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Magnesium in PDB 4qls: Ycp in Complex with Tripeptidic Epoxyketone Inhibitor 11

Enzymatic activity of Ycp in Complex with Tripeptidic Epoxyketone Inhibitor 11

All present enzymatic activity of Ycp in Complex with Tripeptidic Epoxyketone Inhibitor 11:
3.4.25.1;

Protein crystallography data

The structure of Ycp in Complex with Tripeptidic Epoxyketone Inhibitor 11, PDB code: 4qls 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 (°) 136.420, 299.950, 145.960, 90.00, 113.18, 90.00
R / Rfree (%) 17.9 / 19.9

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Ycp in Complex with Tripeptidic Epoxyketone Inhibitor 11 (pdb code 4qls). 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 11, PDB code: 4qls:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 4qls

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Magnesium binding site 1 out of 8 in the Ycp in Complex with Tripeptidic Epoxyketone Inhibitor 11


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

b:59.7
occ:1.00
 O G:MET125 2.3 55.9 1.0
OG1 G:THR8 2.7 39.9 1.0
O G:ARG122 2.7 44.0 1.0
O G:TYR119 2.8 37.4 1.0
O G:ALA123 3.3 49.3 1.0
CG2 G:THR8 3.3 33.6 1.0
C G:MET125 3.5 55.8 1.0
CB G:THR8 3.6 38.0 1.0
C G:ALA123 3.6 46.9 1.0
CA G:ALA123 3.6 42.9 1.0
C G:ARG122 3.7 44.5 1.0
C G:TYR119 4.0 38.5 1.0
N G:THR8 4.1 44.4 1.0
N G:ALA123 4.1 42.3 1.0
N G:MET125 4.2 56.9 1.0
N G:ARG126 4.3 47.5 1.0
CA G:ARG126 4.4 42.1 1.0
CA G:MET125 4.4 60.4 1.0
CA G:THR8 4.5 41.9 1.0
N G:TYR124 4.5 53.7 1.0
CD G:PRO127 4.7 29.9 1.0
CA G:TYR119 4.7 37.6 1.0
CB G:ALA123 4.9 41.1 1.0
C G:TYR124 4.9 54.6 1.0
CB G:MET125 5.0 64.9 1.0
C G:ARG126 5.0 39.5 1.0
CA G:ARG122 5.0 46.0 1.0

Magnesium binding site 2 out of 8 in 4qls

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Magnesium binding site 2 out of 8 in the Ycp in Complex with Tripeptidic Epoxyketone Inhibitor 11


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

b:56.4
occ:1.00
 O I:ASP177 2.5 51.8 1.0
O I:SER180 2.6 49.4 1.0
O I:ALA174 2.7 50.2 1.0
C I:ASP177 3.7 48.7 1.0
C I:ALA174 3.8 50.8 1.0
OXT I:ASP204 3.8 58.0 1.0
C I:SER180 3.8 49.8 1.0
CA I:ASP175 4.2 57.6 1.0
N I:ASP175 4.4 55.0 1.0
CA I:ALA178 4.5 49.1 1.0
N I:ASP177 4.5 47.1 1.0
N I:ALA178 4.5 47.5 1.0
O I:ALA178 4.5 53.8 1.0
C I:ALA178 4.5 49.7 1.0
C I:ASP175 4.5 54.8 1.0
O I:ASP204 4.6 58.9 1.0
C I:ASP204 4.6 56.2 1.0
N I:SER180 4.6 48.0 1.0
OD1 I:ASP175 4.6 59.9 1.0
CA I:ASP177 4.6 49.2 1.0
CA I:GLY181 4.6 46.0 1.0
N I:GLY181 4.7 48.6 1.0
O I:ASP175 4.7 57.7 1.0
CA I:SER180 4.8 50.0 1.0
NH1 Y:ARG19 4.9 72.6 1.0
CA I:ALA174 4.9 46.2 1.0
NH2 Y:ARG19 4.9 68.3 1.0

Magnesium binding site 3 out of 8 in 4qls

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Magnesium binding site 3 out of 8 in the Ycp in Complex with Tripeptidic Epoxyketone Inhibitor 11


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

b:55.0
occ:1.00
 O K:ASP168 2.2 49.5 1.0
O K:ALA165 2.3 46.0 1.0
O W:ASP204 2.4 60.8 1.0
O K:SER171 2.8 52.8 1.0
C W:ASP204 3.1 57.6 1.0
C K:ASP168 3.2 44.7 1.0
C K:ALA165 3.5 48.4 1.0
CA W:ASP204 3.6 52.8 1.0
CA K:ALA169 3.7 42.3 1.0
O K:HIS166 3.8 45.2 1.0
N K:ALA169 3.8 43.6 1.0
C K:ALA169 3.9 45.0 1.0
O K:ALA169 4.0 47.5 1.0
OXT W:ASP204 4.0 64.0 1.0
C K:SER171 4.0 53.0 1.0
CB W:ASP204 4.0 53.0 1.0
C K:HIS166 4.1 47.4 1.0
NH1 K:ARG19 4.1 60.3 1.0
N K:ASP168 4.2 43.1 1.0
CA K:ASP168 4.3 42.7 1.0
N K:HIS166 4.3 44.6 1.0
CA K:ALA165 4.4 52.2 1.0
N K:SER171 4.4 47.6 1.0
CA K:HIS166 4.4 46.4 1.0
O K:ALA164 4.5 50.6 1.0
C K:ARG167 4.6 43.9 1.0
N K:TYR170 4.7 45.1 1.0
CZ K:ARG19 4.7 64.4 1.0
CA K:SER171 4.8 47.8 1.0
N K:ARG167 4.8 45.6 1.0
NH2 K:ARG19 4.8 75.5 1.0
N W:ASP204 5.0 47.9 1.0
N K:GLY172 5.0 56.1 1.0

Magnesium binding site 4 out of 8 in 4qls

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Magnesium binding site 4 out of 8 in the Ycp in Complex with Tripeptidic Epoxyketone Inhibitor 11


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

b:53.2
occ:1.00
 O N:ILE163 2.3 46.9 1.0
O N:SER169 2.7 52.1 1.0
O N:ASP166 3.1 31.2 1.0
C N:ILE163 3.5 45.4 1.0
CG2 N:ILE163 3.7 41.0 1.0
CD1 a:LEU34 3.7 46.3 1.0
C N:SER169 3.8 49.5 1.0
NH1 N:ARG19 4.0 50.1 1.0
C N:ASP166 4.1 24.4 1.0
CA N:ILE163 4.2 45.0 1.0
CA N:GLY170 4.3 49.9 1.0
CA N:GLY167 4.4 34.9 1.0
CZ N:ARG19 4.4 45.3 1.0
N N:GLY170 4.5 49.1 1.0
N N:LYS164 4.5 45.1 1.0
CB N:ILE163 4.6 44.1 1.0
O N:GLY167 4.6 42.0 1.0
NH2 N:ARG19 4.6 39.5 1.0
N N:GLY167 4.7 35.4 1.0
C N:GLY167 4.7 39.3 1.0
CA N:LYS164 4.8 47.1 1.0
C N:LYS164 4.8 48.6 1.0
CA N:SER169 4.8 45.1 1.0
O N:LYS164 4.9 50.3 1.0
N N:SER169 4.9 47.7 1.0

Magnesium binding site 5 out of 8 in 4qls

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Magnesium binding site 5 out of 8 in the Ycp in Complex with Tripeptidic Epoxyketone Inhibitor 11


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

b:78.8
occ:1.00
 OD1 N:ASP51 2.5 51.7 1.0
O N:ASN92 2.7 58.1 1.0
OE1 H:GLN91 3.1 73.5 1.0
CG N:ASP51 3.3 56.5 1.0
NE2 H:GLN91 3.4 69.3 1.0
OD2 N:ASP51 3.5 58.8 1.0
CD H:GLN91 3.6 67.8 1.0
C N:ASN92 3.9 54.5 1.0
CZ H:PHE88 4.0 39.0 1.0
CE1 H:PHE88 4.1 41.7 1.0
CD2 N:LEU93 4.4 48.9 1.0
CB N:ASP51 4.6 54.7 1.0
CB N:ASN92 4.7 55.4 1.0
CA N:LEU93 4.8 49.8 1.0
N N:LEU93 4.8 53.2 1.0
CA N:ASN92 4.8 52.7 1.0
CE2 H:PHE88 5.0 37.4 1.0

Magnesium binding site 6 out of 8 in 4qls

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Magnesium binding site 6 out of 8 in the Ycp in Complex with Tripeptidic Epoxyketone Inhibitor 11


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

b:64.1
occ:1.00
 OXT L:ASP222 2.1 63.1 1.0
O V:ASP166 2.2 44.6 1.0
O V:ILE163 2.3 51.3 1.0
O V:SER169 2.9 50.4 1.0
C L:ASP222 2.9 62.8 1.0
C V:ASP166 3.1 49.0 1.0
C V:ILE163 3.4 54.1 1.0
O L:ASP222 3.7 61.1 1.0
O V:TRP164 3.7 53.8 1.0
CA V:LEU167 3.7 55.4 1.0
N V:LEU167 3.7 53.7 1.0
CA L:ASP222 3.7 61.4 1.0
N V:ASP166 3.9 47.6 1.0
C V:TRP164 3.9 52.8 1.0
O V:GLY162 4.0 52.4 1.0
C V:SER169 4.1 49.3 1.0
NH1 V:ARG19 4.1 81.7 1.0
CA V:ASP166 4.1 47.1 1.0
N V:TRP164 4.2 53.0 1.0
CA V:TRP164 4.3 52.1 1.0
C V:LEU167 4.4 53.1 1.0
CA V:ILE163 4.4 57.7 1.0
N V:ASN165 4.4 50.7 1.0
CB L:ASP222 4.5 61.8 1.0
C V:ASN165 4.6 48.4 1.0
CD2 V:LEU167 4.7 51.9 1.0
N V:SER169 4.7 49.0 1.0
O L:ARG221 4.7 49.9 1.0
O V:LEU167 4.7 53.2 1.0
CZ V:ARG19 4.8 73.6 1.0
NH2 V:ARG19 4.9 70.2 1.0
CA V:SER169 4.9 45.9 1.0
CB V:LEU167 4.9 57.2 1.0
N L:ASP222 5.0 57.0 1.0
CA V:ASN165 5.0 48.9 1.0
N V:GLY170 5.0 52.0 1.0
C V:GLY162 5.0 52.3 1.0

Magnesium binding site 7 out of 8 in 4qls

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Magnesium binding site 7 out of 8 in the Ycp in Complex with Tripeptidic Epoxyketone Inhibitor 11


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

b:53.5
occ:1.00
 O Y:ASP168 2.3 54.5 1.0
O I:ASP204 2.4 58.9 1.0
O Y:ALA165 2.6 45.2 1.0
O Y:SER171 2.7 47.6 1.0
C I:ASP204 3.2 56.2 1.0
C Y:ASP168 3.2 49.2 1.0
CA Y:ALA169 3.5 43.4 1.0
O Y:ALA169 3.7 49.3 1.0
C Y:ALA169 3.7 46.0 1.0
N Y:ALA169 3.7 46.5 1.0
C Y:ALA165 3.7 47.9 1.0
CA I:ASP204 3.7 53.2 1.0
NH1 Y:ARG19 3.8 72.6 1.0
C Y:SER171 3.9 48.0 1.0
OXT I:ASP204 4.0 58.0 1.0
O Y:HIS166 4.1 51.0 1.0
CB I:ASP204 4.1 52.5 1.0
N Y:SER171 4.3 46.0 1.0
CA Y:ASP168 4.4 47.7 1.0
CZ Y:ARG19 4.4 64.7 1.0
N Y:ASP168 4.4 50.4 1.0
C Y:HIS166 4.4 51.2 1.0
N Y:TYR170 4.4 46.2 1.0
CA Y:ALA165 4.6 47.5 1.0
NH2 Y:ARG19 4.6 68.3 1.0
N Y:HIS166 4.6 49.4 1.0
CA Y:SER171 4.7 44.3 1.0
O Y:ALA164 4.8 49.1 1.0
CA Y:HIS166 4.8 50.4 1.0
C Y:ARG167 4.9 51.1 1.0
CB Y:ALA169 4.9 41.0 1.0
N Y:GLY172 4.9 49.2 1.0

Magnesium binding site 8 out of 8 in 4qls

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Magnesium binding site 8 out of 8 in the Ycp in Complex with Tripeptidic Epoxyketone Inhibitor 11


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

b:62.4
occ:1.00
 O Z:VAL198 2.6 54.6 1.0
O Z:THR192 2.7 60.2 1.0
O Z:HIS195 3.1 42.1 1.0
C Z:THR192 3.7 57.2 1.0
CG2 Z:THR192 3.7 55.9 1.0
O Z:ASP222 3.8 61.7 1.0
C Z:VAL198 3.8 51.0 1.0
NH2 Z:ARG28 3.9 60.1 1.0
O Z:ILE196 4.0 51.9 1.0
C Z:HIS195 4.0 45.1 1.0
CA Z:ILE196 4.1 49.6 1.0
CA Z:THR192 4.1 55.5 1.0
C Z:ILE196 4.2 50.4 1.0
OD1 Z:ASP222 4.2 61.0 1.0
NH2 H:ARG19 4.3 74.7 1.0
N Z:ILE196 4.5 46.7 1.0
CB Z:THR192 4.5 56.9 1.0
N Z:VAL198 4.6 48.3 1.0
C Z:ASP222 4.7 64.7 1.0
CA Z:GLY199 4.7 51.2 1.0
N Z:GLY199 4.7 50.1 1.0
CA Z:VAL198 4.8 48.4 1.0
N Z:GLU193 4.9 55.6 1.0
CZ Z:ARG28 4.9 58.7 1.0
NH1 H:ARG19 4.9 76.1 1.0
CZ H:ARG19 5.0 71.8 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: Mon Aug 11 22:28:36 2025

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