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Magnesium in PDB 4qwg: Ycp BETA5-A49V Mutant in Complex with Carfilzomib

Protein crystallography data

The structure of Ycp BETA5-A49V Mutant in Complex with Carfilzomib, PDB code: 4qwg 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 / 2.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 136.980, 301.070, 145.940, 90.00, 112.89, 90.00
R / Rfree (%) 21.6 / 24.3

Other elements in 4qwg:

The structure of Ycp BETA5-A49V 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-A49V Mutant in Complex with Carfilzomib (pdb code 4qwg). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Ycp BETA5-A49V Mutant in Complex with Carfilzomib, PDB code: 4qwg:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 4qwg

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Magnesium binding site 1 out of 6 in the Ycp BETA5-A49V 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-A49V Mutant in Complex with Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:48.5
occ:1.00
O G:ARG122 2.3 49.3 1.0
O G:MET125 2.3 50.2 1.0
OG1 G:THR8 2.6 39.9 1.0
O G:TYR119 2.7 37.7 1.0
O G:ALA123 3.2 55.3 1.0
CG2 G:THR8 3.4 41.8 1.0
C G:ARG122 3.4 47.5 1.0
C G:MET125 3.5 47.3 1.0
C G:ALA123 3.6 50.2 1.0
CA G:ALA123 3.6 47.0 1.0
CB G:THR8 3.6 41.8 1.0
C G:TYR119 3.9 38.8 1.0
N G:ALA123 3.9 44.2 1.0
N G:MET125 4.2 50.2 1.0
N G:THR8 4.4 44.4 1.0
N G:ARG126 4.4 41.3 1.0
CA G:ARG126 4.4 40.2 1.0
CA G:MET125 4.4 50.6 1.0
N G:TYR124 4.5 51.1 1.0
CA G:THR8 4.6 44.1 1.0
CA G:TYR119 4.6 37.7 1.0
CA G:ARG122 4.7 49.6 1.0
CD G:PRO127 4.7 38.5 1.0
N G:ARG122 4.8 46.3 1.0
CB G:ALA123 4.9 46.5 1.0
N G:THR120 4.9 39.6 1.0
C G:ARG126 5.0 39.6 1.0
CB G:MET125 5.0 56.9 1.0

Magnesium binding site 2 out of 6 in 4qwg

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Magnesium binding site 2 out of 6 in the Ycp BETA5-A49V 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-A49V Mutant in Complex with Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:60.8
occ:1.00
O I:ASP177 2.5 37.9 1.0
O I:SER180 2.7 43.2 1.0
O I:ALA174 3.1 44.6 1.0
OXT I:ASP204 3.6 50.6 1.0
C I:ASP177 3.6 38.3 1.0
C I:SER180 4.0 39.7 1.0
O I:HOH409 4.0 40.2 1.0
O I:ALA178 4.1 37.5 1.0
CA I:ALA178 4.2 37.2 1.0
C I:ALA174 4.2 44.0 1.0
C I:ALA178 4.3 37.6 1.0
N I:ALA178 4.4 37.2 1.0
CA I:ASP175 4.4 44.1 1.0
O I:ASP204 4.4 53.2 1.0
C I:ASP204 4.5 52.7 1.0
NH1 Y:ARG19 4.5 49.5 1.0
C I:ASP175 4.6 43.3 1.0
O I:ASP175 4.6 44.7 1.0
N I:ASP177 4.6 37.8 1.0
N I:SER180 4.7 36.8 1.0
CA I:ASP177 4.7 39.3 1.0
N I:ASP175 4.8 43.1 1.0
CA I:GLY181 4.8 40.5 1.0
NH2 Y:ARG19 4.8 48.8 1.0
N I:GLY181 4.8 40.2 1.0
CA I:SER180 4.9 38.8 1.0

Magnesium binding site 3 out of 6 in 4qwg

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Magnesium binding site 3 out of 6 in the Ycp BETA5-A49V 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-A49V Mutant in Complex with Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg302

b:48.6
occ:1.00
O K:ASP168 2.1 37.7 1.0
O K:ALA165 2.2 39.6 1.0
O W:ASP204 2.4 46.9 1.0
O K:SER171 2.6 39.4 1.0
C W:ASP204 3.2 48.1 1.0
C K:ASP168 3.2 37.3 1.0
C K:ALA165 3.3 39.2 1.0
CA W:ASP204 3.6 47.0 1.0
C K:SER171 3.8 38.0 1.0
CA K:ALA169 3.8 37.3 1.0
CB W:ASP204 3.9 47.3 1.0
N K:ALA169 3.9 36.7 1.0
O K:HIS166 3.9 40.0 1.0
C K:ALA169 4.0 37.9 1.0
O K:ALA169 4.1 37.5 1.0
OXT W:ASP204 4.1 49.1 1.0
C K:HIS166 4.2 39.0 1.0
CA K:ALA165 4.2 39.0 1.0
NH1 K:ARG19 4.2 44.2 1.0
N K:ASP168 4.3 38.6 1.0
N K:SER171 4.3 37.0 1.0
N K:HIS166 4.3 38.6 1.0
CA K:ASP168 4.3 38.2 1.0
O K:ALA164 4.4 38.0 1.0
CA K:HIS166 4.4 38.7 1.0
CA K:SER171 4.5 36.6 1.0
C K:ARG167 4.7 38.9 1.0
CZ K:ARG19 4.7 43.1 1.0
N K:ARG167 4.7 39.7 1.0
N K:GLY172 4.8 39.4 1.0
N K:TYR170 4.8 38.2 1.0
CA K:GLY172 4.9 39.9 1.0
CB K:SER171 4.9 34.9 1.0
NH2 K:ARG19 4.9 46.9 1.0
CG W:ASP204 5.0 48.1 1.0
N W:ASP204 5.0 46.1 1.0

Magnesium binding site 4 out of 6 in 4qwg

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Magnesium binding site 4 out of 6 in the Ycp BETA5-A49V 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-A49V Mutant in Complex with Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg202

b:49.0
occ:1.00
O N:ILE163 2.6 37.7 1.0
O N:SER169 2.6 40.9 1.0
O N:ASP166 2.9 43.4 1.0
CD1 a:LEU34 3.7 47.8 1.0
C N:ILE163 3.7 43.3 1.0
C N:SER169 3.8 40.1 1.0
NH1 N:ARG19 3.8 46.4 1.0
CG2 N:ILE163 3.9 45.3 1.0
C N:ASP166 4.0 42.3 1.0
CA N:GLY167 4.3 40.7 1.0
CA N:ILE163 4.4 44.3 1.0
CA N:GLY170 4.5 43.0 1.0
CZ N:ARG19 4.5 44.4 1.0
N N:GLY167 4.6 40.1 1.0
N N:GLY170 4.6 42.0 1.0
O a:HOH322 4.6 42.3 1.0
O N:GLY167 4.6 41.7 1.0
C N:GLY167 4.6 39.6 1.0
N N:LYS164 4.7 45.1 1.0
CB N:ILE163 4.8 44.2 1.0
N N:SER169 4.8 39.2 1.0
NH2 N:ARG19 4.8 44.6 1.0
CA N:SER169 4.8 38.9 1.0
O N:LYS164 4.9 48.2 1.0
C N:LYS164 4.9 47.3 1.0
CA N:LYS164 4.9 46.8 1.0
CG a:LEU34 5.0 46.9 1.0

Magnesium binding site 5 out of 6 in 4qwg

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Magnesium binding site 5 out of 6 in the Ycp BETA5-A49V 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-A49V Mutant in Complex with Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Mg302

b:45.5
occ:1.00
O V:ASP166 2.1 43.6 1.0
OXT L:ASP222 2.3 58.4 1.0
O V:SER169 2.3 41.4 1.0
O V:ILE163 2.3 47.4 1.0
O V:HOH401 2.6 38.7 1.0
C V:ASP166 3.2 43.8 1.0
C L:ASP222 3.3 60.7 1.0
C V:ILE163 3.4 46.7 1.0
C V:SER169 3.4 41.3 1.0
CA L:ASP222 3.8 58.3 1.0
O V:GLY162 3.9 42.1 1.0
CA V:LEU167 3.9 43.1 1.0
N V:LEU167 3.9 43.8 1.0
NH1 V:ARG19 4.0 47.2 1.0
N V:ASP166 4.1 43.6 1.0
CA V:ILE163 4.2 48.0 1.0
O L:ASP222 4.2 63.2 1.0
CA V:ASP166 4.2 44.3 1.0
N V:SER169 4.3 39.6 1.0
CB L:ASP222 4.3 60.1 1.0
N V:GLY170 4.3 43.9 1.0
C V:LEU167 4.3 42.6 1.0
N V:TRP164 4.3 46.4 1.0
CA V:GLY170 4.3 44.9 1.0
C V:TRP164 4.3 47.9 1.0
CA V:SER169 4.3 40.4 1.0
O V:TRP164 4.4 48.6 1.0
CZ V:ARG19 4.5 46.0 1.0
CA V:TRP164 4.5 48.3 1.0
O V:LEU167 4.6 41.9 1.0
N V:ASN165 4.7 47.6 1.0
NH2 V:ARG19 4.7 48.0 1.0
CB V:SER169 4.8 40.5 1.0
C V:GLY162 4.8 45.9 1.0
C V:ASN165 4.8 43.1 1.0
CB V:ASP166 4.9 43.7 1.0
N V:GLY168 4.9 40.8 1.0

Magnesium binding site 6 out of 6 in 4qwg

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Magnesium binding site 6 out of 6 in the Ycp BETA5-A49V 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-A49V Mutant in Complex with Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
Y:Mg302

b:42.9
occ:1.00
O Y:ASP168 2.2 38.4 1.0
O Y:ALA165 2.3 37.9 1.0
O Y:SER171 2.4 40.5 1.0
O I:ASP204 2.5 53.2 1.0
O Y:HOH415 2.5 41.2 1.0
C I:ASP204 3.2 52.7 1.0
C Y:ASP168 3.3 37.0 1.0
C Y:ALA165 3.4 37.3 1.0
C Y:SER171 3.6 38.3 1.0
CA I:ASP204 3.6 52.4 1.0
CA Y:ALA169 3.8 36.6 1.0
CB I:ASP204 3.9 53.0 1.0
C Y:ALA169 4.0 36.6 1.0
N Y:ALA169 4.0 36.7 1.0
O Y:ALA169 4.0 38.3 1.0
NH1 Y:ARG19 4.0 49.5 1.0
N Y:SER171 4.1 35.4 1.0
O Y:HIS166 4.1 39.1 1.0
OXT I:ASP204 4.2 50.6 1.0
CA Y:ALA165 4.2 37.2 1.0
C Y:HIS166 4.3 39.9 1.0
CA Y:SER171 4.4 35.6 1.0
N Y:HIS166 4.4 37.9 1.0
N Y:ASP168 4.4 37.4 1.0
CA Y:ASP168 4.4 36.1 1.0
O Y:ALA164 4.5 33.8 1.0
CZ Y:ARG19 4.5 46.4 1.0
N Y:GLY172 4.6 39.5 1.0
CA Y:HIS166 4.6 38.3 1.0
N Y:TYR170 4.7 35.6 1.0
CA Y:GLY172 4.7 40.9 1.0
NH2 Y:ARG19 4.7 48.8 1.0
CB Y:SER171 4.8 35.8 1.0
C Y:ARG167 4.9 38.0 1.0
N Y:ARG167 4.9 40.0 1.0
CG I:ASP204 4.9 53.8 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 19:27:00 2020

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