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Vanadium in PDB 4brl: Legionella Pneumophila NTPDASE1 Crystal Form III (Closed) in Complex with Transition State Mimic Guanosine 5'-Phosphovanadate

Enzymatic activity of Legionella Pneumophila NTPDASE1 Crystal Form III (Closed) in Complex with Transition State Mimic Guanosine 5'-Phosphovanadate

All present enzymatic activity of Legionella Pneumophila NTPDASE1 Crystal Form III (Closed) in Complex with Transition State Mimic Guanosine 5'-Phosphovanadate:
3.6.1.5;

Protein crystallography data

The structure of Legionella Pneumophila NTPDASE1 Crystal Form III (Closed) in Complex with Transition State Mimic Guanosine 5'-Phosphovanadate, PDB code: 4brl was solved by M.Zebisch, P.Schaefer, P.Lauble, N.Straeter, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.88 / 1.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 80.994, 83.463, 109.289, 90.00, 90.00, 90.00
R / Rfree (%) 14.416 / 19.773

Other elements in 4brl:

The structure of Legionella Pneumophila NTPDASE1 Crystal Form III (Closed) in Complex with Transition State Mimic Guanosine 5'-Phosphovanadate also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Chlorine (Cl) 3 atoms

Vanadium Binding Sites:

The binding sites of Vanadium atom in the Legionella Pneumophila NTPDASE1 Crystal Form III (Closed) in Complex with Transition State Mimic Guanosine 5'-Phosphovanadate (pdb code 4brl). This binding sites where shown within 5.0 Angstroms radius around Vanadium atom.
In total 2 binding sites of Vanadium where determined in the Legionella Pneumophila NTPDASE1 Crystal Form III (Closed) in Complex with Transition State Mimic Guanosine 5'-Phosphovanadate, PDB code: 4brl:
Jump to Vanadium binding site number: 1; 2;

Vanadium binding site 1 out of 2 in 4brl

Go back to Vanadium Binding Sites List in 4brl
Vanadium binding site 1 out of 2 in the Legionella Pneumophila NTPDASE1 Crystal Form III (Closed) in Complex with Transition State Mimic Guanosine 5'-Phosphovanadate


Mono view


Stereo pair view

A full contact list of Vanadium with other atoms in the V binding site number 1 of Legionella Pneumophila NTPDASE1 Crystal Form III (Closed) in Complex with Transition State Mimic Guanosine 5'-Phosphovanadate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:V1395

b:16.6
occ:1.00
VB A:GMV1395 0.0 16.6 1.0
O1B A:GMV1395 1.7 18.1 1.0
O2B A:GMV1395 1.7 19.9 1.0
O3B A:GMV1395 1.9 15.6 1.0
O3A A:GMV1395 2.0 16.1 1.0
O4B A:GMV1395 2.2 15.9 1.0
PA A:GMV1395 3.3 15.4 1.0
O2A A:GMV1395 3.6 14.7 1.0
MG A:MG1396 3.6 16.1 1.0
OG1 A:THR118 3.7 20.3 1.0
O A:HOH2006 3.8 13.9 1.0
O A:HOH2106 3.9 15.9 1.0
OG A:SER52 3.9 18.4 1.0
N A:GLY189 3.9 13.1 1.0
N A:SER52 4.0 15.1 1.0
OE2 A:GLU159 4.1 15.0 1.0
CA A:GLY188 4.1 13.4 1.0
O5' A:GMV1395 4.1 15.4 1.0
N A:ALA119 4.2 13.9 1.0
CB A:ALA119 4.2 14.2 1.0
CB A:SER52 4.2 14.0 1.0
N A:ALA190 4.3 13.1 1.0
OG A:SER191 4.3 14.9 1.0
O1A A:GMV1395 4.4 18.6 1.0
O A:HOH2105 4.5 14.7 1.0
N A:SER191 4.5 11.9 1.0
C A:GLY188 4.5 13.3 1.0
CB A:THR118 4.6 17.0 1.0
CA A:GLY51 4.7 14.0 1.0
O A:SER191 4.7 14.4 1.0
O A:HOH2117 4.7 15.6 1.0
CA A:ALA119 4.8 12.4 1.0
CA A:SER52 4.8 16.7 1.0
C A:GLY51 4.9 15.6 1.0
CA A:GLY189 4.9 12.3 1.0

Vanadium binding site 2 out of 2 in 4brl

Go back to Vanadium Binding Sites List in 4brl
Vanadium binding site 2 out of 2 in the Legionella Pneumophila NTPDASE1 Crystal Form III (Closed) in Complex with Transition State Mimic Guanosine 5'-Phosphovanadate


Mono view


Stereo pair view

A full contact list of Vanadium with other atoms in the V binding site number 2 of Legionella Pneumophila NTPDASE1 Crystal Form III (Closed) in Complex with Transition State Mimic Guanosine 5'-Phosphovanadate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:V1396

b:19.0
occ:1.00
VB B:GMV1396 0.0 19.0 1.0
O1B B:GMV1396 1.6 17.3 1.0
O2B B:GMV1396 1.7 23.4 1.0
O3B B:GMV1396 1.9 19.2 1.0
O3A B:GMV1396 2.0 18.8 1.0
O4B B:GMV1396 2.2 20.6 1.0
PA B:GMV1396 3.4 18.0 1.0
MG B:MG1397 3.6 17.5 1.0
O2A B:GMV1396 3.6 19.0 1.0
OG1 B:THR118 3.6 21.3 1.0
O B:HOH2090 3.8 19.3 1.0
O B:HOH2004 3.9 15.7 1.0
OG B:SER52 3.9 17.8 1.0
N B:GLY189 4.0 14.8 1.0
CB B:ALA119 4.0 16.9 1.0
N B:SER52 4.1 14.9 1.0
OE2 B:GLU159 4.1 16.7 1.0
CA B:GLY188 4.2 14.0 1.0
O5' B:GMV1396 4.2 19.6 1.0
N B:ALA119 4.2 15.3 1.0
CB B:SER52 4.2 17.4 1.0
OG B:SER191 4.3 14.3 1.0
N B:ALA190 4.3 13.6 1.0
N B:SER191 4.4 13.8 1.0
O1A B:GMV1396 4.4 22.6 1.0
O B:HOH2091 4.5 17.0 1.0
CB B:THR118 4.5 18.3 1.0
C B:GLY188 4.5 14.6 1.0
O B:SER191 4.7 15.2 1.0
CA B:ALA119 4.7 13.8 1.0
O B:HOH2105 4.7 18.1 1.0
CA B:GLY51 4.7 15.8 1.0
CA B:SER52 4.8 16.7 1.0
CA B:GLY189 4.9 14.2 1.0
C B:GLY51 5.0 18.5 1.0
N B:GLY120 5.0 16.1 1.0

Reference:

M.Zebisch, M.Krauss, P.Schaefer, P.Lauble, N.Straeter. Crystallographic Snapshots Along the Reaction Pathway of Nucleoside Triphosphate Diphosphohydrolases Structure V. 21 1460 2013.
ISSN: ISSN 0969-2126
PubMed: 23830739
DOI: 10.1016/J.STR.2013.05.016
Page generated: Wed Dec 16 02:31:06 2020

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