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Magnesium in PDB 4brq: Legionella Pneumophila NTPDASE1 Crystal Form II, Closed, in Complex with Two Phosphates Bound to Active Site Mg and Product Amp

Enzymatic activity of Legionella Pneumophila NTPDASE1 Crystal Form II, Closed, in Complex with Two Phosphates Bound to Active Site Mg and Product Amp

All present enzymatic activity of Legionella Pneumophila NTPDASE1 Crystal Form II, Closed, in Complex with Two Phosphates Bound to Active Site Mg and Product Amp:
3.6.1.5;

Protein crystallography data

The structure of Legionella Pneumophila NTPDASE1 Crystal Form II, Closed, in Complex with Two Phosphates Bound to Active Site Mg and Product Amp, PDB code: 4brq 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) 29.14 / 1.45
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 62.737, 85.497, 70.336, 90.00, 106.20, 90.00
R / Rfree (%) 13.875 / 18.711

Other elements in 4brq:

The structure of Legionella Pneumophila NTPDASE1 Crystal Form II, Closed, in Complex with Two Phosphates Bound to Active Site Mg and Product Amp also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Legionella Pneumophila NTPDASE1 Crystal Form II, Closed, in Complex with Two Phosphates Bound to Active Site Mg and Product Amp (pdb code 4brq). 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 II, Closed, in Complex with Two Phosphates Bound to Active Site Mg and Product Amp, PDB code: 4brq:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 4brq

Go back to Magnesium Binding Sites List in 4brq
Magnesium binding site 1 out of 3 in the Legionella Pneumophila NTPDASE1 Crystal Form II, Closed, in Complex with Two Phosphates Bound to Active Site Mg and Product 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 II, Closed, in Complex with Two Phosphates Bound to Active Site Mg and Product Amp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1401

b:9.1
occ:1.00
 O4 A:PO41399 2.0 9.0 0.9
O3 A:PO41398 2.1 10.0 0.9
O A:HOH2134 2.1 8.3 1.0
O A:HOH2004 2.1 9.0 1.0
O A:HOH2144 2.1 9.1 1.0
O A:HOH2005 2.1 10.0 1.0
P A:PO41398 3.3 11.5 0.9
P A:PO41399 3.5 11.6 0.9
O1 A:PO41398 3.6 10.8 0.9
O3 A:PO41399 3.9 12.1 0.9
OE2 A:GLU159 4.0 9.4 1.0
NH1 A:ARG56 4.0 12.9 1.0
O A:HOH2145 4.0 11.2 1.0
O A:HOH2338 4.1 16.6 1.0
O4 A:PO41398 4.1 13.1 0.9
NE1 A:TRP384 4.1 11.1 1.0
OD2 A:ASP49 4.1 10.7 1.0
O A:HOH2019 4.2 22.2 1.0
O2 A:PO41399 4.2 10.9 0.9
OD2 A:ASP186 4.3 9.9 1.0
OD1 A:ASP49 4.3 10.7 1.0
OD1 A:ASP186 4.4 10.0 1.0
OG1 A:THR118 4.4 10.1 1.0
O2 A:PO41398 4.5 11.6 0.9
CD1 A:TRP384 4.5 11.4 1.0
O1 A:PO41399 4.6 8.7 0.9
CA A:GLY188 4.6 8.9 1.0
CG A:ASP49 4.7 9.2 1.0
CA A:GLY51 4.7 10.1 1.0
CG A:ASP186 4.8 8.8 1.0

Magnesium binding site 2 out of 3 in 4brq

Go back to Magnesium Binding Sites List in 4brq
Magnesium binding site 2 out of 3 in the Legionella Pneumophila NTPDASE1 Crystal Form II, Closed, in Complex with Two Phosphates Bound to Active Site Mg and Product 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 II, Closed, in Complex with Two Phosphates Bound to Active Site Mg and Product Amp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1402

b:27.8
occ:1.00
 O A:HOH2339 2.0 32.7 1.0
O A:HOH2340 2.0 36.7 1.0
O A:HOH2341 2.0 32.1 1.0
O A:HOH2123 2.1 25.4 1.0
O A:HOH2122 2.4 37.9 1.0
O A:VAL149 4.1 19.2 1.0
O A:HOH2125 4.2 32.5 1.0
O A:LEU148 4.6 30.9 1.0

Magnesium binding site 3 out of 3 in 4brq

Go back to Magnesium Binding Sites List in 4brq
Magnesium binding site 3 out of 3 in the Legionella Pneumophila NTPDASE1 Crystal Form II, Closed, in Complex with Two Phosphates Bound to Active Site Mg and Product 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 II, Closed, in Complex with Two Phosphates Bound to Active Site Mg and Product Amp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1400

b:8.1
occ:1.00
 O B:HOH2123 2.0 8.1 1.0
O3 B:PO41398 2.0 8.6 0.9
O B:HOH2006 2.1 8.7 1.0
O B:HOH2134 2.1 8.6 1.0
O2 B:PO41399 2.1 11.4 0.9
O B:HOH2007 2.1 9.6 1.0
P B:PO41398 3.3 11.3 0.9
P B:PO41399 3.5 11.2 0.9
O4 B:PO41398 3.6 11.5 0.9
O1 B:PO41399 3.9 11.8 0.9
NH1 B:ARG56 4.0 12.0 1.0
O B:HOH2135 4.1 11.4 1.0
OE2 B:GLU159 4.1 8.3 1.0
O B:HOH2287 4.1 16.1 1.0
O1 B:PO41398 4.1 12.5 0.9
O B:HOH2021 4.1 20.9 1.0
NE1 B:TRP384 4.1 8.6 1.0
OD2 B:ASP49 4.2 10.8 1.0
OD1 B:ASP49 4.3 8.9 1.0
O4 B:PO41399 4.3 9.4 0.9
OD2 B:ASP186 4.3 9.4 1.0
OD1 B:ASP186 4.4 9.5 1.0
OG1 B:THR118 4.5 9.9 1.0
CD1 B:TRP384 4.5 9.3 1.0
O2 B:PO41398 4.5 10.9 0.9
O3 B:PO41399 4.6 7.6 0.9
CA B:GLY188 4.6 9.0 1.0
CG B:ASP49 4.7 8.0 1.0
CA B:GLY51 4.7 9.3 1.0
CG B:ASP186 4.8 8.1 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: Mon Dec 14 09:12:38 2020

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