Sodium in PDB 6b2x: Apo Yiua Crystal Form 1

The structure of Apo Yiua Crystal Form 1, PDB code: 6b2x 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)	41.47 / 2.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	40.515, 94.732, 171.564, 90.00, 90.00, 90.00
R / Rfree (%)	19.6 / 24.6

The structure of Apo Yiua Crystal Form 1 also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Sodium atom in the Apo Yiua Crystal Form 1 (pdb code 6b2x). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Apo Yiua Crystal Form 1, PDB code: 6b2x:
Jump to Sodium binding site number: 1; 2;

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


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 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:35.1 occ:1.00 OH A:TYR61 2.7 27.1 1.0 OH A:TYR300 2.8 30.6 1.0 O A:HOH581 3.1 29.1 1.0 CE2 A:TYR61 3.2 23.2 1.0 CZ A:TYR61 3.4 25.9 1.0 CZ A:TYR300 3.8 32.5 1.0 CD1 A:LEU334 4.0 27.9 1.0 CE2 A:TYR300 4.0 31.6 1.0 CG2 A:THR57 4.1 19.5 1.0 OG A:SER32 4.2 25.0 1.0 CE2 A:PHE28 4.6 28.2 1.0 CD2 A:LEU334 4.6 26.4 1.0 CD2 A:TYR61 4.6 23.1 1.0 CG2 A:VAL336 4.6 32.2 1.0 CB A:SER32 4.6 25.6 1.0 OH A:TYR330 4.8 32.4 1.0 CE1 A:TYR61 4.8 25.9 1.0 CG A:LEU334 4.9 31.7 1.0 O A:HOH538 4.9 29.0 1.0 CD1 A:TYR29 4.9 29.7 1.0 O A:HOH623 5.0 32.8 1.0

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


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 1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na402 b:39.9 occ:1.00 OH B:TYR300 2.9 39.1 1.0 OH B:TYR61 2.9 26.3 1.0 O B:HOH516 3.0 31.4 1.0 CE1 B:TYR61 3.4 25.9 1.0 CZ B:TYR61 3.6 30.7 1.0 CZ B:TYR300 3.8 37.2 1.0 CE2 B:TYR300 4.0 30.9 1.0 CG B:LEU334 4.1 26.5 1.0 CG2 B:THR57 4.2 27.3 1.0 CD2 B:LEU334 4.3 29.5 1.0 OG B:SER32 4.3 23.1 1.0 OH B:TYR330 4.3 28.3 1.0 CG2 B:VAL336 4.4 22.3 1.0 CD1 B:TYR61 4.6 25.5 1.0 O B:HOH548 4.6 24.0 1.0 CE2 B:TYR330 4.7 26.2 1.0 CB B:SER32 4.7 18.3 1.0 CD1 B:LEU334 4.7 23.3 1.0 CZ B:TYR330 4.8 26.6 1.0 CD1 B:TYR29 4.9 31.1 1.0 CE2 B:TYR61 4.9 25.7 1.0 CE1 B:TYR300 5.0 35.1 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