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Magnesium in PDB 4qz6: Ycp BETA5-A49T-A50V Double Mutant in Complex with the Epoxyketone Inhibitor Onx 0914

Enzymatic activity of Ycp BETA5-A49T-A50V Double Mutant in Complex with the Epoxyketone Inhibitor Onx 0914

All present enzymatic activity of Ycp BETA5-A49T-A50V Double Mutant in Complex with the Epoxyketone Inhibitor Onx 0914:
3.4.25.1;

Protein crystallography data

The structure of Ycp BETA5-A49T-A50V Double Mutant in Complex with the Epoxyketone Inhibitor Onx 0914, PDB code: 4qz6 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 / 2.90
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 (%) 17.4 / 20.4

Other elements in 4qz6:

The structure of Ycp BETA5-A49T-A50V Double 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-A49T-A50V Double Mutant in Complex with the Epoxyketone Inhibitor Onx 0914 (pdb code 4qz6). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Ycp BETA5-A49T-A50V Double Mutant in Complex with the Epoxyketone Inhibitor Onx 0914, PDB code: 4qz6:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 4qz6

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Magnesium binding site 1 out of 8 in the Ycp BETA5-A49T-A50V Double 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-A49T-A50V Double Mutant in Complex with the Epoxyketone Inhibitor Onx 0914 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:56.0
occ:1.00
 O G:MET125 2.4 63.6 1.0
OG1 G:THR8 2.7 52.0 1.0
O G:ARG122 2.9 49.5 1.0
O G:TYR119 3.0 47.9 1.0
O G:ALA123 3.0 62.2 1.0
CG2 G:THR8 3.3 54.3 1.0
C G:MET125 3.5 60.5 1.0
CB G:THR8 3.5 53.6 1.0
C G:ALA123 3.6 57.0 1.0
CA G:ALA123 3.7 55.0 1.0
C G:ARG122 3.9 51.2 1.0
N G:THR8 4.0 59.5 1.0
CA G:ARG126 4.1 53.5 1.0
N G:ARG126 4.2 56.5 1.0
C G:TYR119 4.2 49.0 1.0
N G:ALA123 4.3 52.2 1.0
N G:MET125 4.3 60.4 1.0
CA G:THR8 4.4 55.8 1.0
CD G:PRO127 4.5 50.2 1.0
CA G:MET125 4.5 62.4 1.0
N G:TYR124 4.6 58.7 1.0
C G:ARG126 4.8 51.6 1.0
CA G:TYR119 5.0 47.7 1.0
C G:TYR124 5.0 58.1 1.0
CB G:ALA123 5.0 55.6 1.0
N G:PRO127 5.0 49.8 1.0

Magnesium binding site 2 out of 8 in 4qz6

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Magnesium binding site 2 out of 8 in the Ycp BETA5-A49T-A50V Double 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-A49T-A50V Double Mutant in Complex with the Epoxyketone Inhibitor Onx 0914 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:82.4
occ:1.00
 O I:SER180 2.6 58.8 1.0
O I:ASP177 2.9 55.6 1.0
O I:ALA174 3.0 60.5 1.0
OXT I:ASP204 3.3 80.3 1.0
C I:SER180 3.8 55.5 1.0
C I:ALA174 3.9 61.4 1.0
C I:ASP177 4.1 55.3 1.0
CA I:ASP175 4.1 61.8 1.0
C I:ASP204 4.3 76.7 1.0
O I:ASP204 4.4 80.7 1.0
CA I:GLY181 4.4 55.4 1.0
N I:ASP175 4.5 61.6 1.0
O I:ALA178 4.5 61.7 1.0
C I:ASP175 4.6 59.8 1.0
N I:GLY181 4.6 54.1 1.0
OD1 I:ASP175 4.6 69.6 1.0
O I:ASP175 4.7 60.4 1.0
C I:ALA178 4.7 54.9 1.0
CA I:ALA178 4.7 53.9 1.0
N I:SER180 4.8 52.0 1.0
N I:ALA178 4.9 52.9 1.0
NH1 Y:ARG19 4.9 72.8 1.0
N I:ASP177 4.9 53.6 1.0
CA I:SER180 4.9 54.8 1.0
NH2 Y:ARG19 4.9 71.2 1.0

Magnesium binding site 3 out of 8 in 4qz6

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Magnesium binding site 3 out of 8 in the Ycp BETA5-A49T-A50V Double 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-A49T-A50V Double Mutant in Complex with the Epoxyketone Inhibitor Onx 0914 within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg302

b:60.2
occ:1.00
 O K:ASP168 2.1 59.5 1.0
O K:ALA165 2.2 56.2 1.0
O W:ASP204 2.6 79.3 1.0
O K:SER171 2.8 55.2 1.0
C K:ASP168 3.1 58.9 1.0
C W:ASP204 3.2 74.4 1.0
C K:ALA165 3.4 58.5 1.0
CA W:ASP204 3.6 71.2 1.0
O K:HIS166 3.6 59.3 1.0
CA K:ALA169 3.7 61.4 1.0
N K:ALA169 3.8 60.7 1.0
C K:HIS166 3.9 55.7 1.0
C K:ALA169 4.0 61.5 1.0
O K:ALA169 4.0 57.2 1.0
CB W:ASP204 4.0 69.1 1.0
C K:SER171 4.0 59.4 1.0
OXT W:ASP204 4.1 77.7 1.0
N K:ASP168 4.2 57.2 1.0
N K:HIS166 4.2 57.4 1.0
CA K:ASP168 4.3 57.4 1.0
CA K:ALA165 4.3 59.5 1.0
CA K:HIS166 4.3 58.0 1.0
NH1 K:ARG19 4.4 66.9 1.0
O K:ALA164 4.4 57.3 1.0
C K:ARG167 4.4 57.2 1.0
N K:SER171 4.4 60.3 1.0
N K:ARG167 4.6 55.9 1.0
O K:ARG167 4.7 57.9 1.0
CA K:SER171 4.8 58.3 1.0
N K:TYR170 4.8 62.6 1.0
CZ K:ARG19 4.9 67.4 1.0
N W:ASP204 4.9 71.6 1.0
N K:GLY172 5.0 59.9 1.0

Magnesium binding site 4 out of 8 in 4qz6

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Magnesium binding site 4 out of 8 in the Ycp BETA5-A49T-A50V Double 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-A49T-A50V Double Mutant in Complex with the Epoxyketone Inhibitor Onx 0914 within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg202

b:52.9
occ:1.00
 O N:SER169 2.5 60.3 1.0
O N:ILE163 2.6 56.9 1.0
O N:ASP166 3.0 59.4 1.0
NH1 N:ARG19 3.5 62.9 1.0
CD1 a:LEU34 3.7 60.8 1.0
C N:SER169 3.7 58.3 1.0
C N:ILE163 3.8 58.8 1.0
CG2 N:ILE163 4.0 58.0 1.0
C N:ASP166 4.1 57.5 1.0
CZ N:ARG19 4.2 62.3 1.0
CA N:GLY170 4.3 58.5 1.0
CA N:GLY167 4.3 58.4 1.0
NH2 N:ARG19 4.4 58.8 1.0
O N:GLY167 4.5 55.2 1.0
CA N:ILE163 4.5 58.1 1.0
N N:GLY170 4.5 58.3 1.0
C N:GLY167 4.6 57.3 1.0
N N:GLY167 4.7 55.6 1.0
N N:SER169 4.8 54.9 1.0
N N:LYS164 4.8 58.3 1.0
CA N:SER169 4.8 54.0 1.0
CB N:ILE163 4.8 57.5 1.0
O N:LYS164 4.9 61.3 1.0
C N:LYS164 4.9 60.6 1.0
CA N:LYS164 5.0 60.5 1.0

Magnesium binding site 5 out of 8 in 4qz6

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Magnesium binding site 5 out of 8 in the Ycp BETA5-A49T-A50V Double 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-A49T-A50V Double Mutant in Complex with the Epoxyketone Inhibitor Onx 0914 within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg203

b:78.0
occ:1.00
 OE1 H:GLN91 2.7 70.0 1.0
OD1 N:ASP51 2.8 37.6 1.0
OD2 N:ASP51 3.4 52.0 1.0
CG N:ASP51 3.5 26.2 1.0
CD H:GLN91 3.6 63.9 1.0
O N:ASN92 3.6 75.3 1.0
NE2 H:GLN91 3.9 63.5 1.0
CE1 H:PHE88 4.7 44.9 1.0
C N:ASN92 4.8 69.9 1.0
ND1 H:HIS116 4.9 54.5 1.0
CB N:ASP51 5.0 42.0 1.0

Magnesium binding site 6 out of 8 in 4qz6

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Magnesium binding site 6 out of 8 in the Ycp BETA5-A49T-A50V Double 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-A49T-A50V Double Mutant in Complex with the Epoxyketone Inhibitor Onx 0914 within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Mg302

b:73.8
occ:1.00
 OXT L:ASP222 2.1 81.6 1.0
O V:ASP166 2.1 56.1 1.0
O V:ILE163 2.3 58.1 1.0
O V:SER169 2.8 55.9 1.0
C L:ASP222 3.0 79.8 1.0
C V:ASP166 3.1 58.3 1.0
C V:ILE163 3.3 61.6 1.0
CA L:ASP222 3.6 77.4 1.0
O V:TRP164 3.7 68.9 1.0
C V:TRP164 3.8 66.4 1.0
N V:LEU167 3.8 57.6 1.0
O L:ASP222 3.8 85.9 1.0
CA V:LEU167 3.8 60.7 1.0
O V:GLY162 3.9 57.4 1.0
N V:ASP166 3.9 61.0 1.0
C V:SER169 4.0 57.1 1.0
CA V:ASP166 4.1 59.8 1.0
N V:TRP164 4.1 61.8 1.0
CA V:TRP164 4.2 64.7 1.0
NH1 V:ARG19 4.3 72.4 1.0
CA V:ILE163 4.3 63.2 1.0
CB L:ASP222 4.3 77.0 1.0
N V:ASN165 4.3 65.5 1.0
C V:LEU167 4.4 59.7 1.0
C V:ASN165 4.5 61.6 1.0
N V:SER169 4.7 56.9 1.0
O L:ARG221 4.7 69.2 1.0
CD2 V:LEU167 4.7 61.3 1.0
O V:LEU167 4.8 64.7 1.0
CZ V:ARG19 4.8 68.5 1.0
CA V:SER169 4.9 56.5 1.0
C V:GLY162 4.9 61.6 1.0
CA V:GLY170 4.9 61.7 1.0
N V:GLY170 4.9 58.0 1.0
N L:ASP222 4.9 75.4 1.0
NH2 V:ARG19 4.9 76.2 1.0
CA V:ASN165 4.9 62.2 1.0
CB V:ASP166 5.0 57.1 1.0

Magnesium binding site 7 out of 8 in 4qz6

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Magnesium binding site 7 out of 8 in the Ycp BETA5-A49T-A50V Double 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-A49T-A50V Double Mutant in Complex with the Epoxyketone Inhibitor Onx 0914 within 5.0Å range:
probe atom residue distance (Å) B Occ
Y:Mg302

b:61.2
occ:1.00
 O Y:ASP168 2.2 60.7 1.0
O Y:ALA165 2.4 54.8 1.0
O I:ASP204 2.4 80.7 1.0
O Y:SER171 3.1 56.2 1.0
C I:ASP204 3.1 76.7 1.0
C Y:ASP168 3.2 58.8 1.0
O Y:HIS166 3.5 53.7 1.0
C Y:ALA165 3.5 55.6 1.0
CA I:ASP204 3.6 73.2 1.0
CA Y:ALA169 3.6 59.6 1.0
N Y:ALA169 3.8 59.0 1.0
C Y:HIS166 3.9 54.5 1.0
OXT I:ASP204 4.0 80.3 1.0
O Y:ALA169 4.0 61.5 1.0
C Y:ALA169 4.0 58.5 1.0
CB I:ASP204 4.1 73.4 1.0
C Y:SER171 4.3 60.2 1.0
N Y:ASP168 4.3 56.4 1.0
CA Y:HIS166 4.3 54.3 1.0
N Y:HIS166 4.4 53.8 1.0
CA Y:ASP168 4.4 57.4 1.0
NH1 Y:ARG19 4.4 72.8 1.0
C Y:ARG167 4.4 56.5 1.0
CA Y:ALA165 4.5 57.6 1.0
N Y:ARG167 4.6 54.8 1.0
O Y:ARG167 4.6 55.1 1.0
O Y:ALA164 4.6 50.6 1.0
N Y:SER171 4.7 58.6 1.0
N Y:TYR170 4.9 58.7 1.0
CB Y:ALA169 4.9 60.1 1.0
N I:ASP204 4.9 71.9 1.0
CZ Y:ARG19 5.0 69.5 1.0

Magnesium binding site 8 out of 8 in 4qz6

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Magnesium binding site 8 out of 8 in the Ycp BETA5-A49T-A50V Double 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 8 of Ycp BETA5-A49T-A50V Double Mutant in Complex with the Epoxyketone Inhibitor Onx 0914 within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg301

b:73.4
occ:1.00
 O Z:VAL198 2.5 59.2 1.0
O Z:THR192 2.8 58.6 1.0
O Z:HIS195 3.0 54.9 1.0
NH2 Z:ARG28 3.5 72.8 1.0
O Z:ASP222 3.5 87.3 1.0
CG2 Z:THR192 3.6 67.1 1.0
C Z:VAL198 3.7 61.9 1.0
C Z:THR192 3.8 66.1 1.0
O Z:ILE196 3.8 59.7 1.0
CA Z:THR192 4.1 66.4 1.0
C Z:HIS195 4.1 54.5 1.0
CA Z:ILE196 4.1 57.1 1.0
OD1 Z:ASP222 4.1 72.9 1.0
C Z:ILE196 4.2 56.8 1.0
NH2 H:ARG19 4.4 72.1 1.0
N Z:VAL198 4.5 57.4 1.0
CB Z:THR192 4.5 66.3 1.0
CZ Z:ARG28 4.5 69.5 1.0
C Z:ASP222 4.5 81.8 1.0
CA Z:GLY199 4.5 63.6 1.0
N Z:GLY199 4.5 60.8 1.0
N Z:ILE196 4.6 53.9 1.0
CA Z:VAL198 4.6 60.4 1.0
NH1 Z:ARG28 4.7 72.4 1.0
O Z:LYS220 4.8 72.7 1.0
N Z:GLU193 5.0 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 02:39:29 2024

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