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Magnesium in PDB 5l5h: Yeast 20S Proteasome with Human BETA5I (1-138) and Human BETA6 (97- 111; 118-133) in Complex with Pr-924

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

All present enzymatic activity of Yeast 20S Proteasome with Human BETA5I (1-138) and Human BETA6 (97- 111; 118-133) in Complex with Pr-924:
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 Pr-924, PDB code: 5l5h 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 (°) 135.070, 300.220, 145.500, 90.00, 112.87, 90.00
R / Rfree (%) 19.4 / 21.6

Other elements in 5l5h:

The structure of Yeast 20S Proteasome with Human BETA5I (1-138) and Human 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 Human BETA5I (1-138) and Human BETA6 (97- 111; 118-133) in Complex with Pr-924 (pdb code 5l5h). 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 BETA5I (1-138) and Human BETA6 (97- 111; 118-133) in Complex with Pr-924, PDB code: 5l5h:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Magnesium binding site 1 out of 9 in 5l5h

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Magnesium binding site 1 out of 9 in the Yeast 20S Proteasome with Human BETA5I (1-138) and Human 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 Human BETA5I (1-138) and Human BETA6 (97- 111; 118-133) in Complex with Pr-924 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:58.4
occ:1.00
 O G:MET125 2.2 45.0 1.0
O G:ARG122 2.4 43.2 1.0
OG1 G:THR8 2.6 42.8 1.0
O G:TYR119 2.7 39.2 1.0
CG2 G:THR8 3.3 44.6 1.0
C G:MET125 3.4 46.9 1.0
O G:ALA123 3.4 50.0 1.0
CB G:THR8 3.5 44.0 1.0
C G:ARG122 3.5 44.5 1.0
C G:ALA123 3.7 47.8 1.0
CA G:ALA123 3.7 46.1 1.0
C G:TYR119 3.8 39.1 1.0
N G:ALA123 4.1 44.6 1.0
N G:MET125 4.1 47.9 1.0
N G:ARG126 4.2 45.1 1.0
N G:THR8 4.2 45.2 1.0
CA G:ARG126 4.3 43.6 1.0
CA G:MET125 4.3 49.6 1.0
CA G:THR8 4.5 44.9 1.0
N G:TYR124 4.6 48.2 1.0
CA G:TYR119 4.6 37.6 1.0
CD G:PRO127 4.6 39.7 1.0
CA G:ARG122 4.8 47.0 1.0
N G:ARG122 4.8 44.1 1.0
N G:THR120 4.9 38.5 1.0
CB G:MET125 4.9 54.8 1.0
C G:ARG126 4.9 41.9 1.0
C G:TYR124 4.9 47.2 1.0
CA G:THR120 5.0 38.4 1.0

Magnesium binding site 2 out of 9 in 5l5h

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Magnesium binding site 2 out of 9 in the Yeast 20S Proteasome with Human BETA5I (1-138) and Human 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 Human BETA5I (1-138) and Human BETA6 (97- 111; 118-133) in Complex with Pr-924 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:57.1
occ:1.00
 O I:SER180 2.5 48.8 1.0
O I:ASP177 2.5 48.9 1.0
O I:ALA174 3.0 46.5 1.0
OXT I:ASP204 3.6 54.7 1.0
C I:ASP177 3.7 45.9 1.0
C I:SER180 3.7 47.5 1.0
O I:HOH406 3.7 47.5 1.0
C I:ALA174 4.1 47.3 1.0
O I:ALA178 4.1 51.8 1.0
C I:ALA178 4.2 47.4 1.0
CA I:ALA178 4.3 45.2 1.0
CD1 Y:ILE26 4.3 48.8 1.0
N I:ALA178 4.4 44.0 1.0
N I:SER180 4.4 45.4 1.0
C I:ASP204 4.5 52.6 1.0
O I:ASP204 4.5 51.6 1.0
N I:GLY181 4.6 47.1 1.0
CA I:GLY181 4.6 47.4 1.0
CA I:ASP175 4.6 49.2 1.0
CA I:SER180 4.6 46.0 1.0
N I:ASP177 4.7 46.3 1.0
CA I:ASP177 4.7 46.0 1.0
NH1 Y:ARG19 4.8 60.3 1.0
N I:ASP175 4.8 48.0 1.0
NH2 Y:ARG19 4.9 60.5 1.0
N I:LEU179 5.0 46.6 1.0
C I:ASP175 5.0 50.5 1.0

Magnesium binding site 3 out of 9 in 5l5h

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Magnesium binding site 3 out of 9 in the Yeast 20S Proteasome with Human BETA5I (1-138) and Human 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 Human BETA5I (1-138) and Human BETA6 (97- 111; 118-133) in Complex with Pr-924 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg302

b:50.7
occ:1.00
 O Y:ASP167 2.2 45.3 1.0
O I:ASP204 2.3 51.6 1.0
O Y:ALA164 2.4 44.0 1.0
O Y:SER170 2.5 47.0 1.0
C I:ASP204 3.2 52.6 1.0
C Y:ASP167 3.2 43.8 1.0
NH1 Y:ARG19 3.4 60.3 1.0
C Y:ALA164 3.5 42.2 1.0
CA Y:ALA168 3.6 45.9 1.0
C Y:SER170 3.7 45.6 1.0
CA I:ASP204 3.7 53.2 1.0
O Y:ALA168 3.7 50.7 1.0
C Y:ALA168 3.8 46.9 1.0
N Y:ALA168 3.8 45.4 1.0
CB I:ASP204 3.9 54.0 1.0
O Y:HIS165 4.1 47.2 1.0
N Y:SER170 4.1 43.9 1.0
OXT I:ASP204 4.1 54.7 1.0
CA Y:ALA164 4.3 42.3 1.0
CZ Y:ARG19 4.3 58.0 1.0
CA Y:ASP167 4.4 43.1 1.0
C Y:HIS165 4.4 44.1 1.0
N Y:ASP167 4.5 43.3 1.0
CA Y:SER170 4.5 44.3 1.0
N Y:HIS165 4.5 43.2 1.0
N Y:TYR169 4.6 46.7 1.0
O Y:ALA163 4.7 41.3 1.0
N Y:GLY171 4.7 47.1 1.0
CA Y:HIS165 4.8 43.6 1.0
NH2 Y:ARG19 4.8 60.5 1.0
CA Y:GLY171 4.8 49.0 1.0
C Y:ARG166 4.8 43.8 1.0
CG I:ASP204 4.9 52.4 1.0
CB Y:SER170 5.0 44.2 1.0

Magnesium binding site 4 out of 9 in 5l5h

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Magnesium binding site 4 out of 9 in the Yeast 20S Proteasome with Human BETA5I (1-138) and Human 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 Human BETA5I (1-138) and Human BETA6 (97- 111; 118-133) in Complex with Pr-924 within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mg201

b:56.1
occ:1.00
 OE1 J:GLN118 3.2 42.1 1.0
O J:THR124 3.4 39.0 1.0
CB J:ASP120 3.7 40.4 1.0
N J:ASP120 3.8 37.6 1.0
OD2 J:ASP120 3.8 46.8 1.0
CG J:ASP120 3.8 43.0 1.0
CD J:GLN118 4.1 38.4 1.0
CG J:GLN118 4.1 37.5 1.0
CB J:THR124 4.1 40.4 1.0
CE1 J:HIS133 4.2 39.6 1.0
O J:GLN118 4.3 38.1 1.0
CG2 J:THR124 4.3 39.9 1.0
CA J:ASP120 4.4 38.2 1.0
C J:THR124 4.4 39.4 1.0
C J:ILE119 4.5 37.1 1.0
OD1 J:ASP120 4.5 47.8 1.0
C J:GLN118 4.6 36.6 1.0
CA J:ILE119 4.7 34.9 1.0
N J:ILE119 4.8 35.1 1.0
CG1 I:VAL35 4.9 52.9 1.0
ND1 J:HIS133 4.9 39.4 1.0
CB J:GLN118 4.9 36.7 1.0
CA J:THR124 4.9 39.6 1.0

Magnesium binding site 5 out of 9 in 5l5h

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Magnesium binding site 5 out of 9 in the Yeast 20S Proteasome with Human BETA5I (1-138) and Human 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 Human BETA5I (1-138) and Human BETA6 (97- 111; 118-133) in Complex with Pr-924 within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg302

b:56.2
occ:1.00
 O K:ASP167 2.2 49.0 1.0
O W:ASP204 2.3 57.4 1.0
O K:ALA164 2.3 45.5 1.0
O K:SER170 2.7 48.4 1.0
C W:ASP204 3.1 56.6 1.0
C K:ASP167 3.2 48.3 1.0
C K:ALA164 3.5 46.0 1.0
NH1 K:ARG19 3.6 59.8 1.0
CA W:ASP204 3.6 56.8 1.0
CA K:ALA168 3.6 48.7 1.0
N K:ALA168 3.8 48.1 1.0
O K:ALA168 3.8 50.9 1.0
C K:ALA168 3.8 48.4 1.0
CB W:ASP204 3.9 57.3 1.0
O K:HIS165 3.9 49.8 1.0
C K:SER170 3.9 47.9 1.0
OXT W:ASP204 4.0 59.0 1.0
C K:HIS165 4.3 47.7 1.0
CA K:ALA164 4.3 45.6 1.0
N K:SER170 4.3 46.9 1.0
CA K:ASP167 4.4 47.6 1.0
N K:ASP167 4.4 50.7 1.0
N K:HIS165 4.5 46.2 1.0
CZ K:ARG19 4.5 57.8 1.0
CA K:HIS165 4.6 47.6 1.0
N K:TYR169 4.7 48.0 1.0
O K:ALA163 4.7 45.1 1.0
C K:ARG166 4.7 50.9 1.0
CA K:SER170 4.7 46.3 1.0
N K:ARG166 4.9 47.6 1.0
CG W:ASP204 4.9 57.3 1.0
NH2 K:ARG19 4.9 59.7 1.0
N K:GLY171 4.9 49.2 1.0
O K:ARG166 4.9 53.0 1.0
CB K:ALA168 5.0 48.0 1.0
N W:ASP204 5.0 55.3 1.0

Magnesium binding site 6 out of 9 in 5l5h

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Magnesium binding site 6 out of 9 in the Yeast 20S Proteasome with Human BETA5I (1-138) and Human 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 Human BETA5I (1-138) and Human BETA6 (97- 111; 118-133) in Complex with Pr-924 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg301

b:56.0
occ:1.00
 OXT L:ASP222 2.0 72.0 1.0
O V:ASP166 2.2 45.8 1.0
O V:ILE163 2.2 46.1 1.0
O V:SER169 2.3 50.8 1.0
C L:ASP222 3.0 70.6 1.0
C V:ASP166 3.2 45.4 1.0
C V:ILE163 3.4 46.2 1.0
C V:SER169 3.5 47.4 1.0
NH1 V:ARG19 3.7 55.3 1.0
CA L:ASP222 3.7 68.2 1.0
CA V:LEU167 3.7 45.5 1.0
N V:LEU167 3.8 44.8 1.0
O L:ASP222 3.9 77.7 1.0
O V:GLY162 4.0 46.8 1.0
CA V:ILE163 4.1 46.1 1.0
N V:ASP166 4.2 43.4 1.0
C V:LEU167 4.2 45.7 1.0
CA V:ASP166 4.3 44.5 1.0
N V:SER169 4.3 45.3 1.0
CB L:ASP222 4.3 68.0 1.0
O V:TRP164 4.3 54.3 1.0
N V:TRP164 4.4 47.1 1.0
O V:LEU167 4.4 48.1 1.0
C V:TRP164 4.4 49.1 1.0
N V:GLY170 4.4 48.1 1.0
CA V:GLY170 4.4 48.9 1.0
CA V:SER169 4.4 46.1 1.0
CZ V:ARG19 4.4 52.9 1.0
CA V:TRP164 4.6 48.8 1.0
NH2 V:ARG19 4.6 55.9 1.0
N V:ASN165 4.8 47.7 1.0
CB V:SER169 4.8 47.2 1.0
N V:GLY168 4.9 45.7 1.0
C V:GLY162 4.9 45.1 1.0
CD2 V:LEU167 4.9 45.0 1.0
C V:ASN165 4.9 44.1 1.0

Magnesium binding site 7 out of 9 in 5l5h

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Magnesium binding site 7 out of 9 in the Yeast 20S Proteasome with Human BETA5I (1-138) and Human 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 Human BETA5I (1-138) and Human BETA6 (97- 111; 118-133) in Complex with Pr-924 within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg201

b:53.9
occ:1.00
 O N:ILE163 2.6 42.4 1.0
O N:SER169 2.7 42.4 1.0
O N:ASP166 3.1 44.1 1.0
CD1 a:LEU34 3.6 47.7 1.0
NH1 N:ARG19 3.7 45.6 1.0
C N:ILE163 3.7 43.1 1.0
C N:SER169 3.9 40.9 1.0
CG2 N:ILE163 3.9 41.6 1.0
C N:ASP166 4.1 40.8 1.0
CZ N:ARG19 4.2 43.3 1.0
CA N:GLY167 4.2 40.6 1.0
NH2 N:ARG19 4.4 42.6 1.0
CA N:GLY170 4.4 42.5 1.0
CA N:ILE163 4.4 42.2 1.0
O N:GLY167 4.5 40.3 1.0
N N:GLY167 4.6 40.2 1.0
N N:GLY170 4.6 41.3 1.0
C N:GLY167 4.6 39.7 1.0
CB N:ILE163 4.8 41.3 1.0
N N:LYS164 4.8 44.6 1.0
CG a:LEU34 4.8 48.5 1.0
CA N:SER169 4.9 39.8 1.0
N N:SER169 5.0 40.3 1.0

Magnesium binding site 8 out of 9 in 5l5h

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Magnesium binding site 8 out of 9 in the Yeast 20S Proteasome with Human BETA5I (1-138) and Human 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 Human BETA5I (1-138) and Human BETA6 (97- 111; 118-133) in Complex with Pr-924 within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg202

b:49.1
occ:1.00
 OD1 N:ASP51 2.3 28.1 1.0
O H:HOH315 2.5 48.7 1.0
O H:HOH321 2.9 35.8 1.0
CG N:ASP51 3.2 19.8 1.0
OD2 N:ASP51 3.4 38.5 1.0
NE2 H:GLN91 3.4 58.6 1.0
O N:ASN92 3.7 49.6 1.0
CE1 H:PHE88 4.2 40.0 1.0
CZ H:PHE88 4.5 39.7 1.0
CD H:GLN91 4.6 56.1 1.0
CB N:ASP51 4.6 30.1 1.0
OG N:SER48 4.8 40.2 1.0
C N:ASN92 5.0 50.8 1.0
CD1 H:PHE88 5.0 39.5 1.0

Magnesium binding site 9 out of 9 in 5l5h

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Magnesium binding site 9 out of 9 in the Yeast 20S Proteasome with Human BETA5I (1-138) and Human 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 Human BETA5I (1-138) and Human BETA6 (97- 111; 118-133) in Complex with Pr-924 within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg301

b:76.0
occ:1.00
 O Z:VAL198 2.5 50.5 1.0
O Z:THR192 2.7 57.4 1.0
O Z:HIS195 3.1 49.2 1.0
O Z:ASP222 3.5 71.2 1.0
NH2 Z:ARG28 3.6 59.6 1.0
CG2 Z:THR192 3.7 63.4 1.0
C Z:VAL198 3.7 53.7 1.0
C Z:THR192 3.7 61.9 1.0
O Z:ILE196 4.1 59.4 1.0
OD1 Z:ASP222 4.1 71.0 1.0
CA Z:THR192 4.1 62.7 1.0
C Z:HIS195 4.2 52.0 1.0
CA Z:ILE196 4.2 55.2 1.0
NH2 H:ARG19 4.2 56.1 1.0
C Z:ILE196 4.3 54.9 1.0
C Z:ASP222 4.5 71.0 1.0
CA Z:GLY199 4.5 55.1 1.0
CB Z:THR192 4.5 62.4 1.0
CZ Z:ARG28 4.6 61.5 1.0
N Z:GLY199 4.6 53.9 1.0
N Z:VAL198 4.6 52.9 1.0
N Z:ILE196 4.6 52.5 1.0
CA Z:VAL198 4.7 54.2 1.0
NH1 Z:ARG28 4.7 64.5 1.0
O Z:LYS220 4.8 64.3 1.0
N Z:GLU193 4.9 62.1 1.0
OXT Z:ASP222 4.9 67.0 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 19:24:03 2024

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