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Sodium 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:

Magnesium (Mg) 2 atoms
Vanadium (V) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium 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 Sodium atom.
In total only one binding site of Sodium was determined in the Legionella Pneumophila NTPDASE1 Crystal Form II (Closed) in Complex with Transition State Mimic Adenosine 5' Phosphovanadate, PDB code: 4bre:

Sodium binding site 1 out of 1 in 4bre

Go back to Sodium Binding Sites List in 4bre
Sodium binding site 1 out of 1 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 Sodium with other atoms in the Na 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:Na1395

b:37.4
occ:1.00
OE1 A:GLU233 2.3 13.7 1.0
OE1 B:GLU233 2.4 13.6 1.0
O A:HOH2114 2.6 22.8 1.0
CD A:GLU233 3.3 12.1 1.0
CD B:GLU233 3.4 11.6 1.0
ND1 A:HIS236 3.6 6.3 1.0
ND1 B:HIS236 3.6 7.5 1.0
O A:GLU233 3.7 9.1 1.0
CA A:GLU233 3.8 7.9 1.0
O B:GLU233 3.8 5.9 1.0
CA B:GLU233 3.8 6.8 1.0
OE2 A:GLU233 4.0 13.7 1.0
CB A:HIS236 4.0 5.5 1.0
CB A:GLU233 4.0 8.3 1.0
CB B:GLU233 4.0 7.6 1.0
OE2 B:GLU233 4.0 13.3 1.0
CB B:HIS236 4.1 6.7 1.0
C A:GLU233 4.2 7.2 1.0
CG A:HIS236 4.2 5.9 1.0
CG A:GLU233 4.2 10.1 1.0
CG B:HIS236 4.2 6.9 1.0
CG B:GLU233 4.3 9.2 1.0
C B:GLU233 4.3 6.5 1.0
O A:HOH2119 4.5 38.7 1.0
CE1 A:HIS236 4.6 6.2 1.0
CE1 B:HIS236 4.6 8.4 1.0
O A:HOH2115 4.7 35.2 1.0
NE2 B:GLN237 4.9 5.6 1.0
N A:GLU233 5.0 8.0 1.0
NE2 A:GLN237 5.0 5.1 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: Tue Dec 15 06:34:46 2020

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