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Magnesium in PDB 4brh: Legionella Pneumophila NTPDASE1 Crystal Form II (Closed) in Complex with Mg and Thiamine Phosphovanadate

Enzymatic activity of Legionella Pneumophila NTPDASE1 Crystal Form II (Closed) in Complex with Mg and Thiamine Phosphovanadate

All present enzymatic activity of Legionella Pneumophila NTPDASE1 Crystal Form II (Closed) in Complex with Mg and Thiamine Phosphovanadate:
3.6.1.5;

Protein crystallography data

The structure of Legionella Pneumophila NTPDASE1 Crystal Form II (Closed) in Complex with Mg and Thiamine Phosphovanadate, PDB code: 4brh 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) 29.04 / 1.69
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 62.435, 85.759, 72.306, 90.00, 106.44, 90.00
R / Rfree (%) 15.9 / 19.2

Other elements in 4brh:

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

Chlorine (Cl) 2 atoms
Vanadium (V) 22 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Legionella Pneumophila NTPDASE1 Crystal Form II (Closed) in Complex with Mg and Thiamine Phosphovanadate (pdb code 4brh). 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 Crystal Form II (Closed) in Complex with Mg and Thiamine Phosphovanadate, PDB code: 4brh:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 4brh

Go back to Magnesium Binding Sites List in 4brh
Magnesium binding site 1 out of 2 in the Legionella Pneumophila NTPDASE1 Crystal Form II (Closed) in Complex with Mg and Thiamine Phosphovanadate


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 Mg and Thiamine Phosphovanadate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1396

b:10.9
occ:1.00
O1B A:TMV1395 2.0 9.9 1.0
O A:HOH2008 2.0 10.0 1.0
O1A A:TMV1395 2.0 11.4 1.0
O A:HOH2109 2.1 8.6 1.0
O A:HOH2007 2.1 8.4 1.0
O A:HOH2117 2.1 11.2 1.0
PA A:TMV1395 3.3 10.9 1.0
VB A:TMV1395 3.6 10.5 1.0
O3A A:TMV1395 3.7 10.7 1.0
OE2 A:GLU159 3.9 11.2 1.0
O A:HOH2118 3.9 24.5 1.0
O7 A:TMV1395 3.9 11.2 0.3
O7 A:TMV1395 3.9 12.6 0.7
NH1 A:ARG56 4.0 14.1 1.0
NE1 A:TRP384 4.1 13.3 1.0
C7 A:TMV1395 4.1 11.6 0.3
OD2 A:ASP49 4.2 14.4 1.0
O A:HOH2108 4.2 9.9 1.0
OD1 A:ASP49 4.3 12.4 1.0
OD1 A:ASP186 4.3 10.3 1.0
OD2 A:ASP186 4.3 11.1 1.0
C7 A:TMV1395 4.3 15.0 0.7
O4B A:TMV1395 4.3 11.6 1.0
O3B A:TMV1395 4.4 12.1 1.0
OG1 A:THR118 4.5 10.4 1.0
O2A A:TMV1395 4.5 10.9 1.0
CD1 A:TRP384 4.6 13.4 1.0
CG A:ASP49 4.7 13.0 1.0
CG A:ASP186 4.8 10.6 1.0
CA A:GLY188 4.8 9.2 1.0
CA A:GLY51 5.0 11.0 1.0

Magnesium binding site 2 out of 2 in 4brh

Go back to Magnesium Binding Sites List in 4brh
Magnesium binding site 2 out of 2 in the Legionella Pneumophila NTPDASE1 Crystal Form II (Closed) in Complex with Mg and Thiamine Phosphovanadate


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 Mg and Thiamine Phosphovanadate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1396

b:10.6
occ:1.00
O1B B:TMV1395 2.0 9.8 1.0
O1A B:TMV1395 2.0 9.9 1.0
O B:HOH2093 2.1 9.7 1.0
O B:HOH2006 2.1 9.8 1.0
O B:HOH2098 2.1 10.3 1.0
O B:HOH2005 2.2 9.8 1.0
PA B:TMV1395 3.3 10.5 1.0
VB B:TMV1395 3.6 10.0 1.0
O3A B:TMV1395 3.7 10.8 1.0
O7 B:TMV1395 3.8 11.1 1.0
O B:HOH2099 3.9 22.2 1.0
NH1 B:ARG56 3.9 11.2 1.0
OE2 B:GLU159 3.9 10.9 1.0
NE1 B:TRP384 4.1 10.4 1.0
O B:HOH2008 4.1 23.0 1.0
C7 B:TMV1395 4.1 12.7 1.0
O B:HOH2092 4.2 10.3 1.0
OD2 B:ASP49 4.2 14.1 1.0
OD1 B:ASP186 4.2 10.3 1.0
OD1 B:ASP49 4.3 10.8 1.0
OD2 B:ASP186 4.3 11.1 1.0
O3B B:TMV1395 4.3 11.1 1.0
O4B B:TMV1395 4.4 11.6 1.0
OG1 B:THR118 4.5 10.2 1.0
CD1 B:TRP384 4.5 10.7 1.0
O2A B:TMV1395 4.5 9.9 1.0
CG B:ASP49 4.7 11.4 1.0
CG B:ASP186 4.7 10.0 1.0
CA B:GLY188 4.9 8.8 1.0
CA B:GLY51 4.9 9.9 1.0
O2B B:TMV1395 5.0 10.5 1.0

Reference:

M.Zebisch, M.Krauss, P.Schafer, P.Lauble, N.Strater. Crystallographic Snapshots Along the Reaction Pathway of Nucleoside Triphosphate Diphosphohydrolases. Structure V. 21 1460 2013.
ISSN: ISSN 1878-4186
PubMed: 23830739
DOI: 10.1016/J.STR.2013.05.016
Page generated: Mon Dec 14 09:12:27 2020

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