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Magnesium in PDB 4qlt: Ycp in Complex with Tripeptidic Epoxyketone Inhibitor 2 (PR924)

Enzymatic activity of Ycp in Complex with Tripeptidic Epoxyketone Inhibitor 2 (PR924)

All present enzymatic activity of Ycp in Complex with Tripeptidic Epoxyketone Inhibitor 2 (PR924):
3.4.25.1;

Protein crystallography data

The structure of Ycp in Complex with Tripeptidic Epoxyketone Inhibitor 2 (PR924), PDB code: 4qlt 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 (°) 135.650, 298.660, 145.460, 90.00, 112.83, 90.00
R / Rfree (%) 17.6 / 20.2

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Ycp in Complex with Tripeptidic Epoxyketone Inhibitor 2 (PR924) (pdb code 4qlt). 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 2 (PR924), PDB code: 4qlt:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 4qlt

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Magnesium binding site 1 out of 8 in the Ycp in Complex with Tripeptidic Epoxyketone Inhibitor 2 (PR924)


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 2 (PR924) within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:52.4
occ:1.00
 O G:MET125 2.2 53.6 1.0
OG1 G:THR8 2.6 41.9 1.0
O G:ARG122 2.6 45.6 1.0
O G:TYR119 2.6 43.9 1.0
CG2 G:THR8 3.3 40.2 1.0
C G:MET125 3.4 52.1 1.0
O G:ALA123 3.4 53.1 1.0
CB G:THR8 3.5 42.3 1.0
C G:ARG122 3.7 48.1 1.0
C G:ALA123 3.7 50.7 1.0
CA G:ALA123 3.7 48.5 1.0
C G:TYR119 3.8 44.1 1.0
N G:THR8 4.1 44.2 1.0
N G:ALA123 4.2 47.6 1.0
N G:MET125 4.2 51.7 1.0
N G:ARG126 4.2 48.1 1.0
CA G:ARG126 4.2 45.1 1.0
CA G:MET125 4.3 54.5 1.0
CA G:THR8 4.4 44.6 1.0
CA G:TYR119 4.6 43.0 1.0
N G:TYR124 4.6 53.8 1.0
CD G:PRO127 4.7 38.4 1.0
N G:THR120 4.9 42.8 1.0
C G:ARG126 4.9 43.5 1.0
CB G:MET125 4.9 58.8 1.0
CA G:ARG122 4.9 49.7 1.0
N G:ARG122 5.0 46.0 1.0
C G:TYR124 5.0 52.1 1.0
CA G:THR120 5.0 40.3 1.0

Magnesium binding site 2 out of 8 in 4qlt

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Magnesium binding site 2 out of 8 in the Ycp in Complex with Tripeptidic Epoxyketone Inhibitor 2 (PR924)


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 2 (PR924) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:60.2
occ:1.00
 O I:ALA174 2.4 45.8 1.0
O I:ASP177 2.5 47.5 1.0
O I:SER180 2.6 49.5 1.0
O I:HOH419 2.7 57.5 1.0
O I:HOH413 3.2 49.1 1.0
C I:ALA174 3.5 48.6 1.0
C I:ASP177 3.6 46.9 1.0
C I:SER180 3.7 49.2 1.0
O I:HOH417 3.9 62.5 1.0
CA I:ASP175 3.9 55.0 1.0
OXT I:ASP204 4.0 54.5 1.0
N I:ASP175 4.1 51.5 1.0
C I:ASP175 4.3 55.7 1.0
N I:ASP177 4.4 48.2 1.0
CA I:GLY181 4.5 45.8 1.0
N I:ALA178 4.5 45.6 1.0
CA I:ASP177 4.6 48.2 1.0
N I:GLY181 4.6 49.4 1.0
O I:ALA178 4.6 48.3 1.0
CA I:ALA178 4.6 44.2 1.0
CA I:ALA174 4.6 45.2 1.0
OD1 I:ASP175 4.6 54.9 1.0
O I:ASP175 4.6 57.6 1.0
C I:ALA178 4.6 46.7 1.0
N I:SER180 4.6 46.0 1.0
CA I:SER180 4.7 46.5 1.0
CB I:ALA174 4.8 44.0 1.0
NH2 Y:ARG19 4.8 64.3 1.0
C I:ASP204 4.9 54.9 1.0
O I:ASP204 4.9 53.1 1.0
N I:ARG176 4.9 54.5 1.0
NH1 Y:ARG19 5.0 61.0 1.0

Magnesium binding site 3 out of 8 in 4qlt

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Magnesium binding site 3 out of 8 in the Ycp in Complex with Tripeptidic Epoxyketone Inhibitor 2 (PR924)


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 2 (PR924) within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg301

b:64.5
occ:1.00
 O K:ASP168 2.2 47.8 1.0
O K:ALA165 2.4 52.4 1.0
O W:ASP204 2.4 57.6 1.0
O K:SER171 2.8 54.9 1.0
C K:ASP168 3.1 45.6 1.0
C W:ASP204 3.2 55.2 1.0
C K:ALA165 3.5 54.7 1.0
CA K:ALA169 3.5 42.2 1.0
O K:HIS166 3.6 47.6 1.0
CA W:ASP204 3.6 54.3 1.0
N K:ALA169 3.6 43.2 1.0
C K:ALA169 3.8 45.4 1.0
O K:ALA169 3.9 47.7 1.0
C K:SER171 4.0 53.9 1.0
OXT W:ASP204 4.0 57.6 1.0
CB W:ASP204 4.1 54.3 1.0
C K:HIS166 4.1 49.0 1.0
NH1 K:ARG19 4.1 70.5 1.0
N K:ASP168 4.2 49.7 1.0
CA K:ASP168 4.2 47.4 1.0
N K:SER171 4.4 52.2 1.0
N K:HIS166 4.4 50.9 1.0
CA K:ALA165 4.4 58.4 1.0
CA K:HIS166 4.4 49.8 1.0
O K:ALA164 4.6 57.7 1.0
N K:TYR170 4.6 46.9 1.0
C K:ARG167 4.6 51.0 1.0
CZ K:ARG19 4.7 66.8 1.0
CA K:SER171 4.7 50.7 1.0
N K:ARG167 4.8 48.1 1.0
CB K:ALA169 4.9 38.1 1.0
N K:GLY172 4.9 53.1 1.0
N W:ASP204 5.0 50.9 1.0

Magnesium binding site 4 out of 8 in 4qlt

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Magnesium binding site 4 out of 8 in the Ycp in Complex with Tripeptidic Epoxyketone Inhibitor 2 (PR924)


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 2 (PR924) within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg201

b:55.6
occ:1.00
 O N:ILE163 2.4 49.2 1.0
O N:SER169 2.6 52.1 1.0
O N:ASP166 2.9 40.7 1.0
C N:ILE163 3.6 45.9 1.0
CD1 a:LEU34 3.6 44.4 1.0
C N:SER169 3.7 48.3 1.0
NH1 N:ARG19 3.8 48.9 1.0
CG2 N:ILE163 3.9 40.6 1.0
C N:ASP166 3.9 28.1 1.0
CA N:GLY167 4.2 42.7 1.0
CA N:ILE163 4.2 43.7 1.0
CA N:GLY170 4.3 50.1 1.0
CZ N:ARG19 4.3 48.9 1.0
N N:GLY170 4.5 49.6 1.0
O N:GLY167 4.5 44.0 1.0
N N:GLY167 4.5 39.9 1.0
NH2 N:ARG19 4.5 47.2 1.0
C N:GLY167 4.6 43.4 1.0
N N:LYS164 4.6 47.2 1.0
CB N:ILE163 4.7 42.2 1.0
CA N:SER169 4.8 44.8 1.0
N N:SER169 4.8 46.6 1.0
C N:LYS164 4.8 50.2 1.0
O N:LYS164 4.9 51.7 1.0
CA N:LYS164 4.9 49.6 1.0
CG a:LEU34 4.9 46.9 1.0

Magnesium binding site 5 out of 8 in 4qlt

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Magnesium binding site 5 out of 8 in the Ycp in Complex with Tripeptidic Epoxyketone Inhibitor 2 (PR924)


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 2 (PR924) within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg202

b:66.1
occ:1.00
 OE1 H:GLN91 2.7 57.5 1.0
O N:HOH304 3.3 42.1 1.0
O N:ASN92 3.4 51.0 1.0
OD1 N:ASP51 3.4 50.8 1.0
CD H:GLN91 3.7 56.8 1.0
OD2 N:ASP51 3.8 51.8 1.0
CG N:ASP51 4.0 51.7 1.0
NE2 H:GLN91 4.3 58.0 1.0
C N:ASN92 4.5 50.2 1.0
CG H:GLN91 5.0 53.3 1.0

Magnesium binding site 6 out of 8 in 4qlt

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Magnesium binding site 6 out of 8 in the Ycp in Complex with Tripeptidic Epoxyketone Inhibitor 2 (PR924)


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 2 (PR924) within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Mg301

b:67.4
occ:1.00
 O V:ASP166 2.0 52.4 1.0
OXT L:ASP222 2.1 63.4 1.0
O V:ILE163 2.2 55.2 1.0
O V:SER169 2.4 51.2 1.0
C L:ASP222 3.1 64.3 1.0
C V:ASP166 3.1 53.1 1.0
C V:ILE163 3.3 56.5 1.0
C V:SER169 3.5 50.3 1.0
O V:GLY162 3.7 53.2 1.0
NH1 V:ARG19 3.8 63.5 1.0
CA L:ASP222 3.8 63.5 1.0
N V:LEU167 3.9 55.8 1.0
O L:ASP222 3.9 64.3 1.0
CA V:LEU167 3.9 55.1 1.0
N V:ASP166 3.9 49.8 1.0
CA V:ILE163 4.1 56.0 1.0
CA V:ASP166 4.1 50.3 1.0
O V:TRP164 4.1 56.9 1.0
C V:TRP164 4.1 53.0 1.0
O V:HOH415 4.2 57.0 1.0
N V:TRP164 4.2 54.8 1.0
N V:SER169 4.3 48.6 1.0
C V:LEU167 4.4 53.3 1.0
CB L:ASP222 4.4 66.5 1.0
CA V:TRP164 4.4 54.1 1.0
CA V:SER169 4.4 47.4 1.0
N V:GLY170 4.4 53.4 1.0
CA V:GLY170 4.4 58.3 1.0
CZ V:ARG19 4.5 61.7 1.0
N V:ASN165 4.5 50.3 1.0
O V:LEU167 4.6 53.8 1.0
NH2 V:ARG19 4.6 63.6 1.0
C V:GLY162 4.7 50.2 1.0
C V:ASN165 4.8 48.9 1.0
CB V:SER169 4.8 45.9 1.0
CB V:ASP166 4.8 49.0 1.0
N V:ILE163 4.9 51.5 1.0

Magnesium binding site 7 out of 8 in 4qlt

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Magnesium binding site 7 out of 8 in the Ycp in Complex with Tripeptidic Epoxyketone Inhibitor 2 (PR924)


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 2 (PR924) within 5.0Å range:
probe atom residue distance (Å) B Occ
Y:Mg301

b:48.9
occ:1.00
 O Y:ASP168 2.2 47.2 1.0
O I:ASP204 2.3 53.1 1.0
O Y:SER171 2.4 52.4 1.0
O Y:ALA165 2.6 52.7 1.0
O Y:HOH415 2.6 57.5 1.0
C Y:ASP168 3.2 44.8 1.0
C I:ASP204 3.2 54.9 1.0
CA Y:ALA169 3.5 40.5 1.0
C Y:SER171 3.6 52.2 1.0
O Y:ALA169 3.6 45.5 1.0
C Y:ALA169 3.6 42.8 1.0
C Y:ALA165 3.7 50.7 1.0
NH1 Y:ARG19 3.7 61.0 1.0
N Y:ALA169 3.7 43.3 1.0
CA I:ASP204 3.7 54.9 1.0
N Y:SER171 4.0 46.5 1.0
CB I:ASP204 4.0 53.8 1.0
O Y:HIS166 4.1 47.5 1.0
OXT I:ASP204 4.2 54.5 1.0
CZ Y:ARG19 4.3 61.8 1.0
O I:HOH419 4.3 57.5 1.0
CA Y:SER171 4.4 48.7 1.0
N Y:TYR170 4.4 45.2 1.0
CA Y:ASP168 4.4 44.7 1.0
CA Y:ALA165 4.5 50.5 1.0
N Y:ASP168 4.5 46.1 1.0
C Y:HIS166 4.5 48.5 1.0
N Y:GLY172 4.6 52.8 1.0
N Y:HIS166 4.6 48.5 1.0
NH2 Y:ARG19 4.7 64.3 1.0
CA Y:GLY172 4.7 51.8 1.0
O Y:ALA164 4.7 51.4 1.0
CA Y:HIS166 4.8 48.7 1.0
O I:HOH415 4.9 55.7 1.0
CB Y:ALA169 4.9 38.4 1.0
CB Y:SER171 5.0 48.7 1.0

Magnesium binding site 8 out of 8 in 4qlt

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Magnesium binding site 8 out of 8 in the Ycp in Complex with Tripeptidic Epoxyketone Inhibitor 2 (PR924)


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 2 (PR924) within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg301

b:59.0
occ:1.00
 O Z:HOH412 2.3 40.1 1.0
O Z:HIS195 2.4 45.8 1.0
O Z:THR192 2.4 58.9 1.0
O Z:VAL198 2.8 54.6 1.0
O Z:HOH421 3.1 70.5 1.0
C Z:HIS195 3.4 49.5 1.0
C Z:THR192 3.5 56.5 1.0
CA Z:ILE196 3.7 48.6 1.0
N Z:ILE196 3.9 49.8 1.0
NH2 Z:ARG28 4.0 63.5 1.0
C Z:VAL198 4.0 55.2 1.0
CA Z:THR192 4.0 57.4 1.0
C Z:ILE196 4.0 49.8 1.0
O Z:ILE196 4.0 54.1 1.0
CG2 Z:THR192 4.1 63.8 1.0
NH2 H:ARG19 4.2 63.2 1.0
O Z:ASP222 4.3 68.5 1.0
N Z:HIS195 4.5 51.7 1.0
N Z:VAL198 4.5 53.6 1.0
CA Z:HIS195 4.6 48.4 1.0
OD1 Z:ASP222 4.6 71.1 1.0
N Z:GLU193 4.7 54.8 1.0
CB Z:THR192 4.7 60.7 1.0
CA Z:VAL198 4.7 53.7 1.0
O Z:ALA191 4.8 53.5 1.0
N Z:GLN197 4.9 48.9 1.0
CZ H:ARG19 4.9 65.5 1.0
C Z:GLU193 4.9 54.5 1.0
CB Z:ILE196 4.9 45.2 1.0
O Z:GLU193 4.9 55.7 1.0
NH1 H:ARG19 5.0 68.8 1.0
N Z:GLY199 5.0 54.7 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 02:03:50 2024

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