Magnesium in PDB 4brk: Legionella Pneumophila NTPDASE1 N302Y Variant Crystal Form III (Closed) in Complex with Mg Umppnp

All present enzymatic activity of Legionella Pneumophila NTPDASE1 N302Y Variant Crystal Form III (Closed) in Complex with Mg Umppnp:
3.6.1.5;

The structure of Legionella Pneumophila NTPDASE1 N302Y Variant Crystal Form III (Closed) in Complex with Mg Umppnp, PDB code: 4brk 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)	27.43 / 1.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	80.600, 82.967, 109.578, 90.00, 90.00, 90.00
R / Rfree (%)	12.877 / 17.791

The structure of Legionella Pneumophila NTPDASE1 N302Y Variant Crystal Form III (Closed) in Complex with Mg Umppnp also contains other interesting chemical elements:

Chlorine

(Cl)

3 atoms

The binding sites of Magnesium atom in the Legionella Pneumophila NTPDASE1 N302Y Variant Crystal Form III (Closed) in Complex with Mg Umppnp (pdb code 4brk). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Legionella Pneumophila NTPDASE1 N302Y Variant Crystal Form III (Closed) in Complex with Mg Umppnp, PDB code: 4brk:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Legionella Pneumophila NTPDASE1 N302Y Variant Crystal Form III (Closed) in Complex with Mg Umppnp


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 N302Y Variant Crystal Form III (Closed) in Complex with Mg Umppnp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1396 b:8.5 occ:1.00 O3G A:UNP1395 2.0 7.1 1.0 O3B A:UNP1395 2.1 7.8 1.0 O A:HOH2199 2.1 7.1 1.0 O A:HOH2219 2.1 8.3 1.0 O A:HOH2007 2.1 6.9 1.0 O A:HOH2008 2.2 6.8 1.0 PG A:UNP1395 3.3 7.7 1.0 PB A:UNP1395 3.3 7.7 1.0 N2B A:UNP1395 3.7 7.6 1.0 O A:HOH2198 3.9 7.8 1.0 O1G A:UNP1395 3.9 9.5 1.0 O3A A:UNP1395 4.0 8.1 1.0 O A:HOH2220 4.1 8.7 1.0 NE1 A:TRP384 4.1 7.2 1.0 NH1 A:ARG56 4.1 8.0 1.0 O2A A:UNP1395 4.1 9.1 1.0 OE2 A:GLU159 4.2 9.6 1.0 O A:HOH2027 4.2 11.2 1.0 OD2 A:ASP49 4.2 9.7 1.0 OD2 A:ASP186 4.3 8.0 1.0 OD1 A:ASP49 4.3 8.4 1.0 OG1 A:THR118 4.4 8.4 1.0 OD1 A:ASP186 4.4 8.8 1.0 O2G A:UNP1395 4.5 8.3 1.0 PA A:UNP1395 4.5 8.8 1.0 O1B A:UNP1395 4.5 8.7 1.0 CD1 A:TRP384 4.5 6.1 1.0 CA A:GLY188 4.6 7.6 1.0 CG A:ASP49 4.7 7.3 1.0 O A:HOH2127 4.8 8.9 1.0 O1A A:UNP1395 4.8 9.0 1.0 CG A:ASP186 4.8 7.3 1.0 CA A:GLY51 4.9 7.3 1.0

Magnesium binding site 2 out of 2 in the Legionella Pneumophila NTPDASE1 N302Y Variant Crystal Form III (Closed) in Complex with Mg Umppnp


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 N302Y Variant Crystal Form III (Closed) in Complex with Mg Umppnp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1398 b:8.1 occ:1.00 O3G B:UNP1397 2.0 7.5 1.0 O3B B:UNP1397 2.1 6.9 1.0 O B:HOH2161 2.1 6.3 1.0 O B:HOH2186 2.1 7.6 1.0 O B:HOH2004 2.1 7.9 1.0 O B:HOH2005 2.1 7.7 1.0 PG B:UNP1397 3.3 7.8 1.0 PB B:UNP1397 3.3 7.4 1.0 N2B B:UNP1397 3.7 6.8 1.0 O B:HOH2162 3.9 7.8 1.0 O1G B:UNP1397 3.9 8.5 1.0 O3A B:UNP1397 3.9 8.7 1.0 O B:HOH2185 4.0 10.1 1.0 NE1 B:TRP384 4.1 8.6 1.0 OE2 B:GLU159 4.1 10.2 1.0 NH1 B:ARG56 4.1 8.3 1.0 O1A B:UNP1397 4.1 11.6 1.0 O B:HOH2022 4.2 17.2 1.0 OD2 B:ASP49 4.2 9.6 1.0 OD2 B:ASP186 4.3 7.7 1.0 OD1 B:ASP49 4.3 8.4 1.0 OG1 B:THR118 4.4 8.5 1.0 OD1 B:ASP186 4.4 8.9 1.0 O2G B:UNP1397 4.5 8.4 1.0 PA B:UNP1397 4.5 9.2 1.0 CD1 B:TRP384 4.5 7.9 1.0 O1B B:UNP1397 4.6 8.0 1.0 CG B:ASP49 4.7 7.3 1.0 CA B:GLY188 4.7 6.3 1.0 O B:HOH2111 4.7 9.8 1.0 CG B:ASP186 4.8 5.9 1.0 CA B:GLY51 4.9 6.7 1.0 O2A B:UNP1397 4.9 9.4 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