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Magnesium in PDB 4qz2: Ycp BETA5-M45I Mutant in Complex with the Epoxyketone Inhibitor Onx 0914

Enzymatic activity of Ycp BETA5-M45I Mutant in Complex with the Epoxyketone Inhibitor Onx 0914

All present enzymatic activity of Ycp BETA5-M45I Mutant in Complex with the Epoxyketone Inhibitor Onx 0914:
3.4.25.1;

Protein crystallography data

The structure of Ycp BETA5-M45I Mutant in Complex with the Epoxyketone Inhibitor Onx 0914, PDB code: 4qz2 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 / 2.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 137.160, 299.330, 145.390, 90.00, 113.09, 90.00
R / Rfree (%) 19.5 / 21.9

Other elements in 4qz2:

The structure of Ycp BETA5-M45I 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-M45I Mutant in Complex with the Epoxyketone Inhibitor Onx 0914 (pdb code 4qz2). 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-M45I Mutant in Complex with the Epoxyketone Inhibitor Onx 0914, PDB code: 4qz2:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 4qz2

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Magnesium binding site 1 out of 7 in the Ycp BETA5-M45I 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-M45I Mutant in Complex with the Epoxyketone Inhibitor Onx 0914 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:57.0
occ:1.00
 O G:MET125 2.4 52.6 1.0
OG1 G:THR8 2.5 44.2 1.0
O G:ARG122 2.7 46.6 1.0
O G:TYR119 3.0 40.7 1.0
O G:ALA123 3.1 50.7 1.0
CG2 G:THR8 3.2 46.4 1.0
CB G:THR8 3.4 46.3 1.0
C G:MET125 3.5 51.7 1.0
C G:ALA123 3.6 51.2 1.0
CA G:ALA123 3.6 49.7 1.0
C G:ARG122 3.8 48.8 1.0
N G:THR8 3.9 50.8 1.0
N G:ALA123 4.2 49.2 1.0
C G:TYR119 4.2 39.6 1.0
CA G:ARG126 4.2 45.6 1.0
CA G:THR8 4.3 48.9 1.0
N G:ARG126 4.3 47.4 1.0
N G:MET125 4.3 52.1 1.0
CA G:MET125 4.5 54.1 1.0
N G:TYR124 4.6 53.9 1.0
CD G:PRO127 4.7 43.5 1.0
CB G:ALA123 4.9 48.3 1.0
CA G:TYR119 4.9 38.1 1.0
C G:ARG126 5.0 44.9 1.0
C G:ILE7 5.0 53.4 1.0
C G:TYR124 5.0 52.0 1.0

Magnesium binding site 2 out of 7 in 4qz2

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Magnesium binding site 2 out of 7 in the Ycp BETA5-M45I 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-M45I Mutant in Complex with the Epoxyketone Inhibitor Onx 0914 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:44.3
occ:1.00
 O I:SER180 2.4 44.8 1.0
O I:ALA174 2.6 48.8 1.0
O I:ASP177 2.6 43.0 1.0
O I:HOH410 3.5 36.9 1.0
C I:ALA174 3.5 50.5 1.0
C I:SER180 3.6 45.7 1.0
OXT I:ASP204 3.6 57.8 1.0
C I:ASP177 3.8 42.5 1.0
CA I:ASP175 4.0 51.4 1.0
N I:ASP175 4.2 51.8 1.0
CA I:GLY181 4.3 48.4 1.0
C I:ASP175 4.4 49.1 1.0
N I:GLY181 4.4 46.9 1.0
N I:ASP177 4.5 42.4 1.0
N I:SER180 4.6 43.5 1.0
O I:ALA178 4.6 44.2 1.0
O I:ASP175 4.6 49.0 1.0
CA I:SER180 4.6 44.9 1.0
C I:ASP204 4.6 62.9 1.0
OD1 I:ASP175 4.6 56.0 1.0
CA I:ALA174 4.6 49.3 1.0
N I:ALA178 4.7 41.4 1.0
CA I:ALA178 4.7 42.2 1.0
C I:ALA178 4.7 43.2 1.0
CA I:ASP177 4.7 43.9 1.0
O I:ASP204 4.7 63.3 1.0
CB I:ALA174 4.8 49.7 1.0

Magnesium binding site 3 out of 7 in 4qz2

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Magnesium binding site 3 out of 7 in the Ycp BETA5-M45I 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-M45I Mutant in Complex with the Epoxyketone Inhibitor Onx 0914 within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg302

b:54.5
occ:1.00
 O K:ASP168 2.2 46.9 1.0
O K:ALA165 2.4 46.5 1.0
O W:ASP204 2.4 67.9 1.0
O K:SER171 2.7 45.1 1.0
C W:ASP204 3.2 65.9 1.0
C K:ASP168 3.2 46.9 1.0
C K:ALA165 3.5 47.8 1.0
CA W:ASP204 3.6 62.4 1.0
CA K:ALA169 3.7 47.8 1.0
O K:HIS166 3.7 48.7 1.0
N K:ALA169 3.9 47.5 1.0
NH1 K:ARG19 3.9 67.1 1.0
C K:SER171 3.9 44.3 1.0
CB W:ASP204 4.0 61.0 1.0
C K:ALA169 4.0 48.2 1.0
O K:ALA169 4.2 48.8 1.0
C K:HIS166 4.2 47.8 1.0
OXT W:ASP204 4.2 63.8 1.0
N K:SER171 4.4 43.2 1.0
CA K:ALA165 4.4 48.7 1.0
N K:ASP168 4.4 46.7 1.0
CA K:ASP168 4.4 45.8 1.0
N K:HIS166 4.4 47.0 1.0
CA K:HIS166 4.5 47.4 1.0
CZ K:ARG19 4.6 65.5 1.0
O K:ALA164 4.6 51.0 1.0
CA K:SER171 4.7 42.9 1.0
C K:ARG167 4.7 47.0 1.0
N K:TYR170 4.7 45.7 1.0
NH2 K:ARG19 4.8 71.1 1.0
N K:ARG167 4.8 46.4 1.0
N K:GLY172 4.9 46.3 1.0
O K:ARG167 5.0 46.1 1.0
N W:ASP204 5.0 59.6 1.0

Magnesium binding site 4 out of 7 in 4qz2

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Magnesium binding site 4 out of 7 in the Ycp BETA5-M45I 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-M45I Mutant in Complex with the Epoxyketone Inhibitor Onx 0914 within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg202

b:55.0
occ:1.00
 O N:SER169 2.7 46.2 1.0
O N:ILE163 2.7 43.5 1.0
O N:ASP166 3.1 48.5 1.0
NH1 N:ARG19 3.5 50.2 1.0
CD1 a:LEU34 3.7 53.2 1.0
C N:ILE163 3.8 45.9 1.0
C N:SER169 3.9 43.2 1.0
CG2 N:ILE163 4.0 45.7 1.0
C N:ASP166 4.1 45.2 1.0
CZ N:ARG19 4.2 49.0 1.0
CA N:GLY167 4.3 44.6 1.0
NH2 N:ARG19 4.4 48.1 1.0
CA N:GLY170 4.4 47.1 1.0
O N:GLY167 4.5 45.6 1.0
CA N:ILE163 4.5 45.7 1.0
N N:GLY170 4.6 44.8 1.0
C N:GLY167 4.6 45.2 1.0
N N:GLY167 4.7 44.0 1.0
N N:LYS164 4.8 47.6 1.0
CB N:ILE163 4.9 45.4 1.0
O N:LYS164 4.9 52.9 1.0
CG a:LEU34 4.9 54.6 1.0
N N:SER169 4.9 40.6 1.0
CA N:SER169 5.0 40.3 1.0
C N:LYS164 5.0 50.6 1.0
CA N:LYS164 5.0 50.0 1.0

Magnesium binding site 5 out of 7 in 4qz2

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Magnesium binding site 5 out of 7 in the Ycp BETA5-M45I 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-M45I Mutant in Complex with the Epoxyketone Inhibitor Onx 0914 within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Mg302

b:63.6
occ:1.00
 O V:ASP166 2.1 45.8 1.0
OXT L:ASP222 2.1 68.3 1.0
O V:ILE163 2.2 53.8 1.0
O V:SER169 2.4 46.1 1.0
C L:ASP222 3.1 69.6 1.0
C V:ASP166 3.2 48.2 1.0
C V:ILE163 3.2 55.6 1.0
C V:SER169 3.6 45.6 1.0
CA L:ASP222 3.7 67.5 1.0
O V:GLY162 3.8 52.8 1.0
N V:LEU167 3.9 48.5 1.0
CA V:LEU167 3.9 48.6 1.0
O V:TRP164 3.9 59.1 1.0
N V:ASP166 4.0 49.8 1.0
C V:TRP164 4.0 55.5 1.0
NH1 V:ARG19 4.1 59.9 1.0
O L:ASP222 4.1 68.5 1.0
CA V:ILE163 4.1 56.2 1.0
N V:TRP164 4.1 53.7 1.0
CA V:ASP166 4.2 48.8 1.0
CB L:ASP222 4.2 67.1 1.0
CA V:TRP164 4.3 54.3 1.0
N V:SER169 4.4 44.7 1.0
C V:LEU167 4.4 47.3 1.0
N V:GLY170 4.5 46.6 1.0
CA V:SER169 4.5 45.1 1.0
CA V:GLY170 4.5 50.0 1.0
N V:ASN165 4.6 53.6 1.0
CZ V:ARG19 4.6 57.7 1.0
O V:LEU167 4.7 48.7 1.0
NH2 V:ARG19 4.7 61.0 1.0
C V:GLY162 4.7 54.7 1.0
C V:ASN165 4.8 50.5 1.0
N V:ILE163 4.9 55.1 1.0
CB V:SER169 4.9 45.1 1.0
CB V:ASP166 5.0 46.6 1.0
O L:ARG221 5.0 64.8 1.0
CD2 V:LEU167 5.0 48.4 1.0

Magnesium binding site 6 out of 7 in 4qz2

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Magnesium binding site 6 out of 7 in the Ycp BETA5-M45I 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-M45I Mutant in Complex with the Epoxyketone Inhibitor Onx 0914 within 5.0Å range:
probe atom residue distance (Å) B Occ
Y:Mg302

b:49.3
occ:1.00
 O Y:ASP168 2.2 46.2 1.0
O I:ASP204 2.3 63.3 1.0
O Y:SER171 2.6 43.8 1.0
O Y:ALA165 2.7 43.4 1.0
O Y:HOH413 2.9 54.2 1.0
C I:ASP204 3.2 62.9 1.0
C Y:ASP168 3.3 43.0 1.0
CA Y:ALA169 3.5 42.7 1.0
NH1 Y:ARG19 3.6 67.3 1.0
CA I:ASP204 3.7 62.9 1.0
C Y:ALA169 3.8 43.4 1.0
C Y:SER171 3.8 42.5 1.0
C Y:ALA165 3.8 43.9 1.0
O Y:ALA169 3.8 44.4 1.0
N Y:ALA169 3.8 42.7 1.0
CB I:ASP204 4.0 63.5 1.0
O Y:HIS166 4.1 47.1 1.0
N Y:SER171 4.1 39.4 1.0
OXT I:ASP204 4.2 57.8 1.0
CZ Y:ARG19 4.3 63.3 1.0
N Y:TYR170 4.5 42.2 1.0
CA Y:ASP168 4.5 42.6 1.0
C Y:HIS166 4.5 44.6 1.0
CA Y:SER171 4.6 39.4 1.0
NH2 Y:ARG19 4.6 65.4 1.0
CA Y:ALA165 4.6 43.9 1.0
N Y:ASP168 4.6 43.4 1.0
N Y:HIS166 4.8 44.1 1.0
N Y:GLY172 4.8 45.7 1.0
O Y:ALA164 4.8 47.5 1.0
CB Y:ALA169 4.9 42.0 1.0
CA Y:HIS166 4.9 44.1 1.0
CA Y:GLY172 4.9 47.8 1.0
C Y:ARG167 5.0 44.5 1.0

Magnesium binding site 7 out of 7 in 4qz2

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Magnesium binding site 7 out of 7 in the Ycp BETA5-M45I 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-M45I Mutant in Complex with the Epoxyketone Inhibitor Onx 0914 within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg301

b:71.2
occ:1.00
 O Z:VAL198 2.6 49.7 1.0
O Z:THR192 2.9 50.0 1.0
O Z:ASP222 3.2 67.8 1.0
O Z:HIS195 3.4 41.4 1.0
NH2 Z:ARG28 3.5 60.6 1.0
CG2 Z:THR192 3.5 56.9 1.0
C Z:VAL198 3.8 50.5 1.0
OD1 Z:ASP222 3.8 61.5 1.0
C Z:THR192 3.8 53.2 1.0
O Z:ILE196 4.1 49.4 1.0
CA Z:THR192 4.2 54.4 1.0
C Z:ASP222 4.2 68.0 1.0
NH2 H:ARG19 4.3 59.9 1.0
C Z:HIS195 4.4 44.0 1.0
CA Z:ILE196 4.4 46.4 1.0
CA Z:GLY199 4.4 53.2 1.0
CZ Z:ARG28 4.4 59.0 1.0
CB Z:THR192 4.5 55.1 1.0
C Z:ILE196 4.5 45.6 1.0
O Z:LYS220 4.5 59.9 1.0
N Z:GLY199 4.6 52.1 1.0
NH1 Z:ARG28 4.6 59.5 1.0
N Z:VAL198 4.7 46.9 1.0
OXT Z:ASP222 4.7 65.1 1.0
CA Z:VAL198 4.8 48.9 1.0
CG Z:ASP222 4.8 62.8 1.0
N Z:ILE196 4.9 44.6 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 02:37:15 2024

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