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Magnesium in PDB 5l5d: Yeast 20S Proteasome with Human BETA5I (1-138) and Human BETA6 (97- 111; 118-133) in Complex with Onx 0914

Enzymatic activity of Yeast 20S Proteasome with Human BETA5I (1-138) and Human BETA6 (97- 111; 118-133) in Complex with Onx 0914

All present enzymatic activity of Yeast 20S Proteasome with Human BETA5I (1-138) and Human BETA6 (97- 111; 118-133) in Complex with Onx 0914:
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 Onx 0914, PDB code: 5l5d 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 (°) 134.740, 300.720, 145.720, 90.00, 112.78, 90.00
R / Rfree (%) 19.2 / 22.1

Other elements in 5l5d:

The structure of Yeast 20S Proteasome with Human BETA5I (1-138) and Human BETA6 (97- 111; 118-133) in Complex with Onx 0914 also contains other interesting chemical elements:

Chlorine (Cl) 2 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 Onx 0914 (pdb code 5l5d). 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 Onx 0914, PDB code: 5l5d:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 5l5d

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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 Onx 0914


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 Onx 0914 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:54.0
occ:1.00
 O G:MET125 2.2 52.3 1.0
OG1 G:THR8 2.5 43.2 1.0
O G:ARG122 2.6 45.4 1.0
O G:TYR119 2.8 48.0 1.0
CG2 G:THR8 3.2 47.6 1.0
O G:ALA123 3.2 55.4 1.0
C G:MET125 3.4 49.9 1.0
CB G:THR8 3.4 46.2 1.0
C G:ALA123 3.6 51.3 1.0
C G:ARG122 3.7 47.1 1.0
CA G:ALA123 3.7 48.6 1.0
C G:TYR119 4.0 43.5 1.0
N G:THR8 4.1 47.9 1.0
N G:ALA123 4.2 47.4 1.0
N G:MET125 4.2 50.9 1.0
N G:ARG126 4.2 45.7 1.0
CA G:ARG126 4.2 44.9 1.0
CA G:MET125 4.3 52.6 1.0
CA G:THR8 4.3 46.7 1.0
CD G:PRO127 4.6 41.8 1.0
N G:TYR124 4.6 51.8 1.0
CA G:TYR119 4.7 41.2 1.0
C G:ARG126 4.9 44.2 1.0
CB G:MET125 4.9 58.9 1.0
N G:THR120 5.0 42.3 1.0
C G:TYR124 5.0 49.9 1.0
CA G:ARG122 5.0 50.0 1.0

Magnesium binding site 2 out of 8 in 5l5d

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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 Onx 0914


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 Onx 0914 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:56.4
occ:1.00
 O I:ASP177 2.6 49.9 1.0
O I:SER180 2.6 51.1 1.0
O I:ALA174 3.2 51.3 1.0
OXT I:ASP204 3.3 64.6 1.0
C I:ASP177 3.7 49.5 1.0
C I:SER180 3.9 53.3 1.0
O I:ALA178 4.1 53.7 1.0
CD1 Y:ILE26 4.2 56.0 1.0
CA I:ALA178 4.2 49.5 1.0
C I:ASP204 4.2 64.5 1.0
C I:ALA178 4.3 50.4 1.0
O I:ASP204 4.3 64.8 1.0
C I:ALA174 4.3 54.5 1.0
NH1 Y:ARG19 4.3 74.2 1.0
N I:ALA178 4.4 49.6 1.0
N I:SER180 4.5 47.9 1.0
NH2 Y:ARG19 4.6 67.6 1.0
CA I:ASP175 4.7 55.2 1.0
CA I:GLY181 4.7 54.1 1.0
N I:GLY181 4.8 52.9 1.0
N I:ASP177 4.8 48.9 1.0
CA I:SER180 4.8 50.4 1.0
CZ Y:ARG19 4.8 69.3 1.0
CA I:ASP177 4.8 49.6 1.0
N I:ASP175 4.9 53.8 1.0

Magnesium binding site 3 out of 8 in 5l5d

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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 Onx 0914


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 Onx 0914 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg302

b:55.0
occ:1.00
 O I:ASP204 2.2 64.8 1.0
O Y:ASP167 2.2 54.7 1.0
O Y:ALA164 2.3 49.6 1.0
O Y:SER170 2.3 62.0 1.0
C I:ASP204 3.1 64.5 1.0
C Y:ASP167 3.4 53.5 1.0
NH1 Y:ARG19 3.4 74.2 1.0
C Y:ALA164 3.4 50.1 1.0
C Y:SER170 3.5 55.9 1.0
CA I:ASP204 3.6 64.0 1.0
CB I:ASP204 3.7 65.2 1.0
O Y:ALA168 3.7 57.0 1.0
CA Y:ALA168 3.8 56.9 1.0
C Y:ALA168 3.8 57.3 1.0
N Y:ALA168 4.0 55.4 1.0
N Y:SER170 4.1 51.5 1.0
CA Y:ALA164 4.1 50.5 1.0
O Y:HIS165 4.1 47.5 1.0
OXT I:ASP204 4.2 64.6 1.0
CZ Y:ARG19 4.2 69.3 1.0
CA Y:SER170 4.4 52.5 1.0
N Y:GLY171 4.5 56.1 1.0
C Y:HIS165 4.5 47.7 1.0
N Y:HIS165 4.5 52.5 1.0
CA Y:ASP167 4.5 51.7 1.0
NH2 Y:ARG19 4.6 67.6 1.0
CA Y:GLY171 4.6 57.6 1.0
N Y:TYR169 4.6 55.9 1.0
N Y:ASP167 4.6 50.5 1.0
CG I:ASP204 4.7 66.1 1.0
O Y:ALA163 4.7 49.4 1.0
CA Y:HIS165 4.8 49.6 1.0
CB Y:SER170 4.9 49.3 1.0
CB Y:ALA164 4.9 50.6 1.0

Magnesium binding site 4 out of 8 in 5l5d

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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 Onx 0914


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 Onx 0914 within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mg201

b:46.3
occ:1.00
 OE1 J:GLN118 3.1 47.0 1.0
O J:THR124 3.5 45.0 1.0
CB J:ASP120 3.7 41.7 1.0
OD2 J:ASP120 3.7 52.2 1.0
CG J:ASP120 3.8 45.5 1.0
N J:ASP120 3.9 39.8 1.0
CD J:GLN118 4.0 43.8 1.0
CE1 J:HIS133 4.2 41.3 1.0
CG J:GLN118 4.2 42.0 1.0
CB J:THR124 4.2 44.0 1.0
CG2 J:THR124 4.4 43.3 1.0
O J:GLN118 4.4 39.3 1.0
CA J:ASP120 4.4 39.8 1.0
C J:THR124 4.5 42.0 1.0
OD1 J:ASP120 4.6 50.2 1.0
C J:ILE119 4.6 38.8 1.0
C J:GLN118 4.8 38.8 1.0
CG1 I:VAL35 4.8 53.8 1.0
CA J:ILE119 4.8 37.7 1.0
ND1 J:HIS133 4.8 40.3 1.0
N J:ILE119 5.0 38.2 1.0

Magnesium binding site 5 out of 8 in 5l5d

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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 Onx 0914


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 Onx 0914 within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg302

b:52.7
occ:1.00
 O K:ASP167 2.0 56.1 1.0
O W:ASP204 2.3 63.6 1.0
O K:ALA164 2.3 48.7 1.0
O K:SER170 2.4 52.0 1.0
C K:ASP167 3.2 53.2 1.0
C W:ASP204 3.2 61.2 1.0
NH1 K:ARG19 3.5 71.5 1.0
C K:ALA164 3.5 48.1 1.0
C K:SER170 3.6 51.3 1.0
O K:ALA168 3.6 50.9 1.0
CA K:ALA168 3.6 57.4 1.0
CA W:ASP204 3.7 60.6 1.0
C K:ALA168 3.7 57.1 1.0
CB W:ASP204 3.8 59.9 1.0
N K:ALA168 3.8 54.2 1.0
N K:SER170 4.0 52.2 1.0
O K:HIS165 4.1 47.8 1.0
CA K:ALA164 4.2 49.6 1.0
OXT W:ASP204 4.2 65.5 1.0
CZ K:ARG19 4.3 68.3 1.0
CA K:SER170 4.4 50.4 1.0
CA K:ASP167 4.4 51.4 1.0
C K:HIS165 4.5 48.8 1.0
N K:ASP167 4.5 50.5 1.0
N K:TYR169 4.5 58.1 1.0
N K:HIS165 4.5 49.7 1.0
N K:GLY171 4.6 51.1 1.0
O K:ALA163 4.7 50.0 1.0
CA K:GLY171 4.8 55.5 1.0
NH2 K:ARG19 4.8 69.8 1.0
CA K:HIS165 4.8 51.2 1.0
C K:ARG166 4.9 51.9 1.0
CB K:SER170 4.9 48.1 1.0
CG W:ASP204 4.9 58.2 1.0
CB K:ASP167 5.0 51.0 1.0

Magnesium binding site 6 out of 8 in 5l5d

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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 Onx 0914


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 Onx 0914 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg301

b:69.0
occ:1.00
 OXT L:ASP222 2.1 74.0 1.0
O V:ASP166 2.3 44.5 1.0
O V:ILE163 2.3 53.1 1.0
C L:ASP222 2.9 74.3 1.0
C V:ASP166 3.1 45.4 1.0
O V:SER169 3.1 51.4 1.0
C V:ILE163 3.4 50.8 1.0
O V:TRP164 3.6 54.9 1.0
CA L:ASP222 3.6 72.4 1.0
O L:ASP222 3.6 79.5 1.0
N V:LEU167 3.7 45.9 1.0
C V:TRP164 3.7 50.5 1.0
N V:ASP166 3.7 43.2 1.0
CA V:LEU167 3.8 46.2 1.0
CA V:ASP166 4.0 43.9 1.0
O V:GLY162 4.1 51.3 1.0
CA V:TRP164 4.2 51.5 1.0
N V:TRP164 4.2 52.5 1.0
N V:ASN165 4.2 47.6 1.0
C V:SER169 4.3 48.9 1.0
C V:ASN165 4.4 43.3 1.0
CB L:ASP222 4.4 69.8 1.0
NH1 V:ARG19 4.4 59.1 1.0
CA V:ILE163 4.4 49.3 1.0
O L:ARG221 4.5 73.7 1.0
CD2 V:LEU167 4.5 44.1 1.0
C V:LEU167 4.5 47.2 1.0
CA V:ASN165 4.8 45.4 1.0
N L:ASP222 4.8 65.5 1.0
O V:LEU167 4.8 50.8 1.0
N V:SER169 4.9 44.7 1.0
CB V:LEU167 5.0 44.4 1.0
CD1 L:ILE35 5.0 58.4 1.0
CB V:ASP166 5.0 43.9 1.0

Magnesium binding site 7 out of 8 in 5l5d

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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 Onx 0914


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 Onx 0914 within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg202

b:52.5
occ:1.00
 O N:SER169 2.5 44.2 1.0
O N:ILE163 2.7 44.0 1.0
O N:ASP166 2.8 44.3 1.0
NH1 N:ARG19 3.5 46.2 1.0
C N:SER169 3.7 41.7 1.0
CD1 a:LEU34 3.7 57.4 1.0
C N:ILE163 3.8 44.0 1.0
C N:ASP166 3.9 43.6 1.0
CG2 N:ILE163 4.0 44.4 1.0
CA N:GLY167 4.1 45.7 1.0
CZ N:ARG19 4.1 44.7 1.0
O N:GLY167 4.3 45.6 1.0
CA N:GLY170 4.3 44.5 1.0
NH2 N:ARG19 4.4 44.6 1.0
CA N:ILE163 4.4 44.4 1.0
N N:GLY167 4.4 44.4 1.0
C N:GLY167 4.4 45.8 1.0
N N:GLY170 4.5 41.6 1.0
N N:SER169 4.7 42.2 1.0
CA N:SER169 4.8 40.8 1.0
CB N:ILE163 4.8 43.9 1.0
N N:LYS164 4.9 46.6 1.0
CG a:LEU34 4.9 56.6 1.0
NE N:ARG19 5.0 46.0 1.0

Magnesium binding site 8 out of 8 in 5l5d

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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 Onx 0914


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 Onx 0914 within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg301

b:72.6
occ:1.00
 O Z:VAL198 2.6 54.3 1.0
O Z:THR192 2.8 61.2 1.0
O Z:HIS195 3.0 54.9 1.0
O Z:ASP222 3.6 76.7 1.0
NH2 Z:ARG28 3.7 63.6 1.0
CG2 Z:THR192 3.8 68.7 1.0
C Z:VAL198 3.8 61.1 1.0
O Z:ILE196 3.9 65.9 1.0
C Z:THR192 3.9 64.3 1.0
CA Z:ILE196 3.9 58.0 1.0
C Z:HIS195 4.0 57.6 1.0
C Z:ILE196 4.0 58.7 1.0
NH2 H:ARG19 4.1 70.5 1.0
OD1 Z:ASP222 4.2 76.4 1.0
CA Z:THR192 4.3 65.3 1.0
N Z:ILE196 4.4 56.2 1.0
N Z:VAL198 4.5 57.2 1.0
C Z:ASP222 4.5 75.2 1.0
CB Z:THR192 4.7 66.1 1.0
CZ Z:ARG28 4.7 63.1 1.0
CA Z:VAL198 4.7 58.6 1.0
N Z:GLY199 4.8 62.2 1.0
CA Z:GLY199 4.8 61.9 1.0
NH1 H:ARG19 4.8 60.7 1.0
CZ H:ARG19 4.8 61.8 1.0
OXT Z:ASP222 4.9 65.7 1.0
N Z:GLN197 4.9 56.9 1.0
NH1 Z:ARG28 4.9 64.4 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 19:21:09 2024

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