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Fluorine in PDB 4y84: Yeast 20S Proteasome in Complex with N3-A(4,4-F2P)Nll-Ep

Enzymatic activity of Yeast 20S Proteasome in Complex with N3-A(4,4-F2P)Nll-Ep

All present enzymatic activity of Yeast 20S Proteasome in Complex with N3-A(4,4-F2P)Nll-Ep:
3.4.25.1;

Protein crystallography data

The structure of Yeast 20S Proteasome in Complex with N3-A(4,4-F2P)Nll-Ep, PDB code: 4y84 was solved by E.M.Huber, M.Groll, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.00 / 2.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 136.950, 299.900, 145.790, 90.00, 113.00, 90.00
R / Rfree (%) 18.5 / 20.3

Other elements in 4y84:

The structure of Yeast 20S Proteasome in Complex with N3-A(4,4-F2P)Nll-Ep also contains other interesting chemical elements:

Magnesium (Mg) 7 atoms
Chlorine (Cl) 2 atoms

Fluorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Fluorine atom in the Yeast 20S Proteasome in Complex with N3-A(4,4-F2P)Nll-Ep (pdb code 4y84). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 12 binding sites of Fluorine where determined in the Yeast 20S Proteasome in Complex with N3-A(4,4-F2P)Nll-Ep, PDB code: 4y84:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 12 in 4y84

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Fluorine binding site 1 out of 12 in the Yeast 20S Proteasome in Complex with N3-A(4,4-F2P)Nll-Ep


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Yeast 20S Proteasome in Complex with N3-A(4,4-F2P)Nll-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
e:F4

b:72.0
occ:1.00
 F1 e:PDF4 0.0 72.0 1.0
CG e:PDF4 1.4 67.8 1.0
F2 e:PDF4 2.2 69.0 1.0
CB e:PDF4 2.3 66.5 1.0
CD e:PDF4 2.4 63.6 1.0
N e:PDF4 3.5 64.5 1.0
CA e:PDF4 3.5 64.5 1.0
CB I:ASP124 3.5 54.6 1.0
OD2 I:ASP124 3.5 62.2 1.0
CG I:ASP124 3.8 58.9 1.0
CB I:CYS128 4.1 61.6 1.0
SG I:CYS128 4.2 70.2 1.0
C e:PDF4 4.4 62.1 1.0
N I:ASP124 4.5 52.0 1.0
CA I:ASP124 4.5 52.5 1.0
O e:PDF4 4.6 57.5 1.0
C e:ALA3 4.7 70.1 1.0
OG H:SER20 4.8 66.8 1.0
OD1 I:ASP124 4.9 57.1 1.0
O I:CYS128 4.9 59.7 1.0

Fluorine binding site 2 out of 12 in 4y84

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Fluorine binding site 2 out of 12 in the Yeast 20S Proteasome in Complex with N3-A(4,4-F2P)Nll-Ep


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Yeast 20S Proteasome in Complex with N3-A(4,4-F2P)Nll-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
e:F4

b:69.0
occ:1.00
 F2 e:PDF4 0.0 69.0 1.0
CG e:PDF4 1.3 67.8 1.0
F1 e:PDF4 2.2 72.0 1.0
CB e:PDF4 2.3 66.5 1.0
CD e:PDF4 2.4 63.6 1.0
CA e:PDF4 3.1 64.5 1.0
N e:PDF4 3.2 64.5 1.0
CB H:ALA27 3.7 64.6 1.0
OE1 H:GLN22 3.9 0.0 1.0
CB H:GLN22 4.0 89.8 1.0
CD H:GLN22 4.3 0.5 1.0
CG H:GLN22 4.3 0.2 1.0
C e:PDF4 4.4 62.1 1.0
C e:ALA3 4.5 70.1 1.0
O H:THR21 4.6 72.5 1.0
CA H:GLN22 4.7 74.9 1.0
CB I:ASP124 4.7 54.6 1.0
OG H:SER20 4.7 66.8 1.0
N H:GLN22 4.9 73.3 1.0
C H:THR21 4.9 69.5 1.0

Fluorine binding site 3 out of 12 in 4y84

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Fluorine binding site 3 out of 12 in the Yeast 20S Proteasome in Complex with N3-A(4,4-F2P)Nll-Ep


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Yeast 20S Proteasome in Complex with N3-A(4,4-F2P)Nll-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
f:F4

b:74.0
occ:1.00
 F1 f:PDF4 0.0 74.0 1.0
CG f:PDF4 0.9 67.2 1.0
F2 f:PDF4 1.4 66.9 1.0
CD f:PDF4 1.9 65.5 1.0
CB f:PDF4 1.9 64.2 1.0
N f:PDF4 3.0 61.0 1.0
CA f:PDF4 3.1 60.8 1.0
O L:HOH417 3.9 51.2 1.0
C f:PDF4 4.0 56.4 1.0
CB L:ASP126 4.1 47.1 1.0
CB K:ALA27 4.2 52.8 1.0
OD2 L:ASP126 4.2 47.5 1.0
C f:ALA3 4.2 63.2 1.0
O f:PDF4 4.3 52.9 1.0
CB K:ALA20 4.6 44.8 1.0
CB K:ALA49 4.6 49.2 1.0
CG L:ASP126 4.7 48.8 1.0
N f:NLE5 4.7 53.0 1.0
CA f:ALA3 4.7 69.1 1.0
O L:HOH414 4.9 50.5 1.0

Fluorine binding site 4 out of 12 in 4y84

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Fluorine binding site 4 out of 12 in the Yeast 20S Proteasome in Complex with N3-A(4,4-F2P)Nll-Ep


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Yeast 20S Proteasome in Complex with N3-A(4,4-F2P)Nll-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
f:F4

b:66.9
occ:1.00
 F2 f:PDF4 0.0 66.9 1.0
CG f:PDF4 0.9 67.2 1.0
F1 f:PDF4 1.4 74.0 1.0
CD f:PDF4 1.9 65.5 1.0
CB f:PDF4 2.0 64.2 1.0
N f:PDF4 2.6 61.0 1.0
CA f:PDF4 2.7 60.8 1.0
C f:ALA3 3.7 63.2 1.0
CB K:ALA27 3.7 52.8 1.0
C f:PDF4 3.9 56.4 1.0
CB K:ALA22 4.2 44.2 1.0
CA f:ALA3 4.3 69.1 1.0
O K:THR21 4.4 52.2 1.0
O f:PDF4 4.5 52.9 1.0
O f:ALA3 4.6 62.4 1.0
N f:NLE5 4.6 53.0 1.0
C K:THR21 4.6 50.3 1.0
CB L:ASP126 4.7 47.1 1.0
N K:ALA22 4.7 49.8 1.0
O f:ACE2 4.8 0.6 1.0
CA K:ALA22 4.9 48.4 1.0
OD2 L:ASP126 5.0 47.5 1.0

Fluorine binding site 5 out of 12 in 4y84

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Fluorine binding site 5 out of 12 in the Yeast 20S Proteasome in Complex with N3-A(4,4-F2P)Nll-Ep


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Yeast 20S Proteasome in Complex with N3-A(4,4-F2P)Nll-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
g:F4

b:58.7
occ:1.00
 F1 g:PDF4 0.0 58.7 1.0
CG g:PDF4 1.4 57.0 1.0
F2 g:PDF4 2.2 57.4 1.0
CB g:PDF4 2.3 54.8 1.0
CD g:PDF4 2.4 53.5 1.0
OG H:SER118 2.7 53.0 1.0
O H:HOH311 3.1 53.5 1.0
CG H:HIS114 3.4 83.3 0.5
CB H:HIS114 3.4 64.0 0.5
N g:PDF4 3.4 54.1 1.0
CA g:PDF4 3.5 52.9 1.0
CG H:HIS114 3.5 83.3 0.5
CD2 H:HIS114 3.6 93.4 0.5
CB H:HIS114 3.6 64.0 0.5
ND1 H:HIS114 3.8 92.2 0.5
ND1 H:HIS114 3.9 92.2 0.5
CB H:SER118 4.0 51.6 1.0
CD2 H:HIS114 4.0 93.4 0.5
NE2 H:HIS114 4.1 94.7 0.5
CE1 H:HIS114 4.2 92.0 0.5
C g:PDF4 4.5 48.6 1.0
O g:HOH102 4.5 45.9 1.0
CE1 H:HIS114 4.5 92.0 0.5
O g:PDF4 4.6 47.8 1.0
NE2 H:HIS114 4.6 94.7 0.5
C g:ALA3 4.7 59.3 1.0
CA H:HIS114 4.9 57.3 0.5
CB N:ALA49 4.9 37.1 1.0
CA H:HIS114 5.0 57.3 0.5

Fluorine binding site 6 out of 12 in 4y84

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Fluorine binding site 6 out of 12 in the Yeast 20S Proteasome in Complex with N3-A(4,4-F2P)Nll-Ep


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Yeast 20S Proteasome in Complex with N3-A(4,4-F2P)Nll-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
g:F4

b:57.4
occ:1.00
 F2 g:PDF4 0.0 57.4 1.0
CG g:PDF4 1.3 57.0 1.0
F1 g:PDF4 2.2 58.7 1.0
CB g:PDF4 2.3 54.8 1.0
CD g:PDF4 2.3 53.5 1.0
CA g:PDF4 3.0 52.9 1.0
N g:PDF4 3.1 54.1 1.0
CE1 H:HIS114 3.6 92.0 0.5
ND1 H:HIS114 3.7 92.2 0.5
NE2 H:HIS114 3.9 94.7 0.5
OG1 N:THR22 3.9 47.5 1.0
CG H:HIS114 4.0 83.3 0.5
CB N:ALA27 4.1 39.6 1.0
ND1 H:HIS114 4.1 92.2 0.5
CD2 H:HIS114 4.1 93.4 0.5
CB N:THR22 4.3 50.0 1.0
C g:ALA3 4.3 59.3 1.0
C g:PDF4 4.4 48.6 1.0
CG H:HIS114 4.5 83.3 0.5
CB H:HIS114 4.6 64.0 0.5
CE1 H:HIS114 4.7 92.0 0.5
CG2 N:THR20 4.8 43.9 1.0
O N:THR21 4.8 48.1 1.0
OG H:SER118 4.8 53.0 1.0
CB H:HIS114 4.8 64.0 0.5
O g:PDF4 5.0 47.8 1.0

Fluorine binding site 7 out of 12 in 4y84

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Fluorine binding site 7 out of 12 in the Yeast 20S Proteasome in Complex with N3-A(4,4-F2P)Nll-Ep


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Yeast 20S Proteasome in Complex with N3-A(4,4-F2P)Nll-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
h:F4

b:76.3
occ:1.00
 F1 h:PDF4 0.0 76.3 1.0
CG h:PDF4 1.1 73.1 1.0
F2 h:PDF4 1.6 75.7 1.0
CD h:PDF4 2.0 70.9 1.0
CB h:PDF4 2.2 68.6 1.0
N h:PDF4 3.2 67.9 1.0
CA h:PDF4 3.3 67.4 1.0
CB W:ASP124 3.8 61.7 1.0
OD2 W:ASP124 3.9 68.0 1.0
O W:HOH305 3.9 59.9 1.0
CG W:ASP124 4.2 65.9 1.0
C h:PDF4 4.3 67.2 1.0
C h:ALA3 4.4 68.5 1.0
SG W:CYS128 4.5 77.1 1.0
CB W:CYS128 4.5 66.3 1.0
O h:PDF4 4.5 65.3 1.0
OG V:SER20 4.6 72.7 1.0
CB V:ALA27 4.8 68.2 1.0
N W:ASP124 4.8 59.0 1.0
CA h:ALA3 4.9 69.9 1.0
CA W:ASP124 4.9 59.5 1.0
O W:HOH301 4.9 50.0 1.0

Fluorine binding site 8 out of 12 in 4y84

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Fluorine binding site 8 out of 12 in the Yeast 20S Proteasome in Complex with N3-A(4,4-F2P)Nll-Ep


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Yeast 20S Proteasome in Complex with N3-A(4,4-F2P)Nll-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
h:F4

b:75.7
occ:1.00
 F2 h:PDF4 0.0 75.7 1.0
CG h:PDF4 1.0 73.1 1.0
F1 h:PDF4 1.6 76.3 1.0
CD h:PDF4 1.9 70.9 1.0
CB h:PDF4 2.1 68.6 1.0
N h:PDF4 2.6 67.9 1.0
CA h:PDF4 2.7 67.4 1.0
C h:ALA3 3.8 68.5 1.0
C h:PDF4 4.0 67.2 1.0
CB V:GLN22 4.0 81.0 1.0
CB V:ALA27 4.3 68.2 1.0
O h:ACE2 4.3 93.0 1.0
OE1 V:GLN22 4.3 1.0 1.0
CA h:ALA3 4.4 69.9 1.0
O V:THR21 4.4 61.4 1.0
CB W:ASP124 4.5 61.7 1.0
O h:PDF4 4.6 65.3 1.0
O h:ALA3 4.7 68.3 1.0
CA V:GLN22 4.7 66.4 1.0
OD2 W:ASP124 4.7 68.0 1.0
CG V:GLN22 4.7 98.0 1.0
O W:HOH305 4.8 59.9 1.0
N h:NLE5 4.8 69.4 1.0
C V:THR21 4.9 61.0 1.0
OG V:SER20 4.9 72.7 1.0
CD V:GLN22 4.9 0.8 1.0
N V:GLN22 4.9 65.3 1.0

Fluorine binding site 9 out of 12 in 4y84

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Fluorine binding site 9 out of 12 in the Yeast 20S Proteasome in Complex with N3-A(4,4-F2P)Nll-Ep


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Yeast 20S Proteasome in Complex with N3-A(4,4-F2P)Nll-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
i:F4

b:82.0
occ:1.00
 F1 i:PDF4 0.0 82.0 1.0
CG i:PDF4 1.0 71.7 1.0
F2 i:PDF4 1.5 70.8 1.0
CD i:PDF4 2.0 66.8 1.0
CB i:PDF4 2.1 72.1 1.0
N i:PDF4 3.1 65.3 1.0
CA i:PDF4 3.2 66.1 1.0
O Z:HOH419 3.9 49.8 1.0
CB Y:ALA27 4.0 39.1 1.0
CB Z:ASP126 4.0 48.2 1.0
C i:PDF4 4.1 59.4 1.0
OD2 Z:ASP126 4.4 53.1 1.0
C i:ALA3 4.4 67.7 1.0
O i:PDF4 4.6 54.2 1.0
N i:ALA3 4.6 83.4 1.0
N2 i:AZI1 4.7 0.6 1.0
N3 i:AZI1 4.7 99.3 1.0
CG Z:ASP126 4.7 52.2 1.0
CB Y:ALA20 4.7 43.4 1.0
CA i:ALA3 4.8 74.0 1.0
N i:NLE5 4.9 52.6 1.0
N1 i:AZI1 4.9 93.4 1.0
O Z:HOH410 4.9 37.0 1.0
CB Y:ALA49 5.0 43.2 1.0

Fluorine binding site 10 out of 12 in 4y84

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Fluorine binding site 10 out of 12 in the Yeast 20S Proteasome in Complex with N3-A(4,4-F2P)Nll-Ep


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of Yeast 20S Proteasome in Complex with N3-A(4,4-F2P)Nll-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
i:F4

b:70.8
occ:1.00
 F2 i:PDF4 0.0 70.8 1.0
CG i:PDF4 0.9 71.7 1.0
F1 i:PDF4 1.5 82.0 1.0
CD i:PDF4 1.9 66.8 1.0
CB i:PDF4 2.0 72.1 1.0
N i:PDF4 2.6 65.3 1.0
CA i:PDF4 2.7 66.1 1.0
N2 i:AZI1 3.7 0.6 1.0
C i:ALA3 3.7 67.7 1.0
N3 i:AZI1 3.8 99.3 1.0
N i:ALA3 3.8 83.4 1.0
CB Y:ALA27 3.8 39.1 1.0
CB Y:ALA22 3.9 47.2 1.0
N1 i:AZI1 3.9 93.4 1.0
C i:PDF4 3.9 59.4 1.0
CA i:ALA3 4.3 74.0 1.0
O Y:THR21 4.3 56.4 1.0
N Y:ALA22 4.5 53.6 1.0
C Y:THR21 4.5 56.7 1.0
C i:ACE2 4.5 89.5 1.0
CA Y:ALA22 4.6 47.7 1.0
O i:PDF4 4.6 54.2 1.0
CH3 i:ACE2 4.6 0.7 1.0
O i:ALA3 4.6 65.2 1.0
N i:NLE5 4.6 52.6 1.0
O Z:HOH419 4.7 49.8 1.0
CB Z:ASP126 4.7 48.2 1.0

Reference:

E.M.Huber, G.De Bruin, W.Heinemeyer, G.Paniagua Soriano, H.S.Overkleeft, M.Groll. Systematic Analyses of Substrate Preferences of 20S Proteasomes Using Peptidic Epoxyketone Inhibitors. J.Am.Chem.Soc. V. 137 7835 2015.
ISSN: ESSN 1520-5126
PubMed: 26020686
DOI: 10.1021/JACS.5B03688
Page generated: Thu Aug 1 06:56:36 2024

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