Zinc in PDB 3vti: Crystal Structure of Hype-Hypf Complex

The structure of Crystal Structure of Hype-Hypf Complex, PDB code: 3vti 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 / 2.56
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	118.739, 119.101, 174.631, 90.00, 90.00, 90.00
R / Rfree (%)	20.6 / 25.1

The structure of Crystal Structure of Hype-Hypf Complex 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 Hype-Hypf Complex (pdb code 3vti). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Hype-Hypf Complex, PDB code: 3vti:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Hype-Hypf Complex


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 Hype-Hypf Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn801 b:42.7 occ:1.00 SG A:CYS139 2.3 39.7 1.0 SG A:CYS114 2.3 43.4 1.0 SG A:CYS136 2.3 42.5 1.0 SG A:CYS117 2.3 47.7 1.0 CB A:CYS117 3.2 47.3 1.0 CB A:CYS139 3.4 38.8 1.0 CB A:CYS136 3.4 44.9 1.0 CB A:CYS114 3.5 42.8 1.0 N A:CYS136 3.6 43.1 1.0 N A:CYS139 3.9 39.8 1.0 CA A:CYS136 4.0 44.2 1.0 N A:CYS114 4.1 41.7 1.0 N A:CYS117 4.1 49.1 1.0 C A:ASN135 4.2 43.2 1.0 CA A:CYS139 4.2 38.5 1.0 CA A:CYS117 4.3 49.0 1.0 NH2 A:ARG177 4.3 52.8 1.0 CA A:CYS114 4.3 42.5 1.0 NE A:ARG177 4.4 54.4 1.0 O A:HOH989 4.4 24.1 1.0 C A:ASN138 4.5 40.8 1.0 CA A:ASN135 4.5 42.2 1.0 C A:CYS136 4.6 44.0 1.0 O A:CYS114 4.8 44.6 1.0 N A:ASN138 4.8 43.3 1.0 O A:CYS136 4.8 43.2 1.0 CZ A:ARG177 4.8 54.5 1.0 C A:CYS114 4.8 44.2 1.0 CB A:ASN138 4.9 42.9 1.0 C A:CYS139 4.9 38.3 1.0 CA A:ASN138 4.9 42.3 1.0 O A:ASN135 5.0 44.7 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Hype-Hypf Complex


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 Hype-Hypf Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn802 b:56.8 occ:1.00 SG A:CYS189 2.2 56.8 1.0 SG A:CYS167 2.3 61.8 1.0 SG A:CYS164 2.3 64.0 1.0 SG A:CYS186 2.5 58.1 1.0 CB A:CYS167 3.3 64.0 1.0 CB A:CYS189 3.4 58.2 1.0 CB A:CYS186 3.5 56.2 1.0 CB A:CYS164 3.6 66.4 1.0 N A:CYS186 3.7 54.1 1.0 N A:CYS189 4.0 58.8 1.0 N A:CYS164 4.1 65.2 1.0 CA A:CYS186 4.2 54.8 1.0 NH1 A:ARG127 4.2 63.4 1.0 CA A:CYS189 4.2 58.2 1.0 N A:CYS167 4.3 66.6 1.0 C A:ALA185 4.3 53.1 1.0 CA A:CYS167 4.4 65.3 1.0 CA A:CYS164 4.4 66.8 1.0 CA A:ALA185 4.6 52.6 1.0 C A:CYS186 4.8 55.4 1.0 C A:ASP188 4.9 60.5 1.0 O A:CYS186 4.9 55.3 1.0 CB A:ASP188 4.9 62.0 1.0 N A:GLY190 4.9 54.7 1.0 C A:CYS164 4.9 67.5 1.0 C A:CYS189 4.9 56.2 1.0 O A:CYS164 5.0 66.5 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Hype-Hypf Complex


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 Hype-Hypf Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn801 b:64.3 occ:1.00 SG B:CYS117 2.1 72.5 1.0 SG B:CYS139 2.3 63.5 1.0 SG B:CYS136 2.3 66.7 1.0 SG B:CYS114 2.4 66.2 1.0 CB B:CYS117 3.2 72.8 1.0 CB B:CYS136 3.2 68.7 1.0 N B:CYS136 3.3 67.4 1.0 CB B:CYS139 3.5 62.2 1.0 CB B:CYS114 3.7 67.0 1.0 CA B:CYS136 3.8 68.6 1.0 NH2 B:ARG177 4.0 79.8 1.0 N B:CYS117 4.1 73.8 1.0 N B:CYS139 4.1 63.8 1.0 N B:CYS114 4.2 65.5 1.0 CA B:CYS117 4.2 73.9 1.0 C B:ASN135 4.2 67.8 1.0 CA B:CYS139 4.3 62.3 1.0 NE B:ARG177 4.4 80.6 1.0 C B:CYS136 4.5 68.2 1.0 CA B:CYS114 4.5 66.2 1.0 CA B:ASN135 4.5 66.7 1.0 CZ B:ARG177 4.7 81.0 1.0 O B:CYS136 4.7 67.6 1.0 C B:ASN138 4.8 64.0 1.0 C B:CYS139 4.8 62.2 1.0 CB B:ASN138 4.9 65.6 1.0 O B:HOH999 4.9 29.2 1.0 O B:CYS139 4.9 63.2 1.0 N B:ASN138 5.0 66.5 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Hype-Hypf Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Hype-Hypf Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn802 b:89.5 occ:1.00 SG B:CYS167 2.1 90.5 1.0 SG B:CYS186 2.3 80.9 1.0 SG B:CYS189 2.5 81.9 1.0 SG B:CYS164 2.6 93.4 1.0 CB B:CYS167 3.2 92.7 1.0 CB B:CYS186 3.3 79.3 1.0 N B:CYS186 3.5 77.7 1.0 NH1 B:ARG127 3.8 89.4 1.0 CB B:CYS164 3.9 96.0 1.0 CB B:CYS189 3.9 83.2 1.0 CA B:CYS186 4.0 77.6 1.0 C B:ALA185 4.2 76.9 1.0 N B:CYS167 4.2 95.8 1.0 CA B:CYS167 4.3 93.8 1.0 N B:CYS189 4.3 82.5 1.0 N B:CYS164 4.4 94.2 1.0 C B:CYS186 4.6 78.0 1.0 CA B:ALA185 4.6 77.1 1.0 CA B:CYS189 4.7 82.2 1.0 CA B:CYS164 4.7 96.6 1.0 CB B:ASP188 4.8 86.3 1.0 O B:CYS186 4.8 77.8 1.0 O B:ALA185 4.9 76.0 1.0 N B:ASP188 5.0 82.5 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