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Magnesium in PDB 4qzx: Ycp BETA5-C63F Mutant in Complex with the Epoxyketone Inhibitor Onx 0914

Enzymatic activity of Ycp BETA5-C63F Mutant in Complex with the Epoxyketone Inhibitor Onx 0914

All present enzymatic activity of Ycp BETA5-C63F Mutant in Complex with the Epoxyketone Inhibitor Onx 0914:
3.4.25.1;

Protein crystallography data

The structure of Ycp BETA5-C63F Mutant in Complex with the Epoxyketone Inhibitor Onx 0914, PDB code: 4qzx 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 / 2.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 137.210, 300.810, 145.090, 90.00, 113.52, 90.00
R / Rfree (%) 19.8 / 22.3

Other elements in 4qzx:

The structure of Ycp BETA5-C63F Mutant in Complex with the Epoxyketone Inhibitor Onx 0914 also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Ycp BETA5-C63F Mutant in Complex with the Epoxyketone Inhibitor Onx 0914 (pdb code 4qzx). 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 BETA5-C63F Mutant in Complex with the Epoxyketone Inhibitor Onx 0914, PDB code: 4qzx:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 4qzx

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Magnesium binding site 1 out of 8 in the Ycp BETA5-C63F Mutant 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 BETA5-C63F Mutant in Complex with the Epoxyketone Inhibitor Onx 0914 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:60.6
occ:1.00
 O G:MET125 2.4 47.5 1.0
OG1 G:THR8 2.5 42.5 1.0
O G:ARG122 2.6 46.7 1.0
O G:TYR119 3.0 45.2 1.0
O G:ALA123 3.2 48.1 1.0
CG2 G:THR8 3.2 47.0 1.0
CB G:THR8 3.4 46.2 1.0
C G:MET125 3.5 48.5 1.0
C G:ALA123 3.6 48.1 1.0
CA G:ALA123 3.6 47.2 1.0
C G:ARG122 3.7 47.8 1.0
N G:THR8 4.0 48.0 1.0
N G:ALA123 4.1 46.5 1.0
C G:TYR119 4.2 42.6 1.0
CA G:ARG126 4.3 44.8 1.0
N G:ARG126 4.3 45.6 1.0
N G:MET125 4.3 49.4 1.0
CA G:THR8 4.3 47.6 1.0
CA G:MET125 4.5 51.6 1.0
N G:TYR124 4.6 50.5 1.0
CD G:PRO127 4.6 42.9 1.0
CB G:ALA123 4.9 45.7 1.0
C G:ARG126 4.9 44.6 1.0
CA G:TYR119 4.9 39.9 1.0
C G:TYR124 5.0 49.3 1.0

Magnesium binding site 2 out of 8 in 4qzx

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Magnesium binding site 2 out of 8 in the Ycp BETA5-C63F Mutant 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 BETA5-C63F Mutant in Complex with the Epoxyketone Inhibitor Onx 0914 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:68.7
occ:1.00
 O I:ASP177 2.5 48.6 1.0
O I:SER180 2.5 51.7 1.0
O I:ALA174 2.7 50.1 1.0
O I:HOH420 3.4 60.1 1.0
OXT I:ASP204 3.6 66.7 1.0
C I:ASP177 3.7 48.9 1.0
C I:SER180 3.7 50.3 1.0
C I:ALA174 3.7 53.5 1.0
CA I:ASP175 4.1 53.9 1.0
N I:ASP175 4.3 54.1 1.0
O I:ALA178 4.4 49.0 1.0
C I:ASP175 4.5 51.2 1.0
N I:ASP177 4.5 45.9 1.0
CA I:ALA178 4.5 47.7 1.0
CA I:GLY181 4.5 51.4 1.0
N I:ALA178 4.5 48.8 1.0
C I:ALA178 4.5 49.2 1.0
N I:GLY181 4.5 50.9 1.0
N I:SER180 4.6 46.6 1.0
C I:ASP204 4.6 67.4 1.0
O I:ASP204 4.6 69.7 1.0
CA I:ASP177 4.6 48.6 1.0
O I:ASP175 4.7 51.9 1.0
CA I:SER180 4.7 48.1 1.0
OD1 I:ASP175 4.8 61.2 1.0
CA I:ALA174 4.8 52.2 1.0
NH1 Y:ARG19 4.9 65.5 1.0

Magnesium binding site 3 out of 8 in 4qzx

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Magnesium binding site 3 out of 8 in the Ycp BETA5-C63F Mutant 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 BETA5-C63F Mutant in Complex with the Epoxyketone Inhibitor Onx 0914 within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg302

b:55.0
occ:1.00
 O K:ASP168 2.3 47.4 1.0
O K:ALA165 2.4 49.2 1.0
O W:ASP204 2.5 65.0 1.0
O K:SER171 2.9 48.7 1.0
C W:ASP204 3.1 66.1 1.0
C K:ASP168 3.3 48.4 1.0
CA W:ASP204 3.5 63.3 1.0
C K:ALA165 3.6 50.3 1.0
O K:HIS166 3.7 51.1 1.0
CA K:ALA169 3.7 50.8 1.0
N K:ALA169 3.9 49.8 1.0
OXT W:ASP204 4.0 68.7 1.0
CB W:ASP204 4.0 62.7 1.0
C K:ALA169 4.0 51.3 1.0
NH1 K:ARG19 4.0 67.1 1.0
C K:HIS166 4.1 51.5 1.0
C K:SER171 4.1 49.3 1.0
O K:ALA169 4.1 50.4 1.0
N K:ASP168 4.4 51.3 1.0
CA K:ASP168 4.5 47.9 1.0
N K:HIS166 4.5 49.6 1.0
CA K:HIS166 4.5 50.6 1.0
N K:SER171 4.5 48.6 1.0
CA K:ALA165 4.5 52.3 1.0
CZ K:ARG19 4.7 63.4 1.0
O K:ALA164 4.7 52.4 1.0
C K:ARG167 4.7 52.0 1.0
N K:TYR170 4.8 48.8 1.0
N K:ARG167 4.8 50.9 1.0
CA K:SER171 4.9 47.2 1.0
N W:ASP204 4.9 62.5 1.0
NH2 K:ARG19 4.9 68.3 1.0
CB K:ALA169 5.0 50.4 1.0

Magnesium binding site 4 out of 8 in 4qzx

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Magnesium binding site 4 out of 8 in the Ycp BETA5-C63F Mutant 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 BETA5-C63F Mutant in Complex with the Epoxyketone Inhibitor Onx 0914 within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg202

b:50.7
occ:1.00
 O N:SER169 2.6 46.5 1.0
O N:ILE163 2.7 47.1 1.0
O N:ASP166 3.0 53.5 1.0
NH1 N:ARG19 3.5 52.3 1.0
CD1 a:LEU34 3.7 56.5 1.0
C N:SER169 3.7 47.7 1.0
C N:ILE163 3.8 51.8 1.0
C N:ASP166 4.0 49.2 1.0
CG2 N:ILE163 4.0 50.1 1.0
CZ N:ARG19 4.2 51.2 1.0
CA N:GLY167 4.2 49.0 1.0
NH2 N:ARG19 4.3 49.3 1.0
O N:GLY167 4.4 46.6 1.0
CA N:GLY170 4.4 50.7 1.0
N N:GLY170 4.5 49.1 1.0
C N:GLY167 4.5 48.8 1.0
CA N:ILE163 4.5 50.9 1.0
N N:GLY167 4.5 47.8 1.0
N N:SER169 4.7 45.8 1.0
CA N:SER169 4.8 45.5 1.0
N N:LYS164 4.9 53.5 1.0
CB N:ILE163 4.9 50.6 1.0
CG a:LEU34 5.0 57.9 1.0

Magnesium binding site 5 out of 8 in 4qzx

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Magnesium binding site 5 out of 8 in the Ycp BETA5-C63F Mutant 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 BETA5-C63F Mutant in Complex with the Epoxyketone Inhibitor Onx 0914 within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg203

b:57.1
occ:1.00
 OD1 N:ASP51 2.5 34.1 1.0
OE1 H:GLN91 2.7 54.8 1.0
O N:ASN92 3.2 58.1 1.0
NE2 H:GLN91 3.3 55.3 1.0
CG N:ASP51 3.3 33.3 1.0
CD H:GLN91 3.3 54.1 1.0
OD2 N:ASP51 3.4 47.6 1.0
CE1 H:PHE88 4.0 38.2 1.0
CZ H:PHE88 4.1 38.7 1.0
C N:ASN92 4.4 57.4 1.0
O N:HOH305 4.6 58.3 1.0
CB N:ASP51 4.7 34.4 1.0
CD2 N:LEU93 4.8 55.7 1.0
CG H:GLN91 4.8 50.5 1.0
CD1 H:PHE88 5.0 37.5 1.0

Magnesium binding site 6 out of 8 in 4qzx

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Magnesium binding site 6 out of 8 in the Ycp BETA5-C63F Mutant 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 BETA5-C63F Mutant in Complex with the Epoxyketone Inhibitor Onx 0914 within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Mg302

b:62.9
occ:1.00
 O V:ILE163 2.1 52.7 1.0
O V:ASP166 2.2 45.6 1.0
OXT L:ASP222 2.2 60.4 1.0
O V:SER169 2.7 50.5 1.0
C L:ASP222 3.1 64.8 1.0
C V:ILE163 3.2 55.1 1.0
C V:ASP166 3.2 49.8 1.0
CA L:ASP222 3.6 64.1 1.0
O V:GLY162 3.7 51.5 1.0
O V:TRP164 3.8 55.8 1.0
C V:TRP164 3.8 55.2 1.0
N V:ASP166 3.8 51.7 1.0
C V:SER169 3.9 50.2 1.0
N V:TRP164 4.0 55.7 1.0
N V:LEU167 4.0 50.3 1.0
O L:ASP222 4.1 65.8 1.0
CA V:LEU167 4.1 51.5 1.0
CA V:ILE163 4.1 56.4 1.0
CA V:TRP164 4.1 57.4 1.0
CA V:ASP166 4.1 51.1 1.0
CB L:ASP222 4.3 64.6 1.0
N V:ASN165 4.3 54.8 1.0
NH1 V:ARG19 4.3 62.0 1.0
C V:ASN165 4.5 52.4 1.0
C V:LEU167 4.6 50.1 1.0
N V:SER169 4.6 47.5 1.0
C V:GLY162 4.7 54.4 1.0
CA V:GLY170 4.7 54.8 1.0
N V:GLY170 4.7 51.5 1.0
O L:ARG221 4.7 57.8 1.0
CA V:SER169 4.8 48.2 1.0
CZ V:ARG19 4.8 58.8 1.0
N V:ILE163 4.9 54.6 1.0
CA V:ASN165 4.9 54.1 1.0
CB V:ASP166 4.9 50.0 1.0
N L:ASP222 4.9 62.5 1.0
NH2 V:ARG19 4.9 63.1 1.0
O V:LEU167 4.9 53.1 1.0
CD2 V:LEU167 5.0 51.9 1.0

Magnesium binding site 7 out of 8 in 4qzx

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Magnesium binding site 7 out of 8 in the Ycp BETA5-C63F Mutant 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 BETA5-C63F Mutant in Complex with the Epoxyketone Inhibitor Onx 0914 within 5.0Å range:
probe atom residue distance (Å) B Occ
Y:Mg302

b:65.2
occ:1.00
 O Y:ASP168 2.3 48.9 1.0
O I:ASP204 2.4 69.7 1.0
O Y:ALA165 2.7 49.7 1.0
O Y:SER171 2.9 55.4 1.0
C I:ASP204 3.2 67.4 1.0
C Y:ASP168 3.3 49.7 1.0
CA Y:ALA169 3.5 50.4 1.0
CA I:ASP204 3.7 65.3 1.0
C Y:ALA169 3.8 50.0 1.0
NH1 Y:ARG19 3.8 65.5 1.0
N Y:ALA169 3.8 51.1 1.0
O Y:ALA169 3.8 52.9 1.0
C Y:ALA165 3.9 50.3 1.0
O Y:HIS166 4.0 50.4 1.0
OXT I:ASP204 4.0 66.7 1.0
C Y:SER171 4.1 50.3 1.0
CB I:ASP204 4.1 65.5 1.0
N Y:SER171 4.3 46.2 1.0
C Y:HIS166 4.4 49.5 1.0
CZ Y:ARG19 4.5 64.3 1.0
CA Y:ASP168 4.5 49.0 1.0
N Y:TYR170 4.6 48.4 1.0
N Y:ASP168 4.6 51.0 1.0
NH2 Y:ARG19 4.7 65.5 1.0
CB Y:ALA169 4.8 49.5 1.0
CA Y:ALA165 4.8 50.8 1.0
CA Y:SER171 4.8 46.6 1.0
N Y:HIS166 4.8 49.9 1.0
CA Y:HIS166 4.8 49.5 1.0
C Y:ARG167 4.9 50.5 1.0
O Y:ALA164 4.9 50.1 1.0

Magnesium binding site 8 out of 8 in 4qzx

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Magnesium binding site 8 out of 8 in the Ycp BETA5-C63F Mutant 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 BETA5-C63F Mutant in Complex with the Epoxyketone Inhibitor Onx 0914 within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg301

b:68.1
occ:1.00
 O Z:VAL198 2.5 53.5 1.0
O Z:THR192 2.6 54.5 1.0
O Z:HIS195 3.1 47.7 1.0
CG2 Z:THR192 3.4 56.6 1.0
O Z:ASP222 3.5 71.0 1.0
C Z:THR192 3.6 58.1 1.0
NH2 Z:ARG28 3.6 64.9 1.0
C Z:VAL198 3.7 53.8 1.0
CA Z:THR192 3.9 58.1 1.0
OD1 Z:ASP222 4.1 66.6 1.0
O Z:ILE196 4.2 57.4 1.0
C Z:HIS195 4.2 47.4 1.0
CB Z:THR192 4.3 56.7 1.0
CA Z:ILE196 4.3 48.3 1.0
C Z:ILE196 4.4 50.1 1.0
CA Z:GLY199 4.5 55.8 1.0
NH2 H:ARG19 4.5 59.4 1.0
N Z:GLY199 4.5 54.8 1.0
N Z:VAL198 4.5 49.9 1.0
C Z:ASP222 4.6 70.9 1.0
CZ Z:ARG28 4.6 63.5 1.0
CA Z:VAL198 4.6 51.3 1.0
N Z:ILE196 4.7 46.8 1.0
O Z:LYS220 4.8 61.4 1.0
NH1 Z:ARG28 4.8 66.3 1.0
N Z:GLU193 4.8 58.9 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 02:42:27 2024

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