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Vanadium in PDB 4bre: Legionella Pneumophila NTPDASE1 Crystal Form II (Closed) in Complex with Transition State Mimic Adenosine 5' Phosphovanadate

Protein crystallography data

The structure of Legionella Pneumophila NTPDASE1 Crystal Form II (Closed) in Complex with Transition State Mimic Adenosine 5' Phosphovanadate, PDB code: 4bre 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) 29.33 / 1.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 62.681, 86.203, 70.879, 90.00, 105.94, 90.00
R / Rfree (%) 17.211 / 20.809

Other elements in 4bre:

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

Magnesium (Mg) 2 atoms
Sodium (Na) 1 atom

Vanadium Binding Sites:

The binding sites of Vanadium atom in the Legionella Pneumophila NTPDASE1 Crystal Form II (Closed) in Complex with Transition State Mimic Adenosine 5' Phosphovanadate (pdb code 4bre). 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 II (Closed) in Complex with Transition State Mimic Adenosine 5' Phosphovanadate, PDB code: 4bre:
Jump to Vanadium binding site number: 1; 2;

Vanadium binding site 1 out of 2 in 4bre

Go back to Vanadium Binding Sites List in 4bre
Vanadium binding site 1 out of 2 in the Legionella Pneumophila NTPDASE1 Crystal Form II (Closed) in Complex with Transition State Mimic Adenosine 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 II (Closed) in Complex with Transition State Mimic Adenosine 5' Phosphovanadate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:V1396

b:17.0
occ:1.00
VB A:50T1396 0.0 17.0 1.0
O2B A:50T1396 1.8 19.1 1.0
O1B A:50T1396 1.8 16.8 1.0
O3A A:50T1396 1.8 18.1 1.0
O4B A:50T1396 1.9 15.0 1.0
O3B A:50T1396 2.1 18.9 1.0
PA A:50T1396 3.3 17.7 1.0
O2A A:50T1396 3.6 17.6 1.0
MG A:MG1397 3.6 16.4 1.0
OG1 A:THR118 3.8 5.7 1.0
O A:HOH2077 3.9 18.2 1.0
OG A:SER52 3.9 4.3 1.0
N A:GLY189 3.9 5.4 1.0
O A:HOH2239 3.9 15.9 1.0
N A:SER52 4.0 3.7 1.0
OE2 A:GLU159 4.0 5.1 1.0
CB A:ALA119 4.1 4.5 1.0
O5' A:50T1396 4.1 18.5 1.0
CA A:GLY188 4.1 4.8 1.0
N A:ALA119 4.2 4.4 1.0
N A:ALA190 4.2 5.2 1.0
CB A:SER52 4.3 4.0 1.0
OG A:SER191 4.3 5.2 1.0
O1A A:50T1396 4.4 17.8 1.0
N A:SER191 4.4 5.1 1.0
C A:GLY188 4.5 5.3 1.0
O A:HOH2241 4.5 15.7 1.0
CB A:THR118 4.5 5.1 1.0
O A:SER191 4.6 5.6 1.0
CA A:GLY51 4.6 4.0 1.0
CA A:ALA119 4.7 4.2 1.0
O A:HOH2242 4.8 15.6 1.0
CA A:SER52 4.8 3.8 1.0
C A:GLY51 4.9 3.7 1.0
CA A:GLY189 4.9 5.6 1.0

Vanadium binding site 2 out of 2 in 4bre

Go back to Vanadium Binding Sites List in 4bre
Vanadium binding site 2 out of 2 in the Legionella Pneumophila NTPDASE1 Crystal Form II (Closed) in Complex with Transition State Mimic Adenosine 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 II (Closed) in Complex with Transition State Mimic Adenosine 5' Phosphovanadate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:V1395

b:16.3
occ:1.00
VB B:50T1395 0.0 16.3 1.0
O1B B:50T1395 1.7 15.6 1.0
O2B B:50T1395 1.8 16.7 1.0
O3A B:50T1395 2.0 14.8 1.0
O3B B:50T1395 2.0 15.2 1.0
O4B B:50T1395 2.2 16.2 1.0
PA B:50T1395 3.3 15.3 1.0
O2A B:50T1395 3.6 17.3 1.0
MG B:MG1396 3.6 15.5 1.0
OG1 B:THR118 3.7 6.3 1.0
N B:GLY189 3.9 4.1 1.0
O B:HOH2092 3.9 16.4 1.0
O B:HOH2234 3.9 14.5 1.0
OG B:SER52 3.9 4.6 1.0
N B:SER52 4.0 4.6 1.0
CA B:GLY188 4.0 4.3 1.0
OE2 B:GLU159 4.0 6.2 1.0
CB B:ALA119 4.1 5.5 1.0
O5' B:50T1395 4.1 16.9 0.6
CB B:SER52 4.1 4.5 1.0
O5' B:50T1395 4.2 16.0 0.4
N B:ALA119 4.2 5.1 1.0
N B:ALA190 4.2 4.6 1.0
OG B:SER191 4.3 4.5 1.0
O1A B:50T1395 4.5 16.4 1.0
C B:GLY188 4.5 4.6 1.0
N B:SER191 4.5 4.5 1.0
O B:HOH2236 4.5 15.2 1.0
CB B:THR118 4.5 6.0 1.0
O B:SER191 4.6 4.7 1.0
CA B:GLY51 4.7 4.9 1.0
CA B:ALA119 4.7 4.8 1.0
CA B:SER52 4.8 4.8 1.0
O B:HOH2237 4.8 15.3 1.0
C B:GLY51 4.9 4.8 1.0
CA B:GLY189 4.9 4.5 1.0
N B:GLY120 5.0 4.9 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 02:31:04 2020

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