Magnesium in PDB 4d6y: Crystal Structure of the Receiver Domain of Ntrx From Brucella Abortus in Complex with Beryllofluoride and Magnesium

The structure of Crystal Structure of the Receiver Domain of Ntrx From Brucella Abortus in Complex with Beryllofluoride and Magnesium, PDB code: 4d6y was solved by L.H.Otero, I.Fernandez, M.C.Carrica, S.Klinke, F.A.Goldbaum, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.99 / 1.70
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	30.395, 39.343, 52.961, 97.30, 96.97, 89.97
R / Rfree (%)	18.36 / 20.41

The structure of Crystal Structure of the Receiver Domain of Ntrx From Brucella Abortus in Complex with Beryllofluoride and Magnesium also contains other interesting chemical elements:

Fluorine

(F)

6 atoms

The binding sites of Magnesium atom in the Crystal Structure of the Receiver Domain of Ntrx From Brucella Abortus in Complex with Beryllofluoride and Magnesium (pdb code 4d6y). 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 the Receiver Domain of Ntrx From Brucella Abortus in Complex with Beryllofluoride and Magnesium, PDB code: 4d6y:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of the Receiver Domain of Ntrx From Brucella Abortus in Complex with Beryllofluoride and Magnesium


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 the Receiver Domain of Ntrx From Brucella Abortus in Complex with Beryllofluoride and Magnesium within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1126 b:16.7 occ:1.00 F3 A:BEF1125 1.9 17.0 1.0 OD2 A:ASP53 2.0 18.8 1.0 O A:HOH2001 2.0 20.0 1.0 O A:HOH2004 2.1 24.0 1.0 OD1 A:ASP10 2.1 19.0 1.0 O A:TRP55 2.1 20.3 1.0 CG A:ASP53 3.0 15.4 1.0 CG A:ASP10 3.1 23.0 1.0 BE A:BEF1125 3.2 19.3 1.0 C A:TRP55 3.3 22.7 1.0 OD1 A:ASP53 3.4 12.8 1.0 OD2 A:ASP10 3.5 28.9 1.0 OD1 A:ASP9 4.0 22.8 1.0 CB A:TRP55 4.0 21.4 1.0 CA A:TRP55 4.1 19.9 1.0 OE2 A:GLU11 4.2 29.3 1.0 N A:TRP55 4.3 17.3 1.0 CB A:ASP53 4.3 13.8 1.0 N A:LEU56 4.3 21.2 1.0 F1 A:BEF1125 4.3 16.1 1.0 CB A:ASP10 4.4 23.5 1.0 F2 A:BEF1125 4.4 18.7 1.0 N A:ASP10 4.4 20.2 1.0 CG A:ASP9 4.5 22.6 1.0 CA A:LEU56 4.5 20.9 1.0 OD2 A:ASP9 4.6 22.0 1.0 NZ A:LYS105 4.6 21.0 1.0 CD2 A:LEU56 4.9 19.8 1.0 CA A:ASP10 5.0 21.8 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of the Receiver Domain of Ntrx From Brucella Abortus in Complex with Beryllofluoride and Magnesium


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 the Receiver Domain of Ntrx From Brucella Abortus in Complex with Beryllofluoride and Magnesium within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1126 b:17.6 occ:1.00 F2 B:BEF1125 1.8 16.8 1.0 OD2 B:ASP53 2.0 18.0 1.0 OD1 B:ASP10 2.0 20.9 1.0 O B:HOH2002 2.1 25.5 1.0 O B:HOH2001 2.1 19.5 1.0 O B:TRP55 2.1 20.3 1.0 CG B:ASP53 3.0 16.6 1.0 CG B:ASP10 3.1 24.5 1.0 BE B:BEF1125 3.2 17.4 1.0 C B:TRP55 3.3 22.2 1.0 OD1 B:ASP53 3.4 13.6 1.0 OD2 B:ASP10 3.5 29.5 1.0 OD1 B:ASP9 4.0 22.9 1.0 CB B:TRP55 4.0 20.4 1.0 CA B:TRP55 4.1 19.3 1.0 OE2 B:GLU11 4.2 29.2 1.0 CB B:ASP53 4.3 12.5 1.0 N B:TRP55 4.3 16.8 1.0 F3 B:BEF1125 4.3 15.2 1.0 N B:LEU56 4.3 20.2 1.0 CB B:ASP10 4.4 21.5 1.0 N B:ASP10 4.4 18.3 1.0 F1 B:BEF1125 4.4 15.6 1.0 CG B:ASP9 4.5 21.3 1.0 CA B:LEU56 4.5 19.9 1.0 OD2 B:ASP9 4.6 19.4 1.0 NZ B:LYS105 4.6 21.2 1.0 O B:HOH2027 4.7 34.6 1.0 CD2 B:LEU56 4.9 19.4 1.0 CA B:ASP10 4.9 19.8 1.0

I.Fernandez, L.H.Otero, S.Klinke, M.C.Carrica, F.A.Goldbaum. Snapshots of Conformational Changes Shed Light Into the Ntrx Receiver Domain Signal Transduction Mechanism J.Mol.Biol. V. 427 3258 2015.
ISSN: ISSN 0022-2836
PubMed: 26113057
DOI: 10.1016/J.JMB.2015.06.010