Magnesium in PDB 4xj3: Crystal Structure of Vibrio Cholerae Dncv Gtp Bound Form

The structure of Crystal Structure of Vibrio Cholerae Dncv Gtp Bound Form, PDB code: 4xj3 was solved by K.Kato, R.Ishii, R.Ishitani, O.Nureki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.95 / 1.65
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	118.780, 49.850, 72.860, 90.00, 93.48, 90.00
R / Rfree (%)	17.6 / 20.7

The binding sites of Magnesium atom in the Crystal Structure of Vibrio Cholerae Dncv Gtp Bound Form (pdb code 4xj3). 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 Vibrio Cholerae Dncv Gtp Bound Form, PDB code: 4xj3:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Vibrio Cholerae Dncv Gtp 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 Vibrio Cholerae Dncv Gtp Bound Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1001 b:21.8 occ:1.00 O A:HOH1320 2.3 19.4 1.0 OD2 A:ASP131 2.3 29.5 1.0 O2B A:GTP1012 2.4 19.2 1.0 OD2 A:ASP133 2.4 23.8 1.0 O2A A:GTP1012 2.4 23.4 1.0 O2G A:GTP1012 2.5 17.9 1.0 MG A:MG1002 3.3 32.6 1.0 CG A:ASP131 3.3 30.4 1.0 CG A:ASP133 3.4 25.7 1.0 PB A:GTP1012 3.5 20.8 1.0 PA A:GTP1012 3.5 23.3 1.0 O A:HOH1322 3.6 26.7 1.0 PG A:GTP1012 3.7 17.3 1.0 OD1 A:ASP133 3.7 26.8 1.0 CB A:ASP131 3.8 25.7 1.0 O3A A:GTP1012 3.9 21.3 1.0 O3B A:GTP1012 3.9 22.7 1.0 OG A:SER114 4.0 17.8 1.0 C5' A:GTP1012 4.0 22.7 1.0 N A:SER114 4.2 19.4 1.0 OD1 A:ASP131 4.3 30.7 1.0 O5' A:GTP1012 4.3 23.4 1.0 O A:HOH1211 4.3 18.1 1.0 O A:ASP131 4.3 19.9 1.0 O3G A:GTP1012 4.4 18.6 1.0 O3' A:GTP1013 4.5 29.9 1.0 C A:ASP131 4.6 23.7 1.0 CA A:GLY113 4.6 19.7 1.0 O A:HOH1292 4.7 22.1 1.0 CB A:ASP133 4.7 22.7 1.0 O1A A:GTP1012 4.8 21.0 1.0 CA A:ASP131 4.8 25.4 1.0 O1B A:GTP1012 4.8 17.8 1.0 CB A:SER114 4.9 17.8 1.0 O1G A:GTP1012 4.9 18.5 1.0 C A:GLY113 5.0 19.1 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Vibrio Cholerae Dncv Gtp 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 Vibrio Cholerae Dncv Gtp Bound Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1002 b:32.6 occ:1.00 O2A A:GTP1012 2.3 23.4 1.0 O A:HOH1322 2.4 26.7 1.0 OD2 A:ASP131 2.4 29.5 1.0 O3' A:GTP1013 2.4 29.9 1.0 O A:HOH1323 2.4 22.9 1.0 O A:HOH1327 2.6 34.8 1.0 MG A:MG1001 3.3 21.8 1.0 CG A:ASP131 3.4 30.4 1.0 C3' A:GTP1013 3.6 30.7 1.0 PA A:GTP1012 3.6 23.3 1.0 O A:HOH1338 3.7 40.7 1.0 OD1 A:ASP133 3.8 26.8 1.0 O1A A:GTP1012 3.9 21.0 1.0 O A:HOH1352 3.9 40.7 1.0 OD2 A:ASP193 3.9 25.7 1.0 O2G A:GTP1012 4.0 17.9 1.0 CB A:ASP131 4.1 25.7 1.0 OD1 A:ASP131 4.2 30.7 1.0 OD2 A:ASP133 4.2 23.8 1.0 CG A:ASP133 4.4 25.7 1.0 C2' A:GTP1013 4.5 31.0 1.0 O5' A:GTP1012 4.6 23.4 1.0 O2' A:GTP1013 4.6 32.5 1.0 C4' A:GTP1013 4.7 32.0 1.0 O3A A:GTP1012 4.8 21.3 1.0 O A:HOH1301 4.8 24.8 1.0 NE2 A:HIS191 4.9 25.2 1.0 C5' A:GTP1012 4.9 22.7 1.0 CG A:ASP193 4.9 26.1 1.0 O2B A:GTP1012 5.0 19.2 1.0

K.Kato, R.Ishii, S.Hirano, R.Ishitani, O.Nureki. Structural Basis For the Catalytic Mechanism of Dncv, Bacterial Homolog of Cyclic Gmp-Amp Synthase Structure V. 23 843 2015.
ISSN: ISSN 0969-2126
PubMed: 25865248
DOI: 10.1016/J.STR.2015.01.023