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Magnesium in PDB 4qz3: Ycp BETA5-A49V Mutant in Complex with the Epoxyketone Inhibitor Onx 0914

Enzymatic activity of Ycp BETA5-A49V Mutant in Complex with the Epoxyketone Inhibitor Onx 0914

All present enzymatic activity of Ycp BETA5-A49V Mutant in Complex with the Epoxyketone Inhibitor Onx 0914:
3.4.25.1;

Protein crystallography data

The structure of Ycp BETA5-A49V Mutant in Complex with the Epoxyketone Inhibitor Onx 0914, PDB code: 4qz3 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 / 2.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 135.760, 300.170, 144.960, 90.00, 112.96, 90.00
R / Rfree (%) 18.1 / 20.7

Other elements in 4qz3:

The structure of Ycp BETA5-A49V 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-A49V Mutant in Complex with the Epoxyketone Inhibitor Onx 0914 (pdb code 4qz3). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the Ycp BETA5-A49V Mutant in Complex with the Epoxyketone Inhibitor Onx 0914, PDB code: 4qz3:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 4qz3

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Magnesium binding site 1 out of 7 in the Ycp BETA5-A49V 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-A49V Mutant in Complex with the Epoxyketone Inhibitor Onx 0914 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:58.6
occ:1.00
 O G:MET125 2.5 54.3 1.0
OG1 G:THR8 2.6 45.0 1.0
O G:ARG122 2.8 45.0 1.0
O G:ALA123 3.0 56.7 1.0
O G:TYR119 3.0 39.8 1.0
CG2 G:THR8 3.3 49.5 1.0
CB G:THR8 3.5 47.9 1.0
C G:MET125 3.5 52.4 1.0
C G:ALA123 3.5 52.9 1.0
CA G:ALA123 3.6 50.2 1.0
C G:ARG122 3.9 47.9 1.0
N G:THR8 4.0 52.4 1.0
N G:ALA123 4.2 47.9 1.0
CA G:ARG126 4.2 47.2 1.0
C G:TYR119 4.2 41.8 1.0
N G:ARG126 4.3 49.0 1.0
N G:MET125 4.3 53.1 1.0
CA G:THR8 4.4 49.8 1.0
CA G:MET125 4.5 55.8 1.0
N G:TYR124 4.6 54.0 1.0
CD G:PRO127 4.6 45.2 1.0
CB G:ALA123 4.9 49.6 1.0
C G:ARG126 4.9 46.5 1.0
C G:TYR124 5.0 51.1 1.0
CA G:TYR119 5.0 41.5 1.0

Magnesium binding site 2 out of 7 in 4qz3

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Magnesium binding site 2 out of 7 in the Ycp BETA5-A49V 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-A49V Mutant in Complex with the Epoxyketone Inhibitor Onx 0914 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:68.0
occ:1.00
 O I:ASP177 2.6 45.4 1.0
O I:SER180 2.6 53.1 1.0
O I:ALA174 2.9 48.3 1.0
OXT I:ASP204 3.6 69.6 1.0
C I:ASP177 3.8 45.3 1.0
C I:SER180 3.9 49.4 1.0
C I:ALA174 3.9 52.4 1.0
CA I:ASP175 4.2 52.5 1.0
O I:ALA178 4.2 52.3 1.0
CA I:ALA178 4.4 46.0 1.0
C I:ALA178 4.4 47.7 1.0
C I:ASP204 4.5 66.0 1.0
C I:ASP175 4.5 50.8 1.0
N I:ASP175 4.5 52.6 1.0
O I:ASP204 4.5 69.5 1.0
N I:ALA178 4.5 44.3 1.0
O I:ASP175 4.5 53.5 1.0
NH1 Y:ARG19 4.6 62.2 1.0
N I:ASP177 4.6 45.8 1.0
N I:SER180 4.7 44.7 1.0
CA I:GLY181 4.7 49.0 1.0
N I:GLY181 4.7 48.6 1.0
CA I:ASP177 4.8 45.4 1.0
NH2 Y:ARG19 4.8 67.6 1.0
CA I:SER180 4.8 47.3 1.0
OD1 I:ASP175 4.9 59.1 1.0

Magnesium binding site 3 out of 7 in 4qz3

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Magnesium binding site 3 out of 7 in the Ycp BETA5-A49V 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-A49V Mutant in Complex with the Epoxyketone Inhibitor Onx 0914 within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg302

b:59.5
occ:1.00
 O W:ASP204 2.1 66.8 1.0
O K:ASP168 2.3 51.3 1.0
O K:ALA165 2.5 46.9 1.0
O K:SER171 2.6 52.3 1.0
C W:ASP204 3.0 62.6 1.0
C K:ASP168 3.3 51.2 1.0
CA W:ASP204 3.5 58.7 1.0
CA K:ALA169 3.6 51.8 1.0
C K:ALA165 3.7 49.3 1.0
O K:ALA169 3.7 54.6 1.0
C K:ALA169 3.7 52.8 1.0
C K:SER171 3.8 51.2 1.0
N K:ALA169 3.8 52.2 1.0
NH1 K:ARG19 3.9 62.3 1.0
CB W:ASP204 3.9 56.4 1.0
OXT W:ASP204 4.0 71.0 1.0
O K:HIS166 4.0 52.0 1.0
N K:SER171 4.2 47.1 1.0
C K:HIS166 4.4 49.6 1.0
CZ K:ARG19 4.4 62.4 1.0
CA K:ALA165 4.5 50.4 1.0
CA K:ASP168 4.5 49.3 1.0
CA K:SER171 4.5 47.9 1.0
N K:TYR170 4.6 51.1 1.0
N K:ASP168 4.6 51.8 1.0
N K:HIS166 4.6 48.8 1.0
NH2 K:ARG19 4.6 67.3 1.0
CA K:HIS166 4.7 50.2 1.0
N K:GLY172 4.8 52.6 1.0
O K:ALA164 4.8 48.4 1.0
CA K:GLY172 4.9 52.1 1.0
C K:ARG167 4.9 52.0 1.0
N W:ASP204 4.9 57.1 1.0
CB K:ALA169 4.9 50.7 1.0
CG W:ASP204 5.0 58.9 1.0

Magnesium binding site 4 out of 7 in 4qz3

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Magnesium binding site 4 out of 7 in the Ycp BETA5-A49V 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-A49V Mutant in Complex with the Epoxyketone Inhibitor Onx 0914 within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg202

b:51.5
occ:1.00
 O N:SER169 2.6 51.2 1.0
O N:ILE163 2.7 51.6 1.0
O N:ASP166 3.1 52.1 1.0
NH1 N:ARG19 3.5 59.6 1.0
CD1 a:LEU34 3.7 57.5 1.0
C N:SER169 3.8 51.5 1.0
C N:ILE163 3.9 54.8 1.0
CG2 N:ILE163 4.1 53.6 1.0
CZ N:ARG19 4.2 58.2 1.0
C N:ASP166 4.2 53.2 1.0
NH2 N:ARG19 4.3 55.6 1.0
CA N:GLY167 4.4 54.8 1.0
CA N:GLY170 4.4 55.3 1.0
O N:GLY167 4.5 52.2 1.0
N N:GLY170 4.6 53.0 1.0
CA N:ILE163 4.6 54.7 1.0
C N:GLY167 4.7 53.5 1.0
N N:GLY167 4.7 53.0 1.0
N N:SER169 4.9 48.2 1.0
N N:LYS164 4.9 55.0 1.0
CA N:SER169 4.9 48.6 1.0
O N:LYS164 4.9 57.2 1.0
CB N:ILE163 5.0 54.0 1.0
CG a:LEU34 5.0 58.0 1.0

Magnesium binding site 5 out of 7 in 4qz3

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Magnesium binding site 5 out of 7 in the Ycp BETA5-A49V 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-A49V Mutant in Complex with the Epoxyketone Inhibitor Onx 0914 within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Mg302

b:69.9
occ:1.00
 O V:ILE163 2.3 57.3 1.0
OXT L:ASP222 2.3 63.9 1.0
O V:ASP166 2.3 47.5 1.0
C L:ASP222 3.0 68.4 1.0
C V:ASP166 3.2 53.1 1.0
O V:SER169 3.3 55.2 1.0
O V:TRP164 3.3 61.7 1.0
C V:ILE163 3.4 59.0 1.0
C V:TRP164 3.5 59.9 1.0
CA L:ASP222 3.6 67.0 1.0
O L:ASP222 3.7 78.7 1.0
N V:ASP166 3.7 53.8 1.0
N V:LEU167 3.9 54.1 1.0
CA V:TRP164 3.9 59.6 1.0
O V:GLY162 3.9 54.0 1.0
CA V:LEU167 4.0 55.8 1.0
N V:ASN165 4.0 57.8 1.0
N V:TRP164 4.0 58.7 1.0
CA V:ASP166 4.1 53.8 1.0
C V:ASN165 4.2 55.0 1.0
O L:ARG221 4.4 60.2 1.0
C V:SER169 4.4 53.4 1.0
CA V:ILE163 4.5 59.8 1.0
CB L:ASP222 4.5 66.8 1.0
CA V:ASN165 4.6 57.1 1.0
CD2 V:LEU167 4.6 57.5 1.0
NH1 V:ARG19 4.6 68.2 1.0
C V:LEU167 4.7 55.0 1.0
N L:ASP222 4.8 64.8 1.0
CD1 L:ILE35 4.8 58.1 1.0
O V:ASN165 4.9 53.1 1.0
C V:GLY162 5.0 56.9 1.0

Magnesium binding site 6 out of 7 in 4qz3

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Magnesium binding site 6 out of 7 in the Ycp BETA5-A49V 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-A49V Mutant in Complex with the Epoxyketone Inhibitor Onx 0914 within 5.0Å range:
probe atom residue distance (Å) B Occ
Y:Mg302

b:49.7
occ:1.00
 O Y:ASP168 2.2 47.7 1.0
O I:ASP204 2.2 69.5 1.0
O Y:ALA165 2.5 45.0 1.0
O Y:SER171 2.5 56.3 1.0
O Y:HOH401 2.6 49.0 1.0
C I:ASP204 3.1 66.0 1.0
C Y:ASP168 3.2 48.1 1.0
CA Y:ALA169 3.6 49.4 1.0
CA I:ASP204 3.6 62.7 1.0
C Y:ALA165 3.6 48.4 1.0
C Y:SER171 3.7 50.6 1.0
O Y:ALA169 3.7 51.3 1.0
C Y:ALA169 3.7 48.2 1.0
N Y:ALA169 3.8 50.8 1.0
NH1 Y:ARG19 3.8 62.2 1.0
CB I:ASP204 3.9 62.5 1.0
OXT I:ASP204 4.1 69.6 1.0
N Y:SER171 4.1 45.1 1.0
O Y:HIS166 4.1 45.4 1.0
CZ Y:ARG19 4.4 61.9 1.0
CA Y:SER171 4.4 46.7 1.0
C Y:HIS166 4.4 46.8 1.0
CA Y:ALA165 4.4 49.5 1.0
CA Y:ASP168 4.5 46.7 1.0
N Y:TYR170 4.5 46.6 1.0
N Y:ASP168 4.5 47.0 1.0
N Y:HIS166 4.6 48.8 1.0
NH2 Y:ARG19 4.7 67.6 1.0
N Y:GLY172 4.7 52.1 1.0
O Y:ALA164 4.7 46.6 1.0
CA Y:HIS166 4.8 47.7 1.0
CA Y:GLY172 4.8 52.7 1.0
C Y:ARG167 4.9 47.2 1.0
CB Y:SER171 4.9 45.8 1.0
CB Y:ALA169 4.9 48.8 1.0

Magnesium binding site 7 out of 7 in 4qz3

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Magnesium binding site 7 out of 7 in the Ycp BETA5-A49V 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-A49V Mutant in Complex with the Epoxyketone Inhibitor Onx 0914 within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg301

b:64.0
occ:1.00
 O Z:VAL198 2.5 55.6 1.0
O Z:THR192 2.8 56.2 1.0
O Z:HIS195 3.2 48.9 1.0
NH2 Z:ARG28 3.4 67.2 1.0
O Z:ASP222 3.5 77.2 1.0
CG2 Z:THR192 3.7 59.8 1.0
C Z:VAL198 3.7 55.7 1.0
C Z:THR192 3.8 58.7 1.0
O Z:ILE196 4.0 49.0 1.0
CA Z:THR192 4.2 58.5 1.0
C Z:HIS195 4.2 49.4 1.0
CA Z:ILE196 4.2 48.9 1.0
OD1 Z:ASP222 4.2 68.2 1.0
C Z:ILE196 4.3 48.0 1.0
NH2 H:ARG19 4.4 68.9 1.0
CZ Z:ARG28 4.4 63.9 1.0
C Z:ASP222 4.5 70.4 1.0
N Z:VAL198 4.5 50.4 1.0
CB Z:THR192 4.5 59.1 1.0
CA Z:GLY199 4.6 57.0 1.0
N Z:GLY199 4.6 56.4 1.0
N Z:ILE196 4.7 47.9 1.0
NH1 Z:ARG28 4.7 64.8 1.0
CA Z:VAL198 4.7 52.3 1.0
O Z:LYS220 4.8 60.9 1.0
OXT Z:ASP222 5.0 65.9 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 02:37:22 2024

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