Magnesium in PDB 4u0n: Structure of the Vibrio Cholerae Di-Nucleotide Cyclase (Dncv) Deletion Mutant D-Loop

All present enzymatic activity of Structure of the Vibrio Cholerae Di-Nucleotide Cyclase (Dncv) Deletion Mutant D-Loop:
2.7.7.86;

The structure of Structure of the Vibrio Cholerae Di-Nucleotide Cyclase (Dncv) Deletion Mutant D-Loop, PDB code: 4u0n was solved by Y.Xiang, D.Y.Zhu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.73 / 2.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	73.605, 49.253, 122.233, 90.00, 98.66, 90.00
R / Rfree (%)	21.8 / 26.4

The binding sites of Magnesium atom in the Structure of the Vibrio Cholerae Di-Nucleotide Cyclase (Dncv) Deletion Mutant D-Loop (pdb code 4u0n). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Structure of the Vibrio Cholerae Di-Nucleotide Cyclase (Dncv) Deletion Mutant D-Loop, PDB code: 4u0n:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Structure of the Vibrio Cholerae Di-Nucleotide Cyclase (Dncv) Deletion Mutant D-Loop


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of the Vibrio Cholerae Di-Nucleotide Cyclase (Dncv) Deletion Mutant D-Loop within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:40.0 occ:1.00 OD1 A:ASP133 2.1 54.1 1.0 OD2 A:ASP193 2.1 41.8 1.0 O A:HOH585 2.1 29.9 1.0 O A:HOH588 2.1 32.4 1.0 OD1 A:ASP131 2.3 37.3 1.0 CG A:ASP133 2.8 52.7 1.0 OD2 A:ASP133 3.0 58.9 1.0 CG A:ASP131 3.1 41.6 1.0 CG A:ASP193 3.1 36.1 1.0 OD2 A:ASP131 3.3 51.2 1.0 CB A:ASP193 3.6 26.3 1.0 NH2 A:ARG182 4.2 27.1 1.0 OD1 A:ASP193 4.2 38.5 1.0 CB A:ASP133 4.3 42.0 1.0 O A:ILE132 4.5 29.5 1.0 CB A:ASP131 4.6 30.4 1.0 O A:HOH600 4.7 47.2 1.0 C A:ILE132 4.7 29.3 1.0 CA A:ASP133 4.8 30.8 1.0 N A:ASP133 4.9 25.6 1.0 CA A:ASP193 4.9 25.0 1.0 NE2 A:HIS191 4.9 28.5 1.0 C A:ASP131 5.0 27.8 1.0

Magnesium binding site 2 out of 2 in the Structure of the Vibrio Cholerae Di-Nucleotide Cyclase (Dncv) Deletion Mutant D-Loop


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of the Vibrio Cholerae Di-Nucleotide Cyclase (Dncv) Deletion Mutant D-Loop within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg401 b:38.0 occ:1.00 OD2 B:ASP193 2.0 35.8 1.0 O B:HOH602 2.1 33.3 1.0 OD1 B:ASP133 2.1 56.8 1.0 OD1 B:ASP131 2.3 41.2 1.0 CG B:ASP193 3.1 32.7 1.0 CG B:ASP131 3.1 39.3 1.0 CG B:ASP133 3.2 53.1 1.0 OD2 B:ASP131 3.2 40.8 1.0 OD2 B:ASP133 3.5 55.2 1.0 CB B:ASP193 3.6 24.0 1.0 NH2 B:ARG182 4.2 29.8 1.0 OD1 B:ASP193 4.2 35.8 1.0 CB B:ASP133 4.5 41.6 1.0 CB B:ASP131 4.6 33.8 1.0 O B:HOH674 4.7 48.4 1.0 NE2 B:HIS191 4.8 22.1 1.0 O B:ILE132 4.9 26.1 1.0 CA B:ASP193 4.9 24.6 1.0 CA B:ASP133 4.9 33.0 1.0 N B:ASP133 4.9 30.0 1.0 C B:ILE132 4.9 26.9 1.0 O B:HOH646 5.0 48.8 1.0

D.Zhu, L.Wang, G.Shang, X.Liu, J.Zhu, D.Lu, L.Wang, B.Kan, J.R.Zhang, Y.Xiang. Structural Biochemistry of A Vibrio Cholerae Dinucleotide Cyclase Reveals Cyclase Activity Regulation By Folates. Mol.Cell V. 55 931 2014.
ISSN: ISSN 1097-2765
PubMed: 25201413
DOI: 10.1016/J.MOLCEL.2014.08.001