Magnesium in PDB 4u0m: Structure of the Vibrio Cholerae Di-Nucleotide Cyclase (Dncv) Mutant D193N in Complex with Atp, Gtp and 5MTHFGLU2

All present enzymatic activity of Structure of the Vibrio Cholerae Di-Nucleotide Cyclase (Dncv) Mutant D193N in Complex with Atp, Gtp and 5MTHFGLU2:
2.7.7.86;

The structure of Structure of the Vibrio Cholerae Di-Nucleotide Cyclase (Dncv) Mutant D193N in Complex with Atp, Gtp and 5MTHFGLU2, PDB code: 4u0m was solved by D.Zhu, Y.Xiang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.57 / 2.30
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	69.898, 59.860, 104.185, 90.00, 95.55, 90.00
R / Rfree (%)	19.9 / 25.3

The binding sites of Magnesium atom in the Structure of the Vibrio Cholerae Di-Nucleotide Cyclase (Dncv) Mutant D193N in Complex with Atp, Gtp and 5MTHFGLU2 (pdb code 4u0m). 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) Mutant D193N in Complex with Atp, Gtp and 5MTHFGLU2, PDB code: 4u0m:
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) Mutant D193N in Complex with Atp, Gtp and 5MTHFGLU2


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) Mutant D193N in Complex with Atp, Gtp and 5MTHFGLU2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:15.0 occ:1.00 O2A A:GTP501 2.0 34.1 1.0 OD1 A:ASP131 2.1 33.5 1.0 O2B A:GTP501 2.1 21.9 1.0 OD2 A:ASP133 2.2 30.9 1.0 O3G A:GTP501 2.3 23.1 1.0 O A:HOH763 2.4 18.4 1.0 CG A:ASP131 3.2 34.9 1.0 CG A:ASP133 3.2 38.6 1.0 PA A:GTP501 3.4 21.6 1.0 PB A:GTP501 3.5 15.4 1.0 OD1 A:ASP133 3.5 44.8 1.0 OD2 A:ASP131 3.6 52.1 1.0 PG A:GTP501 3.6 18.6 1.0 C5' A:GTP501 3.9 28.2 1.0 O3A A:GTP501 3.9 21.7 1.0 O3B A:GTP501 4.0 15.1 1.0 O5' A:GTP501 4.2 29.1 1.0 OG A:SER114 4.2 15.3 1.0 O2G A:GTP501 4.2 14.5 1.0 O A:ASP131 4.2 24.9 1.0 O3' A:ATP502 4.3 0.7 1.0 O A:HOH660 4.4 19.1 1.0 CB A:ASP131 4.4 29.4 1.0 N A:SER114 4.5 16.1 1.0 CB A:ASP133 4.6 35.1 1.0 O1A A:GTP501 4.6 26.7 1.0 CA A:GLY113 4.7 19.6 1.0 O A:HOH661 4.7 28.4 1.0 O1B A:GTP501 4.7 21.3 1.0 C A:ASP131 4.8 21.7 1.0 O1G A:GTP501 4.8 24.1 1.0 C3' A:ATP502 5.0 0.6 1.0

Magnesium binding site 2 out of 2 in the Structure of the Vibrio Cholerae Di-Nucleotide Cyclase (Dncv) Mutant D193N in Complex with Atp, Gtp and 5MTHFGLU2


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) Mutant D193N in Complex with Atp, Gtp and 5MTHFGLU2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg503 b:18.5 occ:1.00 O2B B:GTP501 2.1 17.2 1.0 OD1 B:ASP131 2.2 43.6 1.0 O B:HOH724 2.2 16.8 1.0 OD2 B:ASP133 2.2 30.8 1.0 O2A B:GTP501 2.4 24.9 1.0 O3G B:GTP501 2.9 50.6 1.0 CG B:ASP133 3.2 27.9 1.0 O2G B:GTP501 3.2 46.8 1.0 CG B:ASP131 3.3 38.1 1.0 PB B:GTP501 3.4 17.0 1.0 PG B:GTP501 3.5 26.5 1.0 OD1 B:ASP133 3.5 30.2 1.0 O B:ASP131 3.7 23.2 1.0 PA B:GTP501 3.7 19.5 1.0 O3B B:GTP501 3.8 32.8 1.0 C5' B:GTP501 3.8 28.0 1.0 OD2 B:ASP131 3.9 46.9 1.0 OG B:SER114 3.9 16.8 1.0 O B:HOH665 4.1 22.5 1.0 O3A B:GTP501 4.1 35.7 1.0 N B:SER114 4.1 22.4 1.0 O5' B:GTP501 4.3 28.4 1.0 CA B:GLY113 4.3 19.2 1.0 CB B:ASP133 4.5 28.6 1.0 CB B:ASP131 4.5 38.1 1.0 C B:ASP131 4.5 19.6 1.0 O B:HOH654 4.6 19.5 1.0 O1B B:GTP501 4.7 27.7 1.0 O2' B:ATP502 4.7 59.9 0.7 C B:GLY113 4.8 18.5 1.0 CB B:SER114 4.8 17.1 1.0 O2' B:ATP502 5.0 58.9 0.3 O1G B:GTP501 5.0 28.5 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