Atomistry » Magnesium » PDB 4qw6-4qzw » 4qwr
Atomistry »
  Magnesium »
    PDB 4qw6-4qzw »
      4qwr »

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

Go back to Magnesium Binding Sites List in 4qwr
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

Go back to Magnesium Binding Sites List in 4qwr
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

Go back to Magnesium Binding Sites List in 4qwr
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

Go back to Magnesium Binding Sites List in 4qwr
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

Go back to Magnesium Binding Sites List in 4qwr
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

Go back to Magnesium Binding Sites List in 4qwr
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

Go back to Magnesium Binding Sites List in 4qwr
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

Go back to Magnesium Binding Sites List in 4qwr
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: Mon Dec 14 19:27:32 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy