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Magnesium in PDB 4qz0: Ycp BETA5-M45V Mutant in Complex with the Epoxyketone Inhibitor Onx 0914

Enzymatic activity of Ycp BETA5-M45V Mutant in Complex with the Epoxyketone Inhibitor Onx 0914

All present enzymatic activity of Ycp BETA5-M45V Mutant in Complex with the Epoxyketone Inhibitor Onx 0914:
3.4.25.1;

Protein crystallography data

The structure of Ycp BETA5-M45V Mutant in Complex with the Epoxyketone Inhibitor Onx 0914, PDB code: 4qz0 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 / 3.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 136.050, 299.920, 145.010, 90.00, 112.94, 90.00
R / Rfree (%) 16.9 / 20.1

Other elements in 4qz0:

The structure of Ycp BETA5-M45V 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-M45V Mutant in Complex with the Epoxyketone Inhibitor Onx 0914 (pdb code 4qz0). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Ycp BETA5-M45V Mutant in Complex with the Epoxyketone Inhibitor Onx 0914, PDB code: 4qz0:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 4qz0

Go back to Magnesium Binding Sites List in 4qz0
Magnesium binding site 1 out of 6 in the Ycp BETA5-M45V 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-M45V Mutant in Complex with the Epoxyketone Inhibitor Onx 0914 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:64.6
occ:1.00
 O G:MET125 2.4 61.8 1.0
OG1 G:THR8 2.6 54.7 1.0
O G:ALA123 2.9 59.5 1.0
O G:ARG122 3.0 57.2 1.0
CG2 G:THR8 3.3 53.8 1.0
O G:TYR119 3.3 48.7 1.0
C G:ALA123 3.4 60.0 1.0
CB G:THR8 3.5 54.0 1.0
C G:MET125 3.5 59.8 1.0
CA G:ALA123 3.6 56.9 1.0
N G:THR8 3.8 59.8 1.0
C G:ARG122 4.0 57.4 1.0
CA G:ARG126 4.2 53.8 1.0
N G:ALA123 4.2 56.4 1.0
CA G:THR8 4.3 56.7 1.0
N G:ARG126 4.3 54.8 1.0
N G:MET125 4.3 62.4 1.0
N G:TYR124 4.5 62.8 1.0
CA G:MET125 4.5 63.8 1.0
C G:TYR119 4.5 49.4 1.0
C G:ILE7 4.8 63.3 1.0
CD G:PRO127 4.8 51.6 1.0
CB G:ALA123 4.8 54.4 1.0
C G:TYR124 4.9 61.5 1.0
CA G:ILE7 4.9 62.3 1.0

Magnesium binding site 2 out of 6 in 4qz0

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Magnesium binding site 2 out of 6 in the Ycp BETA5-M45V 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-M45V Mutant in Complex with the Epoxyketone Inhibitor Onx 0914 within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg302

b:60.6
occ:1.00
 O K:ASP168 2.1 51.7 1.0
O W:ASP204 2.4 84.2 1.0
O K:ALA165 2.4 54.4 1.0
O K:SER171 2.7 50.1 1.0
C K:ASP168 3.2 52.6 1.0
C W:ASP204 3.3 79.0 1.0
C K:ALA165 3.6 55.1 1.0
CA K:ALA169 3.6 55.4 1.0
CA W:ASP204 3.7 72.5 1.0
O K:HIS166 3.7 55.0 1.0
N K:ALA169 3.8 53.7 1.0
C K:ALA169 3.9 56.5 1.0
C K:SER171 3.9 50.3 1.0
NH1 K:ARG19 3.9 80.0 1.0
CB W:ASP204 3.9 69.9 1.0
O K:ALA169 4.0 59.9 1.0
C K:HIS166 4.2 53.5 1.0
OXT W:ASP204 4.3 83.9 1.0
N K:SER171 4.3 48.9 1.0
CA K:ASP168 4.4 53.1 1.0
CA K:ALA165 4.4 56.1 1.0
N K:ASP168 4.4 53.9 1.0
N K:HIS166 4.5 53.0 1.0
O K:ALA164 4.6 60.7 1.0
CZ K:ARG19 4.6 78.1 1.0
CA K:HIS166 4.6 53.3 1.0
N K:TYR170 4.6 54.0 1.0
CA K:SER171 4.6 49.2 1.0
C K:ARG167 4.7 55.6 1.0
NH2 K:ARG19 4.8 86.6 1.0
N K:GLY172 4.9 51.8 1.0
N K:ARG167 4.9 51.9 1.0
O K:ARG167 4.9 60.4 1.0
CB K:ALA169 5.0 54.4 1.0

Magnesium binding site 3 out of 6 in 4qz0

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Magnesium binding site 3 out of 6 in the Ycp BETA5-M45V 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-M45V Mutant in Complex with the Epoxyketone Inhibitor Onx 0914 within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg202

b:42.1
occ:1.00
 O N:SER169 2.6 54.8 1.0
O N:ILE163 2.7 50.7 1.0
O N:ASP166 2.9 57.1 1.0
NH1 N:ARG19 3.5 57.9 1.0
CD1 a:LEU34 3.6 65.1 1.0
C N:ILE163 3.8 54.8 1.0
C N:SER169 3.8 53.5 1.0
C N:ASP166 3.9 53.7 1.0
CG2 N:ILE163 4.1 54.8 1.0
CA N:GLY167 4.2 52.6 1.0
CZ N:ARG19 4.2 58.0 1.0
O N:GLY167 4.3 50.9 1.0
NH2 N:ARG19 4.4 58.0 1.0
CA N:GLY170 4.4 58.2 1.0
C N:GLY167 4.5 52.5 1.0
N N:GLY167 4.5 51.5 1.0
CA N:ILE163 4.5 55.9 1.0
N N:GLY170 4.6 55.6 1.0
N N:SER169 4.8 52.0 1.0
CG a:LEU34 4.8 66.1 1.0
N N:LYS164 4.8 57.8 1.0
O N:LYS164 4.8 60.8 1.0
CA N:SER169 4.9 50.7 1.0
C N:LYS164 4.9 59.4 1.0
CB N:ILE163 4.9 54.9 1.0
CA N:LYS164 5.0 58.3 1.0

Magnesium binding site 4 out of 6 in 4qz0

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Magnesium binding site 4 out of 6 in the Ycp BETA5-M45V 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-M45V Mutant in Complex with the Epoxyketone Inhibitor Onx 0914 within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Mg302

b:73.9
occ:1.00
 OXT L:ASP222 2.0 94.6 1.0
O V:ASP166 2.1 57.1 1.0
O V:ILE163 2.2 57.2 1.0
O V:SER169 2.6 57.7 1.0
C L:ASP222 3.0 89.2 1.0
C V:ASP166 3.1 59.4 1.0
C V:ILE163 3.4 63.3 1.0
O V:TRP164 3.6 61.0 1.0
CA L:ASP222 3.7 83.5 1.0
CA V:LEU167 3.7 59.8 1.0
N V:LEU167 3.7 59.7 1.0
C V:SER169 3.8 56.0 1.0
O V:GLY162 3.9 68.1 1.0
C V:TRP164 3.9 64.2 1.0
O L:ASP222 4.0 98.2 1.0
N V:ASP166 4.0 57.3 1.0
NH1 V:ARG19 4.0 69.8 1.0
CA V:ASP166 4.1 58.0 1.0
N V:TRP164 4.2 62.2 1.0
C V:LEU167 4.2 58.4 1.0
CB L:ASP222 4.3 81.1 1.0
CA V:TRP164 4.3 63.7 1.0
CA V:ILE163 4.3 66.1 1.0
O V:LEU167 4.5 61.0 1.0
N V:SER169 4.5 55.6 1.0
N V:ASN165 4.6 63.0 1.0
CZ V:ARG19 4.6 67.7 1.0
C V:ASN165 4.7 58.7 1.0
CA V:SER169 4.7 55.4 1.0
CA V:GLY170 4.7 60.6 1.0
N V:GLY170 4.7 55.5 1.0
CD2 V:LEU167 4.7 60.0 1.0
NH2 V:ARG19 4.7 71.1 1.0
O L:ARG221 4.9 75.7 1.0
C V:GLY162 4.9 66.8 1.0
N V:GLY168 4.9 57.7 1.0
N L:ASP222 5.0 81.2 1.0
CB V:LEU167 5.0 59.5 1.0
CB V:ASP166 5.0 57.1 1.0

Magnesium binding site 5 out of 6 in 4qz0

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Magnesium binding site 5 out of 6 in the Ycp BETA5-M45V 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-M45V Mutant in Complex with the Epoxyketone Inhibitor Onx 0914 within 5.0Å range:
probe atom residue distance (Å) B Occ
Y:Mg302

b:58.1
occ:1.00
 O Y:ASP168 2.2 50.0 1.0
O I:ASP204 2.3 82.7 1.0
O Y:ALA165 2.7 51.9 1.0
O Y:SER171 2.8 58.6 1.0
C I:ASP204 3.2 79.4 1.0
C Y:ASP168 3.2 50.5 1.0
CA Y:ALA169 3.5 52.1 1.0
CA I:ASP204 3.7 77.4 1.0
N Y:ALA169 3.7 51.7 1.0
C Y:ALA169 3.7 51.0 1.0
NH1 Y:ARG19 3.8 81.7 1.0
O Y:ALA169 3.8 52.4 1.0
C Y:ALA165 3.8 54.5 1.0
O Y:HIS166 3.9 50.4 1.0
C Y:SER171 4.0 53.6 1.0
CB I:ASP204 4.0 75.5 1.0
OXT I:ASP204 4.1 83.0 1.0
N Y:SER171 4.3 49.1 1.0
C Y:HIS166 4.4 52.6 1.0
CA Y:ASP168 4.5 50.2 1.0
CZ Y:ARG19 4.5 75.5 1.0
N Y:ASP168 4.5 50.5 1.0
N Y:TYR170 4.6 50.5 1.0
CA Y:ALA165 4.7 53.2 1.0
N Y:HIS166 4.7 56.3 1.0
NH2 Y:ARG19 4.7 78.8 1.0
CA Y:SER171 4.8 49.4 1.0
C Y:ARG167 4.8 51.6 1.0
CA Y:HIS166 4.8 54.1 1.0
CB Y:ALA169 4.8 51.8 1.0
O Y:ALA164 4.8 56.4 1.0
O Y:ARG167 4.9 48.9 1.0

Magnesium binding site 6 out of 6 in 4qz0

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Magnesium binding site 6 out of 6 in the Ycp BETA5-M45V 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-M45V Mutant in Complex with the Epoxyketone Inhibitor Onx 0914 within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg301

b:70.6
occ:1.00
 O Z:VAL198 2.5 60.5 1.0
O Z:THR192 2.7 68.5 1.0
O Z:HIS195 2.9 54.7 1.0
O Z:ASP222 3.4 86.1 1.0
NH2 Z:ARG28 3.5 73.8 1.0
CG2 Z:THR192 3.7 70.8 1.0
C Z:THR192 3.7 68.4 1.0
C Z:VAL198 3.7 62.7 1.0
O Z:ILE196 3.9 67.4 1.0
C Z:HIS195 4.0 57.9 1.0
CA Z:ILE196 4.0 59.7 1.0
CA Z:THR192 4.1 67.9 1.0
C Z:ILE196 4.1 59.5 1.0
OD1 Z:ASP222 4.2 83.8 1.0
NH2 H:ARG19 4.4 74.4 1.0
N Z:VAL198 4.5 59.7 1.0
N Z:ILE196 4.5 57.3 1.0
C Z:ASP222 4.5 87.7 1.0
CB Z:THR192 4.5 67.8 1.0
CZ Z:ARG28 4.6 71.1 1.0
N Z:GLY199 4.6 63.5 1.0
CA Z:VAL198 4.7 61.6 1.0
CA Z:GLY199 4.7 65.9 1.0
NH1 Z:ARG28 4.9 70.3 1.0
O Z:LYS220 4.9 74.0 1.0
N Z:GLU193 4.9 66.3 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 02:36:12 2024

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