Magnesium in PDB 4xj6: Crystal Structure of Escherichia Coli Dncv 3'-Deoxy Gtp Bound Form

The structure of Crystal Structure of Escherichia Coli Dncv 3'-Deoxy Gtp Bound Form, PDB code: 4xj6 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)	37.13 / 2.31
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	136.070, 46.300, 62.560, 90.00, 110.61, 90.00
R / Rfree (%)	18.9 / 23.4

The binding sites of Magnesium atom in the Crystal Structure of Escherichia Coli Dncv 3'-Deoxy Gtp Bound Form (pdb code 4xj6). 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 Escherichia Coli Dncv 3'-Deoxy Gtp Bound Form, PDB code: 4xj6:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Escherichia Coli Dncv 3'-Deoxy 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 Escherichia Coli Dncv 3'-Deoxy Gtp Bound Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:18.6 occ:1.00 OD2 A:ASP129 2.0 22.6 1.0 O2B A:GH3503 2.0 20.5 1.0 O2A A:GH3503 2.0 26.5 1.0 O2G A:GH3503 2.0 22.4 1.0 OD2 A:ASP131 2.1 19.5 1.0 O A:HOH689 2.1 18.2 1.0 CG A:ASP131 3.1 20.8 1.0 PB A:GH3503 3.1 23.1 1.0 CG A:ASP129 3.1 23.5 1.0 PA A:GH3503 3.3 30.1 1.0 PG A:GH3503 3.3 21.7 1.0 OD1 A:ASP131 3.3 18.8 1.0 MG A:MG502 3.5 32.7 1.0 O3A A:GH3503 3.6 20.9 1.0 O3B A:GH3503 3.6 24.2 1.0 CB A:ASP129 3.8 17.7 1.0 C5' A:GH3503 3.8 24.9 1.0 O A:HOH637 3.9 22.5 1.0 O3G A:GH3503 4.0 23.6 1.0 OG A:SER112 4.0 21.1 1.0 O5' A:GH3503 4.0 25.7 1.0 O A:ASP129 4.1 26.9 1.0 OD1 A:ASP129 4.1 28.1 1.0 N A:SER112 4.3 22.7 1.0 O A:HOH691 4.4 31.6 1.0 O1B A:GH3503 4.4 27.8 1.0 CB A:ASP131 4.4 20.3 1.0 O1A A:GH3503 4.4 28.4 1.0 O1G A:GH3503 4.5 17.3 1.0 C A:ASP129 4.5 21.9 1.0 CB A:SER112 4.7 20.6 1.0 CA A:GLY111 4.8 18.8 1.0 N A:ASP131 4.8 20.5 1.0 CA A:ASP129 4.8 20.9 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Escherichia Coli Dncv 3'-Deoxy 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 Escherichia Coli Dncv 3'-Deoxy Gtp Bound Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:32.7 occ:1.00 O A:HOH691 2.1 31.6 1.0 OD1 A:ASP131 2.2 18.8 1.0 OD2 A:ASP191 2.2 25.2 1.0 OD1 A:ASP129 2.5 28.1 1.0 OD2 A:ASP129 2.5 22.6 1.0 CG A:ASP129 2.8 23.5 1.0 O2A A:GH3503 3.1 26.5 1.0 C3' A:GH3504 3.2 26.6 1.0 CG A:ASP131 3.3 20.8 1.0 CG A:ASP191 3.3 25.1 1.0 MG A:MG501 3.5 18.6 1.0 C4' A:GH3504 3.7 32.4 1.0 OD2 A:ASP131 3.7 19.5 1.0 CB A:ASP191 3.9 20.8 1.0 C5' A:GH3504 4.0 37.0 1.0 NH2 A:ARG180 4.0 20.9 1.0 CB A:ASP129 4.3 17.7 1.0 O2' A:GH3504 4.3 25.7 1.0 PA A:GH3503 4.3 30.1 1.0 OD1 A:ASP191 4.3 25.8 1.0 C2' A:GH3504 4.4 27.2 1.0 O2G A:GH3503 4.5 22.4 1.0 CB A:ASP131 4.6 20.3 1.0 O1A A:GH3503 4.7 28.4 1.0 NE2 A:HIS189 4.7 21.0 1.0 O5' A:GH3503 4.8 25.7 1.0 C5' A:GH3503 5.0 24.9 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