Zinc in PDB 3vth: Crystal Structure of Full-Length Hypf in the Phosphate- and Nucleotide-Bound Form

The structure of Crystal Structure of Full-Length Hypf in the Phosphate- and Nucleotide-Bound Form, PDB code: 3vth was solved by Y.Shomura, Y.Higuchi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.00
Space group	P 64
Cell size a, b, c (Å), α, β, γ (°)	232.983, 232.983, 65.665, 90.00, 90.00, 120.00
R / Rfree (%)	20.9 / 23.8

The structure of Crystal Structure of Full-Length Hypf in the Phosphate- and Nucleotide-Bound Form also contains other interesting chemical elements:

Magnesium	(Mg)	2 atoms
Iron	(Fe)	2 atoms

The binding sites of Zinc atom in the Crystal Structure of Full-Length Hypf in the Phosphate- and Nucleotide-Bound Form (pdb code 3vth). 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 Full-Length Hypf in the Phosphate- and Nucleotide-Bound Form, PDB code: 3vth:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Crystal Structure of Full-Length Hypf in the Phosphate- and Nucleotide-Bound Form


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 Full-Length Hypf in the Phosphate- and Nucleotide-Bound Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn801 b:27.7 occ:1.00 SG A:CYS117 2.3 29.4 1.0 SG A:CYS114 2.3 29.5 1.0 SG A:CYS139 2.3 26.3 1.0 SG A:CYS136 2.3 28.3 1.0 CB A:CYS117 3.2 28.4 1.0 CB A:CYS139 3.4 25.7 1.0 CB A:CYS136 3.4 28.4 1.0 CB A:CYS114 3.5 29.0 1.0 N A:CYS136 3.6 26.8 1.0 N A:CYS114 4.0 28.0 1.0 C A:ASN135 4.0 27.1 1.0 CA A:CYS136 4.1 27.3 1.0 N A:CYS117 4.1 30.0 1.0 N A:CYS139 4.1 25.5 1.0 NH2 A:ARG177 4.2 36.4 1.0 CA A:CYS117 4.2 30.2 1.0 CA A:CYS114 4.3 29.0 1.0 CA A:CYS139 4.3 25.8 1.0 CA A:ASN135 4.3 27.1 1.0 NH1 A:ARG177 4.5 37.3 1.0 O A:HOH933 4.5 21.9 1.0 C A:ASN138 4.5 26.1 1.0 C A:CYS136 4.6 27.0 1.0 O A:ASN135 4.7 27.9 1.0 CZ A:ARG177 4.8 37.2 1.0 O A:CYS114 4.8 30.2 1.0 CB A:ASN138 4.8 27.9 1.0 N A:ASN138 4.8 26.9 1.0 O A:CYS136 4.8 26.1 1.0 C A:CYS114 4.8 30.5 1.0 C A:CYS139 4.9 25.3 1.0 CA A:ASN138 5.0 26.8 1.0

Zinc binding site 2 out of 3 in the Crystal Structure of Full-Length Hypf in the Phosphate- and Nucleotide-Bound Form


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 Full-Length Hypf in the Phosphate- and Nucleotide-Bound Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn802 b:35.9 occ:1.00 SG A:CYS186 2.3 35.6 1.0 SG A:CYS167 2.3 32.5 1.0 SG A:CYS189 2.3 34.4 1.0 SG A:CYS164 2.3 37.9 1.0 CB A:CYS167 3.3 32.5 1.0 CB A:CYS186 3.3 34.7 1.0 CB A:CYS189 3.4 34.4 1.0 CB A:CYS164 3.5 37.7 1.0 N A:CYS186 3.6 33.2 1.0 N A:CYS164 3.9 36.5 1.0 N A:CYS189 4.0 36.1 1.0 CA A:CYS186 4.0 34.2 1.0 C A:ALA185 4.1 33.0 1.0 N A:CYS167 4.1 35.1 1.0 CA A:CYS164 4.2 37.6 1.0 CA A:CYS167 4.3 33.7 1.0 CA A:CYS189 4.3 35.1 1.0 CA A:ALA185 4.4 32.7 1.0 NH1 A:ARG127 4.4 36.9 1.0 NH2 A:ARG127 4.4 35.7 1.0 C A:CYS186 4.6 34.8 1.0 O A:HOH1252 4.6 22.9 1.0 CB A:ASP188 4.7 40.4 1.0 O A:CYS186 4.8 34.4 1.0 C A:CYS164 4.8 38.3 1.0 O A:CYS164 4.8 37.4 1.0 C A:ASP188 4.9 38.1 1.0 CZ A:ARG127 4.9 37.4 1.0 O A:ALA185 4.9 32.7 1.0 N A:ASP188 5.0 38.3 1.0

Zinc binding site 3 out of 3 in the Crystal Structure of Full-Length Hypf in the Phosphate- and Nucleotide-Bound Form


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 Full-Length Hypf in the Phosphate- and Nucleotide-Bound Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn802 b:97.4 occ:1.00 SG B:CYS136 2.3 0.8 1.0 SG B:CYS117 2.3 0.1 1.0 SG B:CYS114 2.3 97.6 1.0 SG B:CYS139 2.3 95.8 1.0 CB B:CYS117 3.1 0.9 1.0 CB B:CYS139 3.4 91.9 1.0 CB B:CYS114 3.5 95.9 1.0 CB B:CYS136 3.5 0.1 1.0 N B:CYS136 3.8 0.6 1.0 N B:CYS139 3.9 92.2 1.0 N B:CYS114 4.1 94.5 1.0 CA B:CYS136 4.2 0.1 1.0 N B:CYS117 4.2 0.7 1.0 CA B:CYS117 4.2 0.9 1.0 NH2 B:ARG177 4.3 0.5 1.0 CA B:CYS139 4.3 91.0 1.0 C B:ASN135 4.3 0.5 1.0 NH1 B:ARG177 4.3 0.9 1.0 CA B:CYS114 4.4 95.5 1.0 C B:ASN138 4.4 92.0 1.0 CB B:ASN138 4.5 95.0 1.0 N B:ASN138 4.7 95.5 1.0 C B:CYS136 4.8 0.0 1.0 O B:ASN135 4.8 0.5 1.0 CA B:ASN138 4.8 93.6 1.0 CZ B:ARG177 4.8 0.4 1.0 CA B:ASN135 4.8 1.0 1.0 C B:CYS139 4.9 90.9 1.0

Y.Shomura, Y.Higuchi. Structural Basis For the Reaction Mechanism of S-Carbamoylation of Hype By Hypf in the Maturation of [Nife]-Hydrogenases J.Biol.Chem. V. 287 28409 2012.
ISSN: ISSN 0021-9258
PubMed: 22740694
DOI: 10.1074/JBC.M112.387134