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Magnesium in PDB 4qwr: Ycp BETA5-C52F Mutant in Complex with Carfilzomib

Enzymatic activity of Ycp BETA5-C52F Mutant in Complex with Carfilzomib

All present enzymatic activity of Ycp BETA5-C52F Mutant in Complex with Carfilzomib:
3.4.25.1;

Protein crystallography data

The structure of Ycp BETA5-C52F Mutant in Complex with Carfilzomib, PDB code: 4qwr 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 (°) 136.000, 300.580, 144.520, 90.00, 113.17, 90.00
R / Rfree (%) 18.1 / 20.9

Other elements in 4qwr:

The structure of Ycp BETA5-C52F 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-C52F Mutant in Complex with Carfilzomib (pdb code 4qwr). 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-C52F Mutant in Complex with Carfilzomib, PDB code: 4qwr:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 4qwr

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Magnesium binding site 1 out of 8 in the Ycp BETA5-C52F 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-C52F Mutant in Complex with Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:63.2
occ:1.00
 O G:MET125 2.4 48.1 1.0
OG1 G:THR8 2.9 42.0 1.0
O G:ARG122 2.9 41.5 1.0
O G:ALA123 3.0 53.0 1.0
O G:TYR119 3.2 43.0 1.0
CG2 G:THR8 3.3 44.6 1.0
C G:MET125 3.4 48.8 1.0
C G:ALA123 3.5 51.4 1.0
CB G:THR8 3.6 44.0 1.0
CA G:ALA123 3.7 48.2 1.0
O F:HOH315 3.9 54.5 1.0
C G:ARG122 4.0 46.1 1.0
CA G:ARG126 4.0 42.9 1.0
N G:THR8 4.0 46.0 1.0
N G:ARG126 4.1 45.0 1.0
N G:MET125 4.2 52.8 1.0
N G:ALA123 4.3 46.2 1.0
CD G:PRO127 4.4 40.6 1.0
CA G:MET125 4.4 53.7 1.0
C G:TYR119 4.4 41.7 1.0
CA G:THR8 4.5 45.6 1.0
N G:TYR124 4.6 54.1 1.0
C G:ARG126 4.8 42.4 1.0
C G:TYR124 4.9 52.3 1.0
N G:PRO127 5.0 40.8 1.0

Magnesium binding site 2 out of 8 in 4qwr

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Magnesium binding site 2 out of 8 in the Ycp BETA5-C52F 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-C52F Mutant in Complex with Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:59.7
occ:1.00
 O I:ASP177 2.6 47.8 1.0
O I:SER180 2.6 45.0 1.0
O I:ALA174 2.8 57.2 1.0
OXT I:ASP204 3.6 68.6 1.0
C I:ASP177 3.8 49.9 1.0
C I:ALA174 3.8 56.8 1.0
C I:SER180 3.8 49.0 1.0
CA I:ASP175 4.1 56.4 1.0
N I:ASP175 4.4 56.4 1.0
C I:ASP175 4.4 53.6 1.0
O I:ALA178 4.4 55.5 1.0
O I:ASP175 4.4 53.5 1.0
CA I:ALA178 4.5 48.7 1.0
C I:ASP204 4.5 67.3 1.0
CA I:GLY181 4.6 50.2 1.0
C I:ALA178 4.6 50.0 1.0
N I:ALA178 4.6 48.5 1.0
N I:ASP177 4.6 50.4 1.0
O I:ASP204 4.6 66.9 1.0
N I:GLY181 4.6 48.8 1.0
N I:SER180 4.7 48.0 1.0
CA I:ASP177 4.7 50.4 1.0
OD1 I:ASP175 4.8 60.2 1.0
CA I:SER180 4.8 48.8 1.0
NH1 Y:ARG19 4.9 63.0 1.0
CA I:ALA174 5.0 55.0 1.0

Magnesium binding site 3 out of 8 in 4qwr

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Magnesium binding site 3 out of 8 in the Ycp BETA5-C52F 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-C52F Mutant in Complex with Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg302

b:49.7
occ:1.00
 O K:ASP168 2.3 53.0 1.0
O K:ALA165 2.3 50.8 1.0
O W:ASP204 2.4 66.0 1.0
O K:SER171 2.9 47.6 1.0
C W:ASP204 3.1 62.0 1.0
C K:ASP168 3.3 50.8 1.0
C K:ALA165 3.5 50.8 1.0
CA W:ASP204 3.5 59.8 1.0
O K:HIS166 3.6 48.3 1.0
CA K:ALA169 3.7 52.1 1.0
N K:ALA169 3.9 50.9 1.0
OXT W:ASP204 3.9 59.5 1.0
CB W:ASP204 3.9 58.0 1.0
C K:HIS166 4.0 49.7 1.0
C K:ALA169 4.0 53.5 1.0
O K:ALA169 4.0 53.7 1.0
C K:SER171 4.1 50.1 1.0
NH1 K:ARG19 4.2 61.6 1.0
N K:HIS166 4.3 49.5 1.0
N K:ASP168 4.3 52.4 1.0
CA K:HIS166 4.4 49.9 1.0
CA K:ALA165 4.4 50.7 1.0
CA K:ASP168 4.4 51.2 1.0
C K:ARG167 4.6 52.4 1.0
N K:SER171 4.6 50.4 1.0
O K:ALA164 4.6 50.4 1.0
N K:ARG167 4.6 51.3 1.0
CZ K:ARG19 4.8 61.8 1.0
O K:ARG167 4.8 52.6 1.0
N W:ASP204 4.9 59.6 1.0
N K:TYR170 4.9 54.0 1.0
NH2 K:ARG19 4.9 64.2 1.0
CA K:SER171 4.9 49.1 1.0

Magnesium binding site 4 out of 8 in 4qwr

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Magnesium binding site 4 out of 8 in the Ycp BETA5-C52F 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-C52F Mutant in Complex with Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg202

b:45.7
occ:1.00
 O N:SER169 2.5 43.0 1.0
O N:ILE163 2.6 46.4 1.0
O N:ASP166 2.8 46.3 1.0
NH1 N:ARG19 3.6 48.3 1.0
C N:SER169 3.7 42.5 1.0
CD1 a:LEU34 3.7 48.3 1.0
C N:ILE163 3.7 45.8 1.0
C N:ASP166 3.9 44.2 1.0
CG2 N:ILE163 3.9 46.7 1.0
CA N:GLY167 4.2 42.8 1.0
CZ N:ARG19 4.3 46.9 1.0
CA N:ILE163 4.3 45.9 1.0
O N:GLY167 4.3 43.3 1.0
CA N:GLY170 4.4 44.1 1.0
C N:GLY167 4.5 41.5 1.0
N N:GLY167 4.5 42.1 1.0
N N:GLY170 4.5 43.2 1.0
N N:SER169 4.6 40.0 1.0
NH2 N:ARG19 4.6 48.6 1.0
CA N:SER169 4.7 39.2 1.0
CB N:ILE163 4.7 45.5 1.0
N N:LYS164 4.8 46.7 1.0
CG a:LEU34 4.9 49.3 1.0
C N:LYS164 5.0 47.0 1.0

Magnesium binding site 5 out of 8 in 4qwr

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Magnesium binding site 5 out of 8 in the Ycp BETA5-C52F 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-C52F Mutant in Complex with Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg203

b:43.6
occ:1.00
 OD1 N:ASP51 2.5 26.6 1.0
OE1 H:GLN91 2.8 57.0 1.0
CG N:ASP51 3.2 24.6 1.0
O N:ASN92 3.2 54.1 1.0
OD2 N:ASP51 3.3 29.6 1.0
NE2 H:GLN91 3.5 56.0 1.0
CD H:GLN91 3.6 55.0 1.0
CE1 H:PHE88 4.3 37.7 1.0
C N:ASN92 4.5 53.6 1.0
CZ H:PHE88 4.5 37.7 1.0
C18 N:3BV201 4.7 85.3 1.0
CB N:ASP51 4.7 26.6 1.0

Magnesium binding site 6 out of 8 in 4qwr

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Magnesium binding site 6 out of 8 in the Ycp BETA5-C52F 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 6 of Ycp BETA5-C52F Mutant in Complex with Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Mg302

b:60.6
occ:1.00
 OXT L:ASP222 2.0 66.9 1.0
O V:ASP166 2.1 51.0 1.0
O V:ILE163 2.2 54.2 1.0
O V:SER169 2.6 47.7 1.0
C L:ASP222 3.0 63.5 1.0
C V:ASP166 3.1 50.9 1.0
C V:ILE163 3.3 53.9 1.0
CA L:ASP222 3.7 63.9 1.0
C V:SER169 3.7 47.4 1.0
CA V:LEU167 3.8 50.2 1.0
N V:LEU167 3.8 51.0 1.0
O V:GLY162 3.9 52.2 1.0
O V:TRP164 3.9 54.4 1.0
O L:ASP222 3.9 66.1 1.0
N V:ASP166 4.0 48.7 1.0
NH1 V:ARG19 4.0 57.8 1.0
C V:TRP164 4.0 54.8 1.0
CA V:ASP166 4.1 49.6 1.0
N V:TRP164 4.2 53.6 1.0
CA V:ILE163 4.2 54.5 1.0
CB L:ASP222 4.3 63.8 1.0
C V:LEU167 4.3 48.9 1.0
CA V:TRP164 4.3 54.3 1.0
N V:SER169 4.5 46.3 1.0
N V:ASN165 4.5 52.9 1.0
O V:LEU167 4.6 51.0 1.0
CZ V:ARG19 4.6 54.3 1.0
N V:GLY170 4.6 48.4 1.0
CA V:GLY170 4.6 50.9 1.0
CA V:SER169 4.6 46.5 1.0
C V:ASN165 4.7 48.4 1.0
NH2 V:ARG19 4.7 55.8 1.0
C V:GLY162 4.9 52.3 1.0
CD2 V:LEU167 4.9 48.6 1.0
CB V:ASP166 4.9 47.8 1.0
O L:ARG221 4.9 58.5 1.0
N V:GLY168 4.9 45.8 1.0
N L:ASP222 5.0 62.1 1.0

Magnesium binding site 7 out of 8 in 4qwr

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Magnesium binding site 7 out of 8 in the Ycp BETA5-C52F 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 7 of Ycp BETA5-C52F Mutant in Complex with Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
Y:Mg302

b:51.5
occ:1.00
 O Y:ASP168 2.2 51.1 1.0
O Y:ALA165 2.5 45.4 1.0
O I:ASP204 2.5 66.9 1.0
O Y:SER171 3.1 51.6 1.0
C Y:ASP168 3.1 52.9 1.0
C I:ASP204 3.2 67.3 1.0
CA Y:ALA169 3.5 53.7 1.0
O Y:HIS166 3.6 48.9 1.0
C Y:ALA165 3.6 48.4 1.0
N Y:ALA169 3.7 54.9 1.0
CA I:ASP204 3.7 66.9 1.0
C Y:ALA169 3.9 52.5 1.0
O Y:ALA169 4.0 51.5 1.0
C Y:HIS166 4.0 51.7 1.0
OXT I:ASP204 4.0 68.6 1.0
CB I:ASP204 4.2 68.3 1.0
NH1 Y:ARG19 4.2 63.0 1.0
N Y:ASP168 4.3 52.4 1.0
C Y:SER171 4.3 51.8 1.0
CA Y:ASP168 4.3 52.7 1.0
C Y:ARG167 4.4 52.2 1.0
N Y:HIS166 4.5 50.0 1.0
CA Y:HIS166 4.5 51.7 1.0
CA Y:ALA165 4.6 50.1 1.0
N Y:SER171 4.6 50.3 1.0
N Y:ARG167 4.6 53.0 1.0
O Y:ARG167 4.6 51.7 1.0
O Y:ALA164 4.6 51.9 1.0
N Y:TYR170 4.8 53.0 1.0
CB Y:ALA169 4.8 53.6 1.0
CZ Y:ARG19 4.9 60.2 1.0
CA Y:SER171 5.0 50.1 1.0

Magnesium binding site 8 out of 8 in 4qwr

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Magnesium binding site 8 out of 8 in the Ycp BETA5-C52F 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 8 of Ycp BETA5-C52F Mutant in Complex with Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg301

b:60.1
occ:1.00
 O Z:VAL198 2.7 58.5 1.0
O Z:THR192 2.9 58.5 1.0
O Z:HIS195 3.1 47.3 1.0
O Z:ASP222 3.3 68.6 1.0
NH2 Z:ARG28 3.5 60.4 1.0
CG2 Z:THR192 3.7 59.8 1.0
C Z:VAL198 3.8 56.0 1.0
O Z:ILE196 3.8 46.7 1.0
C Z:THR192 3.9 59.6 1.0
OD1 Z:ASP222 4.1 64.8 1.0
CA Z:ILE196 4.1 48.7 1.0
NH2 H:ARG19 4.2 67.3 1.0
C Z:HIS195 4.2 48.9 1.0
C Z:ILE196 4.2 47.2 1.0
CA Z:THR192 4.2 60.0 1.0
C Z:ASP222 4.3 67.3 1.0
CZ Z:ARG28 4.5 56.7 1.0
N Z:VAL198 4.6 50.5 1.0
CB Z:THR192 4.6 60.5 1.0
N Z:ILE196 4.6 47.8 1.0
CA Z:GLY199 4.6 56.6 1.0
N Z:GLY199 4.7 56.3 1.0
NH1 Z:ARG28 4.7 58.4 1.0
CA Z:VAL198 4.8 52.8 1.0
OXT Z:ASP222 4.8 65.3 1.0
O Z:LYS220 4.8 62.7 1.0
NH1 H:ARG19 4.8 61.1 1.0
CZ H:ARG19 4.9 60.6 1.0
CG Z:ASP222 5.0 63.3 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 02:32:09 2024

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