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Magnesium in PDB 4qwu: Ycp BETA5-C52F Mutant in Complex with Bortezomib

Enzymatic activity of Ycp BETA5-C52F Mutant in Complex with Bortezomib

All present enzymatic activity of Ycp BETA5-C52F Mutant in Complex with Bortezomib:
3.4.25.1;

Protein crystallography data

The structure of Ycp BETA5-C52F Mutant in Complex with Bortezomib, PDB code: 4qwu 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 / 3.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 135.200, 299.250, 144.850, 90.00, 113.01, 90.00
R / Rfree (%) 18.1 / 21.8

Other elements in 4qwu:

The structure of Ycp BETA5-C52F Mutant in Complex with Bortezomib also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Ycp BETA5-C52F Mutant in Complex with Bortezomib (pdb code 4qwu). 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-C52F Mutant in Complex with Bortezomib, PDB code: 4qwu:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 4qwu

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Magnesium binding site 1 out of 7 in the Ycp BETA5-C52F Mutant in Complex with Bortezomib


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Ycp BETA5-C52F Mutant in Complex with Bortezomib within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:56.2
occ:1.00
 O G:MET125 2.1 52.5 1.0
OG1 G:THR8 2.7 45.6 1.0
O G:TYR119 2.9 40.6 1.0
O G:ARG122 2.9 47.5 1.0
O G:ALA123 3.2 52.5 1.0
CG2 G:THR8 3.2 46.0 1.0
C G:MET125 3.3 50.0 1.0
CB G:THR8 3.5 45.5 1.0
C G:ALA123 3.7 52.2 1.0
CA G:ALA123 3.8 49.9 1.0
CA G:ARG126 4.0 43.0 1.0
C G:ARG122 4.0 49.0 1.0
N G:ARG126 4.0 44.6 1.0
N G:THR8 4.0 48.9 1.0
C G:TYR119 4.1 39.5 1.0
N G:MET125 4.2 53.6 1.0
CA G:MET125 4.3 53.9 1.0
N G:ALA123 4.4 50.1 1.0
CA G:THR8 4.4 46.8 1.0
CD G:PRO127 4.5 40.9 1.0
N G:TYR124 4.7 53.9 1.0
C G:ARG126 4.7 42.6 1.0
C G:TYR124 4.8 52.5 1.0
N G:PRO127 4.9 40.9 1.0
CA G:TYR119 4.9 37.9 1.0

Magnesium binding site 2 out of 7 in 4qwu

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Magnesium binding site 2 out of 7 in the Ycp BETA5-C52F Mutant in Complex with Bortezomib


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Ycp BETA5-C52F Mutant in Complex with Bortezomib within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mg201

b:45.8
occ:1.00
 O J:THR124 3.3 41.0 1.0
OE1 J:GLN118 3.4 41.6 1.0
CB J:ASP120 3.7 38.1 1.0
N J:ASP120 3.8 35.6 1.0
CG J:ASP120 3.8 40.8 1.0
OD2 J:ASP120 3.8 44.6 1.0
CB J:THR124 4.0 38.0 1.0
O J:GLN118 4.2 36.9 1.0
CD J:GLN118 4.2 36.6 1.0
CG2 J:THR124 4.2 38.0 1.0
CE1 J:HIS133 4.2 39.6 1.0
CG J:GLN118 4.3 35.3 1.0
CA J:ASP120 4.3 35.9 1.0
C J:THR124 4.3 38.5 1.0
OD1 J:ASP120 4.4 45.0 1.0
C J:ILE119 4.5 34.3 1.0
C J:GLN118 4.6 34.2 1.0
CA J:ILE119 4.6 32.4 1.0
CG1 I:VAL35 4.8 48.1 1.0
CA J:THR124 4.8 37.1 1.0
N J:ILE119 4.8 32.6 1.0
ND1 J:HIS133 5.0 39.0 1.0

Magnesium binding site 3 out of 7 in 4qwu

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Magnesium binding site 3 out of 7 in the Ycp BETA5-C52F Mutant in Complex with Bortezomib


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Ycp BETA5-C52F Mutant in Complex with Bortezomib within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg302

b:59.4
occ:1.00
 O K:ASP168 2.2 51.3 1.0
O K:ALA165 2.2 47.5 1.0
O W:ASP204 2.4 61.7 1.0
O K:SER171 2.8 43.4 1.0
C K:ASP168 3.2 49.1 1.0
C W:ASP204 3.2 61.5 1.0
C K:ALA165 3.3 49.4 1.0
CA W:ASP204 3.6 57.9 1.0
O K:HIS166 3.6 51.5 1.0
CA K:ALA169 3.7 49.6 1.0
N K:ALA169 3.8 49.7 1.0
CB W:ASP204 3.9 54.5 1.0
C K:HIS166 4.0 49.0 1.0
C K:SER171 4.0 44.8 1.0
C K:ALA169 4.0 50.4 1.0
NH1 K:ARG19 4.0 59.9 1.0
O K:ALA169 4.1 51.8 1.0
CA K:ALA165 4.2 49.8 1.0
OXT W:ASP204 4.2 66.3 1.0
N K:HIS166 4.2 48.2 1.0
N K:ASP168 4.3 46.1 1.0
CA K:ASP168 4.3 46.1 1.0
CA K:HIS166 4.4 48.8 1.0
C K:ARG167 4.4 48.4 1.0
O K:ALA164 4.4 49.9 1.0
N K:SER171 4.5 44.6 1.0
O K:ARG167 4.5 50.6 1.0
N K:ARG167 4.6 47.9 1.0
CZ K:ARG19 4.7 57.7 1.0
CA K:SER171 4.8 45.6 1.0
N K:TYR170 4.8 50.7 1.0
N K:GLY172 4.9 45.4 1.0
NH2 K:ARG19 5.0 59.5 1.0
CG W:ASP204 5.0 53.0 1.0

Magnesium binding site 4 out of 7 in 4qwu

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Magnesium binding site 4 out of 7 in the Ycp BETA5-C52F Mutant in Complex with Bortezomib


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Ycp BETA5-C52F Mutant in Complex with Bortezomib within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg202

b:29.0
occ:1.00
 O N:SER169 2.5 40.8 1.0
O N:ILE163 2.7 39.7 1.0
O N:ASP166 2.8 39.3 1.0
NH1 N:ARG19 3.5 39.1 1.0
CD1 a:LEU34 3.6 43.9 1.0
C N:SER169 3.7 37.2 1.0
C N:ILE163 3.8 39.6 1.0
C N:ASP166 3.9 38.1 1.0
CG2 N:ILE163 4.1 37.8 1.0
CZ N:ARG19 4.1 39.1 1.0
CA N:GLY167 4.2 37.5 1.0
O N:GLY167 4.2 35.5 1.0
CA N:GLY170 4.4 37.2 1.0
C N:GLY167 4.4 36.5 1.0
N N:GLY167 4.4 37.7 1.0
NH2 N:ARG19 4.4 40.6 1.0
CA N:ILE163 4.5 38.7 1.0
N N:GLY170 4.5 37.1 1.0
CA N:SER169 4.8 35.3 1.0
N N:SER169 4.8 35.8 1.0
CG a:LEU34 4.8 44.2 1.0
N N:LYS164 4.9 41.6 1.0
CB N:ILE163 4.9 37.2 1.0
N N:ASP166 4.9 38.9 1.0
O N:LYS164 5.0 43.0 1.0
C N:LYS164 5.0 42.9 1.0

Magnesium binding site 5 out of 7 in 4qwu

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Magnesium binding site 5 out of 7 in the Ycp BETA5-C52F Mutant in Complex with Bortezomib


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Ycp BETA5-C52F Mutant in Complex with Bortezomib within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Mg302

b:53.0
occ:1.00
 OXT L:ASP222 2.0 70.0 1.0
O V:ASP166 2.1 41.6 1.0
O V:ILE163 2.2 37.4 1.0
O V:SER169 2.3 42.4 1.0
C L:ASP222 3.1 67.6 1.0
C V:ASP166 3.1 42.3 1.0
C V:ILE163 3.3 41.8 1.0
C V:SER169 3.5 40.5 1.0
NH1 V:ARG19 3.7 56.9 1.0
CA V:LEU167 3.7 41.0 1.0
CA L:ASP222 3.7 65.5 1.0
N V:LEU167 3.8 42.0 1.0
O V:GLY162 3.9 41.0 1.0
O L:ASP222 4.0 68.9 1.0
O V:TRP164 4.0 46.9 1.0
N V:ASP166 4.1 41.6 1.0
CA V:ILE163 4.1 43.8 1.0
C V:LEU167 4.2 40.9 1.0
C V:TRP164 4.2 45.2 1.0
CB L:ASP222 4.2 67.2 1.0
CA V:ASP166 4.2 42.2 1.0
N V:TRP164 4.3 42.6 1.0
N V:SER169 4.3 38.3 1.0
CZ V:ARG19 4.3 55.8 1.0
N V:GLY170 4.3 41.9 1.0
CA V:GLY170 4.3 44.6 1.0
CA V:SER169 4.4 38.4 1.0
O V:LEU167 4.4 42.0 1.0
CA V:TRP164 4.5 44.4 1.0
NH2 V:ARG19 4.5 60.5 1.0
N V:ASN165 4.7 44.7 1.0
CB V:SER169 4.8 37.6 1.0
C V:GLY162 4.8 42.9 1.0
C V:ASN165 4.8 43.0 1.0
CD2 V:LEU167 4.9 38.2 1.0
N V:GLY168 4.9 40.1 1.0
N V:ILE163 5.0 44.0 1.0

Magnesium binding site 6 out of 7 in 4qwu

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Magnesium binding site 6 out of 7 in the Ycp BETA5-C52F Mutant in Complex with Bortezomib


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Ycp BETA5-C52F Mutant in Complex with Bortezomib within 5.0Å range:
probe atom residue distance (Å) B Occ
Y:Mg302

b:55.6
occ:1.00
 O Y:ASP168 2.1 49.8 1.0
O I:ASP204 2.3 61.3 1.0
O Y:ALA165 2.4 45.7 1.0
O Y:SER171 2.7 48.1 1.0
C Y:ASP168 3.2 48.4 1.0
C I:ASP204 3.2 62.2 1.0
CA Y:ALA169 3.5 48.6 1.0
C Y:ALA165 3.6 45.6 1.0
CA I:ASP204 3.7 61.0 1.0
N Y:ALA169 3.7 50.3 1.0
O Y:ALA169 3.8 46.6 1.0
C Y:ALA169 3.8 46.6 1.0
NH1 Y:ARG19 3.8 61.6 1.0
C Y:SER171 3.9 48.3 1.0
O Y:HIS166 3.9 48.3 1.0
CB I:ASP204 4.0 60.7 1.0
OXT I:ASP204 4.2 66.3 1.0
C Y:HIS166 4.3 46.2 1.0
N Y:SER171 4.3 47.9 1.0
CA Y:ASP168 4.4 46.7 1.0
N Y:ASP168 4.4 46.5 1.0
CA Y:ALA165 4.4 45.5 1.0
CZ Y:ARG19 4.5 58.1 1.0
N Y:HIS166 4.5 46.3 1.0
C Y:ARG167 4.6 46.7 1.0
N Y:TYR170 4.6 46.1 1.0
O Y:ALA164 4.6 44.9 1.0
O Y:ARG167 4.6 47.1 1.0
CA Y:SER171 4.7 46.5 1.0
CA Y:HIS166 4.7 46.0 1.0
NH2 Y:ARG19 4.8 57.6 1.0
N Y:ARG167 4.9 44.4 1.0
CB Y:ALA169 4.9 48.9 1.0
N Y:GLY172 4.9 51.3 1.0
CA Y:GLY172 5.0 52.9 1.0

Magnesium binding site 7 out of 7 in 4qwu

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Magnesium binding site 7 out of 7 in the Ycp BETA5-C52F Mutant in Complex with Bortezomib


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Ycp BETA5-C52F Mutant in Complex with Bortezomib within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg301

b:45.6
occ:1.00
 O Z:THR192 2.5 56.0 1.0
O Z:VAL198 2.8 50.2 1.0
O Z:HIS195 2.9 43.0 1.0
C Z:THR192 3.6 55.6 1.0
O Z:ASP222 3.7 69.1 1.0
CG2 Z:THR192 3.8 55.3 1.0
C Z:HIS195 3.8 47.1 1.0
CA Z:ILE196 3.9 48.3 1.0
NH2 Z:ARG28 3.9 53.3 1.0
C Z:VAL198 4.0 49.5 1.0
NH2 H:ARG19 4.0 65.1 1.0
O Z:ILE196 4.0 49.8 1.0
CA Z:THR192 4.1 54.4 1.0
C Z:ILE196 4.2 46.1 1.0
OD1 Z:ASP222 4.2 65.3 1.0
N Z:ILE196 4.3 47.6 1.0
CB Z:THR192 4.6 53.1 1.0
N Z:VAL198 4.6 46.2 1.0
C Z:ASP222 4.7 72.0 1.0
CZ H:ARG19 4.8 60.1 1.0
N Z:GLU193 4.8 54.5 1.0
NH1 H:ARG19 4.8 62.6 1.0
CA Z:VAL198 4.8 48.1 1.0
N Z:HIS195 4.9 46.7 1.0
N Z:GLY199 4.9 48.2 1.0
CZ Z:ARG28 5.0 50.7 1.0
CA Z:GLY199 5.0 49.5 1.0
CA Z:HIS195 5.0 46.7 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 02:32:09 2024

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