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Magnesium in PDB 4brd: Legionella Pneumophila NTPDASE1 Q193E Crystal Form II, Closed, Mg Amppnp Complex

Enzymatic activity of Legionella Pneumophila NTPDASE1 Q193E Crystal Form II, Closed, Mg Amppnp Complex

All present enzymatic activity of Legionella Pneumophila NTPDASE1 Q193E Crystal Form II, Closed, Mg Amppnp Complex:
3.6.1.5;

Protein crystallography data

The structure of Legionella Pneumophila NTPDASE1 Q193E Crystal Form II, Closed, Mg Amppnp Complex, PDB code: 4brd 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) 29.20 / 1.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 62.134, 86.045, 71.977, 90.00, 106.78, 90.00
R / Rfree (%) 14.028 / 19.685

Other elements in 4brd:

The structure of Legionella Pneumophila NTPDASE1 Q193E Crystal Form II, Closed, Mg Amppnp Complex also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Legionella Pneumophila NTPDASE1 Q193E Crystal Form II, Closed, Mg Amppnp Complex (pdb code 4brd). 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 Q193E Crystal Form II, Closed, Mg Amppnp Complex, PDB code: 4brd:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 4brd

Go back to Magnesium Binding Sites List in 4brd
Magnesium binding site 1 out of 5 in the Legionella Pneumophila NTPDASE1 Q193E Crystal Form II, Closed, Mg Amppnp Complex


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 Q193E Crystal Form II, Closed, Mg Amppnp Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg505

b:16.8
occ:1.00
 O B:HOH2157 2.0 18.8 1.0
O A:HOH2273 2.1 18.1 1.0
O A:HOH2274 2.1 16.3 1.0
O B:HOH2156 2.1 17.4 1.0
O A:HOH2152 2.1 16.5 1.0
O A:HOH2154 2.2 18.6 1.0
OE2 B:GLU233 3.9 22.3 1.0
OE2 A:GLU233 4.0 28.3 1.0
O B:HOH2011 4.2 27.7 1.0
O A:HOH2008 4.3 29.1 1.0
CE1 B:HIS236 4.3 14.9 1.0
O B:HOH2160 4.3 21.9 1.0
O A:HOH2158 4.4 20.8 1.0
CE1 A:HIS236 4.4 11.8 1.0
O A:HOH2045 4.4 30.6 1.0
O B:HOH2010 4.7 13.8 1.0
O A:HOH2009 4.8 15.9 1.0
CD B:GLU233 4.8 19.3 1.0
O B:HOH2158 4.8 23.2 1.0
O A:HOH2153 4.8 22.6 1.0
OE1 B:GLU233 4.8 28.6 1.0
CD A:GLU233 4.8 20.9 1.0
ND1 B:HIS236 4.9 11.5 1.0
OE1 A:GLU233 4.9 30.0 1.0
ND1 A:HIS236 5.0 11.2 1.0

Magnesium binding site 2 out of 5 in 4brd

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Magnesium binding site 2 out of 5 in the Legionella Pneumophila NTPDASE1 Q193E Crystal Form II, Closed, Mg Amppnp Complex


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 Q193E Crystal Form II, Closed, Mg Amppnp Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1394

b:12.2
occ:1.00
 O2G A:ANP1393 2.0 11.0 0.5
O3G A:ANP1393 2.1 11.0 0.5
O1B A:ANP1393 2.1 11.1 0.5
O A:HOH2124 2.1 11.4 1.0
O A:HOH2003 2.1 12.3 1.0
O A:HOH2004 2.1 11.2 1.0
O1B A:ANP1393 2.1 11.3 0.5
O A:HOH2112 2.1 11.5 1.0
PG A:ANP1393 3.2 11.9 0.5
PB A:ANP1393 3.3 11.9 0.5
PG A:ANP1393 3.3 12.1 0.5
PB A:ANP1393 3.3 12.0 0.5
N3B A:ANP1393 3.6 10.5 0.5
N3B A:ANP1393 3.8 10.8 0.5
O1G A:ANP1393 3.9 12.8 0.5
O A:HOH2111 3.9 11.0 1.0
O1G A:ANP1393 3.9 11.9 0.5
OE2 A:GLU159 4.0 13.6 1.0
O3A A:ANP1393 4.0 13.2 0.5
O A:HOH2123 4.0 12.9 1.0
O3A A:ANP1393 4.0 13.2 0.5
O1A A:ANP1393 4.1 16.6 0.5
NH1 A:ARG56 4.1 17.1 1.0
O A:HOH2017 4.2 19.1 1.0
NE1 A:TRP384 4.2 13.4 1.0
O2A A:ANP1393 4.2 18.8 0.5
OD2 A:ASP49 4.3 15.3 1.0
OD2 A:ASP186 4.3 10.6 1.0
OD1 A:ASP186 4.3 12.0 1.0
OD1 A:ASP49 4.4 12.9 1.0
O3G A:ANP1393 4.5 11.1 0.5
O2G A:ANP1393 4.5 11.3 0.5
PA A:ANP1393 4.5 14.9 0.5
O2B A:ANP1393 4.5 12.9 0.5
PA A:ANP1393 4.6 14.3 0.5
O2B A:ANP1393 4.6 13.2 0.5
OG1 A:THR118 4.6 13.6 1.0
CD1 A:TRP384 4.7 12.5 1.0
O A:HOH2064 4.7 13.1 1.0
CA A:GLY188 4.7 10.5 1.0
CG A:ASP186 4.7 11.5 1.0
CG A:ASP49 4.8 12.0 1.0
O1A A:ANP1393 4.9 17.9 0.5
CA A:GLY51 4.9 13.2 1.0

Magnesium binding site 3 out of 5 in 4brd

Go back to Magnesium Binding Sites List in 4brd
Magnesium binding site 3 out of 5 in the Legionella Pneumophila NTPDASE1 Q193E Crystal Form II, Closed, Mg Amppnp Complex


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 Q193E Crystal Form II, Closed, Mg Amppnp Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg505

b:34.1
occ:1.00
 O B:HOH2271 1.9 32.9 1.0
O B:HOH2272 1.9 34.0 1.0
O B:HOH2067 2.0 32.2 1.0
O B:HOH2066 2.0 29.1 1.0
O B:HOH2273 2.3 28.1 1.0
O B:HOH2068 2.3 46.1 1.0
OD1 B:ASP96 3.8 23.3 1.0
OG1 B:THR100 4.0 20.6 1.0
OD2 B:ASP96 4.3 36.6 1.0
CG B:ASP96 4.6 22.5 1.0
CG2 B:THR100 4.8 20.7 1.0

Magnesium binding site 4 out of 5 in 4brd

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Magnesium binding site 4 out of 5 in the Legionella Pneumophila NTPDASE1 Q193E Crystal Form II, Closed, Mg Amppnp Complex


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 Q193E Crystal Form II, Closed, Mg Amppnp Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg506

b:44.2
occ:1.00
 O B:HOH2218 2.0 39.2 1.0
O B:HOH2213 2.0 43.1 1.0
O B:HOH2274 2.1 32.3 1.0
O B:HOH2222 2.2 36.9 1.0
O B:HOH2224 2.4 37.4 1.0
O B:PHE309 3.9 28.3 1.0
CD2 B:HIS310 4.1 35.0 1.0
NE2 B:HIS310 4.3 41.3 1.0
O B:SER306 4.3 22.8 1.0
CA B:GLN307 4.4 21.6 0.5
CA B:GLN307 4.5 18.8 0.5
O B:HOH2212 4.5 37.4 1.0
O B:GLN307 4.5 22.1 1.0
C B:GLN307 4.8 21.8 1.0
CG B:HIS310 5.0 32.2 1.0

Magnesium binding site 5 out of 5 in 4brd

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Magnesium binding site 5 out of 5 in the Legionella Pneumophila NTPDASE1 Q193E Crystal Form II, Closed, Mg Amppnp Complex


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 Q193E Crystal Form II, Closed, Mg Amppnp Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1397

b:12.5
occ:1.00
 O2G B:ANP1396 2.0 11.6 1.0
O2B B:ANP1396 2.0 11.6 1.0
O B:HOH2122 2.1 10.0 1.0
O B:HOH2133 2.1 11.4 1.0
O B:HOH2006 2.1 11.3 1.0
O B:HOH2005 2.1 12.1 1.0
PG B:ANP1396 3.3 11.3 1.0
PB B:ANP1396 3.3 10.7 1.0
N3B B:ANP1396 3.7 9.5 1.0
O1G B:ANP1396 3.9 11.3 1.0
O B:HOH2121 3.9 10.8 1.0
OE2 B:GLU159 3.9 12.4 1.0
O3A B:ANP1396 4.0 11.9 1.0
O B:HOH2134 4.0 13.3 1.0
NH1 B:ARG56 4.1 12.7 1.0
O1A B:ANP1396 4.1 15.3 1.0
O B:HOH2020 4.1 19.0 1.0
NE1 B:TRP384 4.2 11.8 1.0
OD2 B:ASP186 4.3 10.9 1.0
OD1 B:ASP186 4.3 12.0 1.0
OD2 B:ASP49 4.3 13.4 1.0
OD1 B:ASP49 4.4 9.6 1.0
O3G B:ANP1396 4.5 12.0 1.0
O1B B:ANP1396 4.5 9.9 1.0
PA B:ANP1396 4.5 13.4 1.0
OG1 B:THR118 4.6 12.2 1.0
O B:HOH2079 4.6 13.3 1.0
CG B:ASP186 4.7 8.0 1.0
CD1 B:TRP384 4.7 12.3 1.0
CA B:GLY188 4.7 10.0 1.0
CG B:ASP49 4.8 11.4 1.0
CA B:GLY51 4.8 9.9 1.0
O2A B:ANP1396 4.9 15.5 1.0

Reference:

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
Page generated: Thu Aug 15 16:31:32 2024

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