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Vanadium 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
Sodium (Na) 6 atoms

Vanadium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40;

Binding sites:

The binding sites of Vanadium atom in the NTPDASE1 in Complex with Decavanadate (pdb code 3zx2). This binding sites where shown within 5.0 Angstroms radius around Vanadium atom.
In total 40 binding sites of Vanadium where determined in the NTPDASE1 in Complex with Decavanadate, PDB code: 3zx2:
Jump to Vanadium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Vanadium binding site 1 out of 40 in 3zx2

Go back to Vanadium Binding Sites List in 3zx2
Vanadium binding site 1 out of 40 in the NTPDASE1 in Complex with Decavanadate


Mono view


Stereo pair view

A full contact list of Vanadium with other atoms in the V binding site number 1 of NTPDASE1 in Complex with Decavanadate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:V531

b:40.7
occ:0.50
V10 A:DVT531 0.0 40.7 0.5
O28 A:DVT531 1.6 35.9 0.5
O15 A:DVT531 1.8 45.1 0.5
O18 A:DVT531 1.9 38.8 0.5
O27 A:DVT531 1.9 44.2 0.5
O23 A:DVT531 2.0 40.1 0.5
O2 A:DVT531 2.3 42.6 0.5
V8 A:DVT531 3.1 39.9 0.5
V1 A:DVT531 3.1 49.9 0.5
V3 A:DVT531 3.1 41.5 0.5
V9 A:DVT531 3.2 43.4 0.5
O17 A:DVT531 3.5 40.4 0.5
O4 A:DVT531 3.5 43.2 0.5
O3 A:DVT531 3.5 42.9 0.5
O24 A:DVT531 3.6 43.5 0.5
CD A:LYS408 4.1 46.9 1.0
O26 A:DVT531 4.4 42.5 0.5
V2 A:DVT531 4.4 43.3 0.5
O5 A:DVT531 4.4 47.0 0.5
O10 A:DVT531 4.4 36.8 0.5
CB A:LYS406 4.5 31.3 1.0
CG A:LYS406 4.5 31.4 1.0
O20 A:DVT531 4.5 37.1 0.5
CG A:LYS408 4.5 43.5 1.0
CB A:LYS408 4.6 36.5 1.0
O8 A:DVT531 4.6 41.6 0.5
O9 A:DVT531 4.6 39.9 0.5
O1 A:DVT531 4.6 42.4 0.5
O7 A:DVT531 4.6 42.2 0.5
N A:GLU407 4.6 32.2 1.0
N A:LYS408 4.7 34.8 1.0
CA A:LYS406 4.8 33.0 1.0
CE A:LYS408 4.9 49.6 1.0
CD A:LYS406 4.9 32.6 1.0
C A:LYS406 5.0 30.8 1.0

Vanadium binding site 2 out of 40 in 3zx2

Go back to Vanadium Binding Sites List in 3zx2
Vanadium binding site 2 out of 40 in the NTPDASE1 in Complex with Decavanadate


Mono view


Stereo pair view

A full contact list of Vanadium with other atoms in the V binding site number 2 of NTPDASE1 in Complex with Decavanadate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:V531

b:49.9
occ:0.50
V1 A:DVT531 0.0 49.9 0.5
O5 A:DVT531 1.6 47.0 0.5
O15 A:DVT531 1.8 45.1 0.5
O3 A:DVT531 1.9 42.9 0.5
O4 A:DVT531 1.9 43.2 0.5
O1 A:DVT531 2.1 42.4 0.5
O2 A:DVT531 2.3 42.6 0.5
V3 A:DVT531 3.0 41.5 0.5
V2 A:DVT531 3.1 43.3 0.5
V9 A:DVT531 3.1 43.4 0.5
V10 A:DVT531 3.1 40.7 0.5
O18 A:DVT531 3.2 38.8 0.5
O27 A:DVT531 3.4 44.2 0.5
O8 A:DVT531 3.6 41.6 0.5
O9 A:DVT531 3.7 39.9 0.5
O10 A:DVT531 4.3 36.8 0.5
O28 A:DVT531 4.4 35.9 0.5
V8 A:DVT531 4.4 39.9 0.5
O26 A:DVT531 4.5 42.5 0.5
O17 A:DVT531 4.5 40.4 0.5
O24 A:DVT531 4.5 43.5 0.5
O23 A:DVT531 4.5 40.1 0.5
O16 A:DVT531 4.5 42.0 0.5
O7 A:DVT531 4.6 42.2 0.5
NZ A:LYS408 4.7 52.3 1.0
CD A:LYS408 4.8 46.9 1.0

Vanadium binding site 3 out of 40 in 3zx2

Go back to Vanadium Binding Sites List in 3zx2
Vanadium binding site 3 out of 40 in the NTPDASE1 in Complex with Decavanadate


Mono view


Stereo pair view

A full contact list of Vanadium with other atoms in the V binding site number 3 of NTPDASE1 in Complex with Decavanadate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:V531

b:43.4
occ:0.50
V9 A:DVT531 0.0 43.4 0.5
O26 A:DVT531 1.6 42.5 0.5
O4 A:DVT531 1.8 43.2 0.5
O27 A:DVT531 1.8 44.2 0.5
O8 A:DVT531 2.0 41.6 0.5
O24 A:DVT531 2.0 43.5 0.5
O2 A:DVT531 2.2 42.6 0.5
V7 A:DVT531 3.0 43.5 0.5
V1 A:DVT531 3.1 49.9 0.5
V10 A:DVT531 3.2 40.7 0.5
V8 A:DVT531 3.2 39.9 0.5
V2 A:DVT531 3.2 43.3 0.5
O25 A:DVT531 3.3 41.3 0.5
O15 A:DVT531 3.3 45.1 0.5
O23 A:DVT531 3.5 40.1 0.5
O1 A:DVT531 3.5 42.4 0.5
O7 A:DVT531 3.6 42.2 0.5
O5 A:DVT531 4.4 47.0 0.5
O28 A:DVT531 4.4 35.9 0.5
O18 A:DVT531 4.4 38.8 0.5
O21 A:DVT531 4.4 45.3 0.5
O11 A:DVT531 4.4 43.2 0.5
V3 A:DVT531 4.4 41.5 0.5
O3 A:DVT531 4.4 42.9 0.5
O17 A:DVT531 4.5 40.4 0.5
O16 A:DVT531 4.5 42.0 0.5
O20 A:DVT531 4.6 37.1 0.5
O9 A:DVT531 4.6 39.9 0.5

Vanadium binding site 4 out of 40 in 3zx2

Go back to Vanadium Binding Sites List in 3zx2
Vanadium binding site 4 out of 40 in the NTPDASE1 in Complex with Decavanadate


Mono view


Stereo pair view

A full contact list of Vanadium with other atoms in the V binding site number 4 of NTPDASE1 in Complex with Decavanadate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:V531

b:43.5
occ:0.50
V7 A:DVT531 0.0 43.5 0.5
O25 A:DVT531 1.6 41.3 0.5
O11 A:DVT531 1.8 43.2 0.5
O21 A:DVT531 1.8 45.3 0.5
O8 A:DVT531 2.0 41.6 0.5
O24 A:DVT531 2.0 43.5 0.5
O7 A:DVT531 2.2 42.2 0.5
V9 A:DVT531 3.0 43.4 0.5
V5 A:DVT531 3.1 49.0 0.5
V8 A:DVT531 3.2 39.9 0.5
V2 A:DVT531 3.2 43.3 0.5
V6 A:DVT531 3.2 40.6 0.5
O26 A:DVT531 3.3 42.5 0.5
O6 A:DVT531 3.5 41.3 0.5
O16 A:DVT531 3.5 42.0 0.5
O20 A:DVT531 3.6 37.1 0.5
O2 A:DVT531 3.6 42.6 0.5
O22 A:DVT531 4.4 37.9 0.5
O4 A:DVT531 4.4 43.2 0.5
O27 A:DVT531 4.4 44.2 0.5
O14 A:DVT531 4.4 47.2 0.5
V4 A:DVT531 4.4 43.6 0.5
O13 A:DVT531 4.5 42.4 0.5
O23 A:DVT531 4.5 40.1 0.5
O1 A:DVT531 4.5 42.4 0.5
O9 A:DVT531 4.5 39.9 0.5
O19 A:DVT531 4.5 34.4 0.5
O17 A:DVT531 4.5 40.4 0.5

Vanadium binding site 5 out of 40 in 3zx2

Go back to Vanadium Binding Sites List in 3zx2
Vanadium binding site 5 out of 40 in the NTPDASE1 in Complex with Decavanadate


Mono view


Stereo pair view

A full contact list of Vanadium with other atoms in the V binding site number 5 of NTPDASE1 in Complex with Decavanadate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:V531

b:40.6
occ:0.50
V6 A:DVT531 0.0 40.6 0.5
O22 A:DVT531 1.6 37.9 0.5
O6 A:DVT531 1.8 41.3 0.5
O21 A:DVT531 1.9 45.3 0.5
O19 A:DVT531 1.9 34.4 0.5
O20 A:DVT531 2.1 37.1 0.5
O7 A:DVT531 2.3 42.2 0.5
V4 A:DVT531 3.0 43.6 0.5
V8 A:DVT531 3.1 39.9 0.5
V5 A:DVT531 3.1 49.0 0.5
V7 A:DVT531 3.2 43.5 0.5
O13 A:DVT531 3.4 42.4 0.5
O11 A:DVT531 3.4 43.2 0.5
O24 A:DVT531 3.7 43.5 0.5
O17 A:DVT531 3.7 40.4 0.5
O25 A:DVT531 4.4 41.3 0.5
O12 A:DVT531 4.4 44.8 0.5
O14 A:DVT531 4.4 47.2 0.5
V2 A:DVT531 4.4 43.3 0.5
O9 A:DVT531 4.5 39.9 0.5
O23 A:DVT531 4.6 40.1 0.5
O16 A:DVT531 4.6 42.0 0.5
O8 A:DVT531 4.6 41.6 0.5
O2 A:DVT531 4.7 42.6 0.5

Vanadium binding site 6 out of 40 in 3zx2

Go back to Vanadium Binding Sites List in 3zx2
Vanadium binding site 6 out of 40 in the NTPDASE1 in Complex with Decavanadate


Mono view


Stereo pair view

A full contact list of Vanadium with other atoms in the V binding site number 6 of NTPDASE1 in Complex with Decavanadate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:V531

b:39.9
occ:0.50
V8 A:DVT531 0.0 39.9 0.5
O20 A:DVT531 1.7 37.1 0.5
O23 A:DVT531 1.7 40.1 0.5
O24 A:DVT531 1.9 43.5 0.5
O17 A:DVT531 1.9 40.4 0.5
O7 A:DVT531 2.1 42.2 0.5
O2 A:DVT531 2.2 42.6 0.5
V10 A:DVT531 3.1 40.7 0.5
V6 A:DVT531 3.1 40.6 0.5
V4 A:DVT531 3.1 43.6 0.5
V7 A:DVT531 3.2 43.5 0.5
V9 A:DVT531 3.2 43.4 0.5
O21 A:DVT531 3.2 45.3 0.5
O19 A:DVT531 3.2 34.4 0.5
V3 A:DVT531 3.2 41.5 0.5
O27 A:DVT531 3.3 44.2 0.5
V2 A:DVT531 3.3 43.3 0.5
O18 A:DVT531 3.4 38.8 0.5
O9 A:DVT531 3.5 39.9 0.5
O8 A:DVT531 3.5 41.6 0.5
O25 A:DVT531 4.2 41.3 0.5
O28 A:DVT531 4.2 35.9 0.5
CG A:LYS406 4.3 31.4 1.0
O22 A:DVT531 4.3 37.9 0.5
O26 A:DVT531 4.3 42.5 0.5
O11 A:DVT531 4.4 43.2 0.5
O15 A:DVT531 4.4 45.1 0.5
O6 A:DVT531 4.4 41.3 0.5
O13 A:DVT531 4.4 42.4 0.5
V1 A:DVT531 4.4 49.9 0.5
V5 A:DVT531 4.4 49.0 0.5
O12 A:DVT531 4.4 44.8 0.5
O4 A:DVT531 4.5 43.2 0.5
O3 A:DVT531 4.5 42.9 0.5
O16 A:DVT531 4.6 42.0 0.5
O10 A:DVT531 4.6 36.8 0.5
O1 A:DVT531 4.6 42.4 0.5
CE A:LYS406 4.6 35.7 1.0
CD A:LYS406 4.8 32.6 1.0

Vanadium binding site 7 out of 40 in 3zx2

Go back to Vanadium Binding Sites List in 3zx2
Vanadium binding site 7 out of 40 in the NTPDASE1 in Complex with Decavanadate


Mono view


Stereo pair view

A full contact list of Vanadium with other atoms in the V binding site number 7 of NTPDASE1 in Complex with Decavanadate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:V531

b:49.0
occ:0.50
V5 A:DVT531 0.0 49.0 0.5
O14 A:DVT531 1.6 47.2 0.5
O6 A:DVT531 1.9 41.3 0.5
O11 A:DVT531 1.9 43.2 0.5
O13 A:DVT531 1.9 42.4 0.5
O16 A:DVT531 2.0 42.0 0.5
O7 A:DVT531 2.4 42.2 0.5
V2 A:DVT531 3.1 43.3 0.5
V6 A:DVT531 3.1 40.6 0.5
V4 A:DVT531 3.1 43.6 0.5
V7 A:DVT531 3.1 43.5 0.5
O21 A:DVT531 3.4 45.3 0.5
O9 A:DVT531 3.5 39.9 0.5
O19 A:DVT531 3.6 34.4 0.5
O8 A:DVT531 3.6 41.6 0.5
O12 A:DVT531 4.4 44.8 0.5
O22 A:DVT531 4.4 37.9 0.5
NZ A:LYS87 4.4 80.0 1.0
V8 A:DVT531 4.4 39.9 0.5
O1 A:DVT531 4.5 42.4 0.5
O17 A:DVT531 4.6 40.4 0.5
O20 A:DVT531 4.6 37.1 0.5
O25 A:DVT531 4.6 41.3 0.5
O24 A:DVT531 4.6 43.5 0.5
O2 A:DVT531 4.6 42.6 0.5

Vanadium binding site 8 out of 40 in 3zx2

Go back to Vanadium Binding Sites List in 3zx2
Vanadium binding site 8 out of 40 in the NTPDASE1 in Complex with Decavanadate


Mono view


Stereo pair view

A full contact list of Vanadium with other atoms in the V binding site number 8 of NTPDASE1 in Complex with Decavanadate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:V531

b:43.3
occ:0.50
V2 A:DVT531 0.0 43.3 0.5
O1 A:DVT531 1.7 42.4 0.5
O16 A:DVT531 1.7 42.0 0.5
O9 A:DVT531 1.9 39.9 0.5
O8 A:DVT531 2.0 41.6 0.5
O2 A:DVT531 2.1 42.6 0.5
O7 A:DVT531 2.2 42.2 0.5
V1 A:DVT531 3.1 49.9 0.5
V3 A:DVT531 3.1 41.5 0.5
V5 A:DVT531 3.1 49.0 0.5
V7 A:DVT531 3.2 43.5 0.5
V4 A:DVT531 3.2 43.6 0.5
V9 A:DVT531 3.2 43.4 0.5
O3 A:DVT531 3.2 42.9 0.5
O11 A:DVT531 3.3 43.2 0.5
O13 A:DVT531 3.3 42.4 0.5
O4 A:DVT531 3.3 43.2 0.5
V8 A:DVT531 3.3 39.9 0.5
O17 A:DVT531 3.4 40.4 0.5
O24 A:DVT531 3.5 43.5 0.5
O14 A:DVT531 4.3 47.2 0.5
O10 A:DVT531 4.3 36.8 0.5
O5 A:DVT531 4.3 47.0 0.5
O18 A:DVT531 4.3 38.8 0.5
O15 A:DVT531 4.4 45.1 0.5
O12 A:DVT531 4.4 44.8 0.5
O21 A:DVT531 4.4 45.3 0.5
O6 A:DVT531 4.4 41.3 0.5
O27 A:DVT531 4.4 44.2 0.5
NZ A:LYS87 4.4 80.0 1.0
V10 A:DVT531 4.4 40.7 0.5
V6 A:DVT531 4.4 40.6 0.5
O19 A:DVT531 4.5 34.4 0.5
O26 A:DVT531 4.5 42.5 0.5
O23 A:DVT531 4.5 40.1 0.5
O20 A:DVT531 4.5 37.1 0.5
O25 A:DVT531 4.5 41.3 0.5

Vanadium binding site 9 out of 40 in 3zx2

Go back to Vanadium Binding Sites List in 3zx2
Vanadium binding site 9 out of 40 in the NTPDASE1 in Complex with Decavanadate


Mono view


Stereo pair view

A full contact list of Vanadium with other atoms in the V binding site number 9 of NTPDASE1 in Complex with Decavanadate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:V531

b:43.6
occ:0.50
V4 A:DVT531 0.0 43.6 0.5
O12 A:DVT531 1.6 44.8 0.5
O19 A:DVT531 1.8 34.4 0.5
O13 A:DVT531 1.8 42.4 0.5
O9 A:DVT531 2.0 39.9 0.5
O17 A:DVT531 2.0 40.4 0.5
O7 A:DVT531 2.2 42.2 0.5
V6 A:DVT531 3.0 40.6 0.5
V3 A:DVT531 3.1 41.5 0.5
V5 A:DVT531 3.1 49.0 0.5
V8 A:DVT531 3.1 39.9 0.5
V2 A:DVT531 3.2 43.3 0.5
O6 A:DVT531 3.3 41.3 0.5
O20 A:DVT531 3.3 37.1 0.5
O10 A:DVT531 3.5 36.8 0.5
O16 A:DVT531 3.5 42.0 0.5
O2 A:DVT531 3.6 42.6 0.5
CE A:LYS406 3.7 35.7 1.0
NZ A:LYS87 3.7 80.0 1.0
NZ A:LYS406 4.3 35.8 1.0
O21 A:DVT531 4.3 45.3 0.5
O11 A:DVT531 4.4 43.2 0.5
O22 A:DVT531 4.4 37.9 0.5
O14 A:DVT531 4.4 47.2 0.5
V7 A:DVT531 4.4 43.5 0.5
O18 A:DVT531 4.5 38.8 0.5
O23 A:DVT531 4.5 40.1 0.5
O24 A:DVT531 4.5 43.5 0.5
O3 A:DVT531 4.6 42.9 0.5
O8 A:DVT531 4.6 41.6 0.5
O1 A:DVT531 4.6 42.4 0.5
CE A:LYS87 4.6 79.4 1.0
CD A:LYS406 4.8 32.6 1.0

Vanadium binding site 10 out of 40 in 3zx2

Go back to Vanadium Binding Sites List in 3zx2
Vanadium binding site 10 out of 40 in the NTPDASE1 in Complex with Decavanadate


Mono view


Stereo pair view

A full contact list of Vanadium with other atoms in the V binding site number 10 of NTPDASE1 in Complex with Decavanadate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:V531

b:41.5
occ:0.50
V3 A:DVT531 0.0 41.5 0.5
O10 A:DVT531 1.6 36.8 0.5
O18 A:DVT531 1.8 38.8 0.5
O3 A:DVT531 1.8 42.9 0.5
O17 A:DVT531 2.0 40.4 0.5
O9 A:DVT531 2.0 39.9 0.5
O2 A:DVT531 2.2 42.6 0.5
V1 A:DVT531 3.0 49.9 0.5
V2 A:DVT531 3.1 43.3 0.5
V4 A:DVT531 3.1 43.6 0.5
V10 A:DVT531 3.1 40.7 0.5
V8 A:DVT531 3.2 39.9 0.5
O15 A:DVT531 3.3 45.1 0.5
O1 A:DVT531 3.4 42.4 0.5
O12 A:DVT531 3.5 44.8 0.5
O23 A:DVT531 3.6 40.1 0.5
O7 A:DVT531 3.6 42.2 0.5
NZ A:LYS408 3.7 52.3 1.0
CE A:LYS406 3.8 35.7 1.0
CD A:LYS406 4.0 32.6 1.0
CE A:LYS408 4.1 49.6 1.0
NZ A:LYS406 4.2 35.8 1.0
O5 A:DVT531 4.3 47.0 0.5
CD A:LYS408 4.3 46.9 1.0
O4 A:DVT531 4.4 43.2 0.5
O27 A:DVT531 4.4 44.2 0.5
V9 A:DVT531 4.4 43.4 0.5
O13 A:DVT531 4.4 42.4 0.5
O28 A:DVT531 4.4 35.9 0.5
O16 A:DVT531 4.4 42.0 0.5
CG A:LYS406 4.4 31.4 1.0
O19 A:DVT531 4.5 34.4 0.5
O8 A:DVT531 4.5 41.6 0.5
O20 A:DVT531 4.5 37.1 0.5
O24 A:DVT531 4.6 43.5 0.5
NZ A:LYS87 4.7 80.0 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: Thu Oct 29 07:05:20 2020

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