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Sodium in PDB 4brg: Legionella Pneumophila NTPDASE1 Crystal Form II (Closed) in Complex with Mg Gmppnp

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

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

Protein crystallography data

The structure of Legionella Pneumophila NTPDASE1 Crystal Form II (Closed) in Complex with Mg Gmppnp, PDB code: 4brg 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) 28.99 / 1.45
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 62.186, 86.166, 71.878, 90.00, 107.02, 90.00
R / Rfree (%) 12.371 / 17.444

Other elements in 4brg:

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

Magnesium (Mg) 2 atoms
Chlorine (Cl) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Legionella Pneumophila NTPDASE1 Crystal Form II (Closed) in Complex with Mg Gmppnp (pdb code 4brg). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Legionella Pneumophila NTPDASE1 Crystal Form II (Closed) in Complex with Mg Gmppnp, PDB code: 4brg:

Sodium binding site 1 out of 1 in 4brg

Go back to Sodium Binding Sites List in 4brg
Sodium binding site 1 out of 1 in the Legionella Pneumophila NTPDASE1 Crystal Form II (Closed) in Complex with Mg Gmppnp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Legionella Pneumophila NTPDASE1 Crystal Form II (Closed) in Complex with Mg Gmppnp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1396

b:38.6
occ:1.00
 OE1 A:GLU233 2.4 19.4 1.0
OE1 B:GLU233 2.5 24.0 1.0
O A:HOH2202 2.6 16.2 1.0
ND1 A:HIS236 3.3 14.9 1.0
CD A:GLU233 3.3 16.5 1.0
CD B:GLU233 3.5 19.6 1.0
ND1 B:HIS236 3.5 14.6 1.0
O A:GLU233 3.6 12.5 1.0
O A:HOH2204 3.9 47.6 1.0
OE2 A:GLU233 3.9 26.8 1.0
CA A:GLU233 3.9 12.0 1.0
O B:GLU233 3.9 12.7 1.0
CB A:HIS236 4.0 10.7 1.0
OE2 B:GLU233 4.0 24.6 1.0
CG A:HIS236 4.0 11.1 1.0
CB B:HIS236 4.0 10.7 1.0
CB A:GLU233 4.1 13.1 1.0
CA B:GLU233 4.1 12.1 1.0
C A:GLU233 4.1 10.7 1.0
CG B:HIS236 4.2 9.5 1.0
CB B:GLU233 4.3 15.2 1.0
CE1 A:HIS236 4.3 18.3 1.0
CG A:GLU233 4.4 15.7 1.0
CG B:GLU233 4.5 16.4 1.0
CE1 B:HIS236 4.5 17.0 1.0
C B:GLU233 4.5 11.5 1.0
NE2 B:GLN237 4.9 10.7 1.0
NE2 A:GLN237 4.9 11.1 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 Oct 7 14:33:56 2024

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