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Sodium in PDB 4brf: Legionella Pneumophila NTPDASE1 Crystal Form II (Closed) in Complex with A Distorted Orthomolybdate Ion and Amp

Enzymatic activity of Legionella Pneumophila NTPDASE1 Crystal Form II (Closed) in Complex with A Distorted Orthomolybdate Ion and Amp

All present enzymatic activity of Legionella Pneumophila NTPDASE1 Crystal Form II (Closed) in Complex with A Distorted Orthomolybdate Ion and Amp:
3.6.1.5;

Protein crystallography data

The structure of Legionella Pneumophila NTPDASE1 Crystal Form II (Closed) in Complex with A Distorted Orthomolybdate Ion and Amp, PDB code: 4brf 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) 29.87 / 1.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 62.144, 85.970, 71.888, 90.00, 106.14, 90.00
R / Rfree (%) 12.546 / 18.43

Other elements in 4brf:

The structure of Legionella Pneumophila NTPDASE1 Crystal Form II (Closed) in Complex with A Distorted Orthomolybdate Ion and Amp also contains other interesting chemical elements:

Molybdenum (Mo) 4 atoms
Magnesium (Mg) 6 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 A Distorted Orthomolybdate Ion and Amp (pdb code 4brf). 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 A Distorted Orthomolybdate Ion and Amp, PDB code: 4brf:

Sodium binding site 1 out of 1 in 4brf

Go back to Sodium Binding Sites List in 4brf
Sodium binding site 1 out of 1 in the Legionella Pneumophila NTPDASE1 Crystal Form II (Closed) in Complex with A Distorted Orthomolybdate Ion and Amp


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 A Distorted Orthomolybdate Ion and Amp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1398

b:35.2
occ:1.00
 O A:HOH2164 2.4 16.2 1.0
OE1 A:GLU233 2.4 22.5 1.0
OE1 B:GLU233 2.5 23.1 1.0
CD A:GLU233 3.4 19.2 1.0
CD B:GLU233 3.4 16.6 1.0
ND1 B:HIS236 3.5 14.9 1.0
ND1 A:HIS236 3.6 13.2 1.0
O A:GLU233 3.7 13.3 1.0
CA A:GLU233 3.7 11.4 1.0
O B:GLU233 3.7 12.3 1.0
O A:HOH2165 3.8 32.5 1.0
CA B:GLU233 3.8 12.2 1.0
CB A:GLU233 3.9 13.6 1.0
CB B:HIS236 3.9 11.6 1.0
CB A:HIS236 4.0 9.6 1.0
CB B:GLU233 4.0 15.0 1.0
OE2 A:GLU233 4.1 24.2 1.0
CG B:HIS236 4.1 11.9 1.0
OE2 B:GLU233 4.1 21.6 1.0
C A:GLU233 4.1 11.8 1.0
CG A:HIS236 4.2 11.4 1.0
C B:GLU233 4.2 9.7 1.0
CG A:GLU233 4.3 18.3 1.0
CG B:GLU233 4.3 15.0 1.0
CE1 B:HIS236 4.5 15.6 1.0
CE1 A:HIS236 4.7 13.4 1.0
NE2 B:GLN237 4.7 11.7 1.0
NE2 A:GLN237 4.7 12.9 1.0
N A:GLU233 5.0 11.0 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 06:34:48 2020

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