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Magnesium in PDB 4qwi: Ycp BETA5-A49S-Mutant in Complex with Carfilzomib

Protein crystallography data

The structure of Ycp BETA5-A49S-Mutant in Complex with Carfilzomib, PDB code: 4qwi 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 (°) 136.150, 300.260, 145.440, 90.00, 113.00, 90.00
R / Rfree (%) 19.2 / 21.4

Other elements in 4qwi:

The structure of Ycp BETA5-A49S-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-A49S-Mutant in Complex with Carfilzomib (pdb code 4qwi). 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-A49S-Mutant in Complex with Carfilzomib, PDB code: 4qwi:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 4qwi

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Magnesium binding site 1 out of 7 in the Ycp BETA5-A49S-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-A49S-Mutant in Complex with Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:58.2
occ:1.00
 O G:MET125 2.3 47.7 1.0
OG1 G:THR8 2.6 42.8 1.0
O G:ARG122 2.6 45.1 1.0
O G:TYR119 2.8 41.0 1.0
O G:ALA123 3.2 47.8 1.0
CG2 G:THR8 3.3 44.9 1.0
C G:MET125 3.5 47.5 1.0
CB G:THR8 3.5 44.5 1.0
C G:ALA123 3.6 47.2 1.0
CA G:ALA123 3.7 45.4 1.0
C G:ARG122 3.7 45.2 1.0
C G:TYR119 4.0 41.2 1.0
N G:THR8 4.1 46.6 1.0
N G:ALA123 4.2 44.2 1.0
CA G:ARG126 4.2 42.9 1.0
N G:ARG126 4.2 44.2 1.0
N G:MET125 4.3 48.0 1.0
CA G:THR8 4.4 46.2 1.0
CA G:MET125 4.4 50.8 1.0
CD G:PRO127 4.5 39.3 1.0
N G:TYR124 4.6 49.7 1.0
CA G:TYR119 4.8 39.2 1.0
C G:ARG126 4.9 42.8 1.0
C G:TYR124 5.0 47.0 1.0
CA G:ARG122 5.0 48.3 1.0

Magnesium binding site 2 out of 7 in 4qwi

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Magnesium binding site 2 out of 7 in the Ycp BETA5-A49S-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-A49S-Mutant in Complex with Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:60.1
occ:1.00
 O I:ASP177 2.4 44.7 1.0
O I:SER180 2.5 49.0 1.0
O I:ALA174 2.7 48.8 1.0
C I:ASP177 3.6 44.9 1.0
C I:SER180 3.7 46.6 1.0
C I:ALA174 3.8 50.1 1.0
OXT I:ASP204 3.9 60.0 1.0
CA I:ASP175 4.1 51.6 1.0
O I:ALA178 4.2 46.8 1.0
CA I:ALA178 4.4 44.2 1.0
N I:ASP175 4.4 51.3 1.0
C I:ALA178 4.4 44.3 1.0
N I:ALA178 4.4 43.7 1.0
C I:ASP175 4.4 48.3 1.0
N I:ASP177 4.5 43.2 1.0
N I:SER180 4.5 44.1 1.0
CA I:GLY181 4.5 47.8 1.0
N I:GLY181 4.6 47.0 1.0
O I:ASP175 4.6 48.6 1.0
CA I:ASP177 4.6 44.8 1.0
CA I:SER180 4.7 45.4 1.0
C I:ASP204 4.8 60.6 1.0
NH1 Y:ARG19 4.8 55.2 1.0
O I:ASP204 4.8 60.8 1.0
CA I:ALA174 4.9 49.8 1.0
OD1 I:ASP175 4.9 56.7 1.0

Magnesium binding site 3 out of 7 in 4qwi

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Magnesium binding site 3 out of 7 in the Ycp BETA5-A49S-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-A49S-Mutant in Complex with Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg302

b:56.4
occ:1.00
 O K:ASP168 2.2 44.3 1.0
O W:ASP204 2.3 57.5 1.0
O K:SER171 2.4 49.4 1.0
O K:ALA165 2.4 47.2 1.0
C W:ASP204 3.1 56.3 1.0
C K:ASP168 3.2 45.3 1.0
C K:ALA165 3.6 48.6 1.0
C K:SER171 3.6 46.7 1.0
CA K:ALA169 3.6 45.6 1.0
CA W:ASP204 3.7 55.7 1.0
O K:ALA169 3.7 48.6 1.0
C K:ALA169 3.7 46.8 1.0
N K:ALA169 3.8 45.4 1.0
NH1 K:ARG19 3.9 51.4 1.0
CB W:ASP204 4.0 56.2 1.0
OXT W:ASP204 4.0 53.7 1.0
N K:SER171 4.0 45.1 1.0
O K:HIS166 4.1 46.2 1.0
CA K:ALA165 4.3 48.3 1.0
CA K:SER171 4.4 44.2 1.0
CZ K:ARG19 4.4 52.1 1.0
CA K:ASP168 4.4 45.3 1.0
C K:HIS166 4.4 46.2 1.0
N K:ASP168 4.5 46.4 1.0
N K:TYR170 4.5 45.4 1.0
N K:HIS166 4.6 47.0 1.0
N K:GLY172 4.6 47.8 1.0
O K:ALA164 4.6 49.2 1.0
NH2 K:ARG19 4.6 56.6 1.0
CA K:HIS166 4.7 46.4 1.0
CA K:GLY172 4.7 49.0 1.0
CB K:SER171 4.9 43.8 1.0
C K:ARG167 4.9 46.7 1.0
CB K:ALA169 5.0 45.3 1.0

Magnesium binding site 4 out of 7 in 4qwi

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Magnesium binding site 4 out of 7 in the Ycp BETA5-A49S-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-A49S-Mutant in Complex with Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg202

b:52.8
occ:1.00
 O N:SER169 2.4 41.8 1.0
O N:ILE163 2.5 41.4 1.0
O N:ASP166 2.8 46.5 1.0
C N:SER169 3.6 40.1 1.0
C N:ILE163 3.6 43.7 1.0
NH1 N:ARG19 3.7 47.2 1.0
CD1 a:LEU34 3.7 46.1 1.0
C N:ASP166 3.9 43.2 1.0
CG2 N:ILE163 3.9 42.4 1.0
CA N:GLY167 4.2 41.6 1.0
CA N:ILE163 4.3 44.0 1.0
CZ N:ARG19 4.4 45.5 1.0
CA N:GLY170 4.4 42.5 1.0
O N:GLY167 4.4 43.9 1.0
N N:GLY170 4.5 41.5 1.0
N N:GLY167 4.5 42.2 1.0
C N:GLY167 4.5 41.6 1.0
N N:SER169 4.6 38.5 1.0
NH2 N:ARG19 4.6 44.6 1.0
CA N:SER169 4.6 37.9 1.0
N N:LYS164 4.7 44.5 1.0
CB N:ILE163 4.7 43.0 1.0
C N:LYS164 4.9 46.2 1.0
O N:LYS164 4.9 47.6 1.0
CA N:LYS164 4.9 46.1 1.0
N N:ASP166 5.0 41.9 1.0

Magnesium binding site 5 out of 7 in 4qwi

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Magnesium binding site 5 out of 7 in the Ycp BETA5-A49S-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-A49S-Mutant in Complex with Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Mg302

b:68.1
occ:1.00
 O V:ASP166 2.2 45.2 1.0
OXT L:ASP222 2.2 65.3 1.0
O V:ILE163 2.2 50.1 1.0
C L:ASP222 3.0 69.3 1.0
O V:SER169 3.1 48.9 1.0
C V:ASP166 3.1 48.7 1.0
C V:ILE163 3.3 52.3 1.0
O V:TRP164 3.5 57.1 1.0
C V:TRP164 3.6 54.5 1.0
CA L:ASP222 3.7 66.9 1.0
N V:ASP166 3.7 47.5 1.0
N V:LEU167 3.8 49.3 1.0
O V:GLY162 3.8 50.7 1.0
O L:ASP222 3.9 75.4 1.0
CA V:LEU167 3.9 48.9 1.0
CA V:ASP166 4.0 48.2 1.0
CA V:TRP164 4.0 54.0 1.0
N V:TRP164 4.1 52.1 1.0
N V:ASN165 4.1 52.5 1.0
C V:SER169 4.2 47.4 1.0
C V:ASN165 4.2 48.0 1.0
CA V:ILE163 4.4 53.0 1.0
CB L:ASP222 4.4 66.1 1.0
NH1 V:ARG19 4.5 57.6 1.0
C V:LEU167 4.6 49.0 1.0
O L:ARG221 4.6 65.0 1.0
CA V:ASN165 4.6 50.3 1.0
CD2 V:LEU167 4.7 47.5 1.0
C V:GLY162 4.9 51.5 1.0
N V:SER169 4.9 43.3 1.0
N L:ASP222 4.9 65.9 1.0
O V:LEU167 4.9 53.2 1.0
O V:ASN165 4.9 46.1 1.0
CB V:ASP166 5.0 47.6 1.0

Magnesium binding site 6 out of 7 in 4qwi

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Magnesium binding site 6 out of 7 in the Ycp BETA5-A49S-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-A49S-Mutant in Complex with Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
Y:Mg302

b:51.4
occ:1.00
 O Y:ASP168 2.2 45.8 1.0
O I:ASP204 2.4 60.8 1.0
O Y:ALA165 2.4 46.3 1.0
O Y:SER171 2.6 50.1 1.0
C I:ASP204 3.1 60.6 1.0
C Y:ASP168 3.2 44.4 1.0
C Y:ALA165 3.5 47.0 1.0
CA Y:ALA169 3.6 44.0 1.0
CA I:ASP204 3.6 59.7 1.0
C Y:SER171 3.8 46.7 1.0
N Y:ALA169 3.8 43.9 1.0
C Y:ALA169 3.8 45.0 1.0
O Y:ALA169 3.8 48.5 1.0
O Y:HIS166 4.0 46.7 1.0
OXT I:ASP204 4.0 60.0 1.0
NH1 Y:ARG19 4.0 55.2 1.0
CB I:ASP204 4.0 60.8 1.0
N Y:SER171 4.2 43.1 1.0
C Y:HIS166 4.3 45.9 1.0
CA Y:ALA165 4.4 47.0 1.0
CA Y:ASP168 4.4 43.8 1.0
N Y:ASP168 4.4 45.3 1.0
N Y:HIS166 4.5 47.1 1.0
CA Y:SER171 4.5 43.3 1.0
CZ Y:ARG19 4.6 53.5 1.0
N Y:TYR170 4.6 44.4 1.0
O Y:ALA164 4.6 45.5 1.0
CA Y:HIS166 4.6 46.8 1.0
NH2 Y:ARG19 4.8 54.8 1.0
N Y:GLY172 4.8 48.0 1.0
C Y:ARG167 4.8 46.6 1.0
N Y:ARG167 4.9 46.7 1.0
CA Y:GLY172 4.9 50.1 1.0
CB Y:ALA169 5.0 43.4 1.0
CB Y:SER171 5.0 42.9 1.0

Magnesium binding site 7 out of 7 in 4qwi

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Magnesium binding site 7 out of 7 in the Ycp BETA5-A49S-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-A49S-Mutant in Complex with Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg301

b:66.1
occ:1.00
 O Z:VAL198 2.5 49.5 1.0
O Z:THR192 2.7 55.9 1.0
O Z:HIS195 3.2 45.0 1.0
O Z:ASP222 3.4 70.3 1.0
NH2 Z:ARG28 3.6 61.9 1.0
CG2 Z:THR192 3.6 57.1 1.0
C Z:THR192 3.7 57.2 1.0
C Z:VAL198 3.7 51.6 1.0
O Z:ILE196 4.0 48.2 1.0
CA Z:THR192 4.1 57.3 1.0
OD1 Z:ASP222 4.1 60.8 1.0
C Z:HIS195 4.3 45.7 1.0
CA Z:ILE196 4.3 46.0 1.0
C Z:ILE196 4.3 45.4 1.0
NH2 H:ARG19 4.4 57.8 1.0
C Z:ASP222 4.5 68.5 1.0
CB Z:THR192 4.5 56.9 1.0
CA Z:GLY199 4.5 54.8 1.0
CZ Z:ARG28 4.5 59.8 1.0
N Z:GLY199 4.6 53.3 1.0
N Z:VAL198 4.6 47.8 1.0
NH1 Z:ARG28 4.7 61.8 1.0
CA Z:VAL198 4.7 50.3 1.0
N Z:ILE196 4.8 45.1 1.0
O Z:LYS220 4.8 59.2 1.0
N Z:GLU193 4.9 57.1 1.0
OXT Z:ASP222 5.0 64.0 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: Tue Aug 20 02:29:52 2024

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