Magnesium 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:

Iron	(Fe)	2 atoms
Zinc	(Zn)	3 atoms

The binding sites of Magnesium 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 Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Full-Length Hypf in the Phosphate- and Nucleotide-Bound Form, PDB code: 3vth:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 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 Magnesium with other atoms in the Mg 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:Mg805 b:45.3 occ:1.00 O1B A:APC804 2.0 33.5 1.0 OG A:SER329 2.1 25.8 1.0 O1G A:APC804 2.1 33.5 1.0 O A:HOH1297 2.2 35.5 1.0 O2A A:APC804 2.2 32.0 1.0 PB A:APC804 2.9 35.1 1.0 PA A:APC804 3.2 31.8 1.0 CB A:SER329 3.2 26.1 1.0 C3A A:APC804 3.2 33.5 1.0 PG A:APC804 3.3 35.0 1.0 O3B A:APC804 3.3 34.1 1.0 O5' A:APC804 3.9 31.4 1.0 NZ A:LYS245 4.0 28.3 1.0 O A:HOH940 4.0 22.7 1.0 O A:HOH1222 4.1 34.6 1.0 OD1 A:ASN331 4.1 29.8 1.0 N A:SER329 4.2 26.7 1.0 O3G A:APC804 4.2 32.9 1.0 CA A:SER329 4.2 26.2 1.0 O2G A:APC804 4.3 35.9 1.0 O2B A:APC804 4.3 37.2 1.0 NH1 A:ARG382 4.4 25.4 1.0 ND2 A:ASN331 4.4 28.8 1.0 O1A A:APC804 4.4 30.8 1.0 OD1 A:ASP367 4.5 25.8 1.0 O A:HOH1218 4.6 23.9 1.0 CG A:ASN331 4.7 30.6 1.0 O A:SER329 4.9 27.8 1.0 C A:SER329 4.9 27.4 1.0 OG1 A:THR328 5.0 26.7 1.0

Magnesium binding site 2 out of 2 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 Magnesium with other atoms in the Mg 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 B:Mg805 b:87.0 occ:1.00 O1B B:APC804 2.3 66.2 1.0 OG B:SER329 2.7 64.3 1.0 O2A B:APC804 2.8 66.2 1.0 O3B B:APC804 3.0 70.6 1.0 PB B:APC804 3.2 66.4 1.0 CB B:SER329 3.3 64.4 1.0 NH2 B:ARG382 3.6 55.4 1.0 OD1 B:ASP367 3.7 60.1 1.0 PA B:APC804 3.8 64.6 1.0 O B:HOH992 3.9 24.1 1.0 C3A B:APC804 4.0 66.6 1.0 O5' B:APC804 4.1 61.5 1.0 CG B:ASP367 4.2 58.3 1.0 PG B:APC804 4.3 72.8 1.0 ND2 B:ASN331 4.4 68.1 1.0 CZ B:ARG382 4.4 54.3 1.0 O1G B:APC804 4.4 74.5 1.0 OD2 B:ASP367 4.5 58.0 1.0 O2B B:APC804 4.5 66.6 1.0 CA B:SER329 4.7 66.6 1.0 O3G B:APC804 4.7 72.6 1.0 NH1 B:ARG382 4.7 53.8 1.0 N B:SER329 4.9 66.0 1.0 OD1 B:ASN331 5.0 70.0 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