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Magnesium in PDB 4qw6: Ycp BETA5-M45V Mutant in Complex with Carfilzomib

Enzymatic activity of Ycp BETA5-M45V Mutant in Complex with Carfilzomib

All present enzymatic activity of Ycp BETA5-M45V Mutant in Complex with Carfilzomib:
3.4.25.1;

Protein crystallography data

The structure of Ycp BETA5-M45V Mutant in Complex with Carfilzomib, PDB code: 4qw6 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 (°) 136.320, 299.760, 145.300, 90.00, 113.04, 90.00
R / Rfree (%) 17.7 / 20.6

Other elements in 4qw6:

The structure of Ycp BETA5-M45V 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-M45V Mutant in Complex with Carfilzomib (pdb code 4qw6). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Ycp BETA5-M45V Mutant in Complex with Carfilzomib, PDB code: 4qw6:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 4qw6

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Magnesium binding site 1 out of 6 in the Ycp BETA5-M45V 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-M45V Mutant in Complex with Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:60.5
occ:1.00
 O G:MET125 2.3 52.0 1.0
OG1 G:THR8 2.5 43.0 1.0
O G:ARG122 2.8 45.6 1.0
O G:TYR119 3.0 39.3 1.0
O G:ALA123 3.1 52.0 1.0
CG2 G:THR8 3.2 45.6 1.0
CB G:THR8 3.4 44.7 1.0
C G:MET125 3.5 51.0 1.0
C G:ALA123 3.6 49.9 1.0
CA G:ALA123 3.7 48.5 1.0
C G:ARG122 3.8 47.9 1.0
N G:THR8 3.9 47.6 1.0
C G:TYR119 4.2 40.1 1.0
CA G:ARG126 4.2 44.1 1.0
N G:ALA123 4.2 47.8 1.0
N G:ARG126 4.2 46.5 1.0
N G:MET125 4.3 52.3 1.0
CA G:THR8 4.3 46.5 1.0
CA G:MET125 4.5 54.2 1.0
N G:TYR124 4.6 52.7 1.0
CD G:PRO127 4.6 41.2 1.0
C G:ARG126 4.9 43.0 1.0
CB G:ALA123 4.9 47.7 1.0
C G:TYR124 4.9 50.3 1.0
CA G:TYR119 4.9 38.9 1.0

Magnesium binding site 2 out of 6 in 4qw6

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Magnesium binding site 2 out of 6 in the Ycp BETA5-M45V 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-M45V Mutant in Complex with Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:50.9
occ:1.00
 O I:ASP177 2.3 47.3 1.0
O I:ALA174 2.6 49.5 1.0
O I:SER180 2.6 45.3 1.0
C I:ASP177 3.5 45.7 1.0
C I:ALA174 3.7 50.8 1.0
OXT I:ASP204 3.8 67.6 1.0
C I:SER180 3.9 46.2 1.0
CA I:ASP175 4.0 50.7 1.0
C I:ASP175 4.2 49.5 1.0
N I:ASP175 4.2 50.7 1.0
N I:ASP177 4.3 45.2 1.0
O I:ASP175 4.3 49.5 1.0
CA I:ALA178 4.3 44.3 1.0
N I:ALA178 4.3 44.0 1.0
O I:ALA178 4.4 51.4 1.0
CA I:ASP177 4.4 45.8 1.0
C I:ALA178 4.5 45.5 1.0
N I:SER180 4.6 43.5 1.0
C I:ASP204 4.7 65.5 1.0
CA I:GLY181 4.7 47.8 1.0
O I:ASP204 4.7 66.8 1.0
N I:GLY181 4.7 47.1 1.0
NH1 Y:ARG19 4.8 60.6 1.0
CA I:SER180 4.8 45.3 1.0
CA I:ALA174 4.8 49.2 1.0
OD1 I:ASP175 4.8 53.8 1.0
N I:ARG176 4.9 47.0 1.0
NH2 Y:ARG19 4.9 60.6 1.0

Magnesium binding site 3 out of 6 in 4qw6

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Magnesium binding site 3 out of 6 in the Ycp BETA5-M45V 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-M45V Mutant in Complex with Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg302

b:57.9
occ:1.00
 O K:ASP168 2.1 46.9 1.0
O W:ASP204 2.4 60.0 1.0
O K:ALA165 2.4 47.9 1.0
O K:SER171 2.8 49.5 1.0
C K:ASP168 3.1 47.0 1.0
C W:ASP204 3.2 59.3 1.0
CA K:ALA169 3.5 47.9 1.0
C K:ALA165 3.6 49.4 1.0
CA W:ASP204 3.6 57.9 1.0
O K:HIS166 3.7 48.9 1.0
N K:ALA169 3.7 47.6 1.0
C K:ALA169 3.8 48.8 1.0
O K:ALA169 3.9 49.0 1.0
C K:SER171 4.0 48.5 1.0
CB W:ASP204 4.0 57.4 1.0
NH1 K:ARG19 4.0 56.6 1.0
OXT W:ASP204 4.1 57.9 1.0
C K:HIS166 4.1 48.1 1.0
CA K:ASP168 4.3 47.4 1.0
N K:ASP168 4.3 48.6 1.0
N K:SER171 4.3 45.7 1.0
CA K:ALA165 4.4 49.6 1.0
N K:HIS166 4.5 47.6 1.0
CA K:HIS166 4.5 47.8 1.0
C K:ARG167 4.6 49.1 1.0
O K:ALA164 4.6 48.2 1.0
CZ K:ARG19 4.6 57.1 1.0
N K:TYR170 4.7 48.2 1.0
CA K:SER171 4.7 46.2 1.0
O K:ARG167 4.8 50.2 1.0
NH2 K:ARG19 4.8 61.2 1.0
N K:ARG167 4.8 47.6 1.0
CB K:ALA169 4.9 46.7 1.0
N W:ASP204 5.0 56.9 1.0

Magnesium binding site 4 out of 6 in 4qw6

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Magnesium binding site 4 out of 6 in the Ycp BETA5-M45V 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-M45V Mutant in Complex with Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg202

b:44.4
occ:1.00
 O N:SER169 2.4 40.4 1.0
O N:ILE163 2.5 43.9 1.0
O N:ASP166 2.8 44.1 1.0
NH1 N:ARG19 3.6 48.3 1.0
C N:ILE163 3.6 44.5 1.0
C N:SER169 3.7 41.1 1.0
CD1 a:LEU34 3.7 48.1 1.0
C N:ASP166 3.9 42.3 1.0
CG2 N:ILE163 3.9 44.5 1.0
CA N:GLY167 4.2 40.5 1.0
CZ N:ARG19 4.3 46.5 1.0
CA N:ILE163 4.3 44.6 1.0
CA N:GLY170 4.3 43.3 1.0
O N:GLY167 4.4 40.4 1.0
N N:GLY170 4.5 42.0 1.0
N N:GLY167 4.5 40.8 1.0
C N:GLY167 4.5 40.4 1.0
NH2 N:ARG19 4.5 46.8 1.0
N N:SER169 4.6 40.6 1.0
CA N:SER169 4.7 39.4 1.0
N N:LYS164 4.7 44.9 1.0
CB N:ILE163 4.7 44.2 1.0
C N:LYS164 4.9 46.2 1.0
O N:LYS164 4.9 46.6 1.0
CA N:LYS164 4.9 45.7 1.0
CG a:LEU34 4.9 48.7 1.0

Magnesium binding site 5 out of 6 in 4qw6

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Magnesium binding site 5 out of 6 in the Ycp BETA5-M45V 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-M45V Mutant in Complex with Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Mg302

b:61.5
occ:1.00
 O V:ASP166 2.2 45.0 1.0
OXT L:ASP222 2.3 72.9 1.0
O V:ILE163 2.4 56.3 1.0
C V:ASP166 3.0 47.8 1.0
C L:ASP222 3.1 71.4 1.0
O V:SER169 3.1 51.1 1.0
O V:TRP164 3.3 51.7 1.0
C V:ILE163 3.4 55.9 1.0
C V:TRP164 3.6 53.8 1.0
N V:LEU167 3.7 47.5 1.0
N V:ASP166 3.7 46.9 1.0
CA L:ASP222 3.7 70.6 1.0
CA V:LEU167 3.8 47.9 1.0
O L:ASP222 3.9 74.2 1.0
O V:GLY162 3.9 51.9 1.0
CA V:ASP166 4.0 47.7 1.0
CA V:TRP164 4.1 54.5 1.0
N V:TRP164 4.1 55.0 1.0
N V:ASN165 4.1 52.6 1.0
C V:ASN165 4.2 48.0 1.0
C V:SER169 4.3 48.9 1.0
CA V:ILE163 4.5 55.0 1.0
NH1 V:ARG19 4.5 61.5 1.0
C V:LEU167 4.5 48.3 1.0
CB L:ASP222 4.5 69.9 1.0
CD2 V:LEU167 4.6 46.0 1.0
O L:ARG221 4.6 63.6 1.0
CA V:ASN165 4.7 50.7 1.0
O V:LEU167 4.8 51.1 1.0
CD1 L:ILE35 4.9 59.3 1.0
O V:ASN165 4.9 44.8 1.0
N L:ASP222 4.9 69.1 1.0
N V:SER169 4.9 46.1 1.0
CB V:ASP166 4.9 47.1 1.0
C V:GLY162 5.0 52.6 1.0
CB V:LEU167 5.0 46.2 1.0

Magnesium binding site 6 out of 6 in 4qw6

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Magnesium binding site 6 out of 6 in the Ycp BETA5-M45V 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-M45V Mutant in Complex with Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
Y:Mg302

b:48.0
occ:1.00
 O Y:ASP168 2.2 47.1 1.0
O I:ASP204 2.2 66.8 1.0
O Y:ALA165 2.5 43.7 1.0
O Y:SER171 2.7 47.6 1.0
C I:ASP204 3.1 65.5 1.0
C Y:ASP168 3.3 44.2 1.0
CA Y:ALA169 3.6 43.9 1.0
CA I:ASP204 3.6 63.5 1.0
C Y:ALA165 3.6 44.8 1.0
O Y:ALA169 3.8 44.2 1.0
C Y:ALA169 3.8 43.5 1.0
N Y:ALA169 3.8 44.3 1.0
NH1 Y:ARG19 3.8 60.6 1.0
O Y:HIS166 3.9 42.7 1.0
C Y:SER171 3.9 46.6 1.0
CB I:ASP204 3.9 64.0 1.0
OXT I:ASP204 4.1 67.6 1.0
N Y:SER171 4.3 43.3 1.0
C Y:HIS166 4.3 43.4 1.0
CZ Y:ARG19 4.4 58.1 1.0
CA Y:ASP168 4.5 44.2 1.0
CA Y:ALA165 4.5 46.0 1.0
N Y:ASP168 4.5 45.0 1.0
N Y:HIS166 4.6 44.9 1.0
NH2 Y:ARG19 4.6 60.6 1.0
N Y:TYR170 4.6 43.5 1.0
CA Y:SER171 4.6 43.5 1.0
CA Y:HIS166 4.7 44.0 1.0
O Y:ALA164 4.7 44.2 1.0
C Y:ARG167 4.8 44.9 1.0
N Y:GLY172 4.9 48.9 1.0
CB Y:ALA169 4.9 43.5 1.0
N Y:ARG167 5.0 42.9 1.0
O Y:ARG167 5.0 45.0 1.0
CG I:ASP204 5.0 62.9 1.0
N I:ASP204 5.0 59.8 1.0
CA Y:GLY172 5.0 49.7 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 02:27:08 2024

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