Atomistry » Sodium » PDB 3zux-4adj » 3zx2
Atomistry »
  Sodium »
    PDB 3zux-4adj »
      3zx2 »

Sodium in PDB 3zx2: NTPDASE1 in Complex with Decavanadate

Enzymatic activity of NTPDASE1 in Complex with Decavanadate

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

Protein crystallography data

The structure of NTPDASE1 in Complex with Decavanadate, PDB code: 3zx2 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) 146.83 / 1.81
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 162.920, 80.985, 165.517, 90.00, 117.49, 90.00
R / Rfree (%) 17.5 / 22.4

Other elements in 3zx2:

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

Chlorine (Cl) 23 atoms
Vanadium (V) 40 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the NTPDASE1 in Complex with Decavanadate (pdb code 3zx2). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the NTPDASE1 in Complex with Decavanadate, PDB code: 3zx2:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in 3zx2

Go back to Sodium Binding Sites List in 3zx2
Sodium binding site 1 out of 6 in the NTPDASE1 in Complex with Decavanadate


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 Decavanadate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na521

b:59.4
occ:1.00
 O B:GLN426 2.4 57.0 1.0
OD1 B:ASN429 2.5 66.4 1.0
O B:ALA343 2.6 42.3 1.0
O B:GLY427 2.7 45.9 1.0
O B:CYS342 3.5 47.1 1.0
CG B:ASN429 3.5 60.6 1.0
C B:GLY427 3.6 44.9 1.0
C B:GLN426 3.6 51.8 1.0
C B:ALA343 3.7 41.0 1.0
CA B:GLY427 4.0 45.2 1.0
CA B:ALA343 4.0 39.3 1.0
ND2 B:ASN429 4.0 58.8 1.0
O B:HOH2125 4.0 55.9 1.0
OXT B:ACY511 4.1 68.3 1.0
ND2 B:ASN334 4.2 61.7 1.0
N B:GLY427 4.3 48.5 1.0
O B:HOH2101 4.4 57.7 1.0
C B:CYS342 4.4 43.4 1.0
N B:ASN429 4.4 47.6 1.0
N B:TYR428 4.7 44.5 1.0
N B:ALA343 4.7 40.2 1.0
CA B:GLN426 4.8 49.2 1.0
CB B:ASN429 4.8 58.4 1.0
CA B:ASN429 4.8 54.3 1.0
N B:PHE344 4.8 36.3 1.0

Sodium binding site 2 out of 6 in 3zx2

Go back to Sodium Binding Sites List in 3zx2
Sodium binding site 2 out of 6 in the NTPDASE1 in Complex with Decavanadate


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 Decavanadate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na521

b:54.0
occ:1.00
 O C:LEU329 2.4 40.1 1.0
O C:PHE332 2.5 42.2 1.0
O C:HOH2128 2.6 54.2 1.0
O C:HOH2129 2.8 53.6 1.0
O C:HOH2130 2.9 43.9 1.0
C C:LEU329 3.4 40.0 1.0
C C:PHE332 3.6 40.1 1.0
CA C:LYS330 3.9 43.1 1.0
CD C:LYS330 4.0 64.0 1.0
N C:LYS330 4.1 39.8 1.0
N C:PHE332 4.3 39.8 1.0
C C:LYS330 4.3 41.8 1.0
O C:LYS330 4.3 44.1 1.0
CA C:PHE332 4.4 39.9 1.0
CA C:LEU329 4.4 37.7 1.0
ND2 C:ASN334 4.5 40.7 1.0
CB C:LEU329 4.5 37.3 1.0
CB C:PHE332 4.5 37.3 1.0
N C:ASN333 4.6 38.2 1.0
CA C:ASN333 4.6 41.1 1.0
N C:ASN334 4.6 40.8 1.0
O C:HOH2042 4.7 51.3 1.0
CE C:LYS330 4.8 70.3 1.0
O C:HOH2127 5.0 50.1 1.0

Sodium binding site 3 out of 6 in 3zx2

Go back to Sodium Binding Sites List in 3zx2
Sodium binding site 3 out of 6 in the NTPDASE1 in Complex with Decavanadate


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 Decavanadate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na522

b:32.0
occ:1.00
 O C:HOH2147 2.3 31.9 1.0
O C:ALA343 2.5 29.1 1.0
OD1 C:ASN429 2.5 27.4 1.0
O C:GLN426 2.5 28.4 1.0
O C:GLY427 2.5 29.9 1.0
O C:CYS342 2.6 26.2 1.0
C C:GLY427 3.3 28.5 1.0
CG C:ASN429 3.3 28.1 1.0
C C:ALA343 3.4 27.2 1.0
C C:GLN426 3.5 28.8 1.0
CA C:ALA343 3.6 26.7 1.0
C C:CYS342 3.6 28.1 1.0
CA C:GLY427 3.6 28.6 1.0
ND2 C:ASN429 3.6 27.7 1.0
N C:GLY427 4.0 27.8 1.0
N C:ALA343 4.1 26.7 1.0
O C:HOH2146 4.1 29.7 1.0
O C:HOH2175 4.2 29.2 1.0
O C:HOH2176 4.3 51.3 1.0
OD1 C:ASN334 4.4 41.6 1.0
N C:TYR428 4.4 28.6 1.0
N C:ASN429 4.5 26.2 1.0
N C:PHE344 4.6 29.6 1.0
CB C:ASN429 4.7 28.1 1.0
O C:HOH2133 4.7 34.1 1.0
CA C:GLN426 4.8 30.4 1.0
CA C:CYS342 4.8 29.5 1.0
CA C:ASN429 4.9 26.4 1.0
OXT C:ACY511 4.9 35.8 1.0
C C:TYR428 5.0 26.8 1.0
CA C:TYR428 5.0 26.6 1.0

Sodium binding site 4 out of 6 in 3zx2

Go back to Sodium Binding Sites List in 3zx2
Sodium binding site 4 out of 6 in the NTPDASE1 in Complex with Decavanadate


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 Decavanadate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na521

b:38.7
occ:1.00
 O D:GLY427 2.4 37.2 1.0
O D:HOH2192 2.4 41.8 1.0
OD1 D:ASN429 2.4 41.1 1.0
O D:CYS342 2.5 41.5 1.0
O D:ALA343 2.5 36.4 1.0
O D:GLN426 2.6 45.5 1.0
CG D:ASN429 3.2 41.9 1.0
C D:GLY427 3.2 36.8 1.0
C D:ALA343 3.4 34.5 1.0
C D:CYS342 3.5 38.9 1.0
ND2 D:ASN429 3.5 40.3 1.0
CA D:ALA343 3.5 34.1 1.0
C D:GLN426 3.5 43.7 1.0
CA D:GLY427 3.6 37.3 1.0
N D:ALA343 4.0 35.5 1.0
N D:GLY427 4.0 40.6 1.0
O D:HOH2191 4.2 43.5 1.0
O D:HOH2214 4.2 47.6 1.0
N D:TYR428 4.3 38.8 1.0
N D:ASN429 4.4 40.8 1.0
ND2 D:ASN334 4.4 44.0 1.0
O D:HOH2185 4.5 64.8 1.0
CB D:ASN429 4.5 42.7 1.0
O D:HOH2184 4.6 47.3 1.0
N D:PHE344 4.6 33.4 1.0
O D:ACY511 4.8 43.9 1.0
CA D:CYS342 4.8 38.4 1.0
CA D:GLN426 4.8 45.0 1.0
CA D:ASN429 4.8 41.4 1.0
CA D:TYR428 4.8 38.1 1.0
C D:TYR428 4.9 40.1 1.0
CB D:ALA343 4.9 30.1 1.0
N D:CYS342 5.0 39.9 1.0

Sodium binding site 5 out of 6 in 3zx2

Go back to Sodium Binding Sites List in 3zx2
Sodium binding site 5 out of 6 in the NTPDASE1 in Complex with Decavanadate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of NTPDASE1 in Complex with Decavanadate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na522

b:60.1
occ:1.00
 O D:HOH2177 2.3 60.3 1.0
O D:PHE332 2.4 42.0 1.0
O D:HOH2179 2.4 53.0 1.0
O D:LEU329 2.5 41.1 1.0
O D:HOH2180 2.8 49.9 1.0
O D:HOH2178 2.9 62.6 1.0
C D:PHE332 3.5 41.8 1.0
C D:LEU329 3.5 42.1 1.0
OD1 D:ASN334 3.9 46.8 1.0
CA D:PHE332 4.2 40.0 1.0
CB D:PHE332 4.2 36.6 1.0
N D:ASN334 4.2 48.6 1.0
CA D:LYS330 4.2 43.5 1.0
N D:LYS330 4.3 42.0 1.0
O D:HOH2110 4.3 60.9 1.0
N D:PHE332 4.3 39.6 1.0
CB D:LEU329 4.3 40.9 1.0
CA D:LEU329 4.4 40.3 1.0
N D:ASN333 4.4 43.2 1.0
CA D:ASN333 4.5 48.1 1.0
C D:LYS330 4.5 42.2 1.0
O C:HOH2135 4.5 59.9 1.0
CB D:ASN334 4.6 52.4 1.0
CG D:ASN334 4.7 46.7 1.0
O D:LYS330 4.8 41.6 1.0
C D:ASN333 4.8 46.1 1.0
OXT D:ACY511 5.0 40.8 1.0

Sodium binding site 6 out of 6 in 3zx2

Go back to Sodium Binding Sites List in 3zx2
Sodium binding site 6 out of 6 in the NTPDASE1 in Complex with Decavanadate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of NTPDASE1 in Complex with Decavanadate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na523

b:63.6
occ:1.00
 O D:HOH2124 2.2 46.3 1.0
O D:HOH2006 2.2 33.0 1.0
O D:HOH2133 2.4 42.1 1.0
O D:HOH2007 2.5 42.4 1.0
O D:HOH2125 3.8 27.4 1.0
CL D:CL501 4.0 47.5 1.0
OE2 D:GLU174 4.0 32.4 1.0
OG1 D:THR131 4.2 26.9 1.0
O D:HOH2012 4.2 25.3 1.0
CA D:GLY214 4.3 27.6 1.0
OD1 D:ASP54 4.4 29.0 1.0
O D:HOH2086 4.4 28.4 1.0
OD2 D:ASP54 4.5 29.9 1.0
O D:HOH2005 4.5 38.4 1.0
NE1 D:TRP451 4.6 25.9 1.0
O D:HOH2132 4.6 39.6 1.0
OD2 D:ASP212 4.7 38.1 1.0
OD1 D:ASP212 4.8 39.3 1.0
CA D:GLY56 4.8 27.9 1.0
CG D:ASP54 4.9 27.8 1.0
N D:GLY214 5.0 28.7 1.0

Reference:

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: ISSN 0022-2836
PubMed: 22100451
DOI: 10.1016/J.JMB.2011.10.050
Page generated: Mon Oct 7 14:14:16 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy