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Magnesium in PDB 4qvm: Ycp BETA5-M45A Mutant in Complex with Bortezomib

Enzymatic activity of Ycp BETA5-M45A Mutant in Complex with Bortezomib

All present enzymatic activity of Ycp BETA5-M45A Mutant in Complex with Bortezomib:
3.4.25.1;

Protein crystallography data

The structure of Ycp BETA5-M45A Mutant in Complex with Bortezomib, PDB code: 4qvm 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 (°) 136.890, 299.880, 145.900, 90.00, 112.96, 90.00
R / Rfree (%) 18.7 / 21.5

Other elements in 4qvm:

The structure of Ycp BETA5-M45A 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-M45A Mutant in Complex with Bortezomib (pdb code 4qvm). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 9 binding sites of Magnesium where determined in the Ycp BETA5-M45A Mutant in Complex with Bortezomib, PDB code: 4qvm:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Magnesium binding site 1 out of 9 in 4qvm

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Magnesium binding site 1 out of 9 in the Ycp BETA5-M45A 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-M45A Mutant in Complex with Bortezomib within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:64.3
occ:1.00
 O G:MET125 2.4 56.6 1.0
OG1 G:THR8 2.6 48.2 1.0
O G:ARG122 2.9 45.1 1.0
O G:ALA123 3.1 57.4 1.0
O G:TYR119 3.2 47.4 1.0
CG2 G:THR8 3.2 50.3 1.0
CB G:THR8 3.4 49.2 1.0
C G:MET125 3.5 56.0 1.0
C G:ALA123 3.6 54.6 1.0
CA G:ALA123 3.7 52.0 1.0
N G:THR8 3.9 50.4 1.0
C G:ARG122 3.9 49.5 1.0
CA G:ARG126 4.1 50.4 1.0
N G:ARG126 4.2 52.1 1.0
N G:ALA123 4.3 50.5 1.0
CA G:THR8 4.3 50.4 1.0
N G:MET125 4.3 56.0 1.0
C G:TYR119 4.4 44.8 1.0
CA G:MET125 4.5 58.4 1.0
CD G:PRO127 4.6 47.2 1.0
N G:TYR124 4.6 55.0 1.0
C G:ARG126 4.9 48.5 1.0
C G:ILE7 4.9 54.1 1.0
CB G:ALA123 4.9 50.9 1.0
C G:TYR124 5.0 53.9 1.0

Magnesium binding site 2 out of 9 in 4qvm

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Magnesium binding site 2 out of 9 in the Ycp BETA5-M45A 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-M45A Mutant in Complex with Bortezomib within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:62.5
occ:1.00
 O I:ASP177 2.5 52.6 1.0
O I:SER180 2.6 55.1 1.0
O I:ALA174 2.9 48.4 1.0
OXT I:ASP204 3.6 68.4 1.0
C I:ASP177 3.7 51.4 1.0
C I:SER180 3.8 53.3 1.0
C I:ALA174 3.9 53.0 1.0
CA I:ASP175 4.2 54.6 1.0
O I:ALA178 4.4 52.8 1.0
NH1 Y:ARG19 4.4 71.5 1.0
CA I:ALA178 4.4 48.9 1.0
O I:ASP204 4.4 69.5 1.0
C I:ASP204 4.4 66.8 1.0
N I:ALA178 4.5 49.1 1.0
C I:ALA178 4.5 49.9 1.0
C I:ASP175 4.5 52.8 1.0
N I:ASP177 4.5 51.4 1.0
N I:ASP175 4.5 55.0 1.0
N I:SER180 4.6 50.2 1.0
O I:ASP175 4.6 52.4 1.0
NH2 Y:ARG19 4.6 74.1 1.0
CA I:GLY181 4.7 54.5 1.0
CA I:ASP177 4.7 50.8 1.0
N I:GLY181 4.7 52.5 1.0
CA I:SER180 4.7 52.1 1.0
CZ Y:ARG19 4.9 67.3 1.0
OD1 I:ASP175 4.9 60.5 1.0

Magnesium binding site 3 out of 9 in 4qvm

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Magnesium binding site 3 out of 9 in the Ycp BETA5-M45A 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-M45A Mutant in Complex with Bortezomib within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mg201

b:44.6
occ:1.00
 OE1 J:GLN118 3.4 51.5 1.0
O J:THR124 3.7 50.0 1.0
CB J:ASP120 3.8 44.9 1.0
OD2 J:ASP120 3.9 56.0 1.0
CG J:ASP120 3.9 49.2 1.0
N J:ASP120 4.1 42.5 1.0
CD J:GLN118 4.2 46.4 1.0
CB J:THR124 4.3 46.5 1.0
CE1 J:HIS133 4.3 42.6 1.0
CG J:GLN118 4.3 43.9 1.0
CG2 J:THR124 4.4 46.0 1.0
O J:GLN118 4.5 41.8 1.0
CA J:ASP120 4.6 42.4 1.0
OD1 J:ASP120 4.7 55.0 1.0
CG1 I:VAL35 4.7 53.0 1.0
C J:THR124 4.7 46.3 1.0
C J:ILE119 4.7 42.4 1.0
OG I:SER30 4.8 61.1 1.0
CD2 I:LEU28 4.8 50.6 1.0
C J:GLN118 4.9 41.9 1.0
CA J:ILE119 4.9 41.2 1.0
ND1 J:HIS133 5.0 41.7 1.0

Magnesium binding site 4 out of 9 in 4qvm

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Magnesium binding site 4 out of 9 in the Ycp BETA5-M45A 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-M45A Mutant in Complex with Bortezomib within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg302

b:60.3
occ:1.00
 O K:ASP168 2.2 49.2 1.0
O K:ALA165 2.4 53.7 1.0
O W:ASP204 2.4 60.6 1.0
O K:SER171 2.9 45.8 1.0
C K:ASP168 3.2 49.4 1.0
C W:ASP204 3.3 61.1 1.0
CA K:ALA169 3.6 50.9 1.0
C K:ALA165 3.6 53.5 1.0
CA W:ASP204 3.7 59.5 1.0
O K:HIS166 3.7 54.3 1.0
N K:ALA169 3.8 49.9 1.0
NH1 K:ARG19 3.8 66.8 1.0
C K:ALA169 3.9 52.3 1.0
O K:ALA169 3.9 51.6 1.0
CB W:ASP204 4.0 58.8 1.0
C K:SER171 4.1 47.6 1.0
C K:HIS166 4.2 53.8 1.0
OXT W:ASP204 4.2 67.3 1.0
N K:ASP168 4.3 50.8 1.0
CA K:ASP168 4.3 49.8 1.0
N K:SER171 4.5 48.2 1.0
CA K:ALA165 4.5 54.4 1.0
N K:HIS166 4.5 53.1 1.0
CZ K:ARG19 4.6 66.4 1.0
C K:ARG167 4.6 51.3 1.0
CA K:HIS166 4.6 53.6 1.0
O K:ALA164 4.7 59.4 1.0
N K:TYR170 4.7 52.0 1.0
CA K:SER171 4.8 48.1 1.0
O K:ARG167 4.8 53.0 1.0
N K:ARG167 4.8 51.9 1.0
NH2 K:ARG19 4.9 73.0 1.0
CB K:ALA169 4.9 50.0 1.0

Magnesium binding site 5 out of 9 in 4qvm

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Magnesium binding site 5 out of 9 in the Ycp BETA5-M45A 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-M45A Mutant in Complex with Bortezomib within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg303

b:55.9
occ:1.00
 O K:ILE82 2.8 42.2 1.0
C K:ILE82 3.6 41.2 1.0
CA K:ILE82 3.6 40.8 1.0
CG2 K:ILE82 3.7 42.8 1.0
CB K:ASN85 3.8 37.8 1.0
N K:LEU86 3.9 38.4 1.0
CB K:ILE82 4.2 42.0 1.0
CB K:LEU86 4.2 38.8 1.0
CA K:LEU86 4.3 38.8 1.0
CH2 K:TRP58 4.3 41.8 1.0
C K:ASN85 4.4 37.9 1.0
CG1 K:ILE82 4.6 43.2 1.0
CA K:ASN85 4.6 37.2 1.0
O K:LYS81 4.7 36.3 1.0
N K:LEU83 4.8 41.3 1.0
N K:ILE82 4.9 39.3 1.0
OD1 K:ASN85 4.9 44.9 1.0
CG K:ASN85 4.9 39.4 1.0

Magnesium binding site 6 out of 9 in 4qvm

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Magnesium binding site 6 out of 9 in the Ycp BETA5-M45A 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-M45A Mutant in Complex with Bortezomib within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg202

b:49.6
occ:1.00
 O N:SER169 2.6 43.8 1.0
O N:ILE163 2.8 43.6 1.0
O N:ASP166 2.9 47.0 1.0
NH1 N:ARG19 3.4 48.7 1.0
CD1 a:LEU34 3.7 51.1 1.0
C N:SER169 3.8 44.1 1.0
C N:ASP166 4.0 44.3 1.0
C N:ILE163 4.0 46.4 1.0
CZ N:ARG19 4.1 47.6 1.0
CA N:GLY167 4.1 44.3 1.0
CG2 N:ILE163 4.2 46.6 1.0
O N:GLY167 4.2 45.4 1.0
C N:GLY167 4.4 44.0 1.0
NH2 N:ARG19 4.4 50.2 1.0
CA N:GLY170 4.4 46.0 1.0
N N:GLY167 4.5 43.7 1.0
N N:GLY170 4.6 44.5 1.0
CA N:ILE163 4.6 46.4 1.0
N N:SER169 4.8 42.0 1.0
CA N:SER169 4.8 41.6 1.0
CG a:LEU34 4.9 52.2 1.0

Magnesium binding site 7 out of 9 in 4qvm

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Magnesium binding site 7 out of 9 in the Ycp BETA5-M45A 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-M45A Mutant in Complex with Bortezomib within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Mg302

b:64.7
occ:1.00
 OXT L:ASP222 2.1 67.6 1.0
O V:ASP166 2.1 48.6 1.0
O V:ILE163 2.3 57.0 1.0
O V:SER169 2.5 53.3 1.0
C L:ASP222 3.1 69.0 1.0
C V:ASP166 3.1 49.3 1.0
C V:ILE163 3.4 54.3 1.0
C V:SER169 3.6 49.5 1.0
CA V:LEU167 3.8 47.5 1.0
CA L:ASP222 3.8 68.0 1.0
N V:LEU167 3.8 48.6 1.0
NH1 V:ARG19 3.9 58.0 1.0
O L:ASP222 3.9 73.9 1.0
O V:GLY162 4.0 45.5 1.0
N V:ASP166 4.0 49.3 1.0
O V:TRP164 4.1 61.1 1.0
C V:TRP164 4.2 55.4 1.0
CA V:ASP166 4.2 48.6 1.0
CA V:ILE163 4.2 52.5 1.0
N V:TRP164 4.3 52.6 1.0
C V:LEU167 4.3 47.4 1.0
CB L:ASP222 4.3 69.5 1.0
N V:SER169 4.4 45.6 1.0
CA V:TRP164 4.4 54.7 1.0
N V:GLY170 4.5 49.5 1.0
CZ V:ARG19 4.5 57.5 1.0
CA V:GLY170 4.5 52.7 1.0
CA V:SER169 4.5 46.4 1.0
O V:LEU167 4.6 51.8 1.0
N V:ASN165 4.6 53.1 1.0
NH2 V:ARG19 4.7 64.4 1.0
C V:ASN165 4.7 50.1 1.0
CD2 V:LEU167 4.8 46.8 1.0
C V:GLY162 4.9 49.4 1.0
CB V:SER169 4.9 46.5 1.0
N V:GLY168 5.0 45.2 1.0

Magnesium binding site 8 out of 9 in 4qvm

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Magnesium binding site 8 out of 9 in the Ycp BETA5-M45A 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 8 of Ycp BETA5-M45A Mutant in Complex with Bortezomib within 5.0Å range:
probe atom residue distance (Å) B Occ
Y:Mg302

b:57.2
occ:1.00
 O I:ASP204 2.2 69.5 1.0
O Y:ASP168 2.4 45.5 1.0
O Y:ALA165 2.5 49.1 1.0
O Y:SER171 2.9 51.5 1.0
C I:ASP204 3.1 66.8 1.0
C Y:ASP168 3.3 48.1 1.0
CA I:ASP204 3.6 64.2 1.0
CA Y:ALA169 3.6 50.7 1.0
NH1 Y:ARG19 3.7 71.5 1.0
C Y:ALA165 3.7 50.1 1.0
O Y:HIS166 3.8 48.1 1.0
N Y:ALA169 3.9 50.5 1.0
O Y:ALA169 3.9 54.4 1.0
C Y:ALA169 3.9 51.5 1.0
CB I:ASP204 4.0 64.8 1.0
OXT I:ASP204 4.1 68.4 1.0
C Y:SER171 4.1 47.8 1.0
C Y:HIS166 4.3 50.4 1.0
CZ Y:ARG19 4.4 67.3 1.0
N Y:ASP168 4.5 50.3 1.0
CA Y:ASP168 4.5 48.0 1.0
N Y:SER171 4.6 49.1 1.0
CA Y:ALA165 4.6 50.0 1.0
N Y:HIS166 4.7 51.4 1.0
NH2 Y:ARG19 4.7 74.1 1.0
CA Y:HIS166 4.7 50.6 1.0
C Y:ARG167 4.8 52.2 1.0
N Y:TYR170 4.8 50.5 1.0
O Y:ALA164 4.9 51.8 1.0
CA Y:SER171 4.9 46.0 1.0
CB Y:ALA169 4.9 49.9 1.0
CG I:ASP204 5.0 64.3 1.0
O Y:ARG167 5.0 54.7 1.0
N I:ASP204 5.0 61.1 1.0
N Y:ARG167 5.0 50.7 1.0

Magnesium binding site 9 out of 9 in 4qvm

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Magnesium binding site 9 out of 9 in the Ycp BETA5-M45A 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 9 of Ycp BETA5-M45A Mutant in Complex with Bortezomib within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg301

b:68.8
occ:1.00
 O Z:VAL198 2.4 56.3 1.0
O Z:THR192 2.9 57.7 1.0
O Z:HIS195 3.2 47.6 1.0
NH2 Z:ARG28 3.5 64.1 1.0
O Z:ASP222 3.5 72.6 1.0
C Z:VAL198 3.6 56.6 1.0
CG2 Z:THR192 3.6 62.5 1.0
C Z:THR192 3.9 59.5 1.0
O Z:ILE196 3.9 54.2 1.0
CA Z:THR192 4.2 60.9 1.0
CA Z:ILE196 4.2 50.9 1.0
C Z:ILE196 4.2 50.6 1.0
OD1 Z:ASP222 4.2 69.1 1.0
C Z:HIS195 4.2 49.7 1.0
NH2 H:ARG19 4.4 62.9 1.0
N Z:VAL198 4.4 51.1 1.0
CZ Z:ARG28 4.4 61.2 1.0
CA Z:GLY199 4.5 57.8 1.0
N Z:GLY199 4.5 56.6 1.0
C Z:ASP222 4.5 70.2 1.0
CB Z:THR192 4.5 61.5 1.0
CA Z:VAL198 4.6 53.4 1.0
NH1 Z:ARG28 4.6 61.8 1.0
N Z:ILE196 4.7 48.4 1.0
O Z:LYS220 4.7 59.1 1.0
OXT Z:ASP222 5.0 71.9 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 02:19:53 2024

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