Sodium in PDB 3zx0: NTPDASE1 in Complex with Heptamolybdate

All present enzymatic activity of NTPDASE1 in Complex with Heptamolybdate:
3.6.1.5;

The structure of NTPDASE1 in Complex with Heptamolybdate, PDB code: 3zx0 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)	145.73 / 2.50
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	163.807, 80.267, 164.921, 90.00, 117.92, 90.00
R / Rfree (%)	21.3 / 25.7

The structure of NTPDASE1 in Complex with Heptamolybdate also contains other interesting chemical elements:

Molybdenum	(Mo)	28 atoms
Chlorine	(Cl)	22 atoms

The binding sites of Sodium atom in the NTPDASE1 in Complex with Heptamolybdate (pdb code 3zx0). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the NTPDASE1 in Complex with Heptamolybdate, PDB code: 3zx0:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the NTPDASE1 in Complex with Heptamolybdate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of NTPDASE1 in Complex with Heptamolybdate within 5.0Å range: probe atom residue distance (Å) B Occ B:Na521 b:56.9 occ:1.00 O B:GLN426 2.2 86.4 1.0 OD1 B:ASN429 2.5 89.6 1.0 O B:ALA343 2.6 89.0 1.0 O B:CYS342 3.0 95.2 1.0 O B:GLY427 3.2 82.7 1.0 C B:GLN426 3.5 83.6 1.0 CG B:ASN429 3.6 91.5 1.0 C B:ALA343 3.7 87.0 1.0 ND2 B:ASN429 4.0 94.2 1.0 C B:CYS342 4.0 95.5 1.0 C B:GLY427 4.0 78.8 1.0 CA B:GLY427 4.2 78.1 1.0 N B:GLY427 4.3 79.7 1.0 CA B:ALA343 4.3 87.4 1.0 OXT B:ACY512 4.5 61.4 1.0 CA B:GLN426 4.5 82.9 1.0 N B:ALA343 4.6 91.6 1.0 N B:PHE344 4.8 84.2 1.0 CB B:ASN429 4.9 91.7 1.0 N B:ASN429 4.9 83.1 1.0

Sodium binding site 2 out of 4 in the NTPDASE1 in Complex with Heptamolybdate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of NTPDASE1 in Complex with Heptamolybdate within 5.0Å range: probe atom residue distance (Å) B Occ C:Na521 b:58.0 occ:1.00 O C:LEU329 3.0 54.0 1.0 O C:PHE332 3.2 58.6 1.0 C C:LEU329 3.6 54.0 1.0 CB C:LEU329 3.9 53.8 1.0 OD1 C:ASN334 4.1 59.5 1.0 N C:LYS330 4.2 56.5 1.0 CA C:LYS330 4.2 58.3 1.0 CA C:LEU329 4.3 52.1 1.0 C C:PHE332 4.4 56.2 1.0 CB C:ASN334 4.8 58.8 1.0 C C:LYS330 4.9 57.6 1.0 CG C:ASN334 4.9 59.9 1.0 CB C:PHE332 5.0 52.2 1.0 N C:ASN334 5.0 58.5 1.0

Sodium binding site 3 out of 4 in the NTPDASE1 in Complex with Heptamolybdate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of NTPDASE1 in Complex with Heptamolybdate within 5.0Å range: probe atom residue distance (Å) B Occ C:Na522 b:42.6 occ:1.00 O C:ALA343 2.3 41.9 1.0 OD1 C:ASN429 2.4 41.1 1.0 O C:CYS342 2.4 37.6 1.0 O C:GLY427 2.6 40.1 1.0 O C:GLN426 2.6 39.0 1.0 C C:ALA343 3.3 40.5 1.0 CG C:ASN429 3.4 40.0 1.0 C C:CYS342 3.5 38.6 1.0 C C:GLY427 3.6 39.1 1.0 ND2 C:ASN429 3.7 40.1 1.0 C C:GLN426 3.7 40.4 1.0 CA C:ALA343 3.8 38.4 1.0 CA C:GLY427 4.1 39.5 1.0 N C:ALA343 4.1 38.6 1.0 N C:GLY427 4.3 39.3 1.0 N C:ASN429 4.5 39.0 1.0 N C:PHE344 4.5 40.6 1.0 CA C:CYS342 4.7 39.4 1.0 CB C:ASN429 4.7 39.6 1.0 N C:TYR428 4.7 38.3 1.0 ND2 C:ASN334 4.7 53.1 1.0 N C:CYS342 4.9 39.1 1.0 CA C:GLN426 4.9 42.6 1.0 CA C:ASN429 4.9 40.9 1.0 C C:TYR428 5.0 39.3 1.0

Sodium binding site 4 out of 4 in the NTPDASE1 in Complex with Heptamolybdate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of NTPDASE1 in Complex with Heptamolybdate within 5.0Å range: probe atom residue distance (Å) B Occ D:Na521 b:48.0 occ:1.00 O D:CYS342 2.6 55.0 1.0 OD1 D:ASN429 2.6 57.0 1.0 O D:ALA343 2.6 53.4 1.0 O D:GLN426 2.7 58.6 1.0 O D:GLY427 3.2 54.9 1.0 C D:CYS342 3.6 53.3 1.0 CG D:ASN429 3.6 57.4 1.0 C D:ALA343 3.7 50.9 1.0 ND2 D:ASN429 3.9 55.9 1.0 C D:GLN426 3.9 59.1 1.0 CA D:ALA343 4.2 49.9 1.0 C D:GLY427 4.2 53.0 1.0 ND2 D:ASN334 4.3 57.2 1.0 N D:ALA343 4.3 51.3 1.0 CA D:CYS342 4.5 54.5 1.0 CA D:GLY427 4.6 53.4 1.0 N D:GLY427 4.7 56.2 1.0 N D:CYS342 4.7 57.5 1.0 N D:PHE344 4.8 49.2 1.0 CB D:CYS342 4.8 54.6 1.0 CA D:GLN426 4.9 61.9 1.0 CB D:ASN429 5.0 59.4 1.0

M.Zebisch, M.Krauss, P.Schafer, N.Strater. Crystallographic Evidence For A Domain Motion in Rat Nucleoside Triphosphate Diphosphohydrolase (Ntpdase) 1. J. Mol. Biol. V. 415 288 2012.
ISSN: ESSN 1089-8638
PubMed: 22100451
DOI: 10.1016/J.JMB.2011.10.050