Zinc in PDB 5yy0: Crystal Structure of the Hyhl-Hypa Complex (Form II)

The structure of Crystal Structure of the Hyhl-Hypa Complex (Form II), PDB code: 5yy0 was solved by S.Kwon, S.Watanabe, Y.Nishitani, K.Miki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.02 / 3.24
Space group	P 2 3
Cell size a, b, c (Å), α, β, γ (°)	132.046, 132.046, 132.046, 90.00, 90.00, 90.00
R / Rfree (%)	29 / 31.4

The binding sites of Zinc atom in the Crystal Structure of the Hyhl-Hypa Complex (Form II) (pdb code 5yy0). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total only one binding site of Zinc was determined in the Crystal Structure of the Hyhl-Hypa Complex (Form II), PDB code: 5yy0:

Zinc binding site 1 out of 1 in the Crystal Structure of the Hyhl-Hypa Complex (Form II)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of the Hyhl-Hypa Complex (Form II) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn701 b:0.5 occ:1.00 SG B:CYS76 2.0 0.3 1.0 SG B:CYS110 2.1 0.1 1.0 SG B:CYS73 2.6 0.2 1.0 SG B:CYS113 2.6 0.3 1.0 CB B:CYS73 3.1 0.4 1.0 CB B:CYS110 3.2 0.6 1.0 CB B:CYS76 3.5 0.7 1.0 CB B:CYS113 3.6 0.3 1.0 N B:CYS76 3.9 0.3 1.0 CB B:TYR78 4.1 0.2 1.0 N B:CYS113 4.1 0.7 1.0 CA B:CYS76 4.2 0.3 1.0 CA B:CYS73 4.4 1.0 1.0 O B:CYS73 4.4 0.7 1.0 CA B:CYS113 4.5 0.9 1.0 C B:CYS73 4.6 0.3 1.0 C B:ASN75 4.6 1.0 1.0 CA B:CYS110 4.6 0.4 1.0 C B:CYS76 4.6 0.1 1.0 N B:TYR78 4.7 0.8 1.0 CB B:ASN75 4.7 0.9 1.0 CB B:LYS112 4.8 0.5 1.0 N B:ASN75 4.9 0.5 1.0 N B:ASN77 4.9 0.2 1.0 CD2 B:TYR78 4.9 0.1 1.0 CA B:TYR78 5.0 0.5 1.0 CA B:ASN75 5.0 0.5 1.0 CG B:TYR78 5.0 0.2 1.0

S.Kwon, S.Watanabe, Y.Nishitani, T.Kawashima, T.Kanai, H.Atomi, K.Miki. Crystal Structures of A [Nife] Hydrogenase Large Subunit Hyhl in An Immature State in Complex with A Ni Chaperone Hypa. Proc. Natl. Acad. Sci. V. 115 7045 2018U.S.A..
ISSN: ESSN 1091-6490
PubMed: 29915046
DOI: 10.1073/PNAS.1801955115