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Magnesium in PDB 5l5f: Yeast 20S Proteasome with Human BETA5I (1-138) and Human BETA6 (97- 111; 118-133) in Complex with Bortezomib

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

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

Protein crystallography data

The structure of Yeast 20S Proteasome with Human BETA5I (1-138) and Human BETA6 (97- 111; 118-133) in Complex with Bortezomib, PDB code: 5l5f 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 / 2.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 135.510, 300.910, 144.920, 90.00, 112.59, 90.00
R / Rfree (%) 20.5 / 22.8

Other elements in 5l5f:

The structure of Yeast 20S Proteasome with Human BETA5I (1-138) and Human 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 Human BETA5I (1-138) and Human BETA6 (97- 111; 118-133) in Complex with Bortezomib (pdb code 5l5f). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Yeast 20S Proteasome with Human BETA5I (1-138) and Human BETA6 (97- 111; 118-133) in Complex with Bortezomib, PDB code: 5l5f:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 5l5f

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Magnesium binding site 1 out of 8 in the Yeast 20S Proteasome with Human BETA5I (1-138) and Human 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 Human BETA5I (1-138) and Human BETA6 (97- 111; 118-133) in Complex with Bortezomib within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:46.7
occ:1.00
 O G:MET125 2.2 41.6 1.0
O G:ARG122 2.4 40.1 1.0
O G:TYR119 2.5 34.2 1.0
OG1 G:THR8 2.7 39.1 1.0
CG2 G:THR8 3.2 40.3 1.0
C G:MET125 3.4 42.8 1.0
O G:ALA123 3.4 45.2 1.0
C G:ARG122 3.5 40.5 1.0
CB G:THR8 3.5 39.4 1.0
C G:ALA123 3.7 43.5 1.0
CA G:ALA123 3.7 41.2 1.0
C G:TYR119 3.7 34.7 1.0
N G:ALA123 4.1 40.0 1.0
N G:MET125 4.2 44.5 1.0
N G:ARG126 4.2 40.1 1.0
CA G:ARG126 4.3 38.4 1.0
N G:THR8 4.3 40.4 1.0
CA G:MET125 4.3 45.2 1.0
CA G:TYR119 4.5 34.0 1.0
CA G:THR8 4.5 40.1 1.0
CD G:PRO127 4.5 35.7 1.0
N G:TYR124 4.6 44.0 1.0
CA G:ARG122 4.7 43.5 1.0
N G:THR120 4.7 34.4 1.0
N G:ARG122 4.8 40.5 1.0
CB G:MET125 4.9 50.7 1.0
C G:ARG126 4.9 37.2 1.0
CA G:THR120 4.9 34.2 1.0
C G:THR120 4.9 34.6 1.0

Magnesium binding site 2 out of 8 in 5l5f

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Magnesium binding site 2 out of 8 in the Yeast 20S Proteasome with Human BETA5I (1-138) and Human 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 Human BETA5I (1-138) and Human BETA6 (97- 111; 118-133) in Complex with Bortezomib within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:46.8
occ:1.00
 O Y:ASP167 2.1 44.9 1.0
O Y:ALA164 2.3 39.4 1.0
O I:ASP204 2.4 49.2 1.0
O Y:SER170 2.4 47.0 1.0
C Y:ASP167 3.2 41.9 1.0
C I:ASP204 3.3 52.7 1.0
C Y:ALA164 3.4 38.6 1.0
NH1 Y:ARG19 3.5 54.7 1.0
C Y:SER170 3.6 42.7 1.0
CA I:ASP204 3.7 53.5 1.0
CA Y:ALA168 3.8 44.1 1.0
CB I:ASP204 3.9 54.5 1.0
C Y:ALA168 3.9 44.7 1.0
O Y:ALA168 3.9 45.8 1.0
N Y:ALA168 3.9 42.6 1.0
N Y:SER170 4.1 41.5 1.0
CA Y:ALA164 4.1 38.8 1.0
O Y:HIS165 4.2 40.4 1.0
OXT I:ASP204 4.2 53.7 1.0
CZ Y:ARG19 4.3 52.0 1.0
CA Y:SER170 4.3 40.5 1.0
CA Y:ASP167 4.4 40.0 1.0
N Y:ASP167 4.4 41.6 1.0
C Y:HIS165 4.4 40.0 1.0
N Y:HIS165 4.5 39.4 1.0
N Y:GLY171 4.6 43.5 1.0
O Y:ALA163 4.6 37.9 1.0
N Y:TYR169 4.6 43.8 1.0
NH2 Y:ARG19 4.7 52.7 1.0
CA Y:GLY171 4.7 44.2 1.0
CA Y:HIS165 4.7 38.9 1.0
CB Y:SER170 4.8 39.0 1.0
CG I:ASP204 4.9 55.1 1.0
C Y:ARG166 4.9 42.1 1.0
CB Y:ALA164 4.9 39.2 1.0

Magnesium binding site 3 out of 8 in 5l5f

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Magnesium binding site 3 out of 8 in the Yeast 20S Proteasome with Human BETA5I (1-138) and Human 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 Human BETA5I (1-138) and Human BETA6 (97- 111; 118-133) in Complex with Bortezomib within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mg201

b:62.5
occ:1.00
 OE1 J:GLN118 3.1 38.9 1.0
O J:THR124 3.5 38.4 1.0
CB J:ASP120 3.8 35.5 1.0
N J:ASP120 3.8 32.0 1.0
OD2 J:ASP120 3.8 40.6 1.0
CG J:ASP120 3.9 38.1 1.0
CD J:GLN118 3.9 36.2 1.0
CG J:GLN118 4.0 34.4 1.0
CE1 J:HIS133 4.1 35.1 1.0
CB J:THR124 4.2 36.5 1.0
O J:GLN118 4.3 33.3 1.0
CA J:ASP120 4.4 33.4 1.0
CG2 J:THR124 4.4 36.9 1.0
C J:THR124 4.5 36.8 1.0
C J:ILE119 4.5 32.4 1.0
C J:GLN118 4.6 32.9 1.0
OD1 J:ASP120 4.6 40.5 1.0
CA J:ILE119 4.7 31.1 1.0
CG1 I:VAL35 4.8 46.8 1.0
N J:ILE119 4.8 31.5 1.0
ND1 J:HIS133 4.8 34.9 1.0
CB J:GLN118 4.8 33.8 1.0
CA J:THR124 5.0 36.2 1.0

Magnesium binding site 4 out of 8 in 5l5f

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Magnesium binding site 4 out of 8 in the Yeast 20S Proteasome with Human BETA5I (1-138) and Human 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 Human BETA5I (1-138) and Human BETA6 (97- 111; 118-133) in Complex with Bortezomib within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg302

b:46.5
occ:1.00
 O K:ASP167 2.2 42.6 1.0
O W:ASP204 2.2 49.4 1.0
O K:ALA164 2.3 40.0 1.0
O K:SER170 2.4 43.1 1.0
C W:ASP204 3.1 49.8 1.0
C K:ASP167 3.3 42.5 1.0
C K:ALA164 3.5 40.3 1.0
NH1 K:ARG19 3.5 55.6 1.0
CA W:ASP204 3.6 49.2 1.0
C K:SER170 3.6 43.1 1.0
CA K:ALA168 3.8 45.4 1.0
CB W:ASP204 3.8 49.7 1.0
O K:ALA168 3.9 46.3 1.0
C K:ALA168 3.9 44.7 1.0
N K:ALA168 3.9 43.6 1.0
OXT W:ASP204 4.1 50.4 1.0
N K:SER170 4.1 42.0 1.0
CA K:ALA164 4.2 40.5 1.0
O K:HIS165 4.2 42.7 1.0
CZ K:ARG19 4.3 53.7 1.0
CA K:SER170 4.4 41.1 1.0
CA K:ASP167 4.5 41.3 1.0
C K:HIS165 4.5 41.4 1.0
N K:ASP167 4.5 42.5 1.0
N K:HIS165 4.5 40.8 1.0
N K:GLY171 4.6 44.7 1.0
N K:TYR169 4.6 43.8 1.0
NH2 K:ARG19 4.7 56.3 1.0
O K:ALA163 4.7 40.4 1.0
CA K:GLY171 4.7 45.9 1.0
CG W:ASP204 4.8 51.0 1.0
CA K:HIS165 4.8 41.3 1.0
CB K:SER170 4.8 39.3 1.0
C K:ARG166 4.9 42.4 1.0
CB K:ALA164 5.0 41.6 1.0

Magnesium binding site 5 out of 8 in 5l5f

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Magnesium binding site 5 out of 8 in the Yeast 20S Proteasome with Human BETA5I (1-138) and Human 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 Human BETA5I (1-138) and Human BETA6 (97- 111; 118-133) in Complex with Bortezomib within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg301

b:49.7
occ:1.00
 OXT L:ASP222 2.1 63.9 1.0
O V:ASP166 2.2 37.6 1.0
O V:ILE163 2.2 42.5 1.0
O V:SER169 2.3 40.6 1.0
C L:ASP222 3.1 63.6 1.0
C V:ASP166 3.1 36.3 1.0
C V:ILE163 3.3 40.8 1.0
C V:SER169 3.4 39.0 1.0
CA L:ASP222 3.8 61.5 1.0
NH1 V:ARG19 3.8 44.6 1.0
CA V:LEU167 3.8 36.5 1.0
O V:GLY162 3.8 39.9 1.0
N V:LEU167 3.8 35.9 1.0
O L:ASP222 3.9 68.1 1.0
N V:ASP166 4.0 36.9 1.0
CA V:ILE163 4.1 40.1 1.0
CA V:ASP166 4.2 36.2 1.0
N V:SER169 4.2 36.3 1.0
C V:LEU167 4.3 37.5 1.0
N V:TRP164 4.3 41.8 1.0
CA V:SER169 4.3 37.3 1.0
C V:TRP164 4.3 41.3 1.0
CB L:ASP222 4.3 60.7 1.0
N V:GLY170 4.3 40.3 1.0
CA V:GLY170 4.4 41.9 1.0
O V:TRP164 4.4 42.5 1.0
O V:LEU167 4.5 38.9 1.0
CZ V:ARG19 4.5 42.9 1.0
CA V:TRP164 4.5 42.2 1.0
N V:ASN165 4.6 39.1 1.0
CB V:SER169 4.7 37.5 1.0
C V:GLY162 4.8 39.3 1.0
C V:ASN165 4.8 37.5 1.0
NH2 V:ARG19 4.8 44.3 1.0
N V:GLY168 4.9 37.2 1.0
N V:ILE163 5.0 39.8 1.0
CB V:ASP166 5.0 35.4 1.0
CD2 V:LEU167 5.0 35.8 1.0

Magnesium binding site 6 out of 8 in 5l5f

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Magnesium binding site 6 out of 8 in the Yeast 20S Proteasome with Human BETA5I (1-138) and Human 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 Human BETA5I (1-138) and Human BETA6 (97- 111; 118-133) in Complex with Bortezomib within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg202

b:31.4
occ:1.00
 O N:ILE163 2.5 35.7 1.0
O N:SER169 2.5 33.1 1.0
O N:ASP166 2.6 34.3 1.0
CD1 a:LEU34 3.5 44.6 1.0
C N:ILE163 3.6 37.4 1.0
C N:ASP166 3.7 34.1 1.0
C N:SER169 3.7 33.4 1.0
NH1 N:ARG19 3.8 38.8 1.0
CG2 N:ILE163 4.0 36.7 1.0
CA N:GLY167 4.1 34.6 1.0
CA N:ILE163 4.3 36.1 1.0
N N:GLY167 4.3 33.6 1.0
O N:GLY167 4.4 35.7 1.0
C N:GLY167 4.4 34.8 1.0
CZ N:ARG19 4.5 37.5 1.0
CA N:GLY170 4.5 35.8 1.0
N N:GLY170 4.6 34.4 1.0
N N:SER169 4.6 33.8 1.0
N N:LYS164 4.7 39.1 1.0
CA N:SER169 4.7 32.8 1.0
N N:ASP166 4.7 33.6 1.0
O N:LYS164 4.8 40.2 1.0
CA N:ASP166 4.8 33.8 1.0
CG a:LEU34 4.8 43.7 1.0
CB N:ILE163 4.8 35.8 1.0
C N:LYS164 4.8 39.5 1.0
NH2 N:ARG19 4.8 37.9 1.0
CA N:LYS164 4.9 40.0 1.0

Magnesium binding site 7 out of 8 in 5l5f

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Magnesium binding site 7 out of 8 in the Yeast 20S Proteasome with Human BETA5I (1-138) and Human 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 Human BETA5I (1-138) and Human BETA6 (97- 111; 118-133) in Complex with Bortezomib within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg301

b:51.5
occ:1.00
 O Z:HOH406 2.4 36.9 1.0
O Z:VAL198 2.5 51.2 1.0
O Z:HIS195 2.6 41.5 1.0
O Z:THR192 2.6 43.1 1.0
C Z:HIS195 3.6 45.2 1.0
C Z:THR192 3.6 52.6 1.0
C Z:VAL198 3.7 49.8 1.0
CA Z:ILE196 3.7 47.5 1.0
O Z:ILE196 3.8 48.8 1.0
NH2 Z:ARG28 3.8 54.4 1.0
CG2 Z:THR192 3.8 56.4 1.0
C Z:ILE196 3.9 47.3 1.0
CA Z:THR192 3.9 54.8 1.0
N Z:ILE196 4.1 44.7 1.0
O Z:ASP222 4.1 63.5 1.0
N Z:VAL198 4.2 47.6 1.0
NH2 H:ARG19 4.3 52.2 1.0
CA Z:VAL198 4.5 49.1 1.0
CB Z:THR192 4.5 55.4 1.0
OD1 Z:ASP222 4.6 56.5 1.0
N Z:GLY199 4.6 50.6 1.0
N Z:GLN197 4.7 46.4 1.0
CA Z:HIS195 4.8 47.7 1.0
N Z:HIS195 4.8 48.3 1.0
CA Z:GLY199 4.8 52.3 1.0
CZ Z:ARG28 4.8 54.1 1.0
CB Z:VAL198 4.8 49.2 1.0
N Z:GLU193 4.9 55.1 1.0
O Z:ALA191 5.0 51.8 1.0

Magnesium binding site 8 out of 8 in 5l5f

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Magnesium binding site 8 out of 8 in the Yeast 20S Proteasome with Human BETA5I (1-138) and Human 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 8 of Yeast 20S Proteasome with Human BETA5I (1-138) and Human BETA6 (97- 111; 118-133) in Complex with Bortezomib within 5.0Å range:
probe atom residue distance (Å) B Occ
b:Mg203

b:30.9
occ:1.00
 O b:SER169 2.5 35.4 1.0
O b:ILE163 2.6 36.8 1.0
O b:ASP166 2.6 35.4 1.0
O b:HOH309 3.1 39.4 1.0
CD1 M:LEU34 3.6 42.5 1.0
NH1 b:ARG19 3.7 41.5 1.0
C b:ASP166 3.7 33.8 1.0
C b:SER169 3.7 34.9 1.0
C b:ILE163 3.7 37.0 1.0
CA b:GLY167 4.1 34.9 1.0
CG2 b:ILE163 4.1 37.4 1.0
N b:GLY167 4.3 33.3 1.0
O b:GLY167 4.3 36.7 1.0
CZ b:ARG19 4.3 40.6 1.0
CA b:ILE163 4.4 36.1 1.0
C b:GLY167 4.4 35.9 1.0
CA b:GLY170 4.5 37.6 1.0
N b:GLY170 4.5 36.4 1.0
N b:SER169 4.6 34.6 1.0
CA b:SER169 4.6 33.8 1.0
NH2 b:ARG19 4.7 41.4 1.0
N b:ASP166 4.8 33.4 1.0
N b:LYS164 4.8 38.4 1.0
CG M:LEU34 4.8 42.4 1.0
CA b:ASP166 4.8 33.2 1.0
CB b:ILE163 4.8 36.6 1.0
O b:LYS164 4.8 40.1 1.0
C b:LYS164 4.9 39.5 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 19:23:19 2024

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