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Magnesium in PDB 4bre: Legionella Pneumophila NTPDASE1 Crystal Form II (Closed) in Complex with Transition State Mimic Adenosine 5' Phosphovanadate

Protein crystallography data

The structure of Legionella Pneumophila NTPDASE1 Crystal Form II (Closed) in Complex with Transition State Mimic Adenosine 5' Phosphovanadate, PDB code: 4bre 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) 29.33 / 1.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 62.681, 86.203, 70.879, 90.00, 105.94, 90.00
R / Rfree (%) 17.211 / 20.809

Other elements in 4bre:

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

Vanadium (V) 2 atoms
Sodium (Na) 1 atom

Magnesium Binding Sites:

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

Magnesium binding site 1 out of 2 in 4bre

Go back to Magnesium Binding Sites List in 4bre
Magnesium binding site 1 out of 2 in the Legionella Pneumophila NTPDASE1 Crystal Form II (Closed) in Complex with Transition State Mimic Adenosine 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 II (Closed) in Complex with Transition State Mimic Adenosine 5' Phosphovanadate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1397

b:16.4
occ:1.00
O2A A:50T1396 1.9 17.6 1.0
O4B A:50T1396 2.0 15.0 1.0
O A:HOH2240 2.1 15.7 1.0
O A:HOH2241 2.2 15.7 1.0
O A:HOH2242 2.2 15.6 1.0
O A:HOH2239 2.2 15.9 1.0
PA A:50T1396 3.3 17.7 1.0
O3A A:50T1396 3.5 18.1 1.0
VB A:50T1396 3.6 17.0 1.0
O5' A:50T1396 3.8 18.5 1.0
O A:HOH2090 3.9 24.6 1.0
NH1 A:ARG56 3.9 5.0 1.0
OE2 A:GLU159 4.0 5.1 1.0
O A:HOH2015 4.0 36.3 1.0
OD2 A:ASP49 4.1 7.3 1.0
NE1 A:TRP384 4.1 8.4 1.0
O A:HOH2077 4.2 18.2 1.0
OD1 A:ASP186 4.3 5.9 1.0
OD1 A:ASP49 4.3 6.7 1.0
OD2 A:ASP186 4.4 5.2 1.0
O3B A:50T1396 4.4 18.9 1.0
O2B A:50T1396 4.4 19.1 1.0
O1A A:50T1396 4.5 17.8 1.0
OG1 A:THR118 4.5 5.7 1.0
CD1 A:TRP384 4.6 7.8 1.0
C5' A:50T1396 4.6 19.3 1.0
CG A:ASP49 4.7 6.6 1.0
CA A:GLY188 4.8 4.8 1.0
CG A:ASP186 4.8 5.8 1.0
CA A:GLY51 4.9 4.0 1.0

Magnesium binding site 2 out of 2 in 4bre

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

b:15.5
occ:1.00
O3B B:50T1395 2.0 15.2 1.0
O2A B:50T1395 2.1 17.3 1.0
O B:HOH2235 2.1 13.5 1.0
O B:HOH2236 2.1 15.2 1.0
O B:HOH2234 2.1 14.5 1.0
O B:HOH2237 2.2 15.3 1.0
PA B:50T1395 3.3 15.3 1.0
VB B:50T1395 3.6 16.3 1.0
O3A B:50T1395 3.7 14.8 1.0
OE2 B:GLU159 3.9 6.2 1.0
O5' B:50T1395 3.9 16.9 0.6
O B:HOH2101 4.0 29.6 1.0
O5' B:50T1395 4.0 16.0 0.4
NH1 B:ARG56 4.0 6.3 1.0
NE1 B:TRP384 4.0 6.8 1.0
O B:HOH2015 4.1 32.1 1.0
OD2 B:ASP49 4.1 9.1 1.0
O B:HOH2092 4.2 16.4 1.0
OD2 B:ASP186 4.3 6.3 1.0
OD1 B:ASP186 4.3 7.1 1.0
OD1 B:ASP49 4.4 7.9 1.0
O4B B:50T1395 4.4 16.2 1.0
O2B B:50T1395 4.4 16.7 1.0
OG1 B:THR118 4.5 6.3 1.0
CD1 B:TRP384 4.5 6.6 1.0
O1A B:50T1395 4.6 16.4 1.0
C5' B:50T1395 4.6 18.2 0.6
CG B:ASP49 4.7 7.6 1.0
CG B:ASP186 4.7 6.7 1.0
C5' B:50T1395 4.7 16.8 0.4
CA B:GLY188 4.8 4.3 1.0
CA B:GLY51 5.0 4.9 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 09:12:23 2020

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