Zinc 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:

Sodium

(Na)

2 atoms

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

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Spelter Bound to ZN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:31.9 occ:1.00 NE2 A:HIS125 2.0 22.1 1.0 OE1 A:GLU200 2.0 29.5 1.0 O A:HOH466 2.1 27.5 1.0 OE1 A:GLU122 2.3 34.5 1.0 CD A:GLU200 2.8 27.2 1.0 CE1 A:HIS125 2.9 22.1 1.0 CD2 A:HIS125 3.0 21.1 1.0 OE2 A:GLU200 3.1 30.9 1.0 CD A:GLU122 3.2 28.9 1.0 OE2 A:GLU122 4.0 32.6 1.0 CG A:GLU122 4.0 32.4 1.0 ND1 A:HIS125 4.0 19.9 1.0 CG A:HIS125 4.1 19.9 1.0 CG A:GLU200 4.2 21.3 1.0 CB A:GLU122 4.3 23.1 1.0 CB A:GLU200 4.6 17.8 1.0 O A:GLU122 4.8 33.5 1.0 NE2 A:GLN129 4.8 28.9 1.0

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Spelter Bound to ZN2+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:38.1 occ:1.00 OE2 B:GLU200 1.9 32.2 1.0 NE2 B:HIS125 2.0 20.0 1.0 OE1 B:GLU122 2.2 41.5 1.0 O B:HOH477 2.2 27.9 1.0 CD B:GLU200 2.9 34.4 1.0 CD2 B:HIS125 2.9 21.4 1.0 CE1 B:HIS125 3.1 22.2 1.0 OE1 B:GLU200 3.2 41.2 1.0 CD B:GLU122 3.3 38.4 1.0 OE2 B:GLU122 4.0 37.1 1.0 CG B:HIS125 4.1 18.9 1.0 CB B:GLU122 4.1 29.9 1.0 ND1 B:HIS125 4.2 21.3 1.0 CG B:GLU200 4.2 26.4 1.0 CG B:GLU122 4.4 36.2 1.0 CB B:GLU200 4.7 21.6 1.0 O B:GLU122 4.7 43.1 1.0 NE2 B:GLN129 4.8 24.7 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