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Sodium in PDB 4bvo: Legionella Pneumophila NTPDASE1 Crystal Form VI (Part-Open) in Complex with Polytungstate Pom-1

Enzymatic activity of Legionella Pneumophila NTPDASE1 Crystal Form VI (Part-Open) in Complex with Polytungstate Pom-1

All present enzymatic activity of Legionella Pneumophila NTPDASE1 Crystal Form VI (Part-Open) in Complex with Polytungstate Pom-1:
3.6.1.5;

Protein crystallography data

The structure of Legionella Pneumophila NTPDASE1 Crystal Form VI (Part-Open) in Complex with Polytungstate Pom-1, PDB code: 4bvo was solved by M.Zebisch, P.Schaefer, N.Straeter, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 124.44 / 1.70
Space group P 63 2 2
Cell size a, b, c (Å), α, β, γ (°) 143.692, 143.692, 75.166, 90.00, 90.00, 120.00
R / Rfree (%) 14.907 / 19.757

Other elements in 4bvo:

The structure of Legionella Pneumophila NTPDASE1 Crystal Form VI (Part-Open) in Complex with Polytungstate Pom-1 also contains other interesting chemical elements:

Tungsten (W) 12 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Legionella Pneumophila NTPDASE1 Crystal Form VI (Part-Open) in Complex with Polytungstate Pom-1 (pdb code 4bvo). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Legionella Pneumophila NTPDASE1 Crystal Form VI (Part-Open) in Complex with Polytungstate Pom-1, PDB code: 4bvo:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 4bvo

Go back to Sodium Binding Sites List in 4bvo
Sodium binding site 1 out of 2 in the Legionella Pneumophila NTPDASE1 Crystal Form VI (Part-Open) in Complex with Polytungstate Pom-1


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 VI (Part-Open) in Complex with Polytungstate Pom-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1396

b:30.7
occ:1.00
O A:HOH2061 2.1 41.1 1.0
O A:GLN143 2.4 47.5 1.0
O A:TRP146 2.6 32.1 1.0
O A:PHE140 2.6 23.2 1.0
O A:HOH2062 2.6 46.8 1.0
O A:HOH2060 2.6 32.3 1.0
C A:GLN143 3.6 37.1 1.0
C A:PHE140 3.6 21.1 1.0
C A:TRP146 3.7 28.8 1.0
O A:ARG141 4.0 26.0 1.0
CA A:ARG141 4.2 23.8 1.0
C A:ARG141 4.2 25.5 1.0
CA A:GLN147 4.3 27.4 1.0
N A:ARG141 4.3 21.7 1.0
N A:GLN143 4.4 29.7 1.0
CA A:GLN143 4.4 29.9 1.0
N A:GLN147 4.5 24.4 1.0
N A:SER144 4.5 37.4 1.0
CA A:SER144 4.6 41.4 1.0
CB A:GLN143 4.6 34.4 1.0
N A:TRP146 4.6 29.5 1.0
N A:LEU148 4.6 20.5 1.0
CA A:PHE140 4.7 21.4 1.0
CA A:TRP146 4.7 27.5 1.0
CB A:PHE140 4.9 20.4 1.0
C A:SER144 4.9 43.9 1.0

Sodium binding site 2 out of 2 in 4bvo

Go back to Sodium Binding Sites List in 4bvo
Sodium binding site 2 out of 2 in the Legionella Pneumophila NTPDASE1 Crystal Form VI (Part-Open) in Complex with Polytungstate Pom-1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Legionella Pneumophila NTPDASE1 Crystal Form VI (Part-Open) in Complex with Polytungstate Pom-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1397

b:46.5
occ:0.50
OE1 A:GLU233 2.3 29.1 1.0
O A:HOH2116 2.5 12.7 0.5
CD A:GLU233 3.2 21.1 1.0
ND1 A:HIS236 3.4 16.4 1.0
OE2 A:GLU233 3.7 27.0 1.0
O A:GLU233 3.7 14.5 1.0
O A:HOH2117 3.7 33.0 0.5
CA A:GLU233 4.0 13.8 1.0
CB A:HIS236 4.0 13.2 1.0
CB A:GLU233 4.1 17.0 1.0
CG A:HIS236 4.1 13.8 1.0
CG A:GLU233 4.3 18.8 1.0
C A:GLU233 4.3 13.0 1.0
CE1 A:HIS236 4.4 18.2 1.0
NE2 A:GLN237 4.9 11.3 1.0

Reference:

M.Zebisch, M.Krauss, P.Schafer, N.Strater. Structures of Legionella Pneumophila NTPDASE1 in Complex with Polyoxometallates. Acta Crystallogr.,Sect.D V. 70 1147 2014.
ISSN: ISSN 0907-4449
PubMed: 24699658
DOI: 10.1107/S1399004714001916
Page generated: Tue Dec 15 06:34:54 2020

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