Atomistry » Magnesium » PDB 4qq8-4qwi » 4qw7
Atomistry »
  Magnesium »
    PDB 4qq8-4qwi »
      4qw7 »

Magnesium in PDB 4qw7: Ycp BETA5-M45T Mutant in Complex with Carfilzomib

Enzymatic activity of Ycp BETA5-M45T Mutant in Complex with Carfilzomib

All present enzymatic activity of Ycp BETA5-M45T Mutant in Complex with Carfilzomib:
3.4.25.1;

Protein crystallography data

The structure of Ycp BETA5-M45T Mutant in Complex with Carfilzomib, PDB code: 4qw7 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 / 2.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 136.630, 300.130, 145.260, 90.00, 113.11, 90.00
R / Rfree (%) 20.5 / 22.6

Other elements in 4qw7:

The structure of Ycp BETA5-M45T 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-M45T Mutant in Complex with Carfilzomib (pdb code 4qw7). 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 BETA5-M45T Mutant in Complex with Carfilzomib, PDB code: 4qw7:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 4qw7

Go back to Magnesium Binding Sites List in 4qw7
Magnesium binding site 1 out of 7 in the Ycp BETA5-M45T 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-M45T Mutant in Complex with Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:57.0
occ:1.00
 O G:MET125 2.4 46.3 1.0
OG1 G:THR8 2.6 40.2 1.0
O G:ARG122 2.7 45.0 1.0
O G:TYR119 3.0 40.4 1.0
O G:ALA123 3.1 46.5 1.0
CG2 G:THR8 3.2 42.3 1.0
CB G:THR8 3.4 41.4 1.0
C G:MET125 3.5 46.4 1.0
C G:ALA123 3.5 47.3 1.0
O F:HOH306 3.6 58.2 1.0
CA G:ALA123 3.6 45.7 1.0
C G:ARG122 3.8 45.7 1.0
N G:THR8 4.0 44.6 1.0
N G:ALA123 4.2 45.7 1.0
C G:TYR119 4.2 39.0 1.0
CA G:ARG126 4.2 41.4 1.0
N G:ARG126 4.3 43.6 1.0
CA G:THR8 4.3 44.0 1.0
N G:MET125 4.4 47.4 1.0
CA G:MET125 4.5 49.5 1.0
CD G:PRO127 4.6 37.8 1.0
N G:TYR124 4.6 49.4 1.0
CB G:ALA123 4.9 45.1 1.0
C G:ARG126 4.9 40.2 1.0
CA G:TYR119 5.0 36.8 1.0
C G:TYR124 5.0 48.3 1.0

Magnesium binding site 2 out of 7 in 4qw7

Go back to Magnesium Binding Sites List in 4qw7
Magnesium binding site 2 out of 7 in the Ycp BETA5-M45T 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-M45T Mutant in Complex with Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:58.0
occ:1.00
 O I:ASP177 2.6 40.1 1.0
O I:SER180 2.7 45.3 1.0
O I:ALA174 2.8 46.4 1.0
O I:HOH427 3.4 48.9 1.0
OXT I:ASP204 3.6 68.0 1.0
C I:ASP177 3.7 40.8 1.0
C I:ALA174 3.9 46.8 1.0
C I:SER180 3.9 43.0 1.0
CA I:ASP175 4.1 47.1 1.0
O I:ALA178 4.2 44.7 1.0
CA I:ALA178 4.4 40.8 1.0
N I:ASP175 4.4 46.0 1.0
C I:ASP204 4.4 60.6 1.0
C I:ASP175 4.4 45.3 1.0
C I:ALA178 4.5 42.3 1.0
N I:ALA178 4.5 40.5 1.0
O I:ASP204 4.5 60.0 1.0
O I:ASP175 4.6 46.7 1.0
N I:ASP177 4.6 39.9 1.0
NH1 Y:ARG19 4.6 55.1 1.0
CA I:GLY181 4.7 43.1 1.0
NH2 Y:ARG19 4.7 54.2 1.0
N I:SER180 4.7 39.8 1.0
CA I:ASP177 4.7 41.3 1.0
N I:GLY181 4.8 42.5 1.0
CA I:SER180 4.9 42.0 1.0
OD1 I:ASP175 4.9 53.5 1.0

Magnesium binding site 3 out of 7 in 4qw7

Go back to Magnesium Binding Sites List in 4qw7
Magnesium binding site 3 out of 7 in the Ycp BETA5-M45T 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-M45T Mutant in Complex with Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg302

b:50.6
occ:1.00
 O K:ASP168 2.3 41.6 1.0
O W:ASP204 2.3 52.1 1.0
O K:ALA165 2.4 42.4 1.0
O K:SER171 2.6 45.7 1.0
C W:ASP204 3.1 51.3 1.0
C K:ASP168 3.3 40.7 1.0
CA W:ASP204 3.5 50.6 1.0
C K:ALA165 3.6 42.9 1.0
CA K:ALA169 3.6 41.1 1.0
O K:ALA169 3.8 45.8 1.0
C K:ALA169 3.8 43.1 1.0
C K:SER171 3.8 41.7 1.0
N K:ALA169 3.9 40.3 1.0
CB W:ASP204 3.9 49.1 1.0
O K:HIS166 3.9 44.2 1.0
NH1 K:ARG19 3.9 50.0 1.0
OXT W:ASP204 4.0 51.7 1.0
N K:SER171 4.3 41.0 1.0
C K:HIS166 4.3 41.8 1.0
CA K:ALA165 4.4 42.7 1.0
CZ K:ARG19 4.5 50.3 1.0
CA K:ASP168 4.5 40.4 1.0
N K:ASP168 4.5 41.2 1.0
N K:HIS166 4.5 41.3 1.0
CA K:SER171 4.6 39.9 1.0
CA K:HIS166 4.6 40.9 1.0
NH2 K:ARG19 4.7 54.2 1.0
O K:ALA164 4.7 42.8 1.0
N K:TYR170 4.7 41.2 1.0
C K:ARG167 4.8 41.9 1.0
N K:GLY172 4.8 42.3 1.0
N W:ASP204 4.9 51.3 1.0
CA K:GLY172 4.9 44.1 1.0
N K:ARG167 5.0 40.6 1.0
CG W:ASP204 5.0 48.3 1.0
CB K:ALA169 5.0 40.2 1.0

Magnesium binding site 4 out of 7 in 4qw7

Go back to Magnesium Binding Sites List in 4qw7
Magnesium binding site 4 out of 7 in the Ycp BETA5-M45T 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-M45T Mutant in Complex with Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg202

b:47.4
occ:1.00
 O N:SER169 2.5 36.7 1.0
O N:ILE163 2.5 37.7 1.0
O N:ASP166 2.9 36.6 1.0
C N:ILE163 3.6 38.7 1.0
NH1 N:ARG19 3.7 40.4 1.0
C N:SER169 3.7 36.0 1.0
CD1 a:LEU34 3.7 41.5 1.0
CG2 N:ILE163 3.9 38.2 1.0
C N:ASP166 3.9 36.8 1.0
CA N:GLY167 4.3 36.0 1.0
CA N:ILE163 4.3 38.7 1.0
CZ N:ARG19 4.3 39.7 1.0
CA N:GLY170 4.3 38.3 1.0
O N:GLY167 4.5 36.0 1.0
N N:GLY170 4.5 37.3 1.0
NH2 N:ARG19 4.5 38.4 1.0
N N:GLY167 4.5 36.1 1.0
C N:GLY167 4.6 36.3 1.0
N N:LYS164 4.7 40.0 1.0
N N:SER169 4.7 33.8 1.0
CA N:SER169 4.7 33.1 1.0
CB N:ILE163 4.7 38.3 1.0
C N:LYS164 4.9 40.6 1.0
CA N:LYS164 4.9 40.8 1.0
O N:LYS164 4.9 39.9 1.0
CG a:LEU34 5.0 42.7 1.0

Magnesium binding site 5 out of 7 in 4qw7

Go back to Magnesium Binding Sites List in 4qw7
Magnesium binding site 5 out of 7 in the Ycp BETA5-M45T 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-M45T Mutant in Complex with Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Mg302

b:57.6
occ:1.00
 O V:ASP166 2.2 37.6 1.0
OXT L:ASP222 2.2 61.0 1.0
O V:ILE163 2.2 41.7 1.0
O V:SER169 2.9 42.5 1.0
C L:ASP222 3.0 64.7 1.0
C V:ASP166 3.1 39.0 1.0
C V:ILE163 3.3 44.4 1.0
O V:TRP164 3.6 47.2 1.0
CA L:ASP222 3.6 62.3 1.0
C V:TRP164 3.7 45.2 1.0
O L:ASP222 3.8 69.0 1.0
N V:LEU167 3.8 38.5 1.0
N V:ASP166 3.8 38.3 1.0
CA V:LEU167 3.8 38.8 1.0
O V:GLY162 3.9 43.4 1.0
CA V:ASP166 4.1 38.9 1.0
N V:TRP164 4.1 43.6 1.0
C V:SER169 4.1 39.7 1.0
CA V:TRP164 4.1 45.2 1.0
N V:ASN165 4.2 43.8 1.0
NH1 V:ARG19 4.3 47.0 1.0
CA V:ILE163 4.4 45.5 1.0
C V:ASN165 4.4 39.6 1.0
CB L:ASP222 4.4 60.2 1.0
C V:LEU167 4.5 39.2 1.0
O L:ARG221 4.6 56.4 1.0
CD2 V:LEU167 4.7 37.1 1.0
O V:LEU167 4.8 41.6 1.0
N V:SER169 4.8 36.6 1.0
CA V:ASN165 4.8 41.6 1.0
N L:ASP222 4.8 61.3 1.0
C V:GLY162 4.9 43.6 1.0
CZ V:ARG19 5.0 45.9 1.0
CA V:SER169 5.0 37.8 1.0
CA V:GLY170 5.0 43.8 1.0
CB V:ASP166 5.0 38.4 1.0

Magnesium binding site 6 out of 7 in 4qw7

Go back to Magnesium Binding Sites List in 4qw7
Magnesium binding site 6 out of 7 in the Ycp BETA5-M45T 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-M45T Mutant in Complex with Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
Y:Mg302

b:59.7
occ:1.00
 O I:ASP204 2.3 60.0 1.0
O Y:ASP168 2.4 43.6 1.0
O Y:ALA165 2.5 42.5 1.0
C I:ASP204 3.0 60.6 1.0
O Y:SER171 3.1 46.1 1.0
C Y:ASP168 3.3 41.8 1.0
CA I:ASP204 3.4 58.5 1.0
O Y:HIS166 3.6 40.5 1.0
CA Y:ALA169 3.6 40.9 1.0
C Y:ALA165 3.6 42.1 1.0
OXT I:ASP204 3.8 68.0 1.0
N Y:ALA169 3.8 41.8 1.0
O Y:ALA169 4.0 40.0 1.0
CB I:ASP204 4.0 59.7 1.0
C Y:ALA169 4.0 40.6 1.0
C Y:HIS166 4.0 40.5 1.0
NH1 Y:ARG19 4.2 55.1 1.0
C Y:SER171 4.3 42.2 1.0
N Y:ASP168 4.4 42.0 1.0
CA Y:HIS166 4.4 41.3 1.0
CA Y:ASP168 4.5 41.0 1.0
N Y:HIS166 4.5 42.0 1.0
C Y:ARG167 4.6 41.7 1.0
CA Y:ALA165 4.6 42.0 1.0
N Y:SER171 4.6 38.7 1.0
N Y:ARG167 4.7 40.4 1.0
O Y:ALA164 4.7 44.3 1.0
O Y:ARG167 4.8 44.7 1.0
N I:ASP204 4.8 56.6 1.0
CZ Y:ARG19 4.8 52.9 1.0
N Y:TYR170 4.9 40.9 1.0
NH2 Y:ARG19 4.9 54.2 1.0
CB Y:ALA169 4.9 40.6 1.0

Magnesium binding site 7 out of 7 in 4qw7

Go back to Magnesium Binding Sites List in 4qw7
Magnesium binding site 7 out of 7 in the Ycp BETA5-M45T 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-M45T Mutant in Complex with Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg301

b:55.5
occ:1.00
 O Z:HOH411 2.3 35.0 1.0
O Z:THR192 2.5 51.5 1.0
O Z:VAL198 2.6 46.7 1.0
O Z:HIS195 2.8 39.0 1.0
C Z:THR192 3.5 52.7 1.0
CG2 Z:THR192 3.7 54.3 1.0
C Z:VAL198 3.8 48.1 1.0
C Z:HIS195 3.8 42.6 1.0
NH2 Z:ARG28 3.8 57.0 1.0
O Z:ASP222 3.8 62.6 1.0
O Z:ILE196 3.9 38.1 1.0
CA Z:THR192 3.9 52.7 1.0
CA Z:ILE196 4.0 42.4 1.0
C Z:ILE196 4.1 40.8 1.0
N Z:ILE196 4.4 43.3 1.0
CB Z:THR192 4.4 52.6 1.0
NH2 H:ARG19 4.4 53.8 1.0
OD1 Z:ASP222 4.4 59.7 1.0
N Z:VAL198 4.4 45.8 1.0
CA Z:VAL198 4.6 47.3 1.0
N Z:GLY199 4.7 49.6 1.0
N Z:GLU193 4.7 53.1 1.0
CA Z:GLY199 4.7 50.0 1.0
C Z:ASP222 4.8 61.5 1.0
CZ Z:ARG28 4.9 55.0 1.0
N Z:HIS195 4.9 45.3 1.0
O Z:ALA191 5.0 48.8 1.0
CA Z:HIS195 5.0 44.0 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: Mon Aug 11 22:47:42 2025

Last articles

Mg in 5FRN
Mg in 5FRM
Mg in 5FPH
Mg in 5FR2
Mg in 5FQ8
Mg in 5FR1
Mg in 5FQO
Mg in 5FQ7
Mg in 5FQ5
Mg in 5FP3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy