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Magnesium in PDB 4qwk: Ycp BETA5-A49T-A50V-Double Mutant in Complex with Carfilzomib

Protein crystallography data

The structure of Ycp BETA5-A49T-A50V-Double Mutant in Complex with Carfilzomib, PDB code: 4qwk 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 / 2.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 136.690, 300.210, 145.620, 90.00, 112.79, 90.00
R / Rfree (%) 18.2 / 20.9

Other elements in 4qwk:

The structure of Ycp BETA5-A49T-A50V-Double 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-A49T-A50V-Double Mutant in Complex with Carfilzomib (pdb code 4qwk). 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-A49T-A50V-Double Mutant in Complex with Carfilzomib, PDB code: 4qwk:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 4qwk

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Magnesium binding site 1 out of 7 in the Ycp BETA5-A49T-A50V-Double 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-A49T-A50V-Double Mutant in Complex with Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:59.2
occ:1.00
 O G:MET125 2.4 55.9 1.0
OG1 G:THR8 2.7 46.0 1.0
O G:ARG122 2.7 52.1 1.0
O G:TYR119 2.9 43.7 1.0
O G:ALA123 3.1 58.6 1.0
CG2 G:THR8 3.3 49.3 1.0
C G:MET125 3.5 54.5 1.0
CB G:THR8 3.6 48.3 1.0
C G:ALA123 3.6 54.6 1.0
CA G:ALA123 3.7 53.1 1.0
C G:ARG122 3.8 50.9 1.0
N G:THR8 4.1 49.9 1.0
C G:TYR119 4.1 44.7 1.0
CA G:ARG126 4.2 48.0 1.0
N G:ALA123 4.2 50.8 1.0
N G:ARG126 4.2 49.5 1.0
N G:MET125 4.3 57.5 1.0
CA G:THR8 4.5 50.2 1.0
CA G:MET125 4.5 58.8 1.0
CD G:PRO127 4.6 44.5 1.0
N G:TYR124 4.6 57.0 1.0
C G:ARG126 4.8 48.2 1.0
CA G:TYR119 4.9 43.8 1.0
CB G:ALA123 5.0 54.6 1.0
C G:TYR124 5.0 54.9 1.0

Magnesium binding site 2 out of 7 in 4qwk

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Magnesium binding site 2 out of 7 in the Ycp BETA5-A49T-A50V-Double 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-A49T-A50V-Double Mutant in Complex with Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:56.8
occ:1.00
 O I:SER180 2.5 55.9 1.0
O I:ASP177 2.5 53.9 1.0
O I:ALA174 2.6 55.5 1.0
C I:ALA174 3.7 57.3 1.0
C I:SER180 3.7 53.2 1.0
C I:ASP177 3.7 52.7 1.0
OXT I:ASP204 3.8 62.6 1.0
CA I:ASP175 4.1 59.3 1.0
N I:ASP175 4.3 58.0 1.0
C I:ASP175 4.4 57.4 1.0
O I:ALA178 4.4 52.8 1.0
CA I:GLY181 4.4 52.8 1.0
O I:ASP175 4.5 58.7 1.0
CA I:ALA178 4.5 50.8 1.0
N I:GLY181 4.5 51.8 1.0
N I:ASP177 4.5 52.5 1.0
C I:ALA178 4.6 51.3 1.0
N I:ALA178 4.6 50.7 1.0
N I:SER180 4.6 50.2 1.0
CA I:ASP177 4.7 52.5 1.0
CA I:SER180 4.7 52.2 1.0
C I:ASP204 4.7 67.9 1.0
O I:ASP204 4.8 69.1 1.0
CA I:ALA174 4.8 55.1 1.0
OD1 I:ASP175 4.8 66.1 1.0
NH1 Y:ARG19 4.9 63.3 1.0

Magnesium binding site 3 out of 7 in 4qwk

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Magnesium binding site 3 out of 7 in the Ycp BETA5-A49T-A50V-Double 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-A49T-A50V-Double Mutant in Complex with Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg302

b:58.9
occ:1.00
 O K:ASP168 2.0 51.9 1.0
O K:ALA165 2.3 51.2 1.0
O W:ASP204 2.4 65.7 1.0
O K:SER171 2.7 52.2 1.0
C K:ASP168 3.1 51.2 1.0
C W:ASP204 3.2 66.0 1.0
C K:ALA165 3.5 52.3 1.0
CA K:ALA169 3.6 51.8 1.0
CA W:ASP204 3.7 63.7 1.0
O K:HIS166 3.7 52.7 1.0
N K:ALA169 3.7 51.3 1.0
C K:ALA169 3.8 53.9 1.0
O K:ALA169 3.9 54.0 1.0
C K:SER171 3.9 51.2 1.0
CB W:ASP204 4.1 61.6 1.0
OXT W:ASP204 4.1 68.1 1.0
C K:HIS166 4.1 50.5 1.0
NH1 K:ARG19 4.1 55.6 1.0
CA K:ASP168 4.3 50.6 1.0
N K:ASP168 4.3 49.4 1.0
N K:SER171 4.3 50.5 1.0
CA K:ALA165 4.4 52.1 1.0
N K:HIS166 4.4 52.1 1.0
CA K:HIS166 4.5 51.4 1.0
O K:ALA164 4.5 50.8 1.0
C K:ARG167 4.6 49.9 1.0
N K:TYR170 4.6 52.7 1.0
CA K:SER171 4.6 49.3 1.0
CZ K:ARG19 4.7 57.6 1.0
N K:ARG167 4.8 49.7 1.0
O K:ARG167 4.9 47.8 1.0
CB K:ALA169 4.9 51.1 1.0
N K:GLY172 4.9 51.8 1.0
NH2 K:ARG19 4.9 59.3 1.0
CB K:ASP168 5.0 51.9 1.0

Magnesium binding site 4 out of 7 in 4qwk

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Magnesium binding site 4 out of 7 in the Ycp BETA5-A49T-A50V-Double 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-A49T-A50V-Double Mutant in Complex with Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg202

b:49.1
occ:1.00
 O N:SER169 2.5 44.8 1.0
O N:ILE163 2.7 46.9 1.0
O N:ASP166 2.8 46.8 1.0
NH1 N:ARG19 3.6 50.3 1.0
CD1 a:LEU34 3.6 55.0 1.0
C N:SER169 3.7 44.4 1.0
C N:ILE163 3.8 48.3 1.0
C N:ASP166 3.8 45.5 1.0
CA N:GLY167 4.1 45.0 1.0
CG2 N:ILE163 4.1 48.1 1.0
O N:GLY167 4.2 48.4 1.0
CZ N:ARG19 4.3 50.4 1.0
C N:GLY167 4.4 45.1 1.0
N N:GLY167 4.4 44.2 1.0
CA N:GLY170 4.5 47.3 1.0
CA N:ILE163 4.5 49.1 1.0
NH2 N:ARG19 4.5 49.9 1.0
N N:GLY170 4.5 45.6 1.0
N N:SER169 4.6 42.2 1.0
CA N:SER169 4.7 41.7 1.0
N N:LYS164 4.8 48.7 1.0
CG a:LEU34 4.9 56.5 1.0
O N:LYS164 4.9 50.3 1.0
CB N:ILE163 4.9 48.6 1.0
C N:LYS164 5.0 50.0 1.0

Magnesium binding site 5 out of 7 in 4qwk

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Magnesium binding site 5 out of 7 in the Ycp BETA5-A49T-A50V-Double 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-A49T-A50V-Double Mutant in Complex with Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Mg302

b:78.0
occ:1.00
 OXT L:ASP222 2.1 87.4 1.0
O V:ASP166 2.1 53.4 1.0
O V:ILE163 2.3 59.0 1.0
O V:SER169 2.8 53.0 1.0
C V:ASP166 3.1 58.2 1.0
C L:ASP222 3.1 85.3 1.0
C V:ILE163 3.4 60.6 1.0
O V:TRP164 3.7 67.3 1.0
CA L:ASP222 3.7 80.3 1.0
N V:LEU167 3.8 59.0 1.0
C V:TRP164 3.8 62.5 1.0
CA V:LEU167 3.8 59.1 1.0
N V:ASP166 3.9 57.3 1.0
O V:GLY162 3.9 53.2 1.0
O L:ASP222 4.0 90.2 1.0
C V:SER169 4.0 52.5 1.0
CA V:ASP166 4.1 57.4 1.0
N V:TRP164 4.1 60.3 1.0
CA V:TRP164 4.2 63.2 1.0
N V:ASN165 4.3 58.8 1.0
CA V:ILE163 4.3 61.7 1.0
NH1 V:ARG19 4.3 69.2 1.0
CB L:ASP222 4.4 79.7 1.0
C V:LEU167 4.4 58.8 1.0
C V:ASN165 4.5 57.8 1.0
O V:LEU167 4.7 62.5 1.0
N V:SER169 4.7 52.7 1.0
O L:ARG221 4.8 69.3 1.0
CD2 V:LEU167 4.8 57.7 1.0
CA V:SER169 4.9 53.3 1.0
CA V:GLY170 4.9 58.2 1.0
C V:GLY162 4.9 59.6 1.0
CA V:ASN165 4.9 59.3 1.0
N V:GLY170 4.9 53.6 1.0
CZ V:ARG19 4.9 65.4 1.0
CB V:ASP166 5.0 55.2 1.0
N L:ASP222 5.0 75.2 1.0
NH2 V:ARG19 5.0 67.4 1.0

Magnesium binding site 6 out of 7 in 4qwk

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Magnesium binding site 6 out of 7 in the Ycp BETA5-A49T-A50V-Double 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-A49T-A50V-Double Mutant in Complex with Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
Y:Mg302

b:49.9
occ:1.00
 O Y:ASP168 2.2 50.4 1.0
O I:ASP204 2.3 69.1 1.0
O Y:ALA165 2.5 43.8 1.0
O Y:SER171 2.8 51.4 1.0
C I:ASP204 3.1 67.9 1.0
C Y:ASP168 3.3 50.6 1.0
CA Y:ALA169 3.5 48.8 1.0
CA I:ASP204 3.6 67.7 1.0
C Y:ALA165 3.7 48.1 1.0
O Y:ALA169 3.8 48.7 1.0
N Y:ALA169 3.8 50.2 1.0
C Y:ALA169 3.8 48.3 1.0
O Y:HIS166 3.8 45.4 1.0
OXT I:ASP204 3.9 62.6 1.0
NH1 Y:ARG19 3.9 63.3 1.0
C Y:SER171 4.0 50.1 1.0
CB I:ASP204 4.0 68.7 1.0
C Y:HIS166 4.3 49.0 1.0
N Y:SER171 4.4 48.1 1.0
CA Y:ASP168 4.5 50.7 1.0
N Y:ASP168 4.5 51.6 1.0
CZ Y:ARG19 4.6 61.8 1.0
CA Y:ALA165 4.6 50.1 1.0
N Y:HIS166 4.6 49.5 1.0
N Y:TYR170 4.6 48.5 1.0
CA Y:HIS166 4.7 49.8 1.0
CA Y:SER171 4.7 47.7 1.0
NH2 Y:ARG19 4.8 63.7 1.0
O Y:ALA164 4.8 50.3 1.0
C Y:ARG167 4.8 50.1 1.0
CB Y:ALA169 4.9 47.8 1.0
N Y:ARG167 5.0 48.7 1.0
N Y:GLY172 5.0 51.6 1.0
N I:ASP204 5.0 66.8 1.0

Magnesium binding site 7 out of 7 in 4qwk

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Magnesium binding site 7 out of 7 in the Ycp BETA5-A49T-A50V-Double 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-A49T-A50V-Double Mutant in Complex with Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg301

b:70.3
occ:1.00
 O Z:VAL198 2.5 60.4 1.0
O Z:THR192 2.8 60.4 1.0
O Z:HIS195 3.3 52.0 1.0
O Z:ASP222 3.3 79.0 1.0
NH2 Z:ARG28 3.5 73.8 1.0
CG2 Z:THR192 3.6 66.0 1.0
C Z:VAL198 3.7 62.1 1.0
C Z:THR192 3.8 65.3 1.0
O Z:ILE196 4.0 53.7 1.0
CA Z:THR192 4.1 64.7 1.0
OD1 Z:ASP222 4.1 77.5 1.0
C Z:HIS195 4.3 53.6 1.0
CA Z:ILE196 4.3 53.9 1.0
C Z:ASP222 4.4 77.9 1.0
C Z:ILE196 4.4 52.8 1.0
NH2 H:ARG19 4.4 75.2 1.0
CA Z:GLY199 4.4 62.2 1.0
CB Z:THR192 4.5 65.2 1.0
CZ Z:ARG28 4.5 68.3 1.0
N Z:GLY199 4.5 62.3 1.0
N Z:VAL198 4.6 56.6 1.0
O Z:LYS220 4.7 67.0 1.0
NH1 Z:ARG28 4.7 69.1 1.0
CA Z:VAL198 4.7 58.8 1.0
N Z:ILE196 4.8 53.0 1.0
OXT Z:ASP222 4.9 74.7 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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