4.7 21.7 1.0 CE2 B:TYR61 4.8 19.0 1.0 CZ B:TYR330 4.8 21.0 1.0 O B:HOH553 4.8 20.2 1.0

C.D.Radka, D.Chen, L.J.Delucas, S.G.Aller. The Crystal Structure of the Yersinia Pestis Iron Chaperone Yiua Reveals A Basic Triad Binding Motif For the Chelated Metal. Acta Crystallogr D Struct V. 73 921 2017BIOL.
ISSN: ISSN 2059-7983
PubMed: 29095164
DOI: 10.1107/S2059798317015236