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Magnesium in PDB 4qwx: Ycp in Complex with the Epoxyketone Inhibitor Onx 0914

Enzymatic activity of Ycp in Complex with the Epoxyketone Inhibitor Onx 0914

All present enzymatic activity of Ycp in Complex with the Epoxyketone Inhibitor Onx 0914:
3.4.25.1;

Protein crystallography data

The structure of Ycp in Complex with the Epoxyketone Inhibitor Onx 0914, PDB code: 4qwx was solved by E.M.Huber, W.Heinemeyer, M.Groll, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.00 / 2.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 135.600, 300.050, 145.620, 90.00, 112.77, 90.00
R / Rfree (%) 17.2 / 21.2

Other elements in 4qwx:

The structure of Ycp in Complex with the Epoxyketone Inhibitor Onx 0914 also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms
Sodium (Na) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Ycp in Complex with the Epoxyketone Inhibitor Onx 0914 (pdb code 4qwx). 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 the Epoxyketone Inhibitor Onx 0914, PDB code: 4qwx:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 4qwx

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Magnesium binding site 1 out of 8 in the Ycp in Complex with the Epoxyketone Inhibitor Onx 0914


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 the Epoxyketone Inhibitor Onx 0914 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:67.4
occ:1.00
 O G:MET125 2.4 60.7 1.0
OG1 G:THR8 2.7 58.3 1.0
O G:ARG122 2.8 55.2 1.0
O G:ALA123 3.0 60.9 1.0
O G:TYR119 3.2 46.8 1.0
CG2 G:THR8 3.3 58.3 1.0
C G:MET125 3.4 61.8 1.0
C G:ALA123 3.5 59.9 1.0
CB G:THR8 3.5 57.5 1.0
CA G:ALA123 3.6 58.2 1.0
C G:ARG122 3.9 57.5 1.0
N G:THR8 3.9 59.8 1.0
CA G:ARG126 4.2 57.7 1.0
N G:ARG126 4.2 57.8 1.0
N G:ALA123 4.2 56.1 1.0
N G:MET125 4.2 63.6 1.0
CA G:THR8 4.3 59.2 1.0
C G:TYR119 4.4 51.8 1.0
CA G:MET125 4.5 65.5 1.0
N G:TYR124 4.5 62.2 1.0
CD G:PRO127 4.7 56.4 1.0
CB G:ALA123 4.9 56.8 1.0
C G:TYR124 4.9 61.3 1.0
C G:ILE7 4.9 63.6 1.0
C G:ARG126 5.0 58.3 1.0

Magnesium binding site 2 out of 8 in 4qwx

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Magnesium binding site 2 out of 8 in the Ycp in Complex with the Epoxyketone Inhibitor Onx 0914


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 the Epoxyketone Inhibitor Onx 0914 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:61.5
occ:1.00
 O I:ASP177 2.5 58.0 1.0
O I:SER180 2.7 54.5 1.0
O I:ALA174 2.8 63.4 1.0
OXT I:ASP204 3.6 84.5 1.0
C I:ASP177 3.7 56.9 1.0
C I:ALA174 3.9 64.8 1.0
C I:SER180 3.9 58.5 1.0
CA I:ASP175 4.1 62.5 1.0
O I:ALA178 4.3 61.4 1.0
CA I:ALA178 4.4 53.8 1.0
C I:ASP175 4.4 60.4 1.0
N I:ASP175 4.4 63.7 1.0
C I:ALA178 4.4 54.5 1.0
N I:ALA178 4.4 54.1 1.0
O I:ASP175 4.5 63.2 1.0
C I:ASP204 4.5 80.9 1.0
N I:ASP177 4.5 56.7 1.0
O I:ASP204 4.6 81.5 1.0
N I:SER180 4.6 53.8 1.0
NH1 Y:ARG19 4.6 74.4 1.0
CA I:ASP177 4.7 56.7 1.0
CA I:GLY181 4.7 59.9 1.0
N I:GLY181 4.7 59.1 1.0
CA I:SER180 4.8 56.0 1.0
NH2 Y:ARG19 4.8 75.9 1.0
OD1 I:ASP175 4.9 70.0 1.0

Magnesium binding site 3 out of 8 in 4qwx

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Magnesium binding site 3 out of 8 in the Ycp in Complex with the Epoxyketone Inhibitor Onx 0914


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 the Epoxyketone Inhibitor Onx 0914 within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg302

b:62.9
occ:1.00
 O K:ASP168 2.2 57.3 1.0
O W:ASP204 2.3 67.9 1.0
O K:ALA165 2.4 55.3 1.0
O K:SER171 2.8 57.5 1.0
C W:ASP204 3.1 68.2 1.0
C K:ASP168 3.2 56.8 1.0
C K:ALA165 3.6 58.4 1.0
CA K:ALA169 3.6 57.9 1.0
CA W:ASP204 3.6 66.2 1.0
O K:HIS166 3.6 52.6 1.0
N K:ALA169 3.8 57.6 1.0
C K:ALA169 3.9 60.0 1.0
O K:ALA169 3.9 62.5 1.0
C K:SER171 4.0 57.2 1.0
NH1 K:ARG19 4.0 71.3 1.0
CB W:ASP204 4.0 64.7 1.0
OXT W:ASP204 4.0 70.3 1.0
C K:HIS166 4.1 54.8 1.0
N K:SER171 4.3 54.5 1.0
CA K:ASP168 4.4 55.5 1.0
N K:ASP168 4.4 56.7 1.0
N K:HIS166 4.5 57.5 1.0
CA K:ALA165 4.5 59.5 1.0
CA K:HIS166 4.5 57.6 1.0
C K:ARG167 4.6 58.3 1.0
O K:ALA164 4.6 61.5 1.0
CZ K:ARG19 4.6 69.7 1.0
N K:TYR170 4.7 58.0 1.0
CA K:SER171 4.7 54.0 1.0
O K:ARG167 4.8 60.9 1.0
N K:ARG167 4.8 53.0 1.0
NH2 K:ARG19 4.9 76.0 1.0
CB K:ALA169 4.9 55.0 1.0
N K:GLY172 5.0 58.6 1.0
N W:ASP204 5.0 64.7 1.0

Magnesium binding site 4 out of 8 in 4qwx

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Magnesium binding site 4 out of 8 in the Ycp in Complex with the Epoxyketone Inhibitor Onx 0914


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 the Epoxyketone Inhibitor Onx 0914 within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg202

b:45.8
occ:1.00
 O N:SER169 2.7 62.0 1.0
O N:ILE163 2.8 59.3 1.0
O N:ASP166 3.0 66.6 1.0
NH1 N:ARG19 3.5 64.6 1.0
CD1 a:LEU34 3.6 64.2 1.0
C N:SER169 3.9 60.6 1.0
C N:ILE163 3.9 61.5 1.0
C N:ASP166 4.1 60.9 1.0
CG2 N:ILE163 4.2 63.1 1.0
CZ N:ARG19 4.2 62.4 1.0
CA N:GLY167 4.3 59.6 1.0
NH2 N:ARG19 4.3 60.2 1.0
O N:GLY167 4.4 59.0 1.0
CA N:GLY170 4.4 64.0 1.0
C N:GLY167 4.6 58.5 1.0
N N:GLY170 4.6 62.3 1.0
N N:GLY167 4.6 57.6 1.0
CA N:ILE163 4.7 63.0 1.0
O N:LYS164 4.9 69.0 1.0
CG a:LEU34 4.9 65.6 1.0
N N:SER169 4.9 57.5 1.0
N N:LYS164 4.9 63.5 1.0
CA N:SER169 4.9 57.3 1.0
C N:LYS164 5.0 67.3 1.0

Magnesium binding site 5 out of 8 in 4qwx

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Magnesium binding site 5 out of 8 in the Ycp in Complex with the Epoxyketone Inhibitor Onx 0914


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 the Epoxyketone Inhibitor Onx 0914 within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Mg302

b:75.1
occ:1.00
 OXT L:ASP222 2.2 77.3 1.0
O V:ASP166 2.2 56.7 1.0
O V:ILE163 2.4 62.3 1.0
C L:ASP222 3.0 74.5 1.0
C V:ASP166 3.1 61.3 1.0
O V:SER169 3.2 61.0 1.0
O V:TRP164 3.4 62.8 1.0
C V:ILE163 3.5 66.4 1.0
C V:TRP164 3.6 65.9 1.0
CA L:ASP222 3.7 75.0 1.0
N V:LEU167 3.7 61.6 1.0
N V:ASP166 3.8 61.7 1.0
CA V:LEU167 3.8 64.3 1.0
O L:ASP222 3.8 79.1 1.0
O V:GLY162 4.0 67.0 1.0
CA V:ASP166 4.0 61.7 1.0
CA V:TRP164 4.1 66.6 1.0
N V:ASN165 4.2 66.0 1.0
N V:TRP164 4.2 66.6 1.0
C V:ASN165 4.3 63.2 1.0
C V:SER169 4.3 60.8 1.0
NH1 V:ARG19 4.4 79.2 1.0
CB L:ASP222 4.5 73.1 1.0
CD2 V:LEU167 4.5 63.5 1.0
C V:LEU167 4.5 61.0 1.0
CA V:ILE163 4.5 69.6 1.0
O L:ARG221 4.6 72.7 1.0
CA V:ASN165 4.7 65.2 1.0
CD1 L:ILE35 4.8 65.6 1.0
O V:LEU167 4.9 64.1 1.0
O V:ASN165 4.9 57.6 1.0
N L:ASP222 4.9 75.0 1.0
N V:SER169 4.9 60.8 1.0
CB V:ASP166 5.0 59.6 1.0
CB V:LEU167 5.0 64.1 1.0

Magnesium binding site 6 out of 8 in 4qwx

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Magnesium binding site 6 out of 8 in the Ycp in Complex with the Epoxyketone Inhibitor Onx 0914


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 the Epoxyketone Inhibitor Onx 0914 within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Mg201

b:29.2
occ:1.00
 OE1 X:GLN118 3.6 59.4 1.0
O X:THR124 3.7 56.6 1.0
CB X:ASP120 3.8 48.5 1.0
CG X:ASP120 4.0 50.5 1.0
OD2 X:ASP120 4.0 47.5 1.0
N X:ASP120 4.0 46.8 1.0
CB X:THR124 4.3 51.2 1.0
CD X:GLN118 4.3 51.5 1.0
CG X:GLN118 4.4 50.8 1.0
CE1 X:HIS133 4.4 53.7 1.0
CG2 X:THR124 4.4 50.4 1.0
O X:GLN118 4.5 53.5 1.0
CA X:ASP120 4.5 46.0 1.0
OD1 X:ASP120 4.6 56.1 1.0
C X:THR124 4.7 53.6 1.0
C X:ILE119 4.8 47.0 1.0
CG1 W:VAL35 4.8 52.2 1.0
C X:GLN118 4.9 50.0 1.0
CD2 W:LEU28 4.9 55.8 1.0

Magnesium binding site 7 out of 8 in 4qwx

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Magnesium binding site 7 out of 8 in the Ycp in Complex with the Epoxyketone Inhibitor Onx 0914


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 the Epoxyketone Inhibitor Onx 0914 within 5.0Å range:
probe atom residue distance (Å) B Occ
Y:Mg302

b:63.9
occ:1.00
 O Y:ASP168 2.2 50.1 1.0
O I:ASP204 2.3 81.5 1.0
O Y:ALA165 2.7 49.4 1.0
O Y:SER171 3.0 58.6 1.0
C Y:ASP168 3.1 51.8 1.0
C I:ASP204 3.1 80.9 1.0
CA Y:ALA169 3.4 54.1 1.0
N Y:ALA169 3.6 52.0 1.0
O Y:HIS166 3.6 52.4 1.0
CA I:ASP204 3.7 75.6 1.0
C Y:ALA169 3.7 55.1 1.0
O Y:ALA169 3.8 56.3 1.0
C Y:ALA165 3.8 55.2 1.0
NH1 Y:ARG19 4.0 74.4 1.0
OXT I:ASP204 4.0 84.5 1.0
C Y:SER171 4.2 55.8 1.0
C Y:HIS166 4.2 56.4 1.0
CB I:ASP204 4.2 75.2 1.0
CA Y:ASP168 4.3 53.8 1.0
N Y:ASP168 4.4 55.1 1.0
N Y:SER171 4.4 49.7 1.0
C Y:ARG167 4.6 56.0 1.0
N Y:TYR170 4.6 55.4 1.0
N Y:HIS166 4.7 58.6 1.0
CA Y:HIS166 4.7 55.3 1.0
CZ Y:ARG19 4.7 70.5 1.0
O Y:ARG167 4.7 56.7 1.0
CB Y:ALA169 4.7 53.0 1.0
CA Y:ALA165 4.8 57.0 1.0
O Y:ALA164 4.8 54.8 1.0
CA Y:SER171 4.9 49.7 1.0
N Y:ARG167 4.9 56.5 1.0
NH2 Y:ARG19 4.9 75.9 1.0

Magnesium binding site 8 out of 8 in 4qwx

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Magnesium binding site 8 out of 8 in the Ycp in Complex with the Epoxyketone Inhibitor Onx 0914


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 the Epoxyketone Inhibitor Onx 0914 within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg301

b:77.1
occ:1.00
 O Z:VAL198 2.6 56.9 1.0
O Z:THR192 2.8 63.4 1.0
O Z:HIS195 3.0 53.8 1.0
NH2 Z:ARG28 3.4 70.2 1.0
O Z:ASP222 3.5 78.0 1.0
C Z:VAL198 3.8 60.0 1.0
CG2 Z:THR192 3.8 66.5 1.0
C Z:THR192 3.9 66.1 1.0
O Z:ILE196 3.9 68.0 1.0
CA Z:ILE196 3.9 56.7 1.0
C Z:HIS195 4.0 57.8 1.0
C Z:ILE196 4.1 58.3 1.0
CA Z:THR192 4.2 65.6 1.0
OD1 Z:ASP222 4.3 77.3 1.0
NH2 H:ARG19 4.3 76.6 1.0
N Z:ILE196 4.4 55.2 1.0
N Z:VAL198 4.4 56.6 1.0
CZ Z:ARG28 4.5 68.3 1.0
C Z:ASP222 4.5 77.8 1.0
CB Z:THR192 4.6 64.7 1.0
CA Z:VAL198 4.7 57.4 1.0
N Z:GLY199 4.7 60.7 1.0
CA Z:GLY199 4.7 64.5 1.0
NH1 Z:ARG28 4.8 72.5 1.0
NH1 H:ARG19 5.0 69.5 1.0
O Z:LYS220 5.0 65.2 1.0
N Z:GLN197 5.0 55.8 1.0
OXT Z:ASP222 5.0 71.3 1.0

Reference:

E.M.Huber, W.Heinemeyer, M.Groll. Bortezomib-Resistant Mutant Proteasomes: Structural and Biochemical Evaluation with Carfilzomib and Onx 0914. Structure 2015.
ISSN: ISSN 0969-2126
PubMed: 25599643
DOI: 10.1016/J.STR.2014.11.019
Page generated: Tue Aug 20 02:32:23 2024

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