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Fluorine in PDB 6eqm: Crystal Structure of Human Bace-1 in Complex with CNP520

Enzymatic activity of Crystal Structure of Human Bace-1 in Complex with CNP520

All present enzymatic activity of Crystal Structure of Human Bace-1 in Complex with CNP520:
3.4.23.46;

Protein crystallography data

The structure of Crystal Structure of Human Bace-1 in Complex with CNP520, PDB code: 6eqm was solved by J.-M.Rondeau, E.Wirth, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.77 / 1.35
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 47.660, 76.650, 104.540, 90.00, 90.00, 90.00
R / Rfree (%) 18.4 / 20

Other elements in 6eqm:

The structure of Crystal Structure of Human Bace-1 in Complex with CNP520 also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Human Bace-1 in Complex with CNP520 (pdb code 6eqm). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 7 binding sites of Fluorine where determined in the Crystal Structure of Human Bace-1 in Complex with CNP520, PDB code: 6eqm:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7;

Fluorine binding site 1 out of 7 in 6eqm

Go back to Fluorine Binding Sites List in 6eqm
Fluorine binding site 1 out of 7 in the Crystal Structure of Human Bace-1 in Complex with CNP520


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of Human Bace-1 in Complex with CNP520 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:21.0
occ:1.00
 F7 A:BUH401 0.0 21.0 1.0
C4 A:BUH401 1.3 18.2 1.0
C3 A:BUH401 2.3 19.5 1.0
C5 A:BUH401 2.4 18.0 1.0
C8 A:BUH401 2.9 16.7 1.0
CE2 A:TYR71 3.0 30.9 0.5
C14 A:BUH401 3.0 17.5 1.0
CZ A:TYR71 3.1 35.2 0.5
C13 A:BUH401 3.1 19.4 1.0
CE1 A:PHE108 3.2 26.7 1.0
CD2 A:TYR71 3.4 30.5 0.5
CD2 A:TYR71 3.4 27.0 0.5
CD1 A:PHE108 3.4 25.8 1.0
OH A:TYR71 3.5 30.0 0.5
CE1 A:TYR71 3.6 31.1 0.5
N6 A:BUH401 3.6 15.6 1.0
C2 A:BUH401 3.6 19.2 1.0
CE2 A:TYR71 3.6 27.2 0.5
CG A:TYR71 3.9 30.4 0.5
CD1 A:TYR71 3.9 32.1 0.5
O12 A:BUH401 4.0 19.0 1.0
CD1 A:ILE118 4.0 19.4 1.0
C1 A:BUH401 4.1 16.2 1.0
CG A:TYR71 4.3 27.4 0.5
N9 A:BUH401 4.4 15.6 1.0
O A:HOH775 4.4 46.1 1.0
CZ A:PHE108 4.4 25.0 1.0
CZ A:TYR71 4.5 34.4 0.5
CG A:PHE108 4.8 25.4 1.0
CB A:TYR71 4.8 28.4 0.5
CB A:TYR71 4.9 30.5 0.5

Fluorine binding site 2 out of 7 in 6eqm

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Fluorine binding site 2 out of 7 in the Crystal Structure of Human Bace-1 in Complex with CNP520


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of Human Bace-1 in Complex with CNP520 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:22.6
occ:1.00
 F28 A:BUH401 0.0 22.6 1.0
C26 A:BUH401 1.3 23.5 1.0
F30 A:BUH401 2.1 23.0 1.0
F29 A:BUH401 2.2 26.6 1.0
C18 A:BUH401 2.3 17.7 1.0
C17 A:BUH401 2.8 16.9 1.0
CD1 A:TYR14 3.4 17.2 1.0
O A:HOH694 3.4 26.9 1.0
O A:HOH659 3.5 15.9 1.0
C19 A:BUH401 3.5 20.5 1.0
CA A:GLY13 3.5 17.3 1.0
O A:SER229 3.6 14.1 1.0
CE1 A:TYR14 3.6 16.7 1.0
N A:GLY13 3.9 19.2 1.0
N A:TYR14 4.0 15.0 1.0
N22 A:BUH401 4.1 16.4 1.0
C A:GLY13 4.2 17.3 1.0
O A:HOH584 4.2 35.2 1.0
CB A:ALA335 4.2 17.2 1.0
CG A:TYR14 4.6 15.9 1.0
C20 A:BUH401 4.6 18.6 1.0
C A:SER229 4.8 14.4 1.0
C21 A:BUH401 4.8 18.3 1.0
C A:GLN12 5.0 23.9 1.0

Fluorine binding site 3 out of 7 in 6eqm

Go back to Fluorine Binding Sites List in 6eqm
Fluorine binding site 3 out of 7 in the Crystal Structure of Human Bace-1 in Complex with CNP520


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of Human Bace-1 in Complex with CNP520 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:26.6
occ:1.00
 F29 A:BUH401 0.0 26.6 1.0
C26 A:BUH401 1.3 23.5 1.0
F28 A:BUH401 2.2 22.6 1.0
F30 A:BUH401 2.2 23.0 1.0
C18 A:BUH401 2.4 17.7 1.0
C19 A:BUH401 2.7 20.5 1.0
CA A:GLY11 3.2 26.7 1.0
O A:HOH584 3.3 35.2 1.0
OG1 A:THR232 3.3 20.2 1.0
O A:HOH694 3.4 26.9 1.0
C A:GLY11 3.5 29.9 1.0
C17 A:BUH401 3.6 16.9 1.0
N A:GLY11 3.7 27.6 1.0
N A:GLN12 3.9 25.9 1.0
N A:GLY13 3.9 19.2 1.0
O A:GLY11 4.0 29.4 1.0
C20 A:BUH401 4.1 18.6 1.0
CB A:THR232 4.2 16.6 1.0
CB A:ALA335 4.2 17.2 1.0
CA A:THR232 4.2 13.6 1.0
CA A:GLY13 4.3 17.3 1.0
CG2 A:THR232 4.4 20.1 1.0
C A:GLN12 4.7 23.9 1.0
N A:THR232 4.7 14.3 1.0
NH2 A:ARG307 4.7 41.7 1.0
N22 A:BUH401 4.7 16.4 1.0
CE1 A:TYR14 4.8 16.7 1.0
CA A:GLN12 4.8 24.0 1.0
C21 A:BUH401 4.9 18.3 1.0
C A:SER10 4.9 30.4 1.0
CD1 A:TYR14 5.0 17.2 1.0

Fluorine binding site 4 out of 7 in 6eqm

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Fluorine binding site 4 out of 7 in the Crystal Structure of Human Bace-1 in Complex with CNP520


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of Human Bace-1 in Complex with CNP520 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:23.0
occ:1.00
 F30 A:BUH401 0.0 23.0 1.0
C26 A:BUH401 1.3 23.5 1.0
F28 A:BUH401 2.1 22.6 1.0
F29 A:BUH401 2.2 26.6 1.0
C18 A:BUH401 2.3 17.7 1.0
C17 A:BUH401 3.0 16.9 1.0
O A:THR231 3.1 14.3 1.0
CB A:ALA335 3.2 17.2 1.0
C19 A:BUH401 3.3 20.5 1.0
CA A:THR232 3.3 13.6 1.0
C A:THR231 3.4 13.7 1.0
N A:THR232 3.4 14.3 1.0
OG1 A:THR232 3.7 20.2 1.0
O A:SER229 3.7 14.1 1.0
CB A:THR232 4.1 16.6 1.0
N A:ALA335 4.2 13.8 1.0
N A:THR231 4.2 13.1 1.0
N22 A:BUH401 4.2 16.4 1.0
CA A:ALA335 4.3 13.9 1.0
CA A:THR231 4.4 13.1 1.0
C20 A:BUH401 4.4 18.6 1.0
C A:THR232 4.5 14.2 1.0
C A:SER229 4.6 14.4 1.0
C A:GLY230 4.6 14.0 1.0
O A:THR232 4.6 14.1 1.0
CG2 A:THR232 4.7 20.1 1.0
C21 A:BUH401 4.8 18.3 1.0
O A:HOH584 4.8 35.2 1.0
O A:HOH659 5.0 15.9 1.0

Fluorine binding site 5 out of 7 in 6eqm

Go back to Fluorine Binding Sites List in 6eqm
Fluorine binding site 5 out of 7 in the Crystal Structure of Human Bace-1 in Complex with CNP520


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Crystal Structure of Human Bace-1 in Complex with CNP520 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:21.9
occ:1.00
 F32 A:BUH401 0.0 21.9 1.0
C31 A:BUH401 1.3 21.9 1.0
F33 A:BUH401 2.2 22.7 1.0
F34 A:BUH401 2.2 22.2 1.0
C11 A:BUH401 2.3 18.6 1.0
C15 A:BUH401 2.8 18.8 1.0
O A:HOH698 2.8 21.2 1.0
OD2 A:ASP228 2.9 14.7 1.0
N16 A:BUH401 2.9 16.0 1.0
C10 A:BUH401 3.0 16.0 1.0
O A:HOH797 3.2 28.6 1.0
O A:HOH774 3.3 24.6 1.0
O A:HOH623 3.5 19.8 1.0
O12 A:BUH401 3.5 19.0 1.0
OG1 A:THR231 3.6 14.9 1.0
CG A:ASP228 4.0 13.9 1.0
N9 A:BUH401 4.2 15.6 1.0
C13 A:BUH401 4.4 19.4 1.0
O A:GLY34 4.6 14.9 1.0
OD1 A:ASP228 4.6 14.3 1.0
O A:HOH800 4.7 44.8 1.0
O A:HOH795 4.7 38.0 1.0
O A:HOH664 4.8 34.6 1.0
C8 A:BUH401 5.0 16.7 1.0
CB A:THR231 5.0 14.9 1.0

Fluorine binding site 6 out of 7 in 6eqm

Go back to Fluorine Binding Sites List in 6eqm
Fluorine binding site 6 out of 7 in the Crystal Structure of Human Bace-1 in Complex with CNP520


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Crystal Structure of Human Bace-1 in Complex with CNP520 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:22.7
occ:1.00
 F33 A:BUH401 0.0 22.7 1.0
C31 A:BUH401 1.4 21.9 1.0
F32 A:BUH401 2.2 21.9 1.0
F34 A:BUH401 2.3 22.2 1.0
C11 A:BUH401 2.3 18.6 1.0
O12 A:BUH401 2.6 19.0 1.0
O A:HOH767 2.9 45.2 1.0
C15 A:BUH401 2.9 18.8 1.0
O A:HOH800 3.3 44.8 1.0
O A:HOH774 3.5 24.6 1.0
C13 A:BUH401 3.6 19.4 1.0
C10 A:BUH401 3.7 16.0 1.0
O A:HOH797 3.8 28.6 1.0
O A:HOH623 4.0 19.8 1.0
O A:HOH795 4.2 38.0 1.0
N16 A:BUH401 4.4 16.0 1.0
O A:HOH664 4.5 34.6 1.0
O A:HOH698 4.6 21.2 1.0
N9 A:BUH401 4.6 15.6 1.0
O A:HOH775 4.6 46.1 1.0
C8 A:BUH401 4.7 16.7 1.0
CD1 A:TYR71 4.8 29.1 0.5
OG1 A:THR231 5.0 14.9 1.0
OD2 A:ASP228 5.0 14.7 1.0

Fluorine binding site 7 out of 7 in 6eqm

Go back to Fluorine Binding Sites List in 6eqm
Fluorine binding site 7 out of 7 in the Crystal Structure of Human Bace-1 in Complex with CNP520


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Crystal Structure of Human Bace-1 in Complex with CNP520 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:22.2
occ:1.00
 F34 A:BUH401 0.0 22.2 1.0
C31 A:BUH401 1.4 21.9 1.0
F32 A:BUH401 2.2 21.9 1.0
F33 A:BUH401 2.3 22.7 1.0
C11 A:BUH401 2.4 18.6 1.0
C10 A:BUH401 2.8 16.0 1.0
O12 A:BUH401 2.8 19.0 1.0
C13 A:BUH401 3.0 19.4 1.0
N16 A:BUH401 3.3 16.0 1.0
O A:HOH698 3.3 21.2 1.0
O A:HOH664 3.4 34.6 1.0
O A:HOH797 3.4 28.6 1.0
N9 A:BUH401 3.5 15.6 1.0
O A:HOH625 3.7 21.4 1.0
O A:GLY34 3.7 14.9 1.0
C15 A:BUH401 3.8 18.8 1.0
C8 A:BUH401 3.8 16.7 1.0
CE1 A:TYR71 4.3 30.1 0.5
O A:HOH767 4.5 45.2 1.0
OD2 A:ASP228 4.6 14.7 1.0
CD1 A:TYR71 4.6 29.1 0.5
O A:HOH774 4.6 24.6 1.0
C A:GLY34 4.6 14.6 1.0
C14 A:BUH401 4.7 17.5 1.0
CZ A:TYR71 4.9 34.4 0.5
O A:HOH800 5.0 44.8 1.0

Reference:

U.Neumann, M.Ufer, L.H.Jacobson, M.L.Rouzade-Dominguez, G.Huledal, C.Kolly, R.M.Luond, R.Machauer, S.J.Veenstra, K.Hurth, H.Rueeger, M.Tintelnot-Blomley, M.Staufenbiel, D.R.Shimshek, L.Perrot, W.Frieauff, V.Dubost, H.Schiller, B.Vogg, K.Beltz, A.Avrameas, S.Kretz, N.Pezous, J.M.Rondeau, N.Beckmann, A.Hartmann, S.Vormfelde, O.J.David, B.Galli, R.Ramos, A.Graf, C.Lopez Lopez. The Bace-1 Inhibitor CNP520 For Prevention Trials in Alzheimer'S Disease. Embo Mol Med V. 10 2018.
ISSN: ESSN 1757-4684
PubMed: 30224383
DOI: 10.15252/EMMM.201809316
Page generated: Thu Aug 1 19:45:24 2024

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