Magnesium in PDB 4brn: Legionella Pneumophila NTPDASE1 Crystal Form III (Closed) in Complex with Mg Amp

The structure of Legionella Pneumophila NTPDASE1 Crystal Form III (Closed) in Complex with Mg Amp, PDB code: 4brn was solved by M.Zebisch, P.Schaefer, P.Lauble, N.Straeter, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.98 / 1.69
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	80.333, 83.577, 104.110, 90.00, 90.00, 90.00
R / Rfree (%)	18.61 / 23.014

The structure of Legionella Pneumophila NTPDASE1 Crystal Form III (Closed) in Complex with Mg Amp also contains other interesting chemical elements:

Chlorine

(Cl)

3 atoms

The binding sites of Magnesium atom in the Legionella Pneumophila NTPDASE1 Crystal Form III (Closed) in Complex with Mg Amp (pdb code 4brn). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Legionella Pneumophila NTPDASE1 Crystal Form III (Closed) in Complex with Mg Amp, PDB code: 4brn:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Legionella Pneumophila NTPDASE1 Crystal Form III (Closed) in Complex with Mg Amp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Legionella Pneumophila NTPDASE1 Crystal Form III (Closed) in Complex with Mg Amp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1394 b:13.4 occ:1.00 O A:HOH2057 2.0 13.0 1.0 O A:HOH2087 2.1 13.0 1.0 O A:HOH2005 2.1 12.7 1.0 O A:HOH2006 2.2 13.5 1.0 O A:HOH2095 2.2 14.6 1.0 O3P A:AMP1393 2.2 15.8 1.0 P A:AMP1393 3.3 16.1 1.0 O2P A:AMP1393 3.6 15.2 1.0 O A:HOH2017 3.7 26.8 1.0 O5' A:AMP1393 3.9 16.7 1.0 NH1 A:ARG56 4.0 15.1 1.0 OE2 A:GLU159 4.0 11.8 1.0 NE1 A:TRP384 4.0 13.6 1.0 O A:HOH2096 4.0 20.6 1.0 O A:HOH2086 4.1 12.5 1.0 OD2 A:ASP49 4.2 12.9 1.0 OD2 A:ASP186 4.2 15.1 1.0 OD1 A:ASP186 4.2 15.9 1.0 OD1 A:ASP49 4.3 13.1 1.0 OG1 A:THR118 4.4 12.2 1.0 CD1 A:TRP384 4.5 13.9 1.0 O1P A:AMP1393 4.6 15.3 1.0 CA A:GLY51 4.7 12.1 1.0 CG A:ASP186 4.7 15.2 1.0 CG A:ASP49 4.7 13.2 1.0 C5' A:AMP1393 4.7 17.0 1.0 O A:HOH2056 4.7 12.1 1.0 CA A:GLY188 4.8 12.8 1.0 O A:HOH2014 5.0 16.5 1.0

Magnesium binding site 2 out of 3 in the Legionella Pneumophila NTPDASE1 Crystal Form III (Closed) in Complex with Mg Amp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Legionella Pneumophila NTPDASE1 Crystal Form III (Closed) in Complex with Mg Amp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1398 b:25.1 occ:1.00 O A:TRP146 2.2 19.8 1.0 O A:GLN143 2.4 29.5 1.0 O A:PHE140 2.4 21.7 1.0 O A:HOH2075 2.8 14.5 1.0 C A:GLN143 3.4 29.2 1.0 C A:TRP146 3.4 19.4 1.0 C A:PHE140 3.5 21.4 1.0 OE1 A:GLN147 4.0 23.9 0.7 O A:ARG141 4.1 28.9 1.0 N A:GLN143 4.2 29.6 1.0 CA A:GLN143 4.2 29.7 1.0 CA A:ARG141 4.2 26.5 1.0 N A:TRP146 4.2 22.1 1.0 C A:ARG141 4.2 28.2 1.0 N A:ARG141 4.3 23.4 1.0 N A:GLN147 4.3 17.9 1.0 CA A:TRP146 4.3 20.1 1.0 CA A:GLN147 4.3 17.8 0.3 CB A:GLN143 4.4 30.6 1.0 N A:SER144 4.4 29.3 1.0 CA A:GLN147 4.4 17.8 0.7 CA A:PHE140 4.5 20.4 1.0 CA A:SER144 4.5 30.3 1.0 CD A:GLN147 4.6 22.1 0.7 CB A:TRP146 4.6 20.6 1.0 C A:SER144 4.8 28.8 1.0 N A:LEU148 4.8 16.8 1.0 CB A:PHE140 4.8 19.5 1.0 NE2 A:GLN147 4.9 21.7 0.7 N A:GLN142 5.0 28.8 1.0

Magnesium binding site 3 out of 3 in the Legionella Pneumophila NTPDASE1 Crystal Form III (Closed) in Complex with Mg Amp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Legionella Pneumophila NTPDASE1 Crystal Form III (Closed) in Complex with Mg Amp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1396 b:12.3 occ:1.00 O B:HOH2043 2.1 12.2 1.0 O B:HOH2080 2.1 10.9 1.0 O2P B:AMP1395 2.1 12.9 1.0 O B:HOH2004 2.1 11.3 1.0 O B:HOH2068 2.1 10.4 1.0 O B:HOH2003 2.2 9.6 1.0 P B:AMP1395 3.3 14.0 1.0 O1P B:AMP1395 3.7 13.7 1.0 O B:HOH2015 3.8 25.2 1.0 NH1 B:ARG56 4.0 14.3 1.0 O B:HOH2067 4.0 13.9 1.0 O5' B:AMP1395 4.0 14.3 1.0 O B:HOH2081 4.0 16.6 1.0 NE1 B:TRP384 4.0 12.0 1.0 OE2 B:GLU159 4.1 11.3 1.0 OD2 B:ASP49 4.1 12.3 1.0 OD1 B:ASP186 4.3 12.2 1.0 OD1 B:ASP49 4.3 12.0 1.0 OD2 B:ASP186 4.3 12.3 1.0 OG1 B:THR118 4.4 11.2 1.0 O3P B:AMP1395 4.5 13.7 1.0 CD1 B:TRP384 4.5 11.8 1.0 CA B:GLY51 4.7 11.5 1.0 CG B:ASP49 4.7 11.8 1.0 CG B:ASP186 4.7 12.0 1.0 C5' B:AMP1395 4.7 16.4 1.0 CA B:GLY188 4.8 11.4 1.0 O B:HOH2044 4.9 11.7 1.0 O B:HOH2011 5.0 14.4 1.0

M.Zebisch, M.Krauss, P.Schaefer, P.Lauble, N.Straeter. Crystallographic Snapshots Along the Reaction Pathway of Nucleoside Triphosphate Diphosphohydrolases Structure V. 21 1460 2013.
ISSN: ISSN 0969-2126
PubMed: 23830739
DOI: 10.1016/J.STR.2013.05.016