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Fluorine in PDB 3zki: BACE2 Mutant Structure with Ligand

Enzymatic activity of BACE2 Mutant Structure with Ligand

All present enzymatic activity of BACE2 Mutant Structure with Ligand:
3.4.23.45;

Protein crystallography data

The structure of BACE2 Mutant Structure with Ligand, PDB code: 3zki was solved by D.W.Banner, A.Kuglstatter, J.Benz, M.Stihle, A.Ruf, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.06 / 2.40
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 47.310, 89.249, 98.850, 90.00, 96.96, 90.00
R / Rfree (%) 18.266 / 24.059

Fluorine Binding Sites:

The binding sites of Fluorine atom in the BACE2 Mutant Structure with Ligand (pdb code 3zki). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the BACE2 Mutant Structure with Ligand, PDB code: 3zki:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 3zki

Go back to Fluorine Binding Sites List in 3zki
Fluorine binding site 1 out of 6 in the BACE2 Mutant Structure with Ligand


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of BACE2 Mutant Structure with Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1398

b:38.4
occ:1.00
 F30 A:WZV1398 0.0 38.4 1.0
C28 A:WZV1398 1.3 38.5 1.0
F29 A:WZV1398 2.1 39.9 1.0
F31 A:WZV1398 2.1 38.5 1.0
C27 A:WZV1398 2.3 37.0 1.0
O26 A:WZV1398 2.9 32.0 1.0
CB A:ALA347 3.0 21.7 1.0
N A:THR348 3.5 23.1 1.0
C A:ALA347 3.6 24.1 1.0
CG2 A:THR348 3.7 25.0 1.0
O A:THR245 3.8 21.5 1.0
CA A:ALA347 3.8 22.8 1.0
CG2 A:THR245 4.0 20.7 1.0
CA A:THR245 4.0 20.7 1.0
CA A:THR348 4.1 23.5 1.0
C18 A:WZV1398 4.2 29.6 1.0
O A:ALA347 4.2 25.9 1.0
OE2 A:GLU351 4.2 23.7 1.0
C A:THR245 4.3 20.6 1.0
N A:ALA347 4.5 21.5 1.0
CB A:THR245 4.5 19.8 1.0
CD A:GLU351 4.5 23.8 1.0
CB A:THR348 4.6 25.1 1.0
O A:GLY27 4.6 51.3 1.0
O A:THR244 4.7 22.7 1.0
OG1 A:THR245 4.7 19.2 1.0
OE1 A:GLU351 4.8 25.2 1.0
CE1 A:TYR30 4.9 21.2 1.0
C23 A:WZV1398 4.9 28.6 1.0
O A:HOH2005 5.0 18.7 1.0

Fluorine binding site 2 out of 6 in 3zki

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Fluorine binding site 2 out of 6 in the BACE2 Mutant Structure with Ligand


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of BACE2 Mutant Structure with Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1398

b:38.5
occ:1.00
 F31 A:WZV1398 0.0 38.5 1.0
C28 A:WZV1398 1.3 38.5 1.0
F30 A:WZV1398 2.1 38.4 1.0
F29 A:WZV1398 2.2 39.9 1.0
C27 A:WZV1398 2.3 37.0 1.0
O26 A:WZV1398 2.6 32.0 1.0
O A:HOH2005 3.0 18.7 1.0
CE1 A:TYR30 3.3 21.2 1.0
CB A:ALA347 3.6 21.7 1.0
OE2 A:GLU351 3.7 23.7 1.0
CD1 A:TYR30 3.7 21.4 1.0
C18 A:WZV1398 3.9 29.6 1.0
O A:GLY27 4.1 51.3 1.0
CA A:GLY27 4.2 49.9 1.0
C A:GLY27 4.3 48.8 1.0
N A:GLY29 4.3 29.9 1.0
CZ A:TYR30 4.4 21.8 1.0
CD A:GLU351 4.5 23.8 1.0
CA A:GLY29 4.5 26.2 1.0
C19 A:WZV1398 4.6 28.5 1.0
OH A:TYR30 4.7 22.9 1.0
C23 A:WZV1398 4.8 28.6 1.0
CA A:ALA347 4.8 22.8 1.0
C A:ALA347 4.9 24.1 1.0
N A:TYR30 4.9 23.1 1.0
C A:GLY29 4.9 24.6 1.0
CE A:MET170 4.9 41.9 1.0
CG A:TYR30 4.9 21.7 1.0

Fluorine binding site 3 out of 6 in 3zki

Go back to Fluorine Binding Sites List in 3zki
Fluorine binding site 3 out of 6 in the BACE2 Mutant Structure with Ligand


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of BACE2 Mutant Structure with Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1398

b:39.9
occ:1.00
 F29 A:WZV1398 0.0 39.9 1.0
C28 A:WZV1398 1.3 38.5 1.0
F30 A:WZV1398 2.1 38.4 1.0
F31 A:WZV1398 2.2 38.5 1.0
C27 A:WZV1398 2.3 37.0 1.0
CA A:GLY27 3.1 49.9 1.0
O A:GLY27 3.3 51.3 1.0
C A:GLY27 3.5 48.8 1.0
O26 A:WZV1398 3.5 32.0 1.0
O A:HOH2005 3.8 18.7 1.0
OE2 A:GLU351 3.9 23.7 1.0
N A:GLY27 4.3 55.1 1.0
CG2 A:THR245 4.3 20.7 1.0
CG2 A:THR348 4.5 25.0 1.0
CD A:GLU351 4.5 23.8 1.0
OE1 A:GLU351 4.7 25.2 1.0
N A:ARG28 4.7 42.7 1.0
C18 A:WZV1398 4.7 29.6 1.0
CB A:ALA347 4.9 21.7 1.0

Fluorine binding site 4 out of 6 in 3zki

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Fluorine binding site 4 out of 6 in the BACE2 Mutant Structure with Ligand


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of BACE2 Mutant Structure with Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1398

b:50.2
occ:1.00
 F30 B:WZV1398 0.0 50.2 1.0
C28 B:WZV1398 1.3 49.4 1.0
F31 B:WZV1398 2.2 47.9 1.0
F29 B:WZV1398 2.2 53.3 1.0
C27 B:WZV1398 2.3 48.2 1.0
O26 B:WZV1398 3.0 47.8 1.0
CG2 B:THR348 3.3 34.0 1.0
CB B:ALA347 3.5 32.5 1.0
O B:THR245 3.6 30.3 1.0
CG2 B:THR245 3.7 26.2 1.0
N B:THR348 3.9 32.2 1.0
CA B:THR245 4.0 28.7 1.0
C B:ALA347 4.1 33.3 1.0
CB B:THR245 4.2 27.6 1.0
OG1 B:THR245 4.2 28.3 1.0
C B:THR245 4.2 28.9 1.0
C18 B:WZV1398 4.3 45.5 1.0
CA B:THR348 4.3 33.4 1.0
CA B:ALA347 4.4 31.3 1.0
OE2 B:GLU351 4.4 43.3 1.0
CB B:THR348 4.5 34.1 1.0
O B:HOH2001 4.6 27.9 1.0
O B:ALA347 4.6 36.3 1.0
CD B:GLU351 4.8 42.7 1.0
O B:GLY27 4.9 61.5 1.0
N B:ALA347 5.0 29.4 1.0
O B:THR244 5.0 26.1 1.0

Fluorine binding site 5 out of 6 in 3zki

Go back to Fluorine Binding Sites List in 3zki
Fluorine binding site 5 out of 6 in the BACE2 Mutant Structure with Ligand


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of BACE2 Mutant Structure with Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1398

b:47.9
occ:1.00
 F31 B:WZV1398 0.0 47.9 1.0
C28 B:WZV1398 1.3 49.4 1.0
F29 B:WZV1398 2.1 53.3 1.0
F30 B:WZV1398 2.2 50.2 1.0
C27 B:WZV1398 2.3 48.2 1.0
O26 B:WZV1398 2.5 47.8 1.0
O B:HOH2001 2.8 27.9 1.0
CE2 B:TYR30 3.4 32.8 1.0
CB B:ALA347 3.4 32.5 1.0
OE2 B:GLU351 3.8 43.3 1.0
CD2 B:TYR30 3.8 33.5 1.0
C18 B:WZV1398 3.9 45.5 1.0
CZ B:TYR30 4.4 33.0 1.0
CD B:GLU351 4.6 42.7 1.0
OH B:TYR30 4.6 33.0 1.0
CA B:ALA347 4.6 31.3 1.0
CE B:MET170 4.6 47.0 1.0
C23 B:WZV1398 4.6 41.1 1.0
C B:ALA347 4.7 33.3 1.0
N B:GLY29 4.7 48.5 1.0
C19 B:WZV1398 4.8 44.8 1.0
CA B:GLY29 4.8 43.5 1.0
CA B:GLY27 4.8 69.1 1.0
O B:ALA347 4.8 36.3 1.0
O B:GLY27 4.8 61.5 1.0
C B:GLY27 4.9 63.8 1.0

Fluorine binding site 6 out of 6 in 3zki

Go back to Fluorine Binding Sites List in 3zki
Fluorine binding site 6 out of 6 in the BACE2 Mutant Structure with Ligand


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of BACE2 Mutant Structure with Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1398

b:53.3
occ:1.00
 F29 B:WZV1398 0.0 53.3 1.0
C28 B:WZV1398 1.3 49.4 1.0
F31 B:WZV1398 2.1 47.9 1.0
F30 B:WZV1398 2.2 50.2 1.0
C27 B:WZV1398 2.4 48.2 1.0
O B:HOH2001 3.1 27.9 1.0
CA B:GLY27 3.2 69.1 1.0
O B:GLY27 3.4 61.5 1.0
O26 B:WZV1398 3.5 47.8 1.0
C B:GLY27 3.5 63.8 1.0
OE2 B:GLU351 3.9 43.3 1.0
N B:GLY27 4.6 75.3 1.0
N B:ARG28 4.6 58.0 1.0
C18 B:WZV1398 4.7 45.5 1.0
CD B:GLU351 4.7 42.7 1.0
CG2 B:THR245 4.8 26.2 1.0
CE2 B:TYR30 4.8 32.8 1.0
CG2 B:THR348 4.9 34.0 1.0
N B:GLY29 4.9 48.5 1.0

Reference:

D.W.Banner, B.Gsell, J.Benz, J.Bertschinger, D.Burger, S.Brack, S.Cuppuleri, M.Debulpaep, A.Gast, D.Grabulovski, M.Hennig, H.Hilpert, W.Huber, A.Kuglstatter, E.Kusznir, T.Laeremans, H.Matile, C.Miscenic, A.Rufer, D.Schlatter, J.Steyeart, M.Stihle, R.Thoma, M.Weber, A.Ruf. Mapping the Conformational Space Accessible to BACE2 Using Surface Mutants and Co-Crystals with Fab-Fragments, Fynomers, and Xaperones Acta Crystallogr.,Sect.D V. 69 1124 2013.
ISSN: ISSN 0907-4449
PubMed: 23695257
DOI: 10.1107/S0907444913006574
Page generated: Wed Jul 31 23:43:22 2024

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