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Magnesium in PDB 4qlu: Ycp in Complex with Tripeptidic Epoxyketone Inhibitor 9

Enzymatic activity of Ycp in Complex with Tripeptidic Epoxyketone Inhibitor 9

All present enzymatic activity of Ycp in Complex with Tripeptidic Epoxyketone Inhibitor 9:
3.4.25.1;

Protein crystallography data

The structure of Ycp in Complex with Tripeptidic Epoxyketone Inhibitor 9, PDB code: 4qlu was solved by G.De Bruin, E.Huber, B.Xin, E.Van Rooden, K.Al-Ayed, K.Kim, A.Kisselev, C.Driessen, G.Van Der Marel, M.Groll, H.Overkleeft, 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 (°) 134.880, 299.380, 144.830, 90.00, 112.78, 90.00
R / Rfree (%) 22.3 / 24.8

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Ycp in Complex with Tripeptidic Epoxyketone Inhibitor 9 (pdb code 4qlu). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Ycp in Complex with Tripeptidic Epoxyketone Inhibitor 9, PDB code: 4qlu:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 4qlu

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Magnesium binding site 1 out of 8 in the Ycp in Complex with Tripeptidic Epoxyketone Inhibitor 9


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Ycp in Complex with Tripeptidic Epoxyketone Inhibitor 9 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:40.1
occ:1.00
 O G:MET125 2.1 23.0 1.0
O G:ARG122 2.4 48.6 1.0
O G:TYR119 2.5 41.1 1.0
OG1 G:THR8 2.8 35.9 1.0
CG2 G:THR8 3.2 32.5 1.0
C G:MET125 3.3 44.1 1.0
O G:ALA123 3.5 47.7 1.0
C G:ARG122 3.5 47.1 1.0
CB G:THR8 3.6 34.5 1.0
C G:ALA123 3.7 47.6 1.0
CA G:ALA123 3.7 45.4 1.0
C G:TYR119 3.7 39.7 1.0
N G:MET125 4.0 45.8 1.0
N G:ALA123 4.1 46.3 1.0
CA G:MET125 4.2 46.4 1.0
N G:ARG126 4.2 41.7 1.0
CA G:ARG126 4.3 41.4 1.0
N G:THR8 4.3 37.0 1.0
CA G:TYR119 4.4 39.0 1.0
N G:TYR124 4.5 50.8 1.0
CA G:THR8 4.6 37.1 1.0
CB G:MET125 4.7 54.3 1.0
CA G:ARG122 4.8 48.1 1.0
N G:ARG122 4.8 42.4 1.0
N G:THR120 4.8 38.1 1.0
CD G:PRO127 4.8 36.9 1.0
C G:TYR124 4.8 45.6 1.0
C G:ARG126 4.9 41.2 1.0
CB G:TYR119 4.9 41.6 1.0
CA G:THR120 5.0 39.0 1.0

Magnesium binding site 2 out of 8 in 4qlu

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Magnesium binding site 2 out of 8 in the Ycp in Complex with Tripeptidic Epoxyketone Inhibitor 9


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Ycp in Complex with Tripeptidic Epoxyketone Inhibitor 9 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg301

b:64.2
occ:1.00
 OD1 N:ASP51 2.4 42.5 1.0
O H:HOH412 2.7 39.6 1.0
OE1 H:GLN91 2.9 57.9 1.0
CG N:ASP51 3.3 44.1 1.0
NE2 H:GLN91 3.4 60.6 1.0
CD H:GLN91 3.5 57.6 1.0
OD2 N:ASP51 3.6 47.3 1.0
O N:ASN92 3.7 51.0 1.0
CE1 H:PHE88 3.9 24.8 1.0
CZ H:PHE88 4.0 25.2 1.0
CB N:ASP51 4.7 43.2 1.0
CD1 H:PHE88 4.7 25.2 1.0
C N:ASN92 4.9 49.1 1.0
CG H:GLN91 4.9 54.0 1.0
CE2 H:PHE88 4.9 25.3 1.0

Magnesium binding site 3 out of 8 in 4qlu

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Magnesium binding site 3 out of 8 in the Ycp in Complex with Tripeptidic Epoxyketone Inhibitor 9


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Ycp in Complex with Tripeptidic Epoxyketone Inhibitor 9 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:54.9
occ:1.00
 O I:ALA174 2.9 40.5 1.0
O I:ASP177 3.0 44.3 1.0
O I:HOH402 3.1 40.7 1.0
O I:SER180 3.2 43.7 1.0
OXT I:ASP204 3.4 52.1 1.0
C I:ALA174 3.8 42.9 1.0
CA I:ASP175 3.9 42.5 1.0
C I:ASP177 4.1 44.5 1.0
C I:ASP175 4.2 42.1 1.0
O I:ASP175 4.2 42.3 1.0
N I:ASP175 4.2 42.2 1.0
C I:ASP204 4.3 49.9 1.0
NH2 Y:ARG19 4.3 54.5 1.0
C I:SER180 4.4 47.3 1.0
O I:ASP204 4.4 52.0 1.0
OD1 I:ASP175 4.6 52.7 1.0
N I:ASP177 4.6 44.0 1.0
NH1 Y:ARG19 4.7 58.6 1.0
CA I:ALA178 4.8 42.4 1.0
N I:ALA178 4.8 43.7 1.0
O I:ALA178 4.8 41.2 1.0
OD1 I:ASP204 4.8 47.2 1.0
CA I:GLY181 4.9 45.3 1.0
CZ Y:ARG19 4.9 53.7 1.0
C I:ALA178 5.0 41.6 1.0
CA I:ASP177 5.0 45.6 1.0
N I:ARG176 5.0 41.6 1.0

Magnesium binding site 4 out of 8 in 4qlu

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Magnesium binding site 4 out of 8 in the Ycp in Complex with Tripeptidic Epoxyketone Inhibitor 9


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Ycp in Complex with Tripeptidic Epoxyketone Inhibitor 9 within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg301

b:52.8
occ:1.00
 O W:ASP204 2.1 49.2 1.0
O K:ASP168 2.2 48.6 1.0
O K:SER171 2.4 42.6 1.0
O K:ALA165 2.5 39.2 1.0
C W:ASP204 3.1 51.4 1.0
C K:ASP168 3.3 44.1 1.0
C K:ALA165 3.6 41.1 1.0
CA W:ASP204 3.6 49.6 1.0
C K:SER171 3.6 44.2 1.0
NH1 K:ARG19 3.6 53.2 1.0
CA K:ALA169 3.7 41.2 1.0
O K:ALA169 3.8 43.3 1.0
C K:ALA169 3.8 42.9 1.0
CB W:ASP204 3.9 51.3 1.0
N K:ALA169 3.9 41.7 1.0
O K:HIS166 4.0 38.1 1.0
OXT W:ASP204 4.1 51.8 1.0
CZ K:ARG19 4.1 54.0 1.0
N K:SER171 4.2 40.3 1.0
CA K:ALA165 4.4 41.4 1.0
NH2 K:ARG19 4.4 55.8 1.0
C K:HIS166 4.4 39.3 1.0
CA K:SER171 4.5 41.5 1.0
CA K:ASP168 4.5 43.6 1.0
N K:HIS166 4.5 41.5 1.0
N K:GLY172 4.6 46.7 1.0
N K:TYR170 4.6 42.1 1.0
CA K:GLY172 4.6 46.9 1.0
N K:ASP168 4.6 42.6 1.0
O K:ALA164 4.7 44.7 1.0
CA K:HIS166 4.7 40.5 1.0
CG W:ASP204 4.9 51.1 1.0
NE K:ARG19 4.9 53.4 1.0

Magnesium binding site 5 out of 8 in 4qlu

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Magnesium binding site 5 out of 8 in the Ycp in Complex with Tripeptidic Epoxyketone Inhibitor 9


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Ycp in Complex with Tripeptidic Epoxyketone Inhibitor 9 within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg201

b:38.7
occ:1.00
 O N:ILE163 2.2 41.6 1.0
O N:SER169 2.6 40.6 1.0
O N:ASP166 2.9 43.5 1.0
C N:ILE163 3.3 40.2 1.0
CD1 a:LEU34 3.7 36.7 1.0
CG2 N:ILE163 3.7 35.7 1.0
C N:SER169 3.8 38.6 1.0
C N:ASP166 3.9 39.1 1.0
CA N:ILE163 4.0 39.7 1.0
NH1 N:ARG19 4.1 35.9 1.0
CA N:GLY170 4.3 40.0 1.0
CA N:GLY167 4.3 36.5 1.0
N N:LYS164 4.4 41.3 1.0
N N:GLY170 4.5 40.4 1.0
CB N:ILE163 4.5 37.6 1.0
N N:GLY167 4.5 36.6 1.0
CA N:LYS164 4.6 42.6 1.0
C N:LYS164 4.6 43.1 1.0
O N:LYS164 4.6 47.3 1.0
CZ N:ARG19 4.6 35.5 1.0
O N:GLY167 4.8 36.9 1.0
C N:GLY167 4.8 37.3 1.0
CG a:LEU34 4.8 36.7 1.0
CA N:SER169 4.9 36.1 1.0
NH2 N:ARG19 4.9 31.1 1.0
N N:ASP166 4.9 36.6 1.0
N N:SER169 4.9 37.8 1.0

Magnesium binding site 6 out of 8 in 4qlu

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Magnesium binding site 6 out of 8 in the Ycp in Complex with Tripeptidic Epoxyketone Inhibitor 9


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Ycp in Complex with Tripeptidic Epoxyketone Inhibitor 9 within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Mg301

b:67.6
occ:1.00
 OXT L:ASP222 2.2 52.8 1.0
O V:ILE163 2.4 44.0 1.0
O V:ASP166 2.5 45.4 1.0
O V:TRP164 3.0 54.6 1.0
C L:ASP222 3.0 56.6 1.0
C V:ASP166 3.1 44.1 1.0
C V:TRP164 3.3 49.3 1.0
C V:ILE163 3.4 41.8 1.0
O V:SER169 3.4 39.2 1.0
N V:ASP166 3.6 42.7 1.0
CA L:ASP222 3.8 56.8 1.0
O L:ASP222 3.8 59.4 1.0
N V:LEU167 3.8 44.2 1.0
CA V:TRP164 3.9 48.0 1.0
O V:GLY162 3.9 41.2 1.0
CA V:LEU167 4.0 43.5 1.0
N V:ASN165 4.0 46.1 1.0
CA V:ASP166 4.0 41.9 1.0
N V:TRP164 4.0 46.0 1.0
C V:ASN165 4.3 43.4 1.0
O L:ARG221 4.5 54.0 1.0
CA V:ILE163 4.5 37.7 1.0
CA V:ASN165 4.5 45.7 1.0
C V:SER169 4.6 38.6 1.0
CD2 V:LEU167 4.6 36.7 1.0
CB L:ASP222 4.6 57.0 1.0
NH1 V:ARG19 4.7 49.6 1.0
CD1 L:ILE35 4.7 51.5 1.0
C V:LEU167 4.8 44.0 1.0
N L:ASP222 4.9 55.5 1.0
C V:GLY162 4.9 36.8 1.0

Magnesium binding site 7 out of 8 in 4qlu

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Magnesium binding site 7 out of 8 in the Ycp in Complex with Tripeptidic Epoxyketone Inhibitor 9


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Ycp in Complex with Tripeptidic Epoxyketone Inhibitor 9 within 5.0Å range:
probe atom residue distance (Å) B Occ
Y:Mg301

b:36.7
occ:1.00
 O I:ASP204 2.2 52.0 1.0
O Y:ASP168 2.2 45.6 1.0
O Y:SER171 2.4 44.2 1.0
O Y:HOH401 2.5 33.2 1.0
O Y:ALA165 2.7 43.6 1.0
C I:ASP204 3.2 49.9 1.0
C Y:ASP168 3.3 45.4 1.0
NH1 Y:ARG19 3.4 58.6 1.0
CA Y:ALA169 3.5 41.8 1.0
O Y:ALA169 3.6 42.1 1.0
C Y:ALA169 3.6 43.5 1.0
C Y:SER171 3.6 43.5 1.0
N Y:ALA169 3.8 44.5 1.0
CA I:ASP204 3.8 47.6 1.0
C Y:ALA165 3.8 44.3 1.0
CZ Y:ARG19 4.0 53.7 1.0
CB I:ASP204 4.1 45.6 1.0
N Y:SER171 4.1 39.1 1.0
OXT I:ASP204 4.2 52.1 1.0
O Y:HIS166 4.2 50.9 1.0
NH2 Y:ARG19 4.3 54.5 1.0
N Y:TYR170 4.4 44.9 1.0
CA Y:SER171 4.5 39.9 1.0
CA Y:ASP168 4.5 44.1 1.0
CA Y:ALA165 4.6 41.0 1.0
N Y:GLY172 4.6 47.2 1.0
C Y:HIS166 4.7 50.6 1.0
CA Y:GLY172 4.7 48.8 1.0
N Y:ASP168 4.7 42.9 1.0
NE Y:ARG19 4.8 52.6 1.0
N Y:HIS166 4.8 47.2 1.0
O Y:ALA164 4.9 45.1 1.0
CB Y:ALA169 4.9 39.5 1.0
CA Y:HIS166 5.0 48.9 1.0

Magnesium binding site 8 out of 8 in 4qlu

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Magnesium binding site 8 out of 8 in the Ycp in Complex with Tripeptidic Epoxyketone Inhibitor 9


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Ycp in Complex with Tripeptidic Epoxyketone Inhibitor 9 within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg301

b:71.3
occ:1.00
 O Z:VAL198 2.7 42.5 1.0
O Z:THR192 3.0 47.5 1.0
O Z:ASP222 3.1 65.3 1.0
O Z:HIS195 3.2 46.4 1.0
NH2 Z:ARG28 3.4 65.9 1.0
O Z:ILE196 3.8 50.1 1.0
OD1 Z:ASP222 3.9 68.8 1.0
C Z:VAL198 3.9 42.6 1.0
NH2 H:ARG19 3.9 60.4 1.0
CG2 Z:THR192 4.0 43.5 1.0
C Z:THR192 4.0 48.1 1.0
CA Z:ILE196 4.1 41.5 1.0
C Z:ASP222 4.2 71.4 1.0
C Z:ILE196 4.2 42.6 1.0
C Z:HIS195 4.2 43.8 1.0
CZ Z:ARG28 4.4 67.2 1.0
CA Z:THR192 4.4 47.1 1.0
NH1 Z:ARG28 4.6 70.4 1.0
CA Z:GLY199 4.6 40.1 1.0
N Z:ILE196 4.7 42.1 1.0
OXT Z:ASP222 4.7 66.4 1.0
N Z:GLY199 4.7 40.7 1.0
N Z:VAL198 4.7 42.4 1.0
NH1 H:ARG19 4.7 58.7 1.0
CZ H:ARG19 4.7 57.9 1.0
CG Z:ASP222 4.8 65.7 1.0
CB Z:THR192 4.8 44.5 1.0
O Z:LYS220 4.8 55.5 1.0
CA Z:VAL198 4.9 41.8 1.0

Reference:

G.De Bruin, E.M.Huber, B.T.Xin, E.J.Van Rooden, K.Al-Ayed, K.B.Kim, A.F.Kisselev, C.Driessen, M.Van Der Stelt, G.A.Van Der Marel, M.Groll, H.S.Overkleeft. Structure-Based Design of Beta 1I or Beta 5I Specific Inhibitors of Human Immunoproteasomes J.Med.Chem. V. 57 6197 2014.
ISSN: ISSN 0022-2623
PubMed: 25006746
DOI: 10.1021/JM500716S
Page generated: Tue Aug 20 02:05:11 2024

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