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Magnesium in PDB 5l67: Yeast 20S Proteasome with Mouse BETA5I (1-138) and Mouse BETA6 (97- 111; 118-133) in Complex with Pr-924

Enzymatic activity of Yeast 20S Proteasome with Mouse BETA5I (1-138) and Mouse BETA6 (97- 111; 118-133) in Complex with Pr-924

All present enzymatic activity of Yeast 20S Proteasome with Mouse BETA5I (1-138) and Mouse BETA6 (97- 111; 118-133) in Complex with Pr-924:
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 Pr-924, PDB code: 5l67 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 (°) 135.560, 300.680, 145.630, 90.00, 112.94, 90.00
R / Rfree (%) 19.1 / 21.3

Other elements in 5l67:

The structure of Yeast 20S Proteasome with Mouse BETA5I (1-138) and Mouse BETA6 (97- 111; 118-133) in Complex with Pr-924 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 Pr-924 (pdb code 5l67). 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 Mouse BETA5I (1-138) and Mouse BETA6 (97- 111; 118-133) in Complex with Pr-924, PDB code: 5l67:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Magnesium binding site 1 out of 9 in 5l67

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Magnesium binding site 1 out of 9 in the Yeast 20S Proteasome with Mouse BETA5I (1-138) and Mouse BETA6 (97- 111; 118-133) in Complex with Pr-924


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 Pr-924 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:60.2
occ:1.00
 O G:MET125 2.2 45.9 1.0
O G:ARG122 2.4 44.2 1.0
OG1 G:THR8 2.6 41.8 1.0
O G:TYR119 2.7 41.3 1.0
CG2 G:THR8 3.3 46.5 1.0
O G:ALA123 3.3 51.0 1.0
C G:MET125 3.4 48.5 1.0
CB G:THR8 3.5 45.1 1.0
C G:ARG122 3.5 45.7 1.0
C G:ALA123 3.6 48.0 1.0
CA G:ALA123 3.7 46.7 1.0
C G:TYR119 3.9 41.3 1.0
N G:ALA123 4.0 45.1 1.0
N G:MET125 4.2 49.5 1.0
N G:ARG126 4.2 45.8 1.0
N G:THR8 4.2 46.4 1.0
CA G:ARG126 4.3 44.6 1.0
CA G:MET125 4.3 51.5 1.0
CA G:THR8 4.5 46.7 1.0
N G:TYR124 4.5 48.5 1.0
CD G:PRO127 4.6 41.8 1.0
CA G:TYR119 4.6 40.0 1.0
CA G:ARG122 4.8 48.3 1.0
N G:ARG122 4.8 45.9 1.0
N G:THR120 4.9 40.9 1.0
C G:ARG126 4.9 43.7 1.0
CB G:MET125 4.9 56.3 1.0
C G:TYR124 4.9 48.2 1.0

Magnesium binding site 2 out of 9 in 5l67

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Magnesium binding site 2 out of 9 in the Yeast 20S Proteasome with Mouse BETA5I (1-138) and Mouse BETA6 (97- 111; 118-133) in Complex with Pr-924


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 Pr-924 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:63.4
occ:1.00
 O I:ASP177 2.5 50.6 1.0
O I:SER180 2.6 57.3 1.0
O I:ALA174 2.9 53.5 1.0
O I:HOH414 3.0 60.2 1.0
OXT I:ASP204 3.6 58.7 1.0
C I:ASP177 3.6 49.9 1.0
O I:HOH406 3.7 46.2 1.0
C I:SER180 3.8 53.0 1.0
O I:ALA178 4.0 52.8 1.0
C I:ALA174 4.1 53.4 1.0
CA I:ALA178 4.2 50.0 1.0
C I:ALA178 4.2 50.5 1.0
N I:ALA178 4.3 48.5 1.0
CD1 Y:ILE26 4.4 54.8 1.0
N I:SER180 4.5 50.7 1.0
C I:ASP204 4.5 59.4 1.0
CA I:ASP175 4.6 54.5 1.0
O I:ASP204 4.6 61.5 1.0
N I:ASP177 4.6 51.6 1.0
N I:GLY181 4.7 51.5 1.0
CA I:GLY181 4.7 52.7 1.0
CA I:ASP177 4.7 50.7 1.0
CA I:SER180 4.7 51.5 1.0
NH1 Y:ARG19 4.7 63.8 1.0
N I:ASP175 4.8 54.2 1.0
NH2 Y:ARG19 4.9 65.3 1.0
C I:ASP175 4.9 55.8 1.0
N I:LEU179 5.0 48.4 1.0

Magnesium binding site 3 out of 9 in 5l67

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Magnesium binding site 3 out of 9 in the Yeast 20S Proteasome with Mouse BETA5I (1-138) and Mouse BETA6 (97- 111; 118-133) in Complex with Pr-924


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 Pr-924 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg302

b:59.9
occ:1.00
 O Y:ASP167 2.2 52.0 1.0
O I:ASP204 2.2 61.5 1.0
O Y:ALA164 2.3 50.7 1.0
O Y:SER170 2.4 52.5 1.0
MG Y:MG301 3.0 80.9 1.0
C I:ASP204 3.2 59.4 1.0
C Y:ASP167 3.3 49.7 1.0
NH1 Y:ARG19 3.3 63.8 1.0
C Y:ALA164 3.5 47.8 1.0
C Y:SER170 3.6 52.2 1.0
CA Y:ALA168 3.7 51.0 1.0
CA I:ASP204 3.8 60.3 1.0
O Y:ALA168 3.8 55.0 1.0
C Y:ALA168 3.8 52.2 1.0
N Y:ALA168 3.9 50.3 1.0
CB I:ASP204 4.0 61.0 1.0
N Y:SER170 4.1 49.0 1.0
OXT I:ASP204 4.1 58.7 1.0
CA Y:ALA164 4.2 47.7 1.0
O Y:HIS165 4.2 48.4 1.0
CZ Y:ARG19 4.3 64.0 1.0
CA Y:SER170 4.4 50.0 1.0
CA Y:ASP167 4.5 48.4 1.0
C Y:HIS165 4.5 47.2 1.0
N Y:HIS165 4.5 48.0 1.0
N Y:ASP167 4.6 48.9 1.0
N Y:TYR169 4.6 52.1 1.0
N Y:GLY171 4.6 53.9 1.0
O Y:ALA163 4.7 43.9 1.0
CA Y:GLY171 4.7 54.6 1.0
NH2 Y:ARG19 4.7 65.3 1.0
CA Y:HIS165 4.8 47.4 1.0
CG I:ASP204 4.9 61.9 1.0
CB Y:SER170 4.9 49.8 1.0
C Y:ARG166 5.0 49.2 1.0
CB Y:ALA164 5.0 48.0 1.0

Magnesium binding site 4 out of 9 in 5l67

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Magnesium binding site 4 out of 9 in the Yeast 20S Proteasome with Mouse BETA5I (1-138) and Mouse BETA6 (97- 111; 118-133) in Complex with Pr-924


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 Pr-924 within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mg201

b:56.4
occ:1.00
 OE1 J:GLN118 3.2 45.7 1.0
O J:THR124 3.3 41.3 1.0
CB J:ASP120 3.7 43.4 1.0
N J:ASP120 3.7 39.9 1.0
CG J:ASP120 3.9 45.9 1.0
OD2 J:ASP120 3.9 50.0 1.0
CD J:GLN118 4.0 42.9 1.0
CG J:GLN118 4.0 41.2 1.0
CB J:THR124 4.1 43.6 1.0
CE1 J:HIS133 4.1 44.7 1.0
O J:GLN118 4.2 39.0 1.0
CA J:ASP120 4.3 41.2 1.0
C J:THR124 4.3 42.4 1.0
CG2 J:THR124 4.4 43.3 1.0
C J:ILE119 4.4 39.8 1.0
C J:GLN118 4.5 38.7 1.0
CA J:ILE119 4.5 37.3 1.0
OD1 J:ASP120 4.6 47.7 1.0
N J:ILE119 4.7 37.7 1.0
CB J:GLN118 4.8 39.7 1.0
ND1 J:HIS133 4.8 44.0 1.0
CA J:THR124 4.9 43.3 1.0
CG1 I:VAL35 4.9 55.1 1.0

Magnesium binding site 5 out of 9 in 5l67

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Magnesium binding site 5 out of 9 in the Yeast 20S Proteasome with Mouse BETA5I (1-138) and Mouse BETA6 (97- 111; 118-133) in Complex with Pr-924


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 Pr-924 within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg302

b:56.7
occ:1.00
 O W:ASP204 2.2 60.0 1.0
O K:ASP167 2.2 48.7 1.0
O K:ALA164 2.3 50.3 1.0
O K:SER170 2.5 49.8 1.0
C W:ASP204 3.1 57.0 1.0
C K:ASP167 3.3 50.0 1.0
NH1 K:ARG19 3.4 62.5 1.0
C K:ALA164 3.5 49.2 1.0
CA W:ASP204 3.6 57.2 1.0
CA K:ALA168 3.7 51.8 1.0
C K:SER170 3.7 50.3 1.0
O K:ALA168 3.8 54.1 1.0
C K:ALA168 3.8 52.4 1.0
CB W:ASP204 3.9 57.0 1.0
N K:ALA168 3.9 50.6 1.0
OXT W:ASP204 4.0 59.4 1.0
O K:HIS165 4.1 48.9 1.0
N K:SER170 4.2 51.0 1.0
CA K:ALA164 4.2 48.6 1.0
CZ K:ARG19 4.3 59.8 1.0
C K:HIS165 4.5 48.1 1.0
CA K:ASP167 4.5 49.6 1.0
CA K:SER170 4.5 49.3 1.0
N K:HIS165 4.5 48.4 1.0
N K:ASP167 4.6 51.2 1.0
N K:TYR169 4.6 52.3 1.0
N K:GLY171 4.7 52.5 1.0
O K:ALA163 4.7 48.1 1.0
CA K:HIS165 4.7 48.7 1.0
NH2 K:ARG19 4.8 61.1 1.0
CA K:GLY171 4.8 52.9 1.0
CG W:ASP204 4.8 56.7 1.0
C K:ARG166 4.9 50.2 1.0

Magnesium binding site 6 out of 9 in 5l67

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Magnesium binding site 6 out of 9 in the Yeast 20S Proteasome with Mouse BETA5I (1-138) and Mouse BETA6 (97- 111; 118-133) in Complex with Pr-924


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 Pr-924 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg301

b:63.7
occ:1.00
 OXT L:ASP222 2.0 71.5 1.0
O V:ILE163 2.1 50.5 1.0
O V:ASP166 2.2 48.8 1.0
O V:SER169 2.5 52.6 1.0
C L:ASP222 3.0 73.5 1.0
C V:ASP166 3.2 49.3 1.0
C V:ILE163 3.3 51.0 1.0
CA L:ASP222 3.7 72.7 1.0
C V:SER169 3.7 50.0 1.0
O L:ASP222 3.8 77.8 1.0
CA V:LEU167 3.9 49.4 1.0
NH1 V:ARG19 3.9 59.9 1.0
N V:LEU167 3.9 49.1 1.0
O V:GLY162 3.9 50.5 1.0
N V:ASP166 4.0 47.7 1.0
O V:TRP164 4.1 56.2 1.0
CA V:ILE163 4.1 50.5 1.0
C V:TRP164 4.1 53.2 1.0
N V:TRP164 4.2 51.0 1.0
CA V:ASP166 4.2 48.4 1.0
CB L:ASP222 4.3 72.2 1.0
C V:LEU167 4.3 50.8 1.0
CA V:TRP164 4.4 53.0 1.0
N V:SER169 4.5 49.3 1.0
O V:LEU167 4.5 52.3 1.0
CA V:GLY170 4.5 52.5 1.0
N V:GLY170 4.6 51.4 1.0
CZ V:ARG19 4.6 55.8 1.0
CA V:SER169 4.6 49.5 1.0
N V:ASN165 4.6 51.4 1.0
NH2 V:ARG19 4.8 56.6 1.0
C V:ASN165 4.8 48.2 1.0
O L:ARG221 4.8 63.2 1.0
C V:GLY162 4.9 50.0 1.0
CD2 V:LEU167 4.9 49.1 1.0
N L:ASP222 4.9 67.5 1.0
CB V:SER169 4.9 50.7 1.0

Magnesium binding site 7 out of 9 in 5l67

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Magnesium binding site 7 out of 9 in the Yeast 20S Proteasome with Mouse BETA5I (1-138) and Mouse BETA6 (97- 111; 118-133) in Complex with Pr-924


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 Pr-924 within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg201

b:55.9
occ:1.00
 O N:ILE163 2.5 45.5 1.0
O N:SER169 2.7 46.3 1.0
O N:ASP166 2.9 47.7 1.0
CD1 a:LEU34 3.6 54.1 1.0
C N:ILE163 3.6 45.8 1.0
NH1 N:ARG19 3.8 49.1 1.0
CG2 N:ILE163 3.8 46.0 1.0
C N:SER169 3.8 45.0 1.0
C N:ASP166 3.9 44.8 1.0
CA N:GLY167 4.1 45.5 1.0
CA N:ILE163 4.3 46.1 1.0
CZ N:ARG19 4.3 46.4 1.0
CA N:GLY170 4.4 46.6 1.0
N N:GLY167 4.4 44.5 1.0
O N:GLY167 4.5 46.4 1.0
C N:GLY167 4.5 45.5 1.0
NH2 N:ARG19 4.5 45.4 1.0
N N:GLY170 4.6 45.2 1.0
CB N:ILE163 4.7 45.4 1.0
N N:LYS164 4.7 47.5 1.0
CG a:LEU34 4.9 53.9 1.0
CA N:SER169 4.9 43.8 1.0
N N:SER169 4.9 45.4 1.0
C N:LYS164 5.0 49.7 1.0

Magnesium binding site 8 out of 9 in 5l67

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Magnesium binding site 8 out of 9 in the Yeast 20S Proteasome with Mouse BETA5I (1-138) and Mouse BETA6 (97- 111; 118-133) in Complex with Pr-924


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 Pr-924 within 5.0Å range:
probe atom residue distance (Å) B Occ
Y:Mg301

b:80.9
occ:1.00
 O Y:HIS165 2.9 48.4 1.0
MG I:MG302 3.0 59.9 1.0
O I:ASP204 3.3 61.5 1.0
C I:ASP204 3.5 59.4 1.0
O Y:ASP167 3.6 52.0 1.0
NE1 I:TRP182 3.7 55.3 1.0
OXT I:ASP204 3.8 58.7 1.0
CA Y:ALA168 3.8 51.0 1.0
C Y:HIS165 3.9 47.2 1.0
C Y:ASP167 3.9 49.7 1.0
O Y:ALA164 3.9 50.7 1.0
O Y:ARG166 4.0 51.3 1.0
N Y:ALA168 4.0 50.3 1.0
CA I:ASP204 4.2 60.3 1.0
CD1 I:TRP182 4.2 54.7 1.0
C Y:ARG166 4.2 49.2 1.0
CE2 I:TRP182 4.3 55.8 1.0
CB Y:ALA168 4.5 50.4 1.0
NE I:ARG27 4.6 48.7 1.0
N Y:ASP167 4.6 48.9 1.0
N Y:ARG166 4.6 47.3 1.0
CZ2 I:TRP182 4.7 57.1 1.0
CA Y:ARG166 4.7 48.0 1.0
CA Y:HIS165 4.8 47.4 1.0
O I:ALA178 4.8 52.8 1.0
C Y:ALA168 4.9 52.2 1.0
CA Y:ASP167 4.9 48.4 1.0
C Y:ALA164 5.0 47.8 1.0

Magnesium binding site 9 out of 9 in 5l67

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Magnesium binding site 9 out of 9 in the Yeast 20S Proteasome with Mouse BETA5I (1-138) and Mouse BETA6 (97- 111; 118-133) in Complex with Pr-924


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 Mouse BETA5I (1-138) and Mouse BETA6 (97- 111; 118-133) in Complex with Pr-924 within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg301

b:64.9
occ:1.00
 O Z:VAL198 2.5 52.9 1.0
O Z:THR192 2.6 60.4 1.0
O Z:HIS195 2.9 54.2 1.0
C Z:THR192 3.6 64.8 1.0
CG2 Z:THR192 3.6 64.8 1.0
C Z:VAL198 3.7 58.2 1.0
NH2 Z:ARG28 3.8 59.3 1.0
O Z:ASP222 3.8 76.7 1.0
C Z:HIS195 3.9 55.7 1.0
CA Z:THR192 3.9 65.4 1.0
O Z:ILE196 4.0 65.0 1.0
CA Z:ILE196 4.0 58.6 1.0
C Z:ILE196 4.2 59.7 1.0
NH2 H:ARG19 4.3 62.3 1.0
OD1 Z:ASP222 4.3 71.8 1.0
CB Z:THR192 4.4 64.1 1.0
N Z:ILE196 4.4 56.2 1.0
N Z:VAL198 4.5 56.3 1.0
CA Z:VAL198 4.6 57.9 1.0
N Z:GLY199 4.6 58.4 1.0
CA Z:GLY199 4.7 60.9 1.0
C Z:ASP222 4.8 74.3 1.0
N Z:GLU193 4.8 63.1 1.0
CZ Z:ARG28 4.8 62.2 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 19:39:24 2024

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