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Magnesium in PDB 4brl: Legionella Pneumophila NTPDASE1 Crystal Form III (Closed) in Complex with Transition State Mimic Guanosine 5'-Phosphovanadate

Enzymatic activity of Legionella Pneumophila NTPDASE1 Crystal Form III (Closed) in Complex with Transition State Mimic Guanosine 5'-Phosphovanadate

All present enzymatic activity of Legionella Pneumophila NTPDASE1 Crystal Form III (Closed) in Complex with Transition State Mimic Guanosine 5'-Phosphovanadate:
3.6.1.5;

Protein crystallography data

The structure of Legionella Pneumophila NTPDASE1 Crystal Form III (Closed) in Complex with Transition State Mimic Guanosine 5'-Phosphovanadate, PDB code: 4brl 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) 19.88 / 1.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 80.994, 83.463, 109.289, 90.00, 90.00, 90.00
R / Rfree (%) 14.416 / 19.773

Other elements in 4brl:

The structure of Legionella Pneumophila NTPDASE1 Crystal Form III (Closed) in Complex with Transition State Mimic Guanosine 5'-Phosphovanadate also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms
Vanadium (V) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Legionella Pneumophila NTPDASE1 Crystal Form III (Closed) in Complex with Transition State Mimic Guanosine 5'-Phosphovanadate (pdb code 4brl). 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 III (Closed) in Complex with Transition State Mimic Guanosine 5'-Phosphovanadate, PDB code: 4brl:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 4brl

Go back to Magnesium Binding Sites List in 4brl
Magnesium binding site 1 out of 2 in the Legionella Pneumophila NTPDASE1 Crystal Form III (Closed) in Complex with Transition State Mimic Guanosine 5'-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 III (Closed) in Complex with Transition State Mimic Guanosine 5'-Phosphovanadate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1396

b:16.1
occ:1.00
O3B A:GMV1395 2.0 15.6 1.0
O2A A:GMV1395 2.1 14.7 1.0
O A:HOH2117 2.1 15.6 1.0
O A:HOH2007 2.1 15.1 1.0
O A:HOH2105 2.1 14.7 1.0
O A:HOH2006 2.2 13.9 1.0
PA A:GMV1395 3.3 15.4 1.0
VB A:GMV1395 3.6 16.6 1.0
O3A A:GMV1395 3.7 16.1 1.0
O A:HOH2017 3.9 36.3 1.0
O5' A:GMV1395 3.9 15.4 1.0
O A:HOH2118 4.0 21.0 1.0
OE2 A:GLU159 4.0 15.0 1.0
NH1 A:ARG56 4.0 17.9 1.0
OD2 A:ASP49 4.1 18.9 1.0
NE1 A:TRP384 4.1 17.6 1.0
O A:HOH2106 4.1 15.9 1.0
OD1 A:ASP186 4.2 17.4 1.0
OD2 A:ASP186 4.3 15.7 1.0
OD1 A:ASP49 4.3 15.0 1.0
O2B A:GMV1395 4.4 19.9 1.0
O4B A:GMV1395 4.4 15.9 1.0
C5' A:GMV1395 4.5 23.2 1.0
O1A A:GMV1395 4.5 18.6 1.0
CD1 A:TRP384 4.5 16.2 1.0
OG1 A:THR118 4.6 20.3 1.0
CG A:ASP49 4.7 17.1 1.0
CG A:ASP186 4.7 13.8 1.0
CA A:GLY188 4.8 13.4 1.0

Magnesium binding site 2 out of 2 in 4brl

Go back to Magnesium Binding Sites List in 4brl
Magnesium binding site 2 out of 2 in the Legionella Pneumophila NTPDASE1 Crystal Form III (Closed) in Complex with Transition State Mimic Guanosine 5'-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 III (Closed) in Complex with Transition State Mimic Guanosine 5'-Phosphovanadate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1397

b:17.5
occ:1.00
O3B B:GMV1396 2.0 19.2 1.0
O2A B:GMV1396 2.1 19.0 1.0
O B:HOH2091 2.1 17.0 1.0
O B:HOH2005 2.1 16.9 1.0
O B:HOH2004 2.2 15.7 1.0
O B:HOH2105 2.2 18.1 1.0
PA B:GMV1396 3.3 18.0 1.0
VB B:GMV1396 3.6 19.0 1.0
O3A B:GMV1396 3.7 18.8 1.0
OE2 B:GLU159 3.9 16.7 1.0
NH1 B:ARG56 4.0 19.4 1.0
O5' B:GMV1396 4.0 19.6 1.0
O B:HOH2090 4.0 19.3 1.0
O B:HOH2106 4.1 21.3 1.0
NE1 B:TRP384 4.1 15.8 1.0
OD2 B:ASP49 4.2 18.5 1.0
OD1 B:ASP186 4.3 19.2 1.0
OD2 B:ASP186 4.3 16.1 1.0
O2B B:GMV1396 4.3 23.4 1.0
O4B B:GMV1396 4.4 20.6 1.0
OD1 B:ASP49 4.4 19.0 1.0
C5' B:GMV1396 4.5 27.4 0.5
OG1 B:THR118 4.5 21.3 1.0
CD1 B:TRP384 4.5 15.7 1.0
O1A B:GMV1396 4.5 22.6 1.0
C5' B:GMV1396 4.6 24.5 0.5
CG B:ASP186 4.7 17.1 1.0
CG B:ASP49 4.8 17.7 1.0
CA B:GLY188 4.8 14.0 1.0
O1B B:GMV1396 4.9 17.3 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 09:12:34 2020

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