Magnesium in PDB 4bvp: Legionella Pneumophila NTPDASE1 Crystal Form II (Closed) in Complex with Heptamolybdate and Octamolybdate

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

Resolution Low / High (Å)	45.34 / 1.49
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	64.564, 85.436, 71.779, 90.00, 103.94, 90.00
R / Rfree (%)	12.608 / 16.858

The structure of Legionella Pneumophila NTPDASE1 Crystal Form II (Closed) in Complex with Heptamolybdate and Octamolybdate also contains other interesting chemical elements:

Molybdenum	(Mo)	46 atoms
Chlorine	(Cl)	2 atoms
Sodium	(Na)	1 atom

The binding sites of Magnesium atom in the Legionella Pneumophila NTPDASE1 Crystal Form II (Closed) in Complex with Heptamolybdate and Octamolybdate (pdb code 4bvp). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Legionella Pneumophila NTPDASE1 Crystal Form II (Closed) in Complex with Heptamolybdate and Octamolybdate, PDB code: 4bvp:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Legionella Pneumophila NTPDASE1 Crystal Form II (Closed) in Complex with Heptamolybdate and Octamolybdate


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 II (Closed) in Complex with Heptamolybdate and Octamolybdate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1404 b:10.0 occ:1.00 O A:HOH2093 2.0 8.3 1.0 O A:HOH2227 2.1 11.1 1.0 O A:HOH2004 2.1 8.5 1.0 O A:HOH2101 2.1 10.0 1.0 O A:HOH2003 2.1 9.4 1.0 O1 A:MOO1403 2.1 8.1 1.0 MO A:MOO1403 3.7 8.8 1.0 O A:HOH2100 3.9 11.8 1.0 OE2 A:GLU159 3.9 8.8 1.0 O A:HOH2092 4.0 9.8 1.0 NE1 A:TRP384 4.0 9.6 1.0 O3 A:MOO1403 4.1 9.3 1.0 OD2 A:ASP49 4.2 15.4 1.0 O A:HOH2104 4.2 17.5 1.0 OD2 A:ASP186 4.3 10.0 1.0 OD1 A:ASP49 4.3 10.3 1.0 OD1 A:ASP186 4.3 9.6 1.0 OG1 A:THR118 4.4 8.6 1.0 O A:HOH2062 4.5 8.6 1.0 CD1 A:TRP384 4.5 8.1 1.0 O4 A:MOO1403 4.5 8.3 1.0 CG A:ASP49 4.6 10.4 1.0 CG A:ASP186 4.7 8.3 1.0 CA A:GLY188 4.9 7.2 1.0

Magnesium binding site 2 out of 5 in the Legionella Pneumophila NTPDASE1 Crystal Form II (Closed) in Complex with Heptamolybdate and Octamolybdate


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 II (Closed) in Complex with Heptamolybdate and Octamolybdate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1406 b:18.5 occ:0.80 O A:HOH2229 2.0 17.7 1.0 O A:HOH2186 2.0 20.7 1.0 O A:HOH2185 2.0 21.3 1.0 OE1 A:GLN307 2.2 18.7 1.0 O A:HOH2187 2.2 17.5 1.0 CD A:GLN307 3.2 15.9 1.0 NE2 A:GLN307 3.5 22.7 1.0 O A:HOH2184 4.3 14.2 1.0 CG A:GLN307 4.6 14.3 1.0

Magnesium binding site 3 out of 5 in the Legionella Pneumophila NTPDASE1 Crystal Form II (Closed) in Complex with Heptamolybdate and Octamolybdate


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 II (Closed) in Complex with Heptamolybdate and Octamolybdate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1405 b:9.7 occ:1.00 O B:HOH2080 2.1 7.9 1.0 O B:HOH2003 2.1 9.4 1.0 O B:HOH2005 2.1 8.8 1.0 O B:HOH2205 2.1 11.9 1.0 O B:HOH2087 2.1 9.9 1.0 O2 B:MOO1404 2.1 9.3 1.0 MO B:MOO1404 3.7 8.9 1.0 OE2 B:GLU159 3.9 9.6 1.0 O B:HOH2088 3.9 12.0 1.0 O B:HOH2081 3.9 9.1 1.0 NE1 B:TRP384 4.0 8.9 1.0 O1 B:MOO1404 4.1 9.5 1.0 O B:HOH2212 4.1 30.8 1.0 O3 B:GOL1417 4.2 32.3 1.0 OD2 B:ASP49 4.2 14.6 1.0 O B:HOH2091 4.2 18.7 1.0 OD1 B:ASP49 4.2 11.1 1.0 OD2 B:ASP186 4.3 9.5 1.0 OD1 B:ASP186 4.3 10.5 1.0 OG1 B:THR118 4.4 8.5 1.0 O B:HOH2050 4.4 8.6 1.0 CD1 B:TRP384 4.5 7.9 1.0 O4 B:MOO1404 4.5 7.7 1.0 CG B:ASP49 4.7 9.3 1.0 O B:HOH2009 4.7 35.0 1.0 CG B:ASP186 4.7 9.8 1.0 CA B:GLY188 4.8 7.9 1.0 O3 B:MOO1404 5.0 7.3 1.0

Magnesium binding site 4 out of 5 in the Legionella Pneumophila NTPDASE1 Crystal Form II (Closed) in Complex with Heptamolybdate and Octamolybdate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Legionella Pneumophila NTPDASE1 Crystal Form II (Closed) in Complex with Heptamolybdate and Octamolybdate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1407 b:20.9 occ:0.80 O B:HOH2156 2.0 24.0 1.0 O B:HOH2154 2.0 19.6 1.0 O B:HOH2206 2.1 23.1 1.0 OE1 B:GLN307 2.2 20.4 1.0 O B:HOH2155 2.3 20.9 1.0 CD B:GLN307 3.1 19.0 1.0 NE2 B:GLN307 3.3 23.2 1.0 O B:HOH2071 4.0 31.0 1.0 O B:HOH2153 4.3 15.1 1.0 CG B:GLN307 4.5 12.7 1.0

Magnesium binding site 5 out of 5 in the Legionella Pneumophila NTPDASE1 Crystal Form II (Closed) in Complex with Heptamolybdate and Octamolybdate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Legionella Pneumophila NTPDASE1 Crystal Form II (Closed) in Complex with Heptamolybdate and Octamolybdate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1418 b:26.3 occ:1.00 O A:HOH2132 1.8 27.8 1.0 O B:HOH2115 2.0 29.1 1.0 O B:HOH2116 2.1 28.7 1.0 O A:HOH2134 2.1 32.7 1.0 OE2 B:GLU233 4.0 17.4 1.0 OE2 A:GLU233 4.0 19.4 1.0 O A:HOH2138 4.1 26.6 1.0 O A:HOH2025 4.2 37.0 1.0 CE1 A:HIS236 4.4 12.5 1.0 CE1 B:HIS236 4.4 12.8 1.0 O A:HOH2048 4.5 32.3 1.0 O B:HOH2016 4.8 20.6 1.0 O A:HOH2015 4.8 19.0 1.0 CD A:GLU233 4.8 15.2 1.0 ND1 A:HIS236 4.8 10.6 1.0 OE1 A:GLU233 4.9 22.3 1.0 CD B:GLU233 4.9 14.6 1.0 OE1 B:GLU233 4.9 20.5 1.0 ND1 B:HIS236 4.9 10.1 1.0

M.Zebisch, M.Krauss, P.Schafer, N.Strater. Structures of Legionella Pneumophila NTPDASE1 in Complex with Polyoxometallates. Acta Crystallogr.,Sect.D V. 70 1147 2014.
ISSN: ISSN 0907-4449
PubMed: 24699658
DOI: 10.1107/S1399004714001916