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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

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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

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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

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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

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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

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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

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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

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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 Dec 14 19:26:44 2020

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