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Magnesium in PDB 5l6b: Yeast 20S Proteasome with Mouse BETA5I (1-138) and Mouse BETA6 (97- 111; 118-133) in Complex with Onx 0914

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

All present enzymatic activity of Yeast 20S Proteasome with Mouse BETA5I (1-138) and Mouse BETA6 (97- 111; 118-133) in Complex with Onx 0914:
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 Onx 0914, PDB code: 5l6b 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 / 2.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 135.190, 300.840, 145.390, 90.00, 112.94, 90.00
R / Rfree (%) 19.6 / 22.1

Other elements in 5l6b:

The structure of Yeast 20S Proteasome with Mouse BETA5I (1-138) and Mouse 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 Mouse BETA5I (1-138) and Mouse BETA6 (97- 111; 118-133) in Complex with Onx 0914 (pdb code 5l6b). 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 Mouse BETA5I (1-138) and Mouse BETA6 (97- 111; 118-133) in Complex with Onx 0914, PDB code: 5l6b:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 5l6b

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Magnesium binding site 1 out of 8 in the Yeast 20S Proteasome with Mouse BETA5I (1-138) and Mouse 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 Mouse BETA5I (1-138) and Mouse BETA6 (97- 111; 118-133) in Complex with Onx 0914 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:63.0
occ:1.00
O G:MET125 2.3 47.6 1.0
OG1 G:THR8 2.5 44.5 1.0
O G:ARG122 2.5 45.4 1.0
O G:TYR119 2.9 41.6 1.0
O G:ALA123 3.1 49.7 1.0
CG2 G:THR8 3.2 45.5 1.0
CB G:THR8 3.4 44.8 1.0
C G:MET125 3.5 48.7 1.0
C G:ALA123 3.5 48.8 1.0
CA G:ALA123 3.6 47.3 1.0
C G:ARG122 3.6 46.0 1.0
N G:THR8 4.0 45.8 1.0
N G:ALA123 4.0 45.6 1.0
C G:TYR119 4.1 40.3 1.0
N G:MET125 4.2 49.0 1.0
N G:ARG126 4.3 46.1 1.0
CA G:THR8 4.3 45.5 1.0
CA G:ARG126 4.3 44.4 1.0
CA G:MET125 4.4 51.6 1.0
N G:TYR124 4.5 49.8 1.0
CD G:PRO127 4.7 40.4 1.0
CA G:TYR119 4.8 39.1 1.0
CB G:ALA123 4.9 46.5 1.0
CA G:ARG122 4.9 48.8 1.0
C G:TYR124 5.0 47.4 1.0
N G:ARG122 5.0 44.7 1.0

Magnesium binding site 2 out of 8 in 5l6b

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Magnesium binding site 2 out of 8 in the Yeast 20S Proteasome with Mouse BETA5I (1-138) and Mouse 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 Mouse BETA5I (1-138) and Mouse BETA6 (97- 111; 118-133) in Complex with Onx 0914 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:63.5
occ:1.00
O I:SER180 2.5 52.0 1.0
O I:ASP177 2.5 50.1 1.0
O I:ALA174 3.3 49.7 1.0
OXT I:ASP204 3.4 63.8 1.0
O I:HOH403 3.6 49.2 1.0
C I:ASP177 3.7 48.5 1.0
C I:SER180 3.8 51.8 1.0
O I:ALA178 3.8 50.0 1.0
C I:ALA178 4.0 49.2 1.0
CA I:ALA178 4.1 48.1 1.0
C I:ASP204 4.3 61.8 1.0
O I:ASP204 4.3 60.1 1.0
N I:ALA178 4.3 46.9 1.0
N I:SER180 4.4 47.9 1.0
C I:ALA174 4.4 53.0 1.0
CD1 Y:ILE26 4.5 59.3 1.0
N I:GLY181 4.7 51.4 1.0
CA I:SER180 4.7 50.2 1.0
CA I:GLY181 4.7 53.9 1.0
NH1 Y:ARG19 4.8 67.5 1.0
NH2 Y:ARG19 4.8 66.8 1.0
N I:LEU179 4.8 48.8 1.0
CA I:ASP177 4.8 49.5 1.0
CA I:ASP175 4.9 55.9 1.0
N I:ASP177 4.9 49.2 1.0

Magnesium binding site 3 out of 8 in 5l6b

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Magnesium binding site 3 out of 8 in the Yeast 20S Proteasome with Mouse BETA5I (1-138) and Mouse 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 Mouse BETA5I (1-138) and Mouse BETA6 (97- 111; 118-133) in Complex with Onx 0914 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg302

b:64.8
occ:1.00
O Y:ASP167 2.2 55.3 1.0
O I:ASP204 2.2 60.1 1.0
O Y:ALA164 2.3 51.6 1.0
O Y:SER170 2.7 58.9 1.0
C I:ASP204 3.2 61.8 1.0
C Y:ASP167 3.3 52.9 1.0
NH1 Y:ARG19 3.4 67.5 1.0
C Y:ALA164 3.5 49.7 1.0
CA Y:ALA168 3.6 56.3 1.0
CA I:ASP204 3.7 62.4 1.0
N Y:ALA168 3.8 54.4 1.0
C Y:ALA168 3.9 56.5 1.0
C Y:SER170 3.9 54.9 1.0
O Y:ALA168 3.9 59.0 1.0
O Y:HIS165 4.0 51.9 1.0
CB I:ASP204 4.0 62.1 1.0
OXT I:ASP204 4.1 63.8 1.0
CA Y:ALA164 4.2 50.5 1.0
C Y:HIS165 4.3 50.6 1.0
N Y:SER170 4.4 53.8 1.0
CA Y:ASP167 4.4 52.9 1.0
N Y:ASP167 4.5 53.7 1.0
N Y:HIS165 4.5 50.0 1.0
CZ Y:ARG19 4.5 66.7 1.0
CA Y:HIS165 4.7 50.3 1.0
O Y:ALA163 4.7 46.5 1.0
CA Y:SER170 4.7 53.3 1.0
N Y:TYR169 4.7 55.9 1.0
C Y:ARG166 4.7 52.1 1.0
N Y:GLY171 4.9 56.4 1.0
N Y:ARG166 4.9 51.1 1.0
CG I:ASP204 4.9 61.4 1.0
O Y:ARG166 4.9 55.3 1.0
NH2 Y:ARG19 5.0 66.8 1.0
CB Y:ALA168 5.0 56.8 1.0

Magnesium binding site 4 out of 8 in 5l6b

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Magnesium binding site 4 out of 8 in the Yeast 20S Proteasome with Mouse BETA5I (1-138) and Mouse 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 Mouse BETA5I (1-138) and Mouse BETA6 (97- 111; 118-133) in Complex with Onx 0914 within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mg201

b:58.2
occ:1.00
OE1 J:GLN118 3.1 41.6 1.0
O J:THR124 3.4 43.5 1.0
CB J:ASP120 3.7 40.5 1.0
N J:ASP120 3.8 37.4 1.0
OD2 J:ASP120 3.8 48.8 1.0
CG J:ASP120 3.9 43.0 1.0
CD J:GLN118 4.0 40.8 1.0
CG J:GLN118 4.0 39.9 1.0
CE1 J:HIS133 4.1 41.2 1.0
CB J:THR124 4.2 42.0 1.0
O J:GLN118 4.3 38.8 1.0
CA J:ASP120 4.3 38.6 1.0
CG2 J:THR124 4.4 41.7 1.0
C J:THR124 4.4 42.0 1.0
C J:ILE119 4.4 37.5 1.0
C J:GLN118 4.6 37.9 1.0
OD1 J:ASP120 4.6 44.2 1.0
CA J:ILE119 4.6 36.1 1.0
N J:ILE119 4.8 36.4 1.0
ND1 J:HIS133 4.8 41.8 1.0
CG1 I:VAL35 4.8 51.9 1.0
CB J:GLN118 4.9 38.3 1.0
CA J:THR124 5.0 41.3 1.0

Magnesium binding site 5 out of 8 in 5l6b

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Magnesium binding site 5 out of 8 in the Yeast 20S Proteasome with Mouse BETA5I (1-138) and Mouse 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 Mouse BETA5I (1-138) and Mouse BETA6 (97- 111; 118-133) in Complex with Onx 0914 within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg302

b:51.0
occ:1.00
O W:ASP204 2.2 60.4 1.0
O K:ASP167 2.2 54.3 1.0
O K:ALA164 2.3 49.0 1.0
O K:SER170 2.6 50.3 1.0
C W:ASP204 3.1 59.4 1.0
C K:ASP167 3.3 51.3 1.0
NH1 K:ARG19 3.3 64.8 1.0
C K:ALA164 3.4 49.2 1.0
CA W:ASP204 3.6 60.3 1.0
CA K:ALA168 3.7 53.9 1.0
C K:SER170 3.8 52.4 1.0
CB W:ASP204 3.9 60.4 1.0
N K:ALA168 3.9 51.0 1.0
C K:ALA168 3.9 53.4 1.0
O K:ALA168 3.9 52.7 1.0
O K:HIS165 4.1 50.4 1.0
OXT W:ASP204 4.1 58.6 1.0
CA K:ALA164 4.2 48.7 1.0
N K:SER170 4.3 51.9 1.0
C K:HIS165 4.4 49.4 1.0
CZ K:ARG19 4.4 63.3 1.0
N K:HIS165 4.5 48.6 1.0
CA K:ASP167 4.5 51.1 1.0
N K:ASP167 4.5 51.0 1.0
CA K:SER170 4.6 51.1 1.0
O K:ALA163 4.7 48.5 1.0
N K:TYR169 4.7 55.1 1.0
CA K:HIS165 4.7 49.4 1.0
N K:GLY171 4.8 54.6 1.0
C K:ARG166 4.8 50.3 1.0
CA K:GLY171 4.9 54.4 1.0
CG W:ASP204 4.9 60.4 1.0
NH2 K:ARG19 4.9 62.5 1.0
CB K:ALA164 5.0 48.5 1.0

Magnesium binding site 6 out of 8 in 5l6b

Go back to Magnesium Binding Sites List in 5l6b
Magnesium binding site 6 out of 8 in the Yeast 20S Proteasome with Mouse BETA5I (1-138) and Mouse 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 Mouse BETA5I (1-138) and Mouse BETA6 (97- 111; 118-133) in Complex with Onx 0914 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg301

b:64.0
occ:1.00
O V:ILE163 2.1 48.2 1.0
OXT L:ASP222 2.2 60.3 1.0
O V:ASP166 2.2 41.1 1.0
O V:SER169 2.6 47.5 1.0
C L:ASP222 3.0 67.7 1.0
C V:ASP166 3.1 43.0 1.0
C V:ILE163 3.2 48.1 1.0
CA L:ASP222 3.7 66.3 1.0
C V:SER169 3.8 46.3 1.0
N V:LEU167 3.8 43.5 1.0
CA V:LEU167 3.9 44.2 1.0
O V:GLY162 3.9 46.7 1.0
O L:ASP222 3.9 75.9 1.0
N V:ASP166 3.9 42.2 1.0
O V:TRP164 4.0 48.8 1.0
C V:TRP164 4.0 48.9 1.0
CA V:ASP166 4.1 42.6 1.0
CA V:ILE163 4.1 47.5 1.0
NH1 V:ARG19 4.1 55.8 1.0
N V:TRP164 4.1 48.9 1.0
CA V:TRP164 4.3 49.5 1.0
CB L:ASP222 4.3 65.1 1.0
C V:LEU167 4.4 45.6 1.0
N V:ASN165 4.4 47.7 1.0
N V:SER169 4.5 43.8 1.0
CA V:SER169 4.6 44.4 1.0
C V:ASN165 4.6 42.6 1.0
N V:GLY170 4.7 47.6 1.0
CA V:GLY170 4.7 48.6 1.0
O V:LEU167 4.7 45.6 1.0
O L:ARG221 4.7 64.9 1.0
CZ V:ARG19 4.8 53.2 1.0
C V:GLY162 4.8 47.4 1.0
CD2 V:LEU167 4.8 42.9 1.0
NH2 V:ARG19 4.9 57.7 1.0
N L:ASP222 4.9 61.9 1.0
CB V:SER169 4.9 45.3 1.0
CB V:ASP166 5.0 42.7 1.0
N V:ILE163 5.0 47.1 1.0

Magnesium binding site 7 out of 8 in 5l6b

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Magnesium binding site 7 out of 8 in the Yeast 20S Proteasome with Mouse BETA5I (1-138) and Mouse 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 Mouse BETA5I (1-138) and Mouse BETA6 (97- 111; 118-133) in Complex with Onx 0914 within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg202

b:52.1
occ:1.00
O N:SER169 2.5 45.4 1.0
O N:ILE163 2.6 42.3 1.0
O N:ASP166 2.8 44.5 1.0
NH1 N:ARG19 3.6 47.6 1.0
C N:SER169 3.7 42.0 1.0
C N:ILE163 3.7 43.7 1.0
CD1 a:LEU34 3.8 56.3 1.0
CG2 N:ILE163 3.8 43.3 1.0
C N:ASP166 3.9 43.3 1.0
CA N:GLY167 4.2 44.8 1.0
CZ N:ARG19 4.2 45.9 1.0
CA N:GLY170 4.2 44.6 1.0
CA N:ILE163 4.3 43.0 1.0
O N:GLY167 4.4 42.5 1.0
N N:GLY170 4.4 42.3 1.0
NH2 N:ARG19 4.4 44.8 1.0
N N:GLY167 4.5 43.0 1.0
C N:GLY167 4.5 43.4 1.0
CB N:ILE163 4.7 42.5 1.0
N N:SER169 4.7 42.6 1.0
CA N:SER169 4.7 40.6 1.0
N N:LYS164 4.8 45.2 1.0
NE N:ARG19 5.0 45.7 1.0

Magnesium binding site 8 out of 8 in 5l6b

Go back to Magnesium Binding Sites List in 5l6b
Magnesium binding site 8 out of 8 in the Yeast 20S Proteasome with Mouse BETA5I (1-138) and Mouse 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 Mouse BETA5I (1-138) and Mouse BETA6 (97- 111; 118-133) in Complex with Onx 0914 within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg301

b:71.7
occ:1.00
O Z:VAL198 2.6 59.5 1.0
O Z:THR192 2.6 56.1 1.0
O Z:HIS195 3.1 49.3 1.0
CG2 Z:THR192 3.5 63.6 1.0
C Z:THR192 3.6 61.5 1.0
O Z:ASP222 3.7 74.2 1.0
C Z:VAL198 3.8 58.4 1.0
NH2 Z:ARG28 3.8 60.9 1.0
CA Z:THR192 4.0 62.8 1.0
C Z:HIS195 4.1 52.3 1.0
OD1 Z:ASP222 4.1 62.7 1.0
O Z:ILE196 4.1 55.8 1.0
CA Z:ILE196 4.2 54.8 1.0
NH2 H:ARG19 4.3 66.2 1.0
C Z:ILE196 4.4 53.5 1.0
CB Z:THR192 4.4 62.5 1.0
N Z:VAL198 4.6 53.1 1.0
C Z:ASP222 4.6 72.0 1.0
N Z:ILE196 4.6 51.9 1.0
CA Z:GLY199 4.7 59.7 1.0
N Z:GLY199 4.7 59.8 1.0
CA Z:VAL198 4.7 56.2 1.0
N Z:GLU193 4.8 61.8 1.0
CZ Z:ARG28 4.8 61.6 1.0
O Z:LYS220 4.9 61.5 1.0
NH1 Z:ARG28 5.0 62.9 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: Mon Dec 14 20:45:12 2020

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