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Magnesium in PDB 5l66: Yeast 20S Proteasome with Mouse BETA5I (1-138) and Mouse BETA6 (97- 111; 118-133) in Complex with Bortezomib

Enzymatic activity of Yeast 20S Proteasome with Mouse BETA5I (1-138) and Mouse BETA6 (97- 111; 118-133) in Complex with Bortezomib

All present enzymatic activity of Yeast 20S Proteasome with Mouse BETA5I (1-138) and Mouse BETA6 (97- 111; 118-133) in Complex with Bortezomib:
3.4.25.1;

Protein crystallography data

The structure of Yeast 20S Proteasome with Mouse BETA5I (1-138) and Mouse BETA6 (97- 111; 118-133) in Complex with Bortezomib, PDB code: 5l66 was solved by M.Groll, E.M.Huber, 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 (°) 135.310, 301.130, 145.750, 90.00, 112.92, 90.00
R / Rfree (%) 18.2 / 21

Other elements in 5l66:

The structure of Yeast 20S Proteasome with Mouse BETA5I (1-138) and Mouse BETA6 (97- 111; 118-133) 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 Yeast 20S Proteasome with Mouse BETA5I (1-138) and Mouse BETA6 (97- 111; 118-133) in Complex with Bortezomib (pdb code 5l66). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the Yeast 20S Proteasome with Mouse BETA5I (1-138) and Mouse BETA6 (97- 111; 118-133) in Complex with Bortezomib, PDB code: 5l66:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 5l66

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Magnesium binding site 1 out of 7 in the Yeast 20S Proteasome with Mouse BETA5I (1-138) and Mouse BETA6 (97- 111; 118-133) 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 Yeast 20S Proteasome with Mouse BETA5I (1-138) and Mouse BETA6 (97- 111; 118-133) in Complex with Bortezomib within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:59.6
occ:1.00
 O G:MET125 2.2 50.8 1.0
O G:ARG122 2.5 43.4 1.0
OG1 G:THR8 2.6 46.9 1.0
O G:TYR119 2.7 43.1 1.0
CG2 G:THR8 3.2 48.0 1.0
O G:ALA123 3.3 54.1 1.0
C G:MET125 3.4 49.9 1.0
CB G:THR8 3.5 46.8 1.0
C G:ARG122 3.6 47.0 1.0
C G:ALA123 3.7 49.6 1.0
CA G:ALA123 3.7 48.0 1.0
C G:TYR119 3.9 42.1 1.0
N G:ALA123 4.1 47.1 1.0
N G:THR8 4.2 47.5 1.0
N G:MET125 4.2 51.5 1.0
CA G:ARG126 4.2 45.7 1.0
N G:ARG126 4.2 46.9 1.0
CA G:MET125 4.4 53.4 1.0
CA G:THR8 4.5 47.6 1.0
CD G:PRO127 4.5 43.3 1.0
CA G:TYR119 4.6 41.0 1.0
N G:TYR124 4.6 49.8 1.0
CA G:ARG122 4.9 49.8 1.0
N G:THR120 4.9 42.4 1.0
C G:ARG126 4.9 44.1 1.0
N G:ARG122 4.9 47.1 1.0
CB G:MET125 4.9 58.6 1.0
CA G:THR120 5.0 42.0 1.0

Magnesium binding site 2 out of 7 in 5l66

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Magnesium binding site 2 out of 7 in the Yeast 20S Proteasome with Mouse BETA5I (1-138) and Mouse BETA6 (97- 111; 118-133) 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 Yeast 20S Proteasome with Mouse BETA5I (1-138) and Mouse BETA6 (97- 111; 118-133) in Complex with Bortezomib within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:55.3
occ:1.00
 O I:ASP204 2.1 61.5 1.0
O Y:ASP167 2.3 51.2 1.0
O Y:ALA164 2.3 47.0 1.0
O Y:SER170 2.6 53.8 1.0
C I:ASP204 3.1 61.3 1.0
C Y:ASP167 3.3 49.8 1.0
NH1 Y:ARG19 3.4 63.8 1.0
C Y:ALA164 3.5 47.5 1.0
CA I:ASP204 3.6 61.7 1.0
CA Y:ALA168 3.7 51.2 1.0
C Y:SER170 3.8 50.6 1.0
CB I:ASP204 3.9 63.4 1.0
N Y:ALA168 3.9 51.3 1.0
C Y:ALA168 3.9 51.8 1.0
O Y:ALA168 3.9 54.5 1.0
O Y:HIS165 4.0 47.3 1.0
OXT I:ASP204 4.0 63.0 1.0
CA Y:ALA164 4.2 47.5 1.0
C Y:HIS165 4.3 48.0 1.0
CZ Y:ARG19 4.4 63.0 1.0
N Y:SER170 4.4 50.6 1.0
N Y:HIS165 4.5 48.8 1.0
CA Y:ASP167 4.5 49.3 1.0
N Y:ASP167 4.5 48.8 1.0
CA Y:HIS165 4.7 48.0 1.0
CA Y:SER170 4.7 49.0 1.0
N Y:TYR169 4.7 50.8 1.0
O Y:ALA163 4.8 48.3 1.0
NH2 Y:ARG19 4.8 65.7 1.0
N Y:GLY171 4.8 51.8 1.0
CG I:ASP204 4.8 65.3 1.0
C Y:ARG166 4.9 49.0 1.0
CA Y:GLY171 4.9 53.0 1.0

Magnesium binding site 3 out of 7 in 5l66

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Magnesium binding site 3 out of 7 in the Yeast 20S Proteasome with Mouse BETA5I (1-138) and Mouse BETA6 (97- 111; 118-133) 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 Yeast 20S Proteasome with Mouse BETA5I (1-138) and Mouse BETA6 (97- 111; 118-133) in Complex with Bortezomib within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mg201

b:50.7
occ:1.00
 OE1 J:GLN118 3.1 47.5 1.0
O J:THR124 3.3 47.0 1.0
CB J:ASP120 3.8 43.4 1.0
OD2 J:ASP120 3.8 52.4 1.0
N J:ASP120 3.8 40.2 1.0
CG J:ASP120 3.9 46.6 1.0
CD J:GLN118 3.9 43.0 1.0
CG J:GLN118 4.0 42.0 1.0
O J:GLN118 4.1 40.2 1.0
CE1 J:HIS133 4.2 44.5 1.0
CB J:THR124 4.2 45.1 1.0
CG2 J:THR124 4.4 44.7 1.0
C J:THR124 4.4 45.4 1.0
CA J:ASP120 4.4 41.0 1.0
C J:ILE119 4.4 40.0 1.0
C J:GLN118 4.5 40.3 1.0
CA J:ILE119 4.6 38.9 1.0
OD1 J:ASP120 4.6 51.8 1.0
N J:ILE119 4.7 39.1 1.0
CB J:GLN118 4.8 40.9 1.0
CG1 I:VAL35 4.8 53.3 1.0
ND1 J:HIS133 4.9 44.2 1.0
CA J:THR124 4.9 44.4 1.0

Magnesium binding site 4 out of 7 in 5l66

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Magnesium binding site 4 out of 7 in the Yeast 20S Proteasome with Mouse BETA5I (1-138) and Mouse BETA6 (97- 111; 118-133) 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 Yeast 20S Proteasome with Mouse BETA5I (1-138) and Mouse BETA6 (97- 111; 118-133) in Complex with Bortezomib within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg302

b:56.9
occ:1.00
 O K:ASP167 2.1 53.0 1.0
O K:ALA164 2.3 49.6 1.0
O W:ASP204 2.3 58.4 1.0
O K:SER170 2.7 50.1 1.0
C W:ASP204 3.1 56.4 1.0
C K:ASP167 3.2 50.0 1.0
C K:ALA164 3.4 47.0 1.0
NH1 K:ARG19 3.6 61.2 1.0
CA K:ALA168 3.6 51.5 1.0
CA W:ASP204 3.7 57.0 1.0
N K:ALA168 3.8 50.1 1.0
O K:HIS165 3.8 51.5 1.0
C K:ALA168 3.9 52.2 1.0
C K:SER170 3.9 49.4 1.0
O K:ALA168 4.0 54.7 1.0
CB W:ASP204 4.0 57.1 1.0
OXT W:ASP204 4.1 59.0 1.0
C K:HIS165 4.2 48.5 1.0
CA K:ALA164 4.2 46.7 1.0
N K:ASP167 4.3 48.8 1.0
CA K:ASP167 4.3 48.4 1.0
N K:HIS165 4.4 46.9 1.0
N K:SER170 4.4 49.8 1.0
CA K:HIS165 4.5 47.8 1.0
CZ K:ARG19 4.6 60.3 1.0
C K:ARG166 4.6 49.6 1.0
O K:ALA163 4.6 49.3 1.0
N K:TYR169 4.7 51.4 1.0
CA K:SER170 4.7 48.8 1.0
N K:ARG166 4.8 47.0 1.0
O K:ARG166 4.9 52.1 1.0
N K:GLY171 4.9 49.9 1.0
CB K:ALA168 5.0 52.1 1.0

Magnesium binding site 5 out of 7 in 5l66

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Magnesium binding site 5 out of 7 in the Yeast 20S Proteasome with Mouse BETA5I (1-138) and Mouse BETA6 (97- 111; 118-133) 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 Yeast 20S Proteasome with Mouse BETA5I (1-138) and Mouse BETA6 (97- 111; 118-133) in Complex with Bortezomib within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg301

b:66.5
occ:1.00
 OXT L:ASP222 2.0 73.5 1.0
O V:ASP166 2.2 44.9 1.0
O V:ILE163 2.2 50.1 1.0
O V:SER169 2.4 49.1 1.0
C L:ASP222 3.0 71.0 1.0
C V:ASP166 3.1 44.6 1.0
C V:ILE163 3.3 47.6 1.0
C V:SER169 3.6 46.8 1.0
CA L:ASP222 3.7 69.9 1.0
CA V:LEU167 3.8 44.2 1.0
N V:LEU167 3.8 45.1 1.0
NH1 V:ARG19 3.9 54.6 1.0
O V:GLY162 3.9 49.6 1.0
O L:ASP222 3.9 73.5 1.0
N V:ASP166 4.0 43.0 1.0
CA V:ILE163 4.1 46.8 1.0
CA V:ASP166 4.2 43.5 1.0
O V:TRP164 4.2 55.1 1.0
C V:TRP164 4.2 49.2 1.0
CB L:ASP222 4.3 67.5 1.0
N V:TRP164 4.3 48.4 1.0
C V:LEU167 4.3 44.3 1.0
N V:SER169 4.3 44.1 1.0
CA V:SER169 4.4 43.2 1.0
N V:GLY170 4.5 47.5 1.0
CA V:GLY170 4.5 48.8 1.0
CA V:TRP164 4.5 48.8 1.0
CZ V:ARG19 4.5 51.6 1.0
O V:LEU167 4.6 43.6 1.0
N V:ASN165 4.6 47.7 1.0
NH2 V:ARG19 4.8 53.7 1.0
CB V:SER169 4.8 43.4 1.0
C V:ASN165 4.8 44.3 1.0
C V:GLY162 4.8 47.5 1.0
CD2 V:LEU167 4.9 42.5 1.0
N V:GLY168 5.0 44.7 1.0
CB V:ASP166 5.0 43.3 1.0
O L:ARG221 5.0 64.5 1.0
N V:ILE163 5.0 46.1 1.0

Magnesium binding site 6 out of 7 in 5l66

Go back to Magnesium Binding Sites List in 5l66
Magnesium binding site 6 out of 7 in the Yeast 20S Proteasome with Mouse BETA5I (1-138) and Mouse BETA6 (97- 111; 118-133) 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 Yeast 20S Proteasome with Mouse BETA5I (1-138) and Mouse BETA6 (97- 111; 118-133) in Complex with Bortezomib within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg202

b:49.8
occ:1.00
 O N:ILE163 2.5 43.2 1.0
O N:SER169 2.5 44.4 1.0
O N:ASP166 2.8 44.3 1.0
C N:ILE163 3.6 44.1 1.0
NH1 N:ARG19 3.7 44.8 1.0
CD1 a:LEU34 3.7 54.9 1.0
C N:SER169 3.7 41.5 1.0
CG2 N:ILE163 3.8 43.7 1.0
C N:ASP166 3.9 42.2 1.0
CA N:ILE163 4.3 43.6 1.0
CA N:GLY167 4.3 42.8 1.0
CZ N:ARG19 4.3 44.8 1.0
CA N:GLY170 4.4 43.5 1.0
N N:GLY170 4.5 41.8 1.0
O N:GLY167 4.5 43.5 1.0
N N:GLY167 4.5 42.0 1.0
NH2 N:ARG19 4.6 45.3 1.0
C N:GLY167 4.6 42.3 1.0
N N:LYS164 4.7 45.3 1.0
CB N:ILE163 4.7 43.4 1.0
CA N:SER169 4.8 39.9 1.0
N N:SER169 4.8 41.8 1.0
O N:LYS164 4.9 48.0 1.0
C N:LYS164 4.9 46.5 1.0
CG a:LEU34 4.9 53.2 1.0
CA N:LYS164 4.9 46.9 1.0
N N:ASP166 5.0 40.9 1.0

Magnesium binding site 7 out of 7 in 5l66

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Magnesium binding site 7 out of 7 in the Yeast 20S Proteasome with Mouse BETA5I (1-138) and Mouse BETA6 (97- 111; 118-133) 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 Yeast 20S Proteasome with Mouse BETA5I (1-138) and Mouse BETA6 (97- 111; 118-133) in Complex with Bortezomib within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg301

b:66.2
occ:1.00
 O Z:THR192 2.5 56.2 1.0
O Z:VAL198 2.6 54.7 1.0
O Z:HIS195 2.9 47.9 1.0
C Z:THR192 3.6 60.4 1.0
CG2 Z:THR192 3.6 63.0 1.0
O Z:ASP222 3.8 71.6 1.0
NH2 Z:ARG28 3.8 61.5 1.0
C Z:VAL198 3.8 57.8 1.0
C Z:HIS195 3.9 51.5 1.0
CA Z:THR192 4.0 61.5 1.0
CA Z:ILE196 4.1 55.0 1.0
O Z:ILE196 4.1 55.4 1.0
C Z:ILE196 4.2 53.3 1.0
NH2 H:ARG19 4.2 65.2 1.0
OD1 Z:ASP222 4.3 68.6 1.0
CB Z:THR192 4.4 61.0 1.0
N Z:ILE196 4.4 52.0 1.0
N Z:VAL198 4.6 54.2 1.0
CA Z:VAL198 4.7 56.4 1.0
N Z:GLY199 4.7 58.0 1.0
CA Z:GLY199 4.7 58.9 1.0
N Z:GLU193 4.8 60.1 1.0
C Z:ASP222 4.8 71.3 1.0
CZ Z:ARG28 4.8 61.6 1.0
N Z:HIS195 5.0 50.5 1.0

Reference:

E.M.Huber, W.Heinemeyer, G.De Bruin, H.S.Overkleeft, M.Groll. A Humanized Yeast Proteasome Identifies Unique Binding Modes of Inhibitors For the Immunosubunit Beta 5I. Embo J. V. 35 2602 2016.
ISSN: ESSN 1460-2075
PubMed: 27789522
DOI: 10.15252/EMBJ.201695222
Page generated: Sun Sep 29 19:39:22 2024

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