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Magnesium in PDB 4qz7: Ycp BETA5-A50V Mutant in Complex with the Epoxyketone Inhibitor Onx 0914

Enzymatic activity of Ycp BETA5-A50V Mutant in Complex with the Epoxyketone Inhibitor Onx 0914

All present enzymatic activity of Ycp BETA5-A50V Mutant in Complex with the Epoxyketone Inhibitor Onx 0914:
3.4.25.1;

Protein crystallography data

The structure of Ycp BETA5-A50V Mutant in Complex with the Epoxyketone Inhibitor Onx 0914, PDB code: 4qz7 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 (°) 135.790, 300.310, 146.090, 90.00, 112.83, 90.00
R / Rfree (%) 17.5 / 21.3

Other elements in 4qz7:

The structure of Ycp BETA5-A50V 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-A50V Mutant in Complex with the Epoxyketone Inhibitor Onx 0914 (pdb code 4qz7). 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-A50V Mutant in Complex with the Epoxyketone Inhibitor Onx 0914, PDB code: 4qz7:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 4qz7

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Magnesium binding site 1 out of 7 in the Ycp BETA5-A50V 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-A50V Mutant in Complex with the Epoxyketone Inhibitor Onx 0914 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:55.5
occ:1.00
 O G:MET125 2.3 58.0 1.0
OG1 G:THR8 2.4 45.9 1.0
O G:ARG122 2.5 54.6 1.0
O G:TYR119 2.5 49.6 1.0
CG2 G:THR8 3.3 49.1 1.0
O G:ALA123 3.4 58.3 1.0
CB G:THR8 3.4 48.0 1.0
C G:MET125 3.5 56.6 1.0
C G:ARG122 3.6 56.2 1.0
CA G:ALA123 3.7 55.7 1.0
C G:TYR119 3.7 48.7 1.0
C G:ALA123 3.7 58.4 1.0
N G:ALA123 4.1 53.5 1.0
N G:THR8 4.2 48.4 1.0
CA G:ARG126 4.3 49.8 1.0
N G:ARG126 4.3 52.5 1.0
N G:MET125 4.3 56.7 1.0
CA G:THR8 4.4 49.4 1.0
CA G:MET125 4.5 60.7 1.0
CA G:TYR119 4.5 46.9 1.0
CD G:PRO127 4.6 43.1 1.0
N G:TYR124 4.7 61.3 1.0
N G:THR120 4.7 47.5 1.0
CA G:ARG122 4.9 59.8 1.0
C G:ARG126 4.9 48.9 1.0
CA G:THR120 4.9 47.4 1.0
N G:ARG122 4.9 53.7 1.0
C G:THR120 4.9 48.9 1.0
CB G:MET125 5.0 67.1 1.0
CB G:TYR119 5.0 48.5 1.0

Magnesium binding site 2 out of 7 in 4qz7

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Magnesium binding site 2 out of 7 in the Ycp BETA5-A50V 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-A50V Mutant in Complex with the Epoxyketone Inhibitor Onx 0914 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:60.2
occ:1.00
 O I:ASP177 2.5 53.0 1.0
O I:SER180 2.7 52.8 1.0
O I:ALA174 2.7 54.0 1.0
OXT I:ASP204 3.6 65.9 1.0
C I:ASP177 3.7 52.2 1.0
C I:ALA174 3.8 57.0 1.0
C I:SER180 3.9 52.2 1.0
CA I:ASP175 4.1 59.0 1.0
N I:ASP175 4.4 58.9 1.0
O I:ASP204 4.4 69.0 1.0
C I:ASP175 4.4 58.5 1.0
C I:ASP204 4.4 65.6 1.0
N I:ASP177 4.4 52.1 1.0
CA I:ALA178 4.5 50.4 1.0
N I:ALA178 4.5 50.0 1.0
O I:ASP175 4.5 60.4 1.0
O I:ALA178 4.5 55.0 1.0
C I:ALA178 4.6 52.5 1.0
CA I:ASP177 4.6 54.0 1.0
N I:SER180 4.7 50.2 1.0
CA I:GLY181 4.7 53.4 1.0
N I:GLY181 4.8 50.4 1.0
NH1 Y:ARG19 4.9 77.5 1.0
CA I:SER180 4.9 50.7 1.0
OD1 I:ASP175 4.9 57.7 1.0
CA I:ALA174 4.9 53.5 1.0

Magnesium binding site 3 out of 7 in 4qz7

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Magnesium binding site 3 out of 7 in the Ycp BETA5-A50V 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-A50V Mutant in Complex with the Epoxyketone Inhibitor Onx 0914 within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg302

b:63.0
occ:1.00
 O K:ASP168 2.2 53.2 1.0
O W:ASP204 2.4 63.9 1.0
O K:SER171 2.5 55.5 1.0
O K:ALA165 2.7 50.1 1.0
C W:ASP204 3.2 60.3 1.0
C K:ASP168 3.3 52.6 1.0
NH1 K:ARG19 3.5 70.9 1.0
CA K:ALA169 3.5 55.8 1.0
O K:ALA169 3.6 61.8 1.0
C K:ALA169 3.6 57.4 1.0
CA W:ASP204 3.7 57.9 1.0
C K:SER171 3.7 57.5 1.0
C K:ALA165 3.8 54.3 1.0
N K:ALA169 3.8 54.4 1.0
OXT W:ASP204 4.0 67.7 1.0
CB W:ASP204 4.1 55.6 1.0
N K:SER171 4.1 54.5 1.0
O K:HIS166 4.1 53.5 1.0
CZ K:ARG19 4.3 70.3 1.0
N K:TYR170 4.4 55.0 1.0
CA K:SER171 4.5 55.2 1.0
CA K:ASP168 4.6 50.3 1.0
NH2 K:ARG19 4.6 72.2 1.0
C K:HIS166 4.6 49.7 1.0
CA K:ALA165 4.6 60.1 1.0
N K:ASP168 4.7 50.9 1.0
N K:GLY172 4.7 57.7 1.0
N K:HIS166 4.8 51.8 1.0
O K:ALA164 4.8 58.0 1.0
CA K:GLY172 4.9 56.0 1.0
CA K:HIS166 4.9 50.9 1.0
CB K:ALA169 4.9 54.8 1.0

Magnesium binding site 4 out of 7 in 4qz7

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Magnesium binding site 4 out of 7 in the Ycp BETA5-A50V 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-A50V Mutant in Complex with the Epoxyketone Inhibitor Onx 0914 within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg202

b:56.4
occ:1.00
 O N:SER169 2.6 50.8 1.0
O N:ILE163 2.7 51.0 1.0
O N:ASP166 3.1 52.1 1.0
NH1 N:ARG19 3.5 50.0 1.0
CD1 a:LEU34 3.7 59.9 1.0
C N:SER169 3.8 47.6 1.0
C N:ILE163 3.9 52.5 1.0
C N:ASP166 4.1 48.1 1.0
CA N:GLY167 4.2 49.0 1.0
CG2 N:ILE163 4.2 52.0 1.0
CZ N:ARG19 4.2 48.4 1.0
O N:GLY167 4.4 50.2 1.0
CA N:GLY170 4.4 49.6 1.0
NH2 N:ARG19 4.4 44.1 1.0
C N:GLY167 4.5 49.3 1.0
N N:GLY167 4.5 47.5 1.0
CA N:ILE163 4.6 52.6 1.0
N N:GLY170 4.6 46.6 1.0
N N:SER169 4.8 48.3 1.0
CA N:SER169 4.9 46.6 1.0
N N:LYS164 4.9 53.3 1.0
CG a:LEU34 4.9 60.7 1.0
CB N:ILE163 5.0 52.5 1.0

Magnesium binding site 5 out of 7 in 4qz7

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Magnesium binding site 5 out of 7 in the Ycp BETA5-A50V 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-A50V Mutant in Complex with the Epoxyketone Inhibitor Onx 0914 within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Mg302

b:81.3
occ:1.00
 O V:ILE163 2.3 61.3 1.0
OXT L:ASP222 2.3 74.3 1.0
O V:ASP166 2.4 49.7 1.0
C L:ASP222 2.9 75.8 1.0
C V:ASP166 3.2 52.9 1.0
O V:SER169 3.2 63.0 1.0
O V:TRP164 3.3 60.7 1.0
C V:ILE163 3.4 63.7 1.0
CA L:ASP222 3.6 75.1 1.0
C V:TRP164 3.6 60.0 1.0
O L:ASP222 3.6 80.4 1.0
N V:ASP166 3.8 53.6 1.0
N V:LEU167 3.8 55.1 1.0
CA V:LEU167 3.9 55.9 1.0
CA V:TRP164 4.0 61.3 1.0
O V:GLY162 4.1 61.7 1.0
CA V:ASP166 4.1 51.9 1.0
N V:TRP164 4.1 62.6 1.0
N V:ASN165 4.2 57.4 1.0
C V:ASN165 4.4 54.9 1.0
C V:SER169 4.4 60.4 1.0
CB L:ASP222 4.4 76.0 1.0
O L:ARG221 4.4 70.6 1.0
CA V:ILE163 4.5 64.1 1.0
CD2 V:LEU167 4.5 55.1 1.0
NH1 V:ARG19 4.6 75.1 1.0
C V:LEU167 4.7 56.9 1.0
CA V:ASN165 4.7 57.2 1.0
N L:ASP222 4.7 73.6 1.0
CD1 L:ILE35 4.8 71.7 1.0
NH2 V:ARG19 5.0 73.2 1.0

Magnesium binding site 6 out of 7 in 4qz7

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Magnesium binding site 6 out of 7 in the Ycp BETA5-A50V 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-A50V Mutant in Complex with the Epoxyketone Inhibitor Onx 0914 within 5.0Å range:
probe atom residue distance (Å) B Occ
Y:Mg302

b:39.8
occ:1.00
 O Y:ASP168 2.2 52.7 1.0
O Y:HOH403 2.3 40.0 1.0
O Y:SER171 2.4 52.7 1.0
O I:ASP204 2.5 69.0 1.0
O Y:ALA165 2.6 47.5 1.0
C I:ASP204 3.2 65.6 1.0
C Y:ASP168 3.3 47.8 1.0
NH1 Y:ARG19 3.5 77.5 1.0
CA Y:ALA169 3.6 45.8 1.0
C Y:SER171 3.6 51.6 1.0
O Y:ALA169 3.6 50.4 1.0
C Y:ALA169 3.7 46.5 1.0
CA I:ASP204 3.7 65.4 1.0
C Y:ALA165 3.7 50.1 1.0
N Y:ALA169 3.8 47.1 1.0
N Y:SER171 4.0 46.4 1.0
CB I:ASP204 4.1 64.2 1.0
OXT I:ASP204 4.1 65.9 1.0
O Y:HIS166 4.2 48.0 1.0
CZ Y:ARG19 4.3 74.3 1.0
N Y:TYR170 4.4 47.1 1.0
CA Y:SER171 4.4 47.5 1.0
CA Y:ALA165 4.5 52.0 1.0
CA Y:ASP168 4.5 46.8 1.0
C Y:HIS166 4.6 48.9 1.0
NH2 Y:ARG19 4.6 78.5 1.0
N Y:ASP168 4.6 48.5 1.0
N Y:GLY172 4.7 54.7 1.0
N Y:HIS166 4.7 51.2 1.0
O Y:ALA164 4.7 55.1 1.0
CA Y:GLY172 4.8 56.7 1.0
CA Y:HIS166 4.9 48.6 1.0
CB Y:ALA169 5.0 46.0 1.0
CB Y:SER171 5.0 46.9 1.0

Magnesium binding site 7 out of 7 in 4qz7

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Magnesium binding site 7 out of 7 in the Ycp BETA5-A50V 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-A50V Mutant in Complex with the Epoxyketone Inhibitor Onx 0914 within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg301

b:70.9
occ:1.00
 O Z:VAL198 2.5 58.8 1.0
O Z:THR192 2.8 70.3 1.0
O Z:HIS195 3.2 48.9 1.0
O Z:ASP222 3.5 74.9 1.0
CG2 Z:THR192 3.5 64.8 1.0
NH2 Z:ARG28 3.6 71.9 1.0
C Z:VAL198 3.7 61.0 1.0
C Z:THR192 3.8 67.3 1.0
O Z:ILE196 4.1 60.6 1.0
OD1 Z:ASP222 4.1 76.6 1.0
CA Z:THR192 4.1 66.0 1.0
C Z:HIS195 4.3 55.6 1.0
CA Z:ILE196 4.3 55.1 1.0
CA Z:GLY199 4.4 55.7 1.0
C Z:ILE196 4.4 56.3 1.0
C Z:ASP222 4.4 75.2 1.0
NH2 H:ARG19 4.4 77.9 1.0
CB Z:THR192 4.5 64.0 1.0
N Z:GLY199 4.5 57.7 1.0
CZ Z:ARG28 4.7 72.2 1.0
N Z:VAL198 4.7 57.7 1.0
O Z:LYS220 4.7 67.9 1.0
CA Z:VAL198 4.7 60.2 1.0
N Z:ILE196 4.8 54.3 1.0
OXT Z:ASP222 4.9 73.9 1.0
NH1 Z:ARG28 4.9 75.6 1.0
N Z:GLU193 4.9 66.4 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 02:39:32 2024

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