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Magnesium in PDB 4qw5: Ycp BETA5-M45A Mutant in Complex with Carfilzomib

Enzymatic activity of Ycp BETA5-M45A Mutant in Complex with Carfilzomib

All present enzymatic activity of Ycp BETA5-M45A Mutant in Complex with Carfilzomib:
3.4.25.1;

Protein crystallography data

The structure of Ycp BETA5-M45A Mutant in Complex with Carfilzomib, PDB code: 4qw5 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 (°) 135.550, 300.110, 145.150, 90.00, 113.00, 90.00
R / Rfree (%) 16.9 / 20.1

Other elements in 4qw5:

The structure of Ycp BETA5-M45A Mutant in Complex with Carfilzomib also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Ycp BETA5-M45A Mutant in Complex with Carfilzomib (pdb code 4qw5). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Ycp BETA5-M45A Mutant in Complex with Carfilzomib, PDB code: 4qw5:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 4qw5

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Magnesium binding site 1 out of 5 in the Ycp BETA5-M45A Mutant in Complex with Carfilzomib


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 Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:62.5
occ:1.00
 O G:MET125 2.4 61.9 1.0
OG1 G:THR8 2.6 51.9 1.0
O G:ARG122 2.9 51.9 1.0
O G:ALA123 3.0 58.8 1.0
O G:TYR119 3.1 49.0 1.0
CG2 G:THR8 3.2 53.8 1.0
C G:MET125 3.4 58.1 1.0
CB G:THR8 3.5 52.9 1.0
C G:ALA123 3.6 57.5 1.0
CA G:ALA123 3.7 55.9 1.0
C G:ARG122 3.9 55.3 1.0
N G:THR8 3.9 53.9 1.0
CA G:ARG126 4.1 51.5 1.0
N G:ARG126 4.2 53.2 1.0
C G:TYR119 4.3 48.5 1.0
N G:ALA123 4.3 54.9 1.0
N G:MET125 4.3 58.4 1.0
CA G:THR8 4.3 53.9 1.0
CA G:MET125 4.5 61.9 1.0
CD G:PRO127 4.5 48.5 1.0
N G:TYR124 4.6 61.3 1.0
C G:ARG126 4.8 51.2 1.0
C G:TYR124 4.9 57.0 1.0
CB G:ALA123 5.0 55.9 1.0
C G:ILE7 5.0 57.2 1.0

Magnesium binding site 2 out of 5 in 4qw5

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Magnesium binding site 2 out of 5 in the Ycp BETA5-M45A Mutant in Complex with Carfilzomib


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 Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg302

b:56.5
occ:1.00
 O K:ASP168 2.1 55.9 1.0
O K:ALA165 2.4 58.1 1.0
O W:ASP204 2.4 71.0 1.0
O K:SER171 2.8 56.6 1.0
C W:ASP204 3.2 67.0 1.0
C K:ASP168 3.2 55.1 1.0
C K:ALA165 3.5 59.0 1.0
CA K:ALA169 3.6 55.9 1.0
CA W:ASP204 3.6 67.3 1.0
O K:HIS166 3.7 55.2 1.0
N K:ALA169 3.8 55.6 1.0
C K:ALA169 3.9 57.3 1.0
O K:ALA169 3.9 59.1 1.0
CB W:ASP204 4.0 64.9 1.0
C K:SER171 4.0 56.3 1.0
NH1 K:ARG19 4.1 64.8 1.0
OXT W:ASP204 4.1 67.9 1.0
C K:HIS166 4.1 55.5 1.0
N K:SER171 4.3 55.2 1.0
CA K:ASP168 4.4 55.2 1.0
N K:ASP168 4.4 57.3 1.0
CA K:ALA165 4.4 59.0 1.0
N K:HIS166 4.4 57.2 1.0
CA K:HIS166 4.5 56.5 1.0
O K:ALA164 4.6 56.1 1.0
C K:ARG167 4.6 58.8 1.0
CZ K:ARG19 4.6 64.3 1.0
N K:TYR170 4.7 56.3 1.0
CA K:SER171 4.7 54.0 1.0
N K:ARG167 4.8 54.4 1.0
O K:ARG167 4.8 60.0 1.0
NH2 K:ARG19 4.8 69.0 1.0
CB K:ALA169 4.9 54.7 1.0
N W:ASP204 5.0 68.2 1.0

Magnesium binding site 3 out of 5 in 4qw5

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Magnesium binding site 3 out of 5 in the Ycp BETA5-M45A Mutant in Complex with Carfilzomib


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 Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg202

b:44.5
occ:1.00
 O N:SER169 2.5 51.1 1.0
O N:ILE163 2.6 50.7 1.0
O N:ASP166 2.9 52.6 1.0
NH1 N:ARG19 3.5 53.2 1.0
CD1 a:LEU34 3.7 54.9 1.0
C N:SER169 3.8 48.9 1.0
C N:ILE163 3.8 51.3 1.0
C N:ASP166 4.0 49.9 1.0
CG2 N:ILE163 4.0 50.1 1.0
CA N:GLY167 4.2 50.0 1.0
CZ N:ARG19 4.2 53.4 1.0
O N:GLY167 4.4 51.1 1.0
CA N:GLY170 4.4 50.3 1.0
NH2 N:ARG19 4.4 56.3 1.0
CA N:ILE163 4.4 51.3 1.0
C N:GLY167 4.5 50.6 1.0
N N:GLY167 4.5 48.7 1.0
N N:GLY170 4.5 49.5 1.0
N N:SER169 4.7 48.8 1.0
N N:LYS164 4.8 52.4 1.0
CA N:SER169 4.8 46.5 1.0
CB N:ILE163 4.8 50.2 1.0
CG a:LEU34 4.9 55.7 1.0
O N:LYS164 5.0 55.1 1.0
C N:LYS164 5.0 53.9 1.0
CA N:LYS164 5.0 53.2 1.0

Magnesium binding site 4 out of 5 in 4qw5

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Magnesium binding site 4 out of 5 in the Ycp BETA5-M45A Mutant in Complex with Carfilzomib


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 Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
Y:Mg302

b:66.6
occ:1.00
 O Y:ASP168 2.2 56.5 1.0
O I:ASP204 2.3 79.9 1.0
O Y:ALA165 2.5 54.2 1.0
O Y:SER171 2.9 58.0 1.0
C I:ASP204 3.1 77.8 1.0
C Y:ASP168 3.2 55.5 1.0
CA Y:ALA169 3.5 54.7 1.0
CA I:ASP204 3.6 73.9 1.0
C Y:ALA165 3.7 55.8 1.0
O Y:HIS166 3.7 51.3 1.0
N Y:ALA169 3.8 57.5 1.0
C Y:ALA169 3.8 54.0 1.0
O Y:ALA169 3.8 56.3 1.0
NH1 Y:ARG19 4.0 71.5 1.0
CB I:ASP204 4.0 74.0 1.0
OXT I:ASP204 4.1 80.0 1.0
C Y:SER171 4.1 55.9 1.0
C Y:HIS166 4.2 52.8 1.0
N Y:SER171 4.4 51.6 1.0
CA Y:ASP168 4.4 54.4 1.0
N Y:ASP168 4.5 56.2 1.0
CA Y:ALA165 4.6 56.4 1.0
N Y:HIS166 4.6 56.5 1.0
CZ Y:ARG19 4.6 70.2 1.0
CA Y:HIS166 4.6 54.4 1.0
N Y:TYR170 4.6 52.8 1.0
C Y:ARG167 4.7 56.0 1.0
O Y:ALA164 4.7 56.4 1.0
CA Y:SER171 4.8 52.2 1.0
NH2 Y:ARG19 4.8 76.5 1.0
O Y:ARG167 4.8 54.1 1.0
CB Y:ALA169 4.8 53.5 1.0
N Y:ARG167 4.9 50.6 1.0

Magnesium binding site 5 out of 5 in 4qw5

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Magnesium binding site 5 out of 5 in the Ycp BETA5-M45A Mutant in Complex with Carfilzomib


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 Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg301

b:65.2
occ:1.00
 O Z:VAL198 2.6 56.7 1.0
O Z:THR192 2.9 65.6 1.0
O Z:HIS195 3.2 52.5 1.0
O Z:ASP222 3.3 73.5 1.0
NH2 Z:ARG28 3.5 74.5 1.0
CG2 Z:THR192 3.6 65.0 1.0
C Z:VAL198 3.8 58.5 1.0
C Z:THR192 3.9 64.6 1.0
O Z:ILE196 3.9 55.7 1.0
OD1 Z:ASP222 4.0 74.2 1.0
CA Z:THR192 4.2 63.8 1.0
CA Z:ILE196 4.2 54.1 1.0
C Z:ILE196 4.3 52.9 1.0
C Z:HIS195 4.3 54.9 1.0
NH2 H:ARG19 4.3 74.5 1.0
C Z:ASP222 4.3 74.8 1.0
CZ Z:ARG28 4.5 69.3 1.0
CA Z:GLY199 4.5 60.3 1.0
CB Z:THR192 4.5 64.1 1.0
N Z:GLY199 4.6 58.1 1.0
N Z:VAL198 4.6 56.8 1.0
NH1 Z:ARG28 4.7 70.1 1.0
O Z:LYS220 4.7 65.3 1.0
N Z:ILE196 4.7 53.8 1.0
CA Z:VAL198 4.8 58.2 1.0
OXT Z:ASP222 4.8 77.5 1.0
CG Z:ASP222 4.9 72.5 1.0
NH1 H:ARG19 5.0 69.0 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 02:26:40 2024

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