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Magnesium in PDB 4qxj: Ycp BETA5-M45A Mutant in Complex with the Epoxyketone Inhibitor Onx 0914

Enzymatic activity of Ycp BETA5-M45A Mutant in Complex with the Epoxyketone Inhibitor Onx 0914

All present enzymatic activity of Ycp BETA5-M45A Mutant in Complex with the Epoxyketone Inhibitor Onx 0914:
3.4.25.1;

Protein crystallography data

The structure of Ycp BETA5-M45A Mutant in Complex with the Epoxyketone Inhibitor Onx 0914, PDB code: 4qxj 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 (°) 137.490, 299.730, 145.610, 90.00, 113.16, 90.00
R / Rfree (%) 18.8 / 22.2

Other elements in 4qxj:

The structure of Ycp BETA5-M45A 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-M45A Mutant in Complex with the Epoxyketone Inhibitor Onx 0914 (pdb code 4qxj). 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-M45A Mutant in Complex with the Epoxyketone Inhibitor Onx 0914, PDB code: 4qxj:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 4qxj

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Magnesium binding site 1 out of 6 in the Ycp BETA5-M45A 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-M45A Mutant in Complex with the Epoxyketone Inhibitor Onx 0914 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:52.1
occ:1.00
 O G:MET125 2.3 60.7 1.0
OG1 G:THR8 2.6 46.1 1.0
O G:ARG122 2.8 49.3 1.0
O G:TYR119 3.0 48.1 1.0
O G:ALA123 3.2 55.2 1.0
CG2 G:THR8 3.2 50.9 1.0
C G:MET125 3.4 57.9 1.0
CB G:THR8 3.5 49.8 1.0
C G:ALA123 3.6 52.4 1.0
CA G:ALA123 3.7 51.6 1.0
C G:ARG122 3.9 51.0 1.0
N G:THR8 4.0 52.6 1.0
CA G:ARG126 4.2 52.5 1.0
N G:ARG126 4.2 54.2 1.0
C G:TYR119 4.2 46.9 1.0
N G:ALA123 4.3 49.7 1.0
N G:MET125 4.3 55.5 1.0
CA G:THR8 4.3 51.4 1.0
CA G:MET125 4.5 60.2 1.0
CD G:PRO127 4.5 49.6 1.0
N G:TYR124 4.7 54.9 1.0
C G:ARG126 4.9 52.3 1.0
CA G:TYR119 4.9 44.5 1.0
C G:TYR124 5.0 52.9 1.0

Magnesium binding site 2 out of 6 in 4qxj

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Magnesium binding site 2 out of 6 in the Ycp BETA5-M45A 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-M45A Mutant in Complex with the Epoxyketone Inhibitor Onx 0914 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:51.6
occ:1.00
 O I:ASP177 2.4 51.8 1.0
O I:SER180 2.6 55.9 1.0
O I:ALA174 2.8 58.7 1.0
O I:HOH401 2.9 49.2 1.0
O I:HOH403 3.6 60.7 1.0
OXT I:ASP204 3.6 74.2 1.0
C I:ASP177 3.6 51.4 1.0
C I:SER180 3.8 53.0 1.0
C I:ALA174 3.9 58.8 1.0
CA I:ASP175 4.2 58.5 1.0
O I:ALA178 4.3 60.2 1.0
CA I:ALA178 4.3 50.2 1.0
N I:ALA178 4.4 49.8 1.0
C I:ALA178 4.4 52.7 1.0
C I:ASP175 4.4 54.2 1.0
O I:ASP204 4.4 80.9 1.0
C I:ASP204 4.4 74.0 1.0
N I:ASP177 4.5 49.2 1.0
N I:ASP175 4.5 59.5 1.0
O I:ASP175 4.5 49.5 1.0
CA I:ASP177 4.6 50.9 1.0
N I:SER180 4.6 48.5 1.0
CA I:GLY181 4.7 56.3 1.0
NH1 Y:ARG19 4.7 75.9 1.0
N I:GLY181 4.7 54.1 1.0
CA I:SER180 4.8 51.2 1.0
NH2 Y:ARG19 4.9 74.5 1.0
OD1 I:ASP175 5.0 67.2 1.0

Magnesium binding site 3 out of 6 in 4qxj

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Magnesium binding site 3 out of 6 in the Ycp BETA5-M45A 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-M45A Mutant in Complex with the Epoxyketone Inhibitor Onx 0914 within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg302

b:63.4
occ:1.00
 O K:ASP168 2.2 50.8 1.0
O W:ASP204 2.4 79.6 1.0
O K:ALA165 2.5 53.0 1.0
O K:SER171 2.8 57.8 1.0
C K:ASP168 3.2 53.4 1.0
C W:ASP204 3.2 76.5 1.0
CA K:ALA169 3.6 57.2 1.0
CA W:ASP204 3.6 70.0 1.0
C K:ALA165 3.6 54.3 1.0
O K:HIS166 3.7 56.1 1.0
N K:ALA169 3.8 56.3 1.0
C K:ALA169 3.9 60.0 1.0
O K:ALA169 4.0 62.1 1.0
CB W:ASP204 4.0 67.2 1.0
NH1 K:ARG19 4.0 68.6 1.0
C K:SER171 4.0 55.4 1.0
OXT W:ASP204 4.2 87.5 1.0
C K:HIS166 4.2 53.7 1.0
N K:SER171 4.4 53.7 1.0
CA K:ASP168 4.4 53.1 1.0
N K:ASP168 4.4 54.6 1.0
CA K:ALA165 4.5 55.6 1.0
N K:HIS166 4.5 53.6 1.0
CA K:HIS166 4.6 54.4 1.0
C K:ARG167 4.6 54.0 1.0
N K:TYR170 4.7 56.0 1.0
O K:ALA164 4.7 60.7 1.0
CZ K:ARG19 4.7 67.5 1.0
CA K:SER171 4.8 52.3 1.0
O K:ARG167 4.8 53.8 1.0
N K:ARG167 4.9 53.0 1.0
CB K:ALA169 4.9 56.1 1.0
NH2 K:ARG19 4.9 74.9 1.0
N W:ASP204 5.0 67.1 1.0

Magnesium binding site 4 out of 6 in 4qxj

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Magnesium binding site 4 out of 6 in the Ycp BETA5-M45A 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-M45A Mutant in Complex with the Epoxyketone Inhibitor Onx 0914 within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg202

b:56.8
occ:1.00
 O N:SER169 2.7 53.4 1.0
O N:ILE163 2.9 51.8 1.0
O N:ASP166 3.2 57.8 1.0
NH1 N:ARG19 3.5 57.0 1.0
CD1 a:LEU34 3.7 59.1 1.0
C N:SER169 3.9 51.9 1.0
C N:ILE163 4.0 55.8 1.0
CG2 N:ILE163 4.1 55.9 1.0
CZ N:ARG19 4.2 56.5 1.0
C N:ASP166 4.3 56.2 1.0
NH2 N:ARG19 4.3 54.0 1.0
CA N:GLY167 4.4 54.2 1.0
CA N:GLY170 4.4 55.1 1.0
O N:GLY167 4.5 52.0 1.0
N N:GLY170 4.6 51.8 1.0
C N:GLY167 4.7 52.8 1.0
CA N:ILE163 4.7 55.4 1.0
N N:GLY167 4.7 53.7 1.0
N N:LYS164 4.9 57.9 1.0
N N:SER169 5.0 51.9 1.0
O N:LYS164 5.0 61.0 1.0

Magnesium binding site 5 out of 6 in 4qxj

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Magnesium binding site 5 out of 6 in the Ycp BETA5-M45A 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-M45A Mutant in Complex with the Epoxyketone Inhibitor Onx 0914 within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Mg302

b:71.0
occ:1.00
 O V:ASP166 2.1 53.4 1.0
OXT L:ASP222 2.2 80.0 1.0
O V:ILE163 2.2 65.3 1.0
O V:SER169 2.7 61.6 1.0
C V:ASP166 3.1 57.9 1.0
C L:ASP222 3.1 80.1 1.0
C V:ILE163 3.3 65.5 1.0
CA L:ASP222 3.7 76.9 1.0
O V:TRP164 3.7 69.8 1.0
O V:GLY162 3.8 58.8 1.0
C V:TRP164 3.8 65.1 1.0
N V:ASP166 3.8 61.0 1.0
N V:LEU167 3.8 58.6 1.0
CA V:LEU167 3.9 58.0 1.0
C V:SER169 3.9 57.9 1.0
CA V:ASP166 4.0 58.5 1.0
O L:ASP222 4.1 83.3 1.0
N V:TRP164 4.1 63.5 1.0
CA V:TRP164 4.1 65.3 1.0
CA V:ILE163 4.2 65.0 1.0
N V:ASN165 4.3 63.7 1.0
NH1 V:ARG19 4.3 70.5 1.0
CB L:ASP222 4.3 75.9 1.0
C V:ASN165 4.5 62.2 1.0
C V:LEU167 4.5 56.3 1.0
N V:SER169 4.6 51.5 1.0
C V:GLY162 4.8 61.1 1.0
CA V:SER169 4.8 53.9 1.0
CA V:GLY170 4.8 63.2 1.0
O L:ARG221 4.8 75.0 1.0
N V:GLY170 4.8 60.5 1.0
O V:LEU167 4.8 61.2 1.0
CZ V:ARG19 4.8 66.8 1.0
CD2 V:LEU167 4.9 60.7 1.0
CA V:ASN165 4.9 62.0 1.0
CB V:ASP166 4.9 55.1 1.0
NH2 V:ARG19 4.9 73.2 1.0
N L:ASP222 5.0 78.0 1.0

Magnesium binding site 6 out of 6 in 4qxj

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Magnesium binding site 6 out of 6 in the Ycp BETA5-M45A 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-M45A Mutant in Complex with the Epoxyketone Inhibitor Onx 0914 within 5.0Å range:
probe atom residue distance (Å) B Occ
Y:Mg302

b:58.4
occ:1.00
 O I:ASP204 2.2 80.9 1.0
O Y:ASP168 2.4 49.5 1.0
O Y:ALA165 2.7 49.2 1.0
O Y:SER171 3.0 55.1 1.0
C I:ASP204 3.0 74.0 1.0
C Y:ASP168 3.4 51.7 1.0
CA I:ASP204 3.5 71.0 1.0
CA Y:ALA169 3.6 52.0 1.0
NH1 Y:ARG19 3.8 75.9 1.0
O Y:HIS166 3.8 53.5 1.0
O Y:ALA169 3.9 58.3 1.0
C Y:ALA169 3.9 53.5 1.0
N Y:ALA169 3.9 52.5 1.0
OXT I:ASP204 3.9 74.2 1.0
C Y:ALA165 3.9 50.0 1.0
CB I:ASP204 4.0 70.7 1.0
C Y:SER171 4.2 52.1 1.0
C Y:HIS166 4.4 51.6 1.0
CZ Y:ARG19 4.5 70.5 1.0
N Y:SER171 4.5 47.5 1.0
CA Y:ASP168 4.6 51.6 1.0
N Y:ASP168 4.7 53.7 1.0
N Y:TYR170 4.7 50.5 1.0
NH2 Y:ARG19 4.8 74.5 1.0
CA Y:HIS166 4.8 50.7 1.0
N Y:HIS166 4.8 49.1 1.0
CA Y:ALA165 4.8 51.8 1.0
CB Y:ALA169 4.8 50.6 1.0
C Y:ARG167 4.9 53.0 1.0
N I:ASP204 4.9 67.3 1.0
CA Y:SER171 5.0 47.3 1.0
O Y:ARG167 5.0 49.3 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 02:34:27 2024

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