Atomistry » Sodium » PDB 4blw-4c44 » 4bvo
Atomistry »
  Sodium »
    PDB 4blw-4c44 »
      4bvo »

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

Last articles

Zn in 7OQY
Zn in 7PEL
Zn in 7OYG
Zn in 7P3S
Zn in 7PE7
Zn in 7RZC
Zn in 7PE9
Zn in 7PE8
Zn in 7RAG
Zn in 7RN5
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy