Sodium in PDB 5kay: Structure of Spelter Bound to ZN2+

The structure of Structure of Spelter Bound to ZN2+, PDB code: 5kay was solved by S.L.Guffy, B.S.Der, B.Kuhlman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.78 / 1.80
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	41.714, 41.496, 61.506, 87.27, 83.09, 79.46
R / Rfree (%)	19.3 / 23.3

The structure of Structure of Spelter Bound to ZN2+ also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Sodium atom in the Structure of Spelter Bound to ZN2+ (pdb code 5kay). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Structure of Spelter Bound to ZN2+, PDB code: 5kay:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Structure of Spelter Bound to ZN2+


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Spelter Bound to ZN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Na302 b:40.2 occ:1.00 OE2 B:GLU196 2.1 31.7 1.0 OE2 A:GLU196 2.4 29.9 1.0 CD B:GLU196 2.7 32.5 1.0 CG B:GLU196 2.7 22.9 1.0 CD A:GLU196 3.0 34.0 1.0 CG A:GLU196 3.1 25.0 1.0 CZ3 B:TRP199 3.4 15.2 1.0 CZ3 A:TRP199 3.5 17.6 1.0 SG A:CYS135 3.8 22.5 0.5 SG B:CYS135 3.8 23.8 0.5 CH2 A:TRP199 3.9 20.2 1.0 OE1 B:GLU196 3.9 29.0 1.0 CH2 B:TRP199 3.9 15.1 1.0 OE2 A:GLU136 4.1 44.5 1.0 OE1 A:GLU196 4.1 34.3 1.0 CB B:GLU196 4.2 17.8 1.0 SG A:CYS137 4.2 36.2 1.0 CE3 B:TRP199 4.4 13.9 1.0 SG B:CYS137 4.4 39.0 1.0 CE3 A:TRP199 4.5 16.8 1.0 CB A:GLU196 4.6 18.6 1.0 CD A:GLU136 4.7 54.8 1.0 CG A:GLU136 4.7 42.5 1.0 CB A:CYS137 4.7 27.4 1.0 O B:HIS192 4.8 16.8 1.0 CA B:GLU196 5.0 16.5 1.0

Sodium binding site 2 out of 2 in the Structure of Spelter Bound to ZN2+


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of Spelter Bound to ZN2+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Na302 b:25.8 occ:1.00 O B:HOH475 2.3 20.2 1.0 O B:SER32 2.4 12.3 1.0 OG1 B:THR36 2.4 16.4 1.0 OG B:SER32 2.7 18.0 1.0 C B:SER32 3.1 14.1 1.0 CB B:THR36 3.5 15.6 1.0 CB B:SER32 3.7 15.4 1.0 CA B:SER32 3.7 14.8 1.0 O B:HOH407 3.8 34.2 1.0 N B:GLN33 4.0 12.8 1.0 N B:THR36 4.1 12.5 1.0 CA B:THR36 4.3 13.9 1.0 CA B:GLN33 4.4 14.4 1.0 O B:HOH423 4.5 20.5 1.0 CG2 B:THR36 4.6 15.9 1.0 CB B:THR35 4.6 13.1 1.0 NH1 B:ARG198 5.0 16.9 1.0

S.L.Guffy, B.S.Der, B.Kuhlman. Probing the Minimal Determinants of Zinc Binding with Computational Protein Design. Protein Eng.Des.Sel. V. 29 327 2016.
ISSN: ESSN 1741-0134
PubMed: 27358168
DOI: 10.1093/PROTEIN/GZW026