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Magnesium in PDB 4qw4: Ycp in Complex with Carfilzomib

Enzymatic activity of Ycp in Complex with Carfilzomib

All present enzymatic activity of Ycp in Complex with Carfilzomib:
3.4.25.1;

Protein crystallography data

The structure of Ycp in Complex with Carfilzomib, PDB code: 4qw4 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 (°) 135.810, 298.690, 145.700, 90.00, 112.69, 90.00
R / Rfree (%) 18.7 / 21.6

Other elements in 4qw4:

The structure of Ycp 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 in Complex with Carfilzomib (pdb code 4qw4). 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 in Complex with Carfilzomib, PDB code: 4qw4:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 4qw4

Go back to Magnesium Binding Sites List in 4qw4
Magnesium binding site 1 out of 7 in the Ycp 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 in Complex with Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:57.1
occ:1.00
 O G:MET125 2.3 50.5 1.0
OG1 G:THR8 2.7 44.0 1.0
O G:ARG122 2.7 49.0 1.0
O G:TYR119 3.0 44.0 1.0
O G:ALA123 3.1 55.5 1.0
CG2 G:THR8 3.3 47.3 1.0
C G:MET125 3.5 50.7 1.0
CB G:THR8 3.5 46.6 1.0
C G:ALA123 3.6 53.3 1.0
CA G:ALA123 3.7 50.1 1.0
C G:ARG122 3.8 50.0 1.0
N G:THR8 4.0 50.2 1.0
C G:TYR119 4.2 43.6 1.0
CA G:ARG126 4.2 45.4 1.0
N G:ALA123 4.2 50.0 1.0
N G:ARG126 4.2 46.8 1.0
N G:MET125 4.3 51.5 1.0
CA G:THR8 4.4 49.4 1.0
CA G:MET125 4.5 52.7 1.0
CD G:PRO127 4.6 42.2 1.0
N G:TYR124 4.6 55.5 1.0
C G:ARG126 4.9 44.9 1.0
CA G:TYR119 4.9 42.5 1.0
C G:TYR124 5.0 51.9 1.0
CB G:ALA123 5.0 48.4 1.0

Magnesium binding site 2 out of 7 in 4qw4

Go back to Magnesium Binding Sites List in 4qw4
Magnesium binding site 2 out of 7 in the Ycp 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 in Complex with Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:61.3
occ:1.00
 O I:ASP177 2.5 42.4 1.0
O I:SER180 2.6 48.4 1.0
O I:ALA174 2.9 46.4 1.0
OXT I:ASP204 3.6 62.6 1.0
C I:ASP177 3.6 42.8 1.0
C I:SER180 3.9 46.1 1.0
C I:ALA174 4.0 48.2 1.0
O I:ALA178 4.1 46.6 1.0
CA I:ALA178 4.2 43.2 1.0
C I:ALA178 4.2 44.3 1.0
N I:ALA178 4.3 41.8 1.0
CA I:ASP175 4.4 49.7 1.0
O I:ASP204 4.4 66.4 1.0
C I:ASP204 4.4 65.0 1.0
NH1 Y:ARG19 4.5 60.4 1.0
N I:SER180 4.6 42.8 1.0
N I:ASP177 4.6 42.0 1.0
C I:ASP175 4.6 48.8 1.0
N I:ASP175 4.6 48.4 1.0
CA I:ASP177 4.7 43.7 1.0
O I:ASP175 4.7 52.4 1.0
N I:GLY181 4.8 44.6 1.0
CA I:SER180 4.8 44.7 1.0
CA I:GLY181 4.8 45.6 1.0
NH2 Y:ARG19 4.9 61.8 1.0

Magnesium binding site 3 out of 7 in 4qw4

Go back to Magnesium Binding Sites List in 4qw4
Magnesium binding site 3 out of 7 in the Ycp 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 in Complex with Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg302

b:51.9
occ:1.00
 O K:ASP168 2.2 47.0 1.0
O W:ASP204 2.4 58.9 1.0
O K:ALA165 2.4 44.4 1.0
O K:SER171 2.9 45.2 1.0
C W:ASP204 3.2 56.2 1.0
C K:ASP168 3.2 45.2 1.0
C K:ALA165 3.5 44.7 1.0
CA W:ASP204 3.6 54.3 1.0
CA K:ALA169 3.6 44.8 1.0
O K:HIS166 3.6 49.8 1.0
N K:ALA169 3.8 44.7 1.0
C K:ALA169 3.9 46.3 1.0
O K:ALA169 4.0 48.1 1.0
CB W:ASP204 4.0 52.6 1.0
C K:HIS166 4.0 45.1 1.0
OXT W:ASP204 4.1 57.5 1.0
C K:SER171 4.1 44.2 1.0
NH1 K:ARG19 4.2 55.4 1.0
N K:ASP168 4.3 44.1 1.0
CA K:ASP168 4.4 43.8 1.0
N K:HIS166 4.4 43.5 1.0
CA K:HIS166 4.4 43.6 1.0
N K:SER171 4.5 43.2 1.0
CA K:ALA165 4.5 45.3 1.0
C K:ARG167 4.6 44.1 1.0
O K:ALA164 4.6 43.2 1.0
N K:ARG167 4.7 42.9 1.0
CZ K:ARG19 4.8 53.2 1.0
N K:TYR170 4.8 45.2 1.0
CA K:SER171 4.8 42.3 1.0
O K:ARG167 4.8 46.2 1.0
NH2 K:ARG19 4.9 57.5 1.0
CB K:ALA169 5.0 43.0 1.0
N W:ASP204 5.0 53.0 1.0

Magnesium binding site 4 out of 7 in 4qw4

Go back to Magnesium Binding Sites List in 4qw4
Magnesium binding site 4 out of 7 in the Ycp 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 in Complex with Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg202

b:43.8
occ:1.00
 O N:SER169 2.5 44.7 1.0
O N:ILE163 2.8 43.1 1.0
O N:ASP166 2.9 41.3 1.0
NH1 N:ARG19 3.4 44.0 1.0
CD1 a:LEU34 3.7 46.0 1.0
C N:SER169 3.7 41.0 1.0
C N:ASP166 4.0 40.6 1.0
C N:ILE163 4.0 42.6 1.0
CA N:GLY167 4.1 41.1 1.0
CZ N:ARG19 4.1 42.6 1.0
O N:GLY167 4.2 42.6 1.0
CG2 N:ILE163 4.2 42.1 1.0
C N:GLY167 4.4 41.2 1.0
CA N:GLY170 4.4 41.6 1.0
NH2 N:ARG19 4.4 42.0 1.0
N N:GLY167 4.5 39.8 1.0
N N:GLY170 4.5 41.2 1.0
N N:SER169 4.7 39.3 1.0
CA N:ILE163 4.7 42.9 1.0
CA N:SER169 4.8 37.6 1.0
CG a:LEU34 5.0 46.5 1.0

Magnesium binding site 5 out of 7 in 4qw4

Go back to Magnesium Binding Sites List in 4qw4
Magnesium binding site 5 out of 7 in the Ycp 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 in Complex with Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Mg302

b:64.1
occ:1.00
 OXT L:ASP222 2.0 76.0 1.0
O V:ASP166 2.2 44.9 1.0
O V:ILE163 2.3 48.4 1.0
O V:SER169 3.0 49.2 1.0
C L:ASP222 3.0 71.4 1.0
C V:ASP166 3.1 45.9 1.0
C V:ILE163 3.3 52.7 1.0
O V:TRP164 3.5 52.7 1.0
CA L:ASP222 3.6 67.4 1.0
C V:TRP164 3.7 50.8 1.0
N V:LEU167 3.8 45.4 1.0
N V:ASP166 3.8 46.8 1.0
CA V:LEU167 3.9 45.8 1.0
O L:ASP222 3.9 77.3 1.0
O V:GLY162 3.9 49.9 1.0
CA V:ASP166 4.1 46.2 1.0
N V:TRP164 4.1 51.6 1.0
CA V:TRP164 4.1 51.6 1.0
C V:SER169 4.1 47.6 1.0
N V:ASN165 4.2 48.1 1.0
CB L:ASP222 4.3 66.4 1.0
NH1 V:ARG19 4.4 56.8 1.0
CA V:ILE163 4.4 52.8 1.0
C V:ASN165 4.4 47.3 1.0
C V:LEU167 4.5 45.0 1.0
CD2 V:LEU167 4.7 44.3 1.0
O L:ARG221 4.7 63.0 1.0
O V:LEU167 4.8 46.2 1.0
N V:SER169 4.8 44.4 1.0
CA V:ASN165 4.8 48.3 1.0
N L:ASP222 4.9 64.2 1.0
C V:GLY162 4.9 51.1 1.0
CA V:SER169 5.0 45.2 1.0
CA V:GLY170 5.0 50.0 1.0
CZ V:ARG19 5.0 53.5 1.0
N V:GLY170 5.0 49.3 1.0

Magnesium binding site 6 out of 7 in 4qw4

Go back to Magnesium Binding Sites List in 4qw4
Magnesium binding site 6 out of 7 in the Ycp 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 in Complex with Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
Y:Mg302

b:48.5
occ:1.00
 O Y:ASP168 2.2 44.4 1.0
O I:ASP204 2.4 66.4 1.0
O Y:ALA165 2.6 38.5 1.0
O Y:SER171 2.6 49.6 1.0
C I:ASP204 3.2 65.0 1.0
C Y:ASP168 3.3 42.3 1.0
CA Y:ALA169 3.5 42.3 1.0
CA I:ASP204 3.7 60.7 1.0
O Y:ALA169 3.7 43.6 1.0
C Y:ALA169 3.7 42.2 1.0
C Y:ALA165 3.8 42.2 1.0
NH1 Y:ARG19 3.8 60.4 1.0
N Y:ALA169 3.8 42.0 1.0
C Y:SER171 3.8 44.3 1.0
CB I:ASP204 4.0 61.3 1.0
O Y:HIS166 4.0 43.9 1.0
OXT I:ASP204 4.1 62.6 1.0
N Y:SER171 4.2 41.5 1.0
CZ Y:ARG19 4.4 57.4 1.0
C Y:HIS166 4.4 43.8 1.0
CA Y:ASP168 4.5 42.1 1.0
N Y:TYR170 4.5 41.6 1.0
N Y:ASP168 4.6 42.5 1.0
CA Y:ALA165 4.6 43.1 1.0
CA Y:SER171 4.6 41.2 1.0
NH2 Y:ARG19 4.6 61.8 1.0
N Y:HIS166 4.7 43.9 1.0
CA Y:HIS166 4.8 43.2 1.0
O Y:ALA164 4.8 43.4 1.0
N Y:GLY172 4.8 45.0 1.0
CB Y:ALA169 4.9 41.2 1.0
C Y:ARG167 4.9 43.0 1.0
CA Y:GLY172 5.0 46.9 1.0

Magnesium binding site 7 out of 7 in 4qw4

Go back to Magnesium Binding Sites List in 4qw4
Magnesium binding site 7 out of 7 in the Ycp 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 in Complex with Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg301

b:61.4
occ:1.00
 O Z:VAL198 2.5 53.9 1.0
O Z:THR192 2.8 51.5 1.0
O Z:HIS195 3.2 44.6 1.0
O Z:ASP222 3.3 64.1 1.0
NH2 Z:ARG28 3.5 60.6 1.0
CG2 Z:THR192 3.6 56.8 1.0
C Z:VAL198 3.7 52.1 1.0
C Z:THR192 3.8 55.0 1.0
O Z:ILE196 4.0 48.6 1.0
CA Z:THR192 4.1 55.1 1.0
OD1 Z:ASP222 4.1 60.7 1.0
C Z:HIS195 4.2 45.4 1.0
CA Z:ILE196 4.3 45.0 1.0
C Z:ILE196 4.3 45.2 1.0
C Z:ASP222 4.4 64.6 1.0
CA Z:GLY199 4.5 52.7 1.0
CB Z:THR192 4.5 56.2 1.0
NH2 H:ARG19 4.5 63.6 1.0
CZ Z:ARG28 4.5 57.5 1.0
N Z:GLY199 4.5 52.3 1.0
N Z:VAL198 4.6 48.0 1.0
CA Z:VAL198 4.7 49.2 1.0
NH1 Z:ARG28 4.7 59.5 1.0
N Z:ILE196 4.7 43.9 1.0
O Z:LYS220 4.8 57.0 1.0
N Z:GLU193 5.0 55.9 1.0
OXT Z:ASP222 5.0 63.6 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 02:26:26 2024

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