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Magnesium in PDB 5l5x: Yeast 20S Proteasome with Human BETA5C (1-138) and Human BETA6 (97- 111; 118-133) in Complex with Onx 0914

Enzymatic activity of Yeast 20S Proteasome with Human BETA5C (1-138) and Human BETA6 (97- 111; 118-133) in Complex with Onx 0914

All present enzymatic activity of Yeast 20S Proteasome with Human BETA5C (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 BETA5C (1-138) and Human BETA6 (97- 111; 118-133) in Complex with Onx 0914, PDB code: 5l5x 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 / 2.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 136.020, 300.510, 145.450, 90.00, 112.97, 90.00
R / Rfree (%) 17.9 / 21.5

Other elements in 5l5x:

The structure of Yeast 20S Proteasome with Human BETA5C (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 BETA5C (1-138) and Human BETA6 (97- 111; 118-133) in Complex with Onx 0914 (pdb code 5l5x). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 9 binding sites of Magnesium where determined in the Yeast 20S Proteasome with Human BETA5C (1-138) and Human BETA6 (97- 111; 118-133) in Complex with Onx 0914, PDB code: 5l5x:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Magnesium binding site 1 out of 9 in 5l5x

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Magnesium binding site 1 out of 9 in the Yeast 20S Proteasome with Human BETA5C (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 BETA5C (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
A:Mg301

b:69.1
occ:1.00
 O A:PRO152 2.5 62.0 1.0
O A:MET118 2.6 55.5 1.0
N A:PHE130 3.1 51.8 1.0
C A:MET118 3.4 52.3 1.0
C A:PRO152 3.5 56.3 1.0
CB A:MET118 3.6 52.1 1.0
CA A:MET118 3.6 50.9 1.0
CA A:PRO129 3.7 51.1 1.0
CB A:PRO129 3.7 51.1 1.0
CD2 A:PHE130 3.7 55.5 1.0
CB A:PHE130 3.8 53.0 1.0
CA A:PRO152 3.8 54.4 1.0
C A:PRO129 3.9 51.6 1.0
CA A:PHE130 4.0 52.0 1.0
O A:PHE130 4.1 55.2 1.0
OG1 A:THR122 4.1 65.3 1.0
CB A:ALA121 4.1 56.0 1.0
CG A:PHE130 4.3 53.0 1.0
CG A:MET118 4.3 53.2 1.0
CB A:PRO152 4.5 53.4 1.0
CE A:MET118 4.5 56.0 1.0
C A:PHE130 4.5 51.7 1.0
N A:GLN119 4.6 51.6 1.0
N A:SER153 4.7 57.7 1.0
CB A:THR122 4.8 57.0 1.0
N A:THR122 4.8 57.9 1.0
C A:ALA121 4.8 58.2 1.0
CE2 A:PHE130 4.8 54.7 1.0
CA A:ALA121 5.0 56.0 1.0
CG A:PRO129 5.0 52.2 1.0

Magnesium binding site 2 out of 9 in 5l5x

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Magnesium binding site 2 out of 9 in the Yeast 20S Proteasome with Human BETA5C (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 BETA5C (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:78.9
occ:1.00
 O G:MET125 2.4 63.3 1.0
OG1 G:THR8 2.5 57.5 1.0
O G:ARG122 2.6 57.0 1.0
O G:TYR119 3.0 56.1 1.0
O G:ALA123 3.1 72.7 1.0
CG2 G:THR8 3.2 60.1 1.0
CB G:THR8 3.4 58.8 1.0
C G:ALA123 3.5 67.0 1.0
C G:MET125 3.5 63.9 1.0
CA G:ALA123 3.6 64.6 1.0
C G:ARG122 3.6 61.6 1.0
N G:THR8 3.9 61.3 1.0
N G:ALA123 4.1 62.6 1.0
C G:TYR119 4.2 55.9 1.0
N G:MET125 4.2 66.9 1.0
CA G:THR8 4.3 61.2 1.0
N G:ARG126 4.4 61.4 1.0
CA G:ARG126 4.4 60.4 1.0
CA G:MET125 4.5 68.8 1.0
N G:TYR124 4.5 66.2 1.0
CD G:PRO127 4.7 56.6 1.0
CB G:ALA123 4.9 65.2 1.0
CA G:ARG122 4.9 65.5 1.0
C G:TYR124 5.0 67.4 1.0
CA G:TYR119 5.0 54.2 1.0

Magnesium binding site 3 out of 9 in 5l5x

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Magnesium binding site 3 out of 9 in the Yeast 20S Proteasome with Human BETA5C (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 BETA5C (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:59.9
occ:1.00
 O I:ASP177 2.5 59.6 1.0
O I:SER180 2.6 63.2 1.0
O I:ALA174 3.0 69.4 1.0
C I:ASP177 3.6 59.0 1.0
OXT I:ASP204 3.6 68.5 1.0
C I:SER180 3.9 60.5 1.0
O I:ALA178 4.1 64.6 1.0
C I:ALA174 4.1 65.6 1.0
CA I:ALA178 4.2 57.6 1.0
C I:ALA178 4.2 58.9 1.0
N I:ALA178 4.3 56.8 1.0
CD1 Y:ILE26 4.4 70.4 1.0
CA I:ASP175 4.5 66.2 1.0
N I:SER180 4.5 60.8 1.0
C I:ASP204 4.6 68.3 1.0
N I:ASP177 4.6 60.5 1.0
NH1 Y:ARG19 4.6 77.3 1.0
O I:ASP204 4.6 68.4 1.0
CA I:ASP177 4.7 59.4 1.0
N I:ASP175 4.7 66.0 1.0
CA I:SER180 4.8 60.1 1.0
N I:GLY181 4.8 58.0 1.0
CA I:GLY181 4.8 60.4 1.0
C I:ASP175 4.8 65.4 1.0
NH2 Y:ARG19 4.8 77.3 1.0
N I:LEU179 5.0 58.1 1.0

Magnesium binding site 4 out of 9 in 5l5x

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Magnesium binding site 4 out of 9 in the Yeast 20S Proteasome with Human BETA5C (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 BETA5C (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:60.1
occ:1.00
 O I:ASP204 2.2 68.4 1.0
O Y:ASP167 2.2 70.1 1.0
O Y:ALA164 2.3 59.4 1.0
O Y:SER170 2.6 63.6 1.0
C I:ASP204 3.1 68.3 1.0
C Y:ASP167 3.3 64.5 1.0
C Y:ALA164 3.4 57.8 1.0
CA I:ASP204 3.6 71.3 1.0
NH1 Y:ARG19 3.8 77.3 1.0
CA Y:ALA168 3.8 65.1 1.0
C Y:SER170 3.8 62.9 1.0
N Y:ALA168 3.9 64.1 1.0
CB I:ASP204 3.9 71.8 1.0
O Y:HIS165 4.0 55.8 1.0
C Y:ALA168 4.0 65.7 1.0
O Y:ALA168 4.0 70.2 1.0
OXT I:ASP204 4.0 68.5 1.0
CA Y:ALA164 4.2 59.2 1.0
C Y:HIS165 4.3 58.7 1.0
N Y:SER170 4.3 61.8 1.0
N Y:ASP167 4.4 63.4 1.0
CA Y:ASP167 4.4 63.1 1.0
CZ Y:ARG19 4.4 76.7 1.0
N Y:HIS165 4.4 57.3 1.0
NH2 Y:ARG19 4.6 77.3 1.0
CA Y:HIS165 4.6 58.9 1.0
CA Y:SER170 4.6 60.7 1.0
C Y:ARG166 4.7 60.3 1.0
O Y:ALA163 4.7 56.5 1.0
N Y:GLY171 4.8 63.3 1.0
N Y:TYR169 4.8 66.4 1.0
CG I:ASP204 4.8 73.7 1.0
CA Y:GLY171 4.8 64.4 1.0
N Y:ARG166 4.9 58.7 1.0
O Y:ARG166 4.9 58.7 1.0

Magnesium binding site 5 out of 9 in 5l5x

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Magnesium binding site 5 out of 9 in the Yeast 20S Proteasome with Human BETA5C (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 BETA5C (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:56.0
occ:1.00
 OE1 J:GLN118 3.1 51.9 1.0
O J:THR124 3.4 51.6 1.0
CB J:ASP120 3.9 52.6 1.0
N J:ASP120 3.9 48.9 1.0
CD J:GLN118 3.9 49.7 1.0
CG J:GLN118 4.0 49.7 1.0
CG J:ASP120 4.1 55.6 1.0
OD2 J:ASP120 4.1 63.0 1.0
O J:GLN118 4.1 50.7 1.0
CE1 J:HIS133 4.2 55.4 1.0
CB J:THR124 4.3 55.8 1.0
CG2 J:THR124 4.4 56.6 1.0
C J:THR124 4.5 53.1 1.0
C J:GLN118 4.5 49.7 1.0
CA J:ASP120 4.5 50.6 1.0
C J:ILE119 4.5 49.1 1.0
CA J:ILE119 4.6 48.0 1.0
CB J:GLN118 4.7 50.0 1.0
CG1 I:VAL35 4.7 60.7 1.0
N J:ILE119 4.7 49.0 1.0
OD1 J:ASP120 4.7 58.1 1.0
NE2 J:HIS133 5.0 55.1 1.0
ND1 J:HIS133 5.0 54.4 1.0

Magnesium binding site 6 out of 9 in 5l5x

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Magnesium binding site 6 out of 9 in the Yeast 20S Proteasome with Human BETA5C (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 BETA5C (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:57.5
occ:1.00
 O K:ASP167 2.1 57.9 1.0
O K:ALA164 2.3 58.1 1.0
O W:ASP204 2.3 70.1 1.0
O K:SER170 3.0 53.0 1.0
C K:ASP167 3.1 60.6 1.0
C W:ASP204 3.1 68.8 1.0
C K:ALA164 3.5 56.9 1.0
O K:HIS165 3.6 57.9 1.0
CA W:ASP204 3.6 69.2 1.0
CA K:ALA168 3.7 65.1 1.0
N K:ALA168 3.7 61.9 1.0
C K:HIS165 4.0 58.9 1.0
OXT W:ASP204 4.0 69.7 1.0
C K:ALA168 4.0 66.5 1.0
NH1 K:ARG19 4.1 69.4 1.0
CB W:ASP204 4.1 67.8 1.0
O K:ALA168 4.1 65.1 1.0
N K:ASP167 4.1 61.3 1.0
C K:SER170 4.2 58.5 1.0
CA K:ASP167 4.2 60.6 1.0
N K:HIS165 4.4 57.5 1.0
C K:ARG166 4.4 61.6 1.0
CA K:ALA164 4.4 56.5 1.0
CA K:HIS165 4.4 59.0 1.0
O K:ARG166 4.6 63.4 1.0
N K:SER170 4.6 58.8 1.0
N K:ARG166 4.6 59.5 1.0
O K:ALA163 4.6 56.8 1.0
CZ K:ARG19 4.8 72.3 1.0
N K:TYR169 4.8 67.3 1.0
CA K:SER170 4.9 58.2 1.0
NH2 K:ARG19 4.9 74.5 1.0
N W:ASP204 4.9 69.2 1.0
CB K:ALA168 5.0 65.3 1.0

Magnesium binding site 7 out of 9 in 5l5x

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Magnesium binding site 7 out of 9 in the Yeast 20S Proteasome with Human BETA5C (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 BETA5C (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:77.3
occ:1.00
 OXT L:ASP222 1.9 86.3 1.0
O V:ASP166 2.1 55.6 1.0
O V:ILE163 2.2 60.6 1.0
O V:SER169 2.3 57.9 1.0
C L:ASP222 3.0 80.7 1.0
C V:ASP166 3.1 56.3 1.0
C V:ILE163 3.3 58.7 1.0
C V:SER169 3.5 57.3 1.0
CA L:ASP222 3.7 82.3 1.0
CA V:LEU167 3.8 56.2 1.0
NH1 V:ARG19 3.8 72.8 1.0
N V:LEU167 3.8 56.1 1.0
O V:GLY162 3.9 59.4 1.0
O L:ASP222 4.0 77.4 1.0
N V:ASP166 4.1 54.3 1.0
CA V:ILE163 4.1 58.6 1.0
N V:SER169 4.2 55.1 1.0
CA V:ASP166 4.2 54.9 1.0
C V:LEU167 4.2 56.5 1.0
CB L:ASP222 4.2 81.0 1.0
O V:TRP164 4.3 64.8 1.0
C V:TRP164 4.3 61.8 1.0
N V:TRP164 4.3 60.0 1.0
CA V:SER169 4.3 54.7 1.0
N V:GLY170 4.4 55.5 1.0
O V:LEU167 4.4 61.5 1.0
CA V:GLY170 4.5 58.0 1.0
CZ V:ARG19 4.5 66.4 1.0
CA V:TRP164 4.5 60.9 1.0
CB V:SER169 4.7 56.1 1.0
N V:ASN165 4.7 59.5 1.0
NH2 V:ARG19 4.8 69.3 1.0
C V:GLY162 4.8 58.4 1.0
N V:GLY168 4.9 54.4 1.0
C V:ASN165 4.9 54.2 1.0
CD2 V:LEU167 4.9 56.3 1.0
O L:ARG221 5.0 79.7 1.0
CB V:ASP166 5.0 55.2 1.0
N V:ILE163 5.0 58.0 1.0
N L:ASP222 5.0 77.7 1.0

Magnesium binding site 8 out of 9 in 5l5x

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Magnesium binding site 8 out of 9 in the Yeast 20S Proteasome with Human BETA5C (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 BETA5C (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:60.6
occ:1.00
 O N:SER169 2.6 62.0 1.0
O N:ILE163 2.7 57.8 1.0
O N:ASP166 2.9 57.0 1.0
CD1 a:LEU34 3.6 66.8 1.0
NH1 N:ARG19 3.6 61.7 1.0
C N:SER169 3.8 57.9 1.0
C N:ILE163 3.8 57.4 1.0
CG2 N:ILE163 3.9 56.9 1.0
C N:ASP166 4.0 54.2 1.0
CA N:GLY167 4.2 56.0 1.0
CZ N:ARG19 4.2 61.0 1.0
CA N:GLY170 4.3 59.6 1.0
NH2 N:ARG19 4.4 60.5 1.0
CA N:ILE163 4.4 58.0 1.0
O N:GLY167 4.4 53.4 1.0
N N:GLY170 4.5 58.8 1.0
N N:GLY167 4.5 53.7 1.0
C N:GLY167 4.5 55.6 1.0
CB N:ILE163 4.8 57.0 1.0
N N:SER169 4.8 55.2 1.0
N N:LYS164 4.8 58.0 1.0
CA N:SER169 4.8 55.4 1.0
CG a:LEU34 4.9 65.8 1.0
O N:LYS164 5.0 62.9 1.0

Magnesium binding site 9 out of 9 in 5l5x

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Magnesium binding site 9 out of 9 in the Yeast 20S Proteasome with Human BETA5C (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 9 of Yeast 20S Proteasome with Human BETA5C (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:95.5
occ:1.00
 O Z:VAL198 2.5 67.9 1.0
O Z:THR192 2.8 63.2 1.0
O Z:HIS195 2.9 67.3 1.0
O Z:ASP222 3.5 83.5 1.0
NH2 Z:ARG28 3.6 78.1 1.0
CG2 Z:THR192 3.6 73.0 1.0
C Z:VAL198 3.7 67.5 1.0
C Z:THR192 3.8 69.2 1.0
O Z:ILE196 3.9 69.5 1.0
C Z:HIS195 4.0 64.3 1.0
CA Z:ILE196 4.0 65.8 1.0
CA Z:THR192 4.1 71.6 1.0
C Z:ILE196 4.1 66.8 1.0
OD1 Z:ASP222 4.2 77.5 1.0
NH2 H:ARG19 4.3 79.0 1.0
N Z:VAL198 4.4 61.1 1.0
N Z:ILE196 4.5 61.3 1.0
CB Z:THR192 4.5 69.9 1.0
C Z:ASP222 4.6 82.6 1.0
N Z:GLY199 4.6 69.2 1.0
CA Z:GLY199 4.6 71.2 1.0
CA Z:VAL198 4.6 65.9 1.0
CZ Z:ARG28 4.7 75.3 1.0
O Z:LYS220 4.9 69.8 1.0
N Z:GLU193 5.0 69.0 1.0
NH1 Z:ARG28 5.0 77.3 1.0
N Z:GLN197 5.0 65.3 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 19:32:16 2024

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