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

The structure of Crystal Structure of the Hyhl-Hypa Complex (Form I), PDB code: 5yxy 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)	48.22 / 3.30
Space group	C 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	245.309, 261.427, 134.870, 90.00, 90.00, 90.00
R / Rfree (%)	30.5 / 32.1

The binding sites of Zinc atom in the Crystal Structure of the Hyhl-Hypa Complex (Form I) (pdb code 5yxy). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure of the Hyhl-Hypa Complex (Form I), PDB code: 5yxy:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Crystal Structure of the Hyhl-Hypa Complex (Form I)


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 I) within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn701 b:43.2 occ:1.00 SG D:CYS73 2.3 76.2 1.0 SG D:CYS76 2.3 70.2 1.0 SG D:CYS113 2.4 79.7 1.0 CB D:CYS113 2.6 48.8 1.0 SG D:CYS110 2.9 63.1 1.0 CB D:CYS110 3.0 59.3 1.0 CB D:CYS73 3.3 25.4 1.0 CB D:CYS76 3.5 60.6 1.0 N D:CYS113 3.7 62.0 1.0 CA D:CYS113 3.7 59.0 1.0 N D:CYS76 3.8 63.1 1.0 CA D:CYS76 4.2 58.9 1.0 CA D:CYS110 4.5 47.6 1.0 CB D:SER115 4.5 71.1 1.0 CB D:ASN75 4.7 41.7 1.0 C D:CYS113 4.7 73.5 1.0 C D:LYS112 4.7 67.2 1.0 CA D:CYS73 4.7 29.9 1.0 C D:ASN75 4.9 63.3 1.0 C D:CYS73 5.0 39.2 1.0

Zinc binding site 2 out of 3 in the Crystal Structure of the Hyhl-Hypa Complex (Form I)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of the Hyhl-Hypa Complex (Form I) within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn701 b:75.2 occ:1.00 SG E:CYS110 2.3 83.5 1.0 CB E:CYS113 2.3 92.7 1.0 SG E:CYS73 2.5 76.4 1.0 SG E:CYS113 2.7 0.0 1.0 CB E:CYS76 2.8 78.7 1.0 CB E:CYS110 2.8 69.5 1.0 SG E:CYS76 2.9 82.6 1.0 N E:CYS113 3.1 89.5 1.0 CA E:CYS113 3.3 91.7 1.0 CB E:CYS73 3.3 79.5 1.0 N E:CYS76 3.9 77.1 1.0 CA E:CYS76 3.9 80.1 1.0 C E:LYS112 4.1 88.1 1.0 CA E:CYS110 4.2 67.4 1.0 C E:CYS113 4.4 95.2 1.0 CB E:LYS112 4.5 70.9 1.0 N E:LYS112 4.5 82.3 1.0 CA E:LYS112 4.6 87.0 1.0 CB E:TYR78 4.6 72.0 1.0 C E:CYS110 4.6 72.2 1.0 O E:CYS113 4.7 94.1 1.0 CA E:CYS73 4.8 73.7 1.0 C E:CYS76 4.8 88.9 1.0 O E:CYS110 4.9 83.6 1.0 O E:SER115 5.0 95.8 1.0 O E:LYS112 5.0 88.2 1.0

Zinc binding site 3 out of 3 in the Crystal Structure of the Hyhl-Hypa Complex (Form I)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of the Hyhl-Hypa Complex (Form I) within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn701 b:43.7 occ:1.00 SG F:CYS113 2.4 55.5 1.0 CB F:CYS113 2.6 63.5 1.0 SG F:CYS110 2.7 81.4 1.0 SG F:CYS73 2.7 52.9 1.0 SG F:CYS76 2.8 75.0 1.0 CB F:CYS76 2.9 59.9 1.0 CB F:CYS110 3.4 42.1 1.0 CB F:CYS73 3.5 67.3 1.0 CB F:TYR78 4.0 60.7 1.0 CA F:CYS113 4.1 73.4 1.0 CA F:CYS76 4.2 64.6 1.0 CD2 F:TYR78 4.5 52.7 1.0 N F:CYS76 4.5 59.6 1.0 N F:CYS113 4.6 75.8 1.0 CG F:TYR78 4.7 45.8 1.0 C F:CYS113 4.8 68.7 1.0 C F:CYS76 4.8 72.7 1.0 N F:TYR78 4.8 67.3 1.0 O F:SER115 4.9 59.6 1.0 CA F:CYS110 4.9 49.5 1.0 O F:TYR78 4.9 65.5 1.0 CA F:CYS73 4.9 72.6 1.0 CA F:TYR78 5.0 55.7 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