Atomistry » Magnesium » PDB 4qpz-4qwg » 4qw3
Atomistry »
  Magnesium »
    PDB 4qpz-4qwg »
      4qw3 »

Magnesium in PDB 4qw3: Ycp BETA5-C63F Mutant in Complex with Bortezomib

Enzymatic activity of Ycp BETA5-C63F Mutant in Complex with Bortezomib

All present enzymatic activity of Ycp BETA5-C63F Mutant in Complex with Bortezomib:
3.4.25.1;

Protein crystallography data

The structure of Ycp BETA5-C63F Mutant in Complex with Bortezomib, PDB code: 4qw3 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 (°) 138.140, 299.960, 146.570, 90.00, 113.18, 90.00
R / Rfree (%) 18.3 / 21.7

Other elements in 4qw3:

The structure of Ycp BETA5-C63F Mutant in Complex with Bortezomib also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Ycp BETA5-C63F Mutant in Complex with Bortezomib (pdb code 4qw3). 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-C63F Mutant in Complex with Bortezomib, PDB code: 4qw3:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 4qw3

Go back to Magnesium Binding Sites List in 4qw3
Magnesium binding site 1 out of 5 in the Ycp BETA5-C63F Mutant in Complex with Bortezomib


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Ycp BETA5-C63F Mutant in Complex with Bortezomib within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:65.2
occ:1.00
 O G:MET125 2.3 59.7 1.0
OG1 G:THR8 2.5 49.8 1.0
O G:ARG122 2.7 44.4 1.0
O G:TYR119 2.9 49.1 1.0
CG2 G:THR8 3.2 53.2 1.0
O G:ALA123 3.3 57.5 1.0
CB G:THR8 3.4 52.1 1.0
C G:MET125 3.4 57.3 1.0
C G:ALA123 3.7 55.9 1.0
CA G:ALA123 3.8 53.6 1.0
C G:ARG122 3.8 50.3 1.0
N G:THR8 4.0 55.0 1.0
C G:TYR119 4.1 48.5 1.0
CA G:ARG126 4.1 53.2 1.0
N G:ARG126 4.2 54.1 1.0
N G:ALA123 4.2 50.5 1.0
N G:MET125 4.3 59.0 1.0
CA G:THR8 4.3 53.4 1.0
CA G:MET125 4.5 60.5 1.0
CD G:PRO127 4.5 50.6 1.0
N G:TYR124 4.7 58.7 1.0
C G:ARG126 4.8 51.8 1.0
CA G:TYR119 4.9 47.5 1.0
N G:PRO127 5.0 50.1 1.0

Magnesium binding site 2 out of 5 in 4qw3

Go back to Magnesium Binding Sites List in 4qw3
Magnesium binding site 2 out of 5 in the Ycp BETA5-C63F Mutant in Complex with Bortezomib


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Ycp BETA5-C63F Mutant in Complex with Bortezomib within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mg201

b:43.6
occ:1.00
 OE1 J:GLN118 3.3 58.7 1.0
O J:THR124 3.7 55.3 1.0
CB J:ASP120 3.9 49.4 1.0
CG J:ASP120 4.0 51.4 1.0
OD2 J:ASP120 4.0 54.1 1.0
N J:ASP120 4.1 50.2 1.0
CD J:GLN118 4.1 53.7 1.0
CB J:THR124 4.3 52.5 1.0
CG J:GLN118 4.3 50.9 1.0
CG2 J:THR124 4.4 52.3 1.0
CE1 J:HIS133 4.4 50.3 1.0
O J:GLN118 4.4 50.6 1.0
CG1 I:VAL35 4.6 56.1 1.0
CA J:ASP120 4.6 48.5 1.0
C J:THR124 4.6 51.4 1.0
OD1 J:ASP120 4.7 56.8 1.0
CD2 I:LEU28 4.7 54.6 1.0
C J:ILE119 4.7 49.4 1.0
C J:GLN118 4.8 47.3 1.0
OG I:SER30 4.9 59.8 1.0
CA J:ILE119 4.9 46.6 1.0

Magnesium binding site 3 out of 5 in 4qw3

Go back to Magnesium Binding Sites List in 4qw3
Magnesium binding site 3 out of 5 in the Ycp BETA5-C63F Mutant in Complex with Bortezomib


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Ycp BETA5-C63F Mutant in Complex with Bortezomib within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg202

b:39.1
occ:1.00
 O N:SER169 2.6 44.9 1.0
O N:ILE163 2.7 49.2 1.0
O N:ASP166 2.8 54.9 1.0
NH1 N:ARG19 3.6 51.3 1.0
CD1 a:LEU34 3.7 56.9 1.0
C N:SER169 3.8 48.3 1.0
C N:ILE163 3.8 51.1 1.0
C N:ASP166 3.9 49.7 1.0
CG2 N:ILE163 4.1 50.9 1.0
CA N:GLY167 4.1 48.6 1.0
CZ N:ARG19 4.3 51.4 1.0
O N:GLY167 4.4 48.7 1.0
N N:GLY167 4.4 47.9 1.0
C N:GLY167 4.5 48.3 1.0
CA N:ILE163 4.5 51.2 1.0
CA N:GLY170 4.5 50.8 1.0
N N:GLY170 4.6 49.4 1.0
NH2 N:ARG19 4.6 56.5 1.0
N N:SER169 4.7 47.3 1.0
CA N:SER169 4.8 45.3 1.0
N N:LYS164 4.9 52.5 1.0
O N:LYS164 4.9 50.8 1.0
N N:ASP166 4.9 50.2 1.0
C N:LYS164 4.9 52.8 1.0
CG a:LEU34 4.9 57.0 1.0
CB N:ILE163 5.0 51.0 1.0

Magnesium binding site 4 out of 5 in 4qw3

Go back to Magnesium Binding Sites List in 4qw3
Magnesium binding site 4 out of 5 in the Ycp BETA5-C63F Mutant in Complex with Bortezomib


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Ycp BETA5-C63F Mutant in Complex with Bortezomib within 5.0Å range:
probe atom residue distance (Å) B Occ
Y:Mg302

b:66.0
occ:1.00
 O Y:ASP168 2.3 50.3 1.0
O I:ASP204 2.3 59.0 1.0
O Y:ALA165 2.4 61.9 1.0
O Y:SER171 2.9 50.2 1.0
C I:ASP204 3.2 62.9 1.0
C Y:ASP168 3.2 52.9 1.0
C Y:ALA165 3.6 57.2 1.0
CA Y:ALA169 3.6 54.6 1.0
CA I:ASP204 3.7 66.1 1.0
O Y:HIS166 3.7 48.4 1.0
N Y:ALA169 3.8 56.3 1.0
NH1 Y:ARG19 3.8 67.7 1.0
CB I:ASP204 3.9 68.6 1.0
C Y:ALA169 3.9 53.0 1.0
O Y:ALA169 4.0 51.3 1.0
C Y:SER171 4.0 51.4 1.0
C Y:HIS166 4.2 54.0 1.0
OXT I:ASP204 4.2 60.9 1.0
N Y:ASP168 4.4 54.0 1.0
CA Y:ASP168 4.4 52.9 1.0
CA Y:ALA165 4.5 55.0 1.0
N Y:SER171 4.5 52.7 1.0
N Y:HIS166 4.5 58.9 1.0
CZ Y:ARG19 4.5 67.3 1.0
CA Y:HIS166 4.6 55.5 1.0
C Y:ARG167 4.6 54.3 1.0
O Y:ALA164 4.7 56.3 1.0
N Y:TYR170 4.8 53.2 1.0
CA Y:SER171 4.8 49.9 1.0
N Y:ARG167 4.8 54.1 1.0
NH2 Y:ARG19 4.9 74.5 1.0
O Y:ARG167 4.9 54.5 1.0
CB Y:ALA169 4.9 55.1 1.0
CG I:ASP204 5.0 67.9 1.0
N Y:GLY172 5.0 49.9 1.0

Magnesium binding site 5 out of 5 in 4qw3

Go back to Magnesium Binding Sites List in 4qw3
Magnesium binding site 5 out of 5 in the Ycp BETA5-C63F Mutant in Complex with Bortezomib


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Ycp BETA5-C63F Mutant in Complex with Bortezomib within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg301

b:66.7
occ:1.00
 O Z:VAL198 2.5 58.1 1.0
O Z:THR192 2.9 62.0 1.0
O Z:HIS195 3.2 47.6 1.0
NH2 Z:ARG28 3.5 66.3 1.0
O Z:ASP222 3.6 70.3 1.0
CG2 Z:THR192 3.6 66.5 1.0
C Z:VAL198 3.6 60.2 1.0
C Z:THR192 3.9 63.5 1.0
O Z:ILE196 3.9 57.1 1.0
OD1 Z:ASP222 4.1 69.0 1.0
CA Z:THR192 4.2 64.7 1.0
C Z:ILE196 4.2 54.7 1.0
CA Z:ILE196 4.2 55.0 1.0
C Z:HIS195 4.2 52.0 1.0
NH2 H:ARG19 4.4 68.0 1.0
CZ Z:ARG28 4.4 63.1 1.0
N Z:VAL198 4.4 55.5 1.0
CA Z:GLY199 4.5 60.2 1.0
N Z:GLY199 4.5 60.0 1.0
CB Z:THR192 4.5 65.2 1.0
C Z:ASP222 4.5 70.1 1.0
NH1 Z:ARG28 4.6 60.0 1.0
O Z:LYS220 4.6 62.4 1.0
CA Z:VAL198 4.6 56.6 1.0
N Z:ILE196 4.7 52.3 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 02:25:04 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy