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Magnesium in PDB 5l54: Yeast 20S Proteasome in Complex with Epoxyketone Inhibitor 16

Enzymatic activity of Yeast 20S Proteasome in Complex with Epoxyketone Inhibitor 16

All present enzymatic activity of Yeast 20S Proteasome in Complex with Epoxyketone Inhibitor 16:
3.4.25.1;

Protein crystallography data

The structure of Yeast 20S Proteasome in Complex with Epoxyketone Inhibitor 16, PDB code: 5l54 was solved by M.Groll, E.M.Huber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.00 / 2.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 136.440, 299.140, 145.470, 90.00, 112.87, 90.00
R / Rfree (%) 18.6 / 20.6

Other elements in 5l54:

The structure of Yeast 20S Proteasome in Complex with Epoxyketone Inhibitor 16 also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Yeast 20S Proteasome in Complex with Epoxyketone Inhibitor 16 (pdb code 5l54). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the Yeast 20S Proteasome in Complex with Epoxyketone Inhibitor 16, PDB code: 5l54:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 5l54

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Magnesium binding site 1 out of 7 in the Yeast 20S Proteasome in Complex with Epoxyketone Inhibitor 16


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Yeast 20S Proteasome in Complex with Epoxyketone Inhibitor 16 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:47.7
occ:1.00
 O G:MET125 2.2 51.5 1.0
OG1 G:THR8 2.6 41.7 1.0
O G:ARG122 2.7 44.6 1.0
O G:TYR119 2.8 42.6 1.0
CG2 G:THR8 3.3 41.6 1.0
O G:ALA123 3.3 51.7 1.0
C G:MET125 3.4 51.9 1.0
CB G:THR8 3.5 42.5 1.0
C G:ALA123 3.6 50.9 1.0
CA G:ALA123 3.7 48.8 1.0
C G:ARG122 3.7 47.5 1.0
C G:TYR119 4.0 42.8 1.0
N G:THR8 4.1 45.0 1.0
N G:ALA123 4.2 47.4 1.0
N G:MET125 4.2 52.0 1.0
N G:ARG126 4.2 48.5 1.0
CA G:ARG126 4.2 45.3 1.0
CA G:MET125 4.4 54.8 1.0
CA G:THR8 4.4 44.7 1.0
N G:TYR124 4.6 53.2 1.0
CD G:PRO127 4.6 39.6 1.0
CA G:TYR119 4.7 42.7 1.0
C G:ARG126 4.9 43.8 1.0
CB G:ALA123 5.0 48.7 1.0
CB G:MET125 5.0 59.3 1.0
N G:THR120 5.0 41.6 1.0
C G:TYR124 5.0 51.5 1.0
CA G:ARG122 5.0 50.1 1.0

Magnesium binding site 2 out of 7 in 5l54

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Magnesium binding site 2 out of 7 in the Yeast 20S Proteasome in Complex with Epoxyketone Inhibitor 16


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Yeast 20S Proteasome in Complex with Epoxyketone Inhibitor 16 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:62.3
occ:1.00
 O I:ASP177 2.6 47.4 1.0
O I:ALA174 2.6 51.0 1.0
O I:SER180 2.7 50.7 1.0
O Y:HOH404 3.2 52.9 1.0
OXT I:ASP204 3.7 60.5 1.0
C I:ALA174 3.7 50.7 1.0
C I:ASP177 3.8 48.4 1.0
C I:SER180 3.8 50.2 1.0
CA I:ASP175 4.1 56.2 1.0
N I:ASP175 4.3 53.3 1.0
C I:ASP175 4.4 56.8 1.0
CA I:GLY181 4.5 48.4 1.0
O I:ALA178 4.5 52.0 1.0
N I:ASP177 4.6 49.9 1.0
CA I:ALA178 4.6 46.9 1.0
OD1 I:ASP175 4.6 55.6 1.0
C I:ASP204 4.6 58.7 1.0
N I:ALA178 4.6 47.0 1.0
N I:GLY181 4.6 50.0 1.0
C I:ALA178 4.6 49.0 1.0
O I:ASP175 4.6 56.0 1.0
O I:ASP204 4.7 61.2 1.0
N I:SER180 4.7 47.5 1.0
CA I:ASP177 4.7 50.1 1.0
NH2 Y:ARG19 4.8 66.8 1.0
CA I:ALA174 4.8 47.8 1.0
CA I:SER180 4.8 48.7 1.0
NH1 Y:ARG19 4.9 66.1 1.0

Magnesium binding site 3 out of 7 in 5l54

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Magnesium binding site 3 out of 7 in the Yeast 20S Proteasome in Complex with Epoxyketone Inhibitor 16


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Yeast 20S Proteasome in Complex with Epoxyketone Inhibitor 16 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg302

b:38.1
occ:1.00
 O Y:ASP168 2.2 44.3 1.0
O I:ASP204 2.3 61.2 1.0
O Y:SER171 2.4 50.6 1.0
O Y:HOH403 2.5 47.5 1.0
O Y:ALA165 2.6 46.0 1.0
C I:ASP204 3.2 58.7 1.0
C Y:ASP168 3.2 44.2 1.0
CA Y:ALA169 3.5 41.1 1.0
C Y:SER171 3.6 50.5 1.0
O Y:ALA169 3.6 42.6 1.0
C Y:ALA169 3.6 42.5 1.0
NH1 Y:ARG19 3.7 66.1 1.0
C Y:ALA165 3.7 47.6 1.0
CA I:ASP204 3.7 57.3 1.0
N Y:ALA169 3.8 43.1 1.0
N Y:SER171 4.0 46.2 1.0
CB I:ASP204 4.0 56.9 1.0
OXT I:ASP204 4.2 60.5 1.0
O Y:HIS166 4.2 46.0 1.0
CZ Y:ARG19 4.3 64.5 1.0
CA Y:SER171 4.3 48.0 1.0
N Y:TYR170 4.4 44.6 1.0
CA Y:ALA165 4.4 48.7 1.0
CA Y:ASP168 4.5 44.4 1.0
N Y:GLY172 4.6 51.7 1.0
N Y:ASP168 4.6 45.2 1.0
C Y:HIS166 4.6 47.5 1.0
NH2 Y:ARG19 4.6 66.8 1.0
N Y:HIS166 4.7 47.7 1.0
CA Y:GLY172 4.7 52.5 1.0
O Y:ALA164 4.8 48.1 1.0
CB Y:SER171 4.8 48.1 1.0
CA Y:HIS166 4.9 48.0 1.0
CB Y:ALA169 4.9 39.6 1.0

Magnesium binding site 4 out of 7 in 5l54

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Magnesium binding site 4 out of 7 in the Yeast 20S Proteasome in Complex with Epoxyketone Inhibitor 16


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Yeast 20S Proteasome in Complex with Epoxyketone Inhibitor 16 within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg302

b:53.5
occ:1.00
 O K:ASP168 2.2 48.2 1.0
O W:ASP204 2.3 57.6 1.0
O K:ALA165 2.4 49.6 1.0
O K:SER171 2.7 49.4 1.0
C W:ASP204 3.1 57.1 1.0
C K:ASP168 3.2 46.1 1.0
C K:ALA165 3.5 51.8 1.0
CA K:ALA169 3.6 42.8 1.0
CA W:ASP204 3.6 56.4 1.0
N K:ALA169 3.7 43.9 1.0
O K:HIS166 3.8 47.5 1.0
C K:ALA169 3.8 45.4 1.0
O K:ALA169 3.9 48.1 1.0
C K:SER171 3.9 51.2 1.0
NH1 K:ARG19 4.0 67.0 1.0
CB W:ASP204 4.0 56.4 1.0
OXT W:ASP204 4.0 58.6 1.0
C K:HIS166 4.2 48.6 1.0
N K:SER171 4.3 51.0 1.0
CA K:ASP168 4.4 46.7 1.0
N K:ASP168 4.4 48.5 1.0
CA K:ALA165 4.4 55.4 1.0
N K:HIS166 4.5 49.6 1.0
CA K:HIS166 4.6 49.5 1.0
CZ K:ARG19 4.6 65.0 1.0
N K:TYR170 4.6 47.0 1.0
CA K:SER171 4.6 50.1 1.0
O K:ALA164 4.7 51.8 1.0
C K:ARG167 4.8 48.9 1.0
N K:GLY172 4.9 50.8 1.0
NH2 K:ARG19 4.9 68.7 1.0
CB K:ALA169 4.9 39.8 1.0
N W:ASP204 4.9 55.0 1.0
N K:ARG167 5.0 47.6 1.0
CA K:GLY172 5.0 51.8 1.0

Magnesium binding site 5 out of 7 in 5l54

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Magnesium binding site 5 out of 7 in the Yeast 20S Proteasome in Complex with Epoxyketone Inhibitor 16


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Yeast 20S Proteasome in Complex with Epoxyketone Inhibitor 16 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg301

b:67.0
occ:1.00
 OXT L:ASP222 2.0 71.9 1.0
O V:ASP166 2.1 55.0 1.0
O V:ILE163 2.1 56.1 1.0
O V:SER169 2.7 52.7 1.0
C L:ASP222 3.0 68.6 1.0
C V:ASP166 3.1 54.4 1.0
C V:ILE163 3.2 57.7 1.0
CA L:ASP222 3.7 66.9 1.0
O V:GLY162 3.8 54.7 1.0
N V:ASP166 3.8 50.9 1.0
C V:SER169 3.8 52.0 1.0
O V:TRP164 3.8 58.7 1.0
N V:LEU167 3.9 55.7 1.0
O L:ASP222 3.9 68.5 1.0
C V:TRP164 3.9 56.0 1.0
CA V:LEU167 3.9 55.1 1.0
NH1 V:ARG19 4.1 65.5 1.0
CA V:ASP166 4.1 51.6 1.0
N V:TRP164 4.1 57.3 1.0
CA V:ILE163 4.1 58.4 1.0
CA V:TRP164 4.2 56.9 1.0
CB L:ASP222 4.3 68.8 1.0
N V:ASN165 4.3 53.6 1.0
C V:LEU167 4.5 54.5 1.0
C V:ASN165 4.6 50.9 1.0
N V:SER169 4.6 49.4 1.0
CA V:SER169 4.7 49.7 1.0
CA V:GLY170 4.7 59.2 1.0
N V:GLY170 4.7 55.4 1.0
C V:GLY162 4.7 53.4 1.0
CZ V:ARG19 4.8 63.2 1.0
O V:LEU167 4.8 54.6 1.0
CB V:ASP166 4.9 50.5 1.0
NH2 V:ARG19 4.9 64.7 1.0
O L:ARG221 4.9 55.7 1.0
N V:ILE163 4.9 54.9 1.0
CD2 V:LEU167 5.0 49.7 1.0
CA V:ASN165 5.0 52.7 1.0
N L:ASP222 5.0 62.1 1.0

Magnesium binding site 6 out of 7 in 5l54

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Magnesium binding site 6 out of 7 in the Yeast 20S Proteasome in Complex with Epoxyketone Inhibitor 16


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Yeast 20S Proteasome in Complex with Epoxyketone Inhibitor 16 within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg201

b:54.0
occ:1.00
 O N:SER169 2.6 54.0 1.0
O N:ILE163 2.6 49.8 1.0
O N:ASP166 3.0 31.2 1.0
NH1 N:ARG19 3.7 50.5 1.0
CD1 a:LEU34 3.7 47.9 1.0
C N:ILE163 3.7 48.0 1.0
C N:SER169 3.7 49.5 1.0
CG2 N:ILE163 3.9 44.0 1.0
C N:ASP166 4.0 30.6 1.0
CA N:GLY167 4.1 41.6 1.0
CZ N:ARG19 4.2 51.4 1.0
CA N:GLY170 4.3 51.9 1.0
CA N:ILE163 4.3 46.2 1.0
NH2 N:ARG19 4.4 50.6 1.0
O N:GLY167 4.4 47.4 1.0
N N:GLY170 4.5 50.6 1.0
N N:GLY167 4.5 37.1 1.0
C N:GLY167 4.5 43.8 1.0
CB N:ILE163 4.8 45.1 1.0
N N:LYS164 4.8 49.2 1.0
CA N:SER169 4.8 46.0 1.0
N N:SER169 4.8 47.3 1.0
C N:LYS164 5.0 51.8 1.0

Magnesium binding site 7 out of 7 in 5l54

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Magnesium binding site 7 out of 7 in the Yeast 20S Proteasome in Complex with Epoxyketone Inhibitor 16


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Yeast 20S Proteasome in Complex with Epoxyketone Inhibitor 16 within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg301

b:62.4
occ:1.00
 O Z:THR192 2.5 61.6 1.0
O Z:VAL198 2.7 55.8 1.0
O Z:HIS195 2.8 49.2 1.0
C Z:THR192 3.6 59.8 1.0
C Z:HIS195 3.7 49.7 1.0
O Z:ASP222 3.8 67.7 1.0
NH2 Z:ARG28 3.8 65.8 1.0
CA Z:ILE196 3.9 49.5 1.0
CG2 Z:THR192 4.0 65.4 1.0
C Z:VAL198 4.0 56.6 1.0
O Z:ILE196 4.0 52.6 1.0
CA Z:THR192 4.1 60.4 1.0
NH2 H:ARG19 4.1 66.9 1.0
C Z:ILE196 4.1 49.8 1.0
N Z:ILE196 4.2 49.0 1.0
OD1 Z:ASP222 4.3 69.5 1.0
N Z:VAL198 4.6 53.6 1.0
CB Z:THR192 4.7 62.8 1.0
C Z:ASP222 4.7 72.0 1.0
N Z:GLU193 4.8 58.4 1.0
CA Z:VAL198 4.8 54.8 1.0
N Z:HIS195 4.8 51.1 1.0
CZ H:ARG19 4.9 66.1 1.0
N Z:GLY199 4.9 56.1 1.0
CA Z:HIS195 4.9 49.5 1.0
CA Z:GLY199 4.9 56.8 1.0
NH1 H:ARG19 5.0 68.6 1.0
CZ Z:ARG28 5.0 66.1 1.0

Reference:

E.M.Huber, W.Heinemeyer, G.De Bruin, H.S.Overkleeft, M.Groll. A Humanized Yeast Proteasome Identifies Unique Binding Modes of Inhibitors For the Immunosubunit Beta 5I. Embo J. V. 35 2602 2016.
ISSN: ESSN 1460-2075
PubMed: 27789522
DOI: 10.15252/EMBJ.201695222
Page generated: Sun Sep 29 19:19:32 2024

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