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Magnesium in PDB 4qwj: Ycp BETA5-A49T-Mutant in Complex with Carfilzomib

Protein crystallography data

The structure of Ycp BETA5-A49T-Mutant in Complex with Carfilzomib, PDB code: 4qwj 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 (°) 136.710, 300.140, 145.280, 90.00, 113.16, 90.00
R / Rfree (%) 19.1 / 22.8

Other elements in 4qwj:

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

Magnesium binding site 1 out of 7 in 4qwj

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

b:58.7
occ:1.00
 O G:MET125 2.3 63.7 1.0
O G:ARG122 2.7 49.5 1.0
OG1 G:THR8 2.7 49.1 1.0
O G:TYR119 2.8 41.4 1.0
O G:ALA123 3.2 56.9 1.0
CG2 G:THR8 3.3 50.0 1.0
C G:MET125 3.4 57.2 1.0
CB G:THR8 3.6 50.7 1.0
C G:ALA123 3.7 54.5 1.0
CA G:ALA123 3.8 53.3 1.0
C G:ARG122 3.8 50.2 1.0
C G:TYR119 4.0 44.0 1.0
CA G:ARG126 4.1 47.2 1.0
N G:ARG126 4.1 48.8 1.0
N G:THR8 4.2 54.7 1.0
N G:ALA123 4.3 50.2 1.0
N G:MET125 4.3 60.5 1.0
CD G:PRO127 4.4 44.9 1.0
CA G:MET125 4.4 59.6 1.0
CA G:THR8 4.5 54.2 1.0
N G:TYR124 4.7 57.1 1.0
C G:ARG126 4.7 46.4 1.0
CA G:TYR119 4.7 44.0 1.0
N G:PRO127 4.9 45.1 1.0
C G:TYR124 5.0 57.6 1.0

Magnesium binding site 2 out of 7 in 4qwj

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

b:66.2
occ:1.00
 O I:ASP177 2.5 51.4 1.0
O I:SER180 2.5 55.1 1.0
O I:ALA174 2.9 61.5 1.0
OXT I:ASP204 3.7 77.4 1.0
C I:ASP177 3.7 55.3 1.0
C I:SER180 3.7 52.6 1.0
C I:ALA174 4.0 61.1 1.0
O I:ALA178 4.2 56.2 1.0
CA I:ASP175 4.2 62.1 1.0
CA I:ALA178 4.4 54.0 1.0
C I:ALA178 4.4 53.6 1.0
N I:ALA178 4.5 53.9 1.0
O I:ASP175 4.5 56.5 1.0
C I:ASP175 4.5 57.4 1.0
CA I:GLY181 4.5 57.1 1.0
N I:ASP175 4.5 63.3 1.0
C I:ASP204 4.6 72.6 1.0
N I:GLY181 4.6 54.2 1.0
O I:ASP204 4.6 75.8 1.0
N I:SER180 4.6 50.4 1.0
N I:ASP177 4.6 55.3 1.0
NH1 Y:ARG19 4.7 58.9 1.0
CA I:SER180 4.7 51.6 1.0
CA I:ASP177 4.7 55.0 1.0

Magnesium binding site 3 out of 7 in 4qwj

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

b:57.9
occ:1.00
 O K:ASP168 2.0 47.9 1.0
O K:SER171 2.4 46.6 1.0
O W:ASP204 2.4 69.7 1.0
O K:ALA165 2.5 52.9 1.0
C K:ASP168 3.1 46.4 1.0
C W:ASP204 3.3 64.3 1.0
CA K:ALA169 3.4 47.0 1.0
O K:ALA169 3.5 45.9 1.0
C K:ALA169 3.5 47.3 1.0
C K:SER171 3.6 48.4 1.0
C K:ALA165 3.7 50.7 1.0
N K:ALA169 3.7 45.8 1.0
CA W:ASP204 3.8 63.5 1.0
NH1 K:ARG19 3.9 50.1 1.0
N K:SER171 3.9 47.5 1.0
OXT W:ASP204 4.1 63.6 1.0
CB W:ASP204 4.2 62.4 1.0
O K:HIS166 4.2 49.2 1.0
CA K:SER171 4.3 47.3 1.0
N K:TYR170 4.3 47.9 1.0
CA K:ASP168 4.3 47.8 1.0
CA K:ALA165 4.4 50.3 1.0
N K:ASP168 4.4 49.3 1.0
CZ K:ARG19 4.5 52.2 1.0
C K:HIS166 4.5 48.4 1.0
O K:ALA164 4.6 49.7 1.0
N K:HIS166 4.6 48.0 1.0
N K:GLY172 4.7 50.7 1.0
NH2 K:ARG19 4.7 57.6 1.0
CB K:SER171 4.8 46.3 1.0
C K:ARG167 4.8 49.6 1.0
CB K:ALA169 4.8 47.7 1.0
CA K:HIS166 4.8 48.5 1.0
CA K:GLY172 4.9 51.4 1.0

Magnesium binding site 4 out of 7 in 4qwj

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

b:51.6
occ:1.00
 O N:SER169 2.4 49.9 1.0
O N:ILE163 2.6 53.6 1.0
O N:ASP166 2.8 51.7 1.0
NH1 N:ARG19 3.6 58.5 1.0
C N:SER169 3.6 49.8 1.0
CD1 a:LEU34 3.7 51.9 1.0
C N:ILE163 3.7 55.1 1.0
C N:ASP166 3.9 50.6 1.0
CG2 N:ILE163 4.0 52.3 1.0
CA N:GLY167 4.2 50.5 1.0
O N:GLY167 4.3 52.1 1.0
CZ N:ARG19 4.3 55.4 1.0
CA N:GLY170 4.3 49.0 1.0
CA N:ILE163 4.4 54.1 1.0
C N:GLY167 4.4 50.3 1.0
N N:GLY170 4.4 49.7 1.0
N N:GLY167 4.5 49.9 1.0
NH2 N:ARG19 4.6 53.7 1.0
N N:SER169 4.6 47.1 1.0
CA N:SER169 4.6 47.2 1.0
N N:LYS164 4.8 53.5 1.0
CB N:ILE163 4.8 51.9 1.0
O N:LYS164 4.9 54.5 1.0
CG a:LEU34 4.9 55.5 1.0
C N:LYS164 4.9 53.5 1.0
CA N:LYS164 5.0 54.7 1.0

Magnesium binding site 5 out of 7 in 4qwj

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

b:70.2
occ:1.00
 O V:ASP166 2.3 60.1 1.0
O V:ILE163 2.3 60.3 1.0
OXT L:ASP222 2.3 78.3 1.0
C L:ASP222 3.1 77.2 1.0
C V:ASP166 3.1 60.5 1.0
O V:SER169 3.1 51.6 1.0
C V:ILE163 3.3 61.0 1.0
O V:TRP164 3.4 67.6 1.0
C V:TRP164 3.6 63.8 1.0
CA L:ASP222 3.7 75.1 1.0
N V:ASP166 3.7 58.0 1.0
N V:LEU167 3.8 60.3 1.0
O V:GLY162 3.9 60.0 1.0
O L:ASP222 3.9 81.1 1.0
CA V:LEU167 3.9 60.3 1.0
CA V:TRP164 4.0 62.7 1.0
CA V:ASP166 4.0 58.6 1.0
N V:ASN165 4.0 62.7 1.0
N V:TRP164 4.1 59.9 1.0
C V:ASN165 4.2 58.9 1.0
C V:SER169 4.3 53.9 1.0
CA V:ILE163 4.4 61.4 1.0
CB L:ASP222 4.5 77.3 1.0
O L:ARG221 4.5 67.8 1.0
CA V:ASN165 4.6 59.5 1.0
NH1 V:ARG19 4.6 68.7 1.0
C V:LEU167 4.6 59.2 1.0
CD2 V:LEU167 4.7 55.9 1.0
O V:ASN165 4.9 55.4 1.0
C V:GLY162 4.9 61.5 1.0
N L:ASP222 4.9 74.2 1.0
O V:LEU167 4.9 64.2 1.0
N V:SER169 5.0 53.1 1.0
CD1 L:ILE35 5.0 62.4 1.0

Magnesium binding site 6 out of 7 in 4qwj

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

b:50.7
occ:1.00
 O Y:ASP168 2.2 51.6 1.0
O Y:ALA165 2.3 43.9 1.0
O I:ASP204 2.7 75.8 1.0
O Y:SER171 3.1 54.9 1.0
C Y:ASP168 3.1 49.3 1.0
C I:ASP204 3.2 72.6 1.0
O Y:HIS166 3.4 58.1 1.0
C Y:ALA165 3.5 48.7 1.0
CA Y:ALA169 3.6 49.0 1.0
CA I:ASP204 3.7 70.5 1.0
N Y:ALA169 3.7 48.0 1.0
C Y:HIS166 3.8 54.6 1.0
OXT I:ASP204 4.0 77.4 1.0
C Y:ALA169 4.0 48.9 1.0
O Y:ALA169 4.1 56.5 1.0
N Y:ASP168 4.1 50.0 1.0
CA Y:ASP168 4.2 48.2 1.0
CB I:ASP204 4.2 69.9 1.0
CA Y:HIS166 4.3 51.0 1.0
N Y:HIS166 4.3 48.7 1.0
C Y:SER171 4.3 51.4 1.0
C Y:ARG167 4.3 52.0 1.0
N Y:ARG167 4.5 52.2 1.0
CA Y:ALA165 4.5 50.9 1.0
NH1 Y:ARG19 4.5 58.9 1.0
O Y:ALA164 4.5 47.4 1.0
O Y:ARG167 4.6 50.7 1.0
N Y:SER171 4.6 45.8 1.0
N Y:TYR170 4.8 45.1 1.0
CB Y:ALA169 4.9 48.1 1.0
CA Y:ARG167 4.9 52.9 1.0
CA Y:SER171 5.0 46.8 1.0

Magnesium binding site 7 out of 7 in 4qwj

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

b:64.2
occ:1.00
 O Z:HIS195 2.5 57.6 1.0
O Z:VAL198 2.6 62.8 1.0
O Z:THR192 2.8 62.0 1.0
O Z:ILE196 3.5 58.3 1.0
C Z:HIS195 3.5 52.8 1.0
NH2 Z:ARG28 3.6 73.2 1.0
CA Z:ILE196 3.6 52.8 1.0
C Z:ILE196 3.7 53.2 1.0
O Z:ASP222 3.8 73.5 1.0
C Z:VAL198 3.8 60.6 1.0
C Z:THR192 3.9 64.3 1.0
N Z:ILE196 4.0 49.6 1.0
CG2 Z:THR192 4.1 66.5 1.0
N Z:VAL198 4.2 57.6 1.0
CA Z:THR192 4.2 64.9 1.0
NH2 H:ARG19 4.5 77.4 1.0
CA Z:VAL198 4.5 57.6 1.0
N Z:GLN197 4.6 51.6 1.0
CZ Z:ARG28 4.7 66.9 1.0
C Z:ASP222 4.8 78.5 1.0
N Z:GLY199 4.8 62.1 1.0
NH1 H:ARG19 4.8 70.5 1.0
CB Z:THR192 4.8 66.3 1.0
CA Z:HIS195 4.8 54.5 1.0
N Z:HIS195 4.8 54.6 1.0
OD1 Z:ASP222 4.8 86.7 1.0
CB Z:ILE196 4.9 52.6 1.0
CA Z:GLY199 4.9 66.2 1.0
CB Z:VAL198 5.0 58.5 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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