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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

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