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Magnesium in PDB 5l5r: Yeast 20S Proteasome with Human BETA5I (1-138;V31M) and Human BETA6 (97-111; 118-133)

Enzymatic activity of Yeast 20S Proteasome with Human BETA5I (1-138;V31M) and Human BETA6 (97-111; 118-133)

All present enzymatic activity of Yeast 20S Proteasome with Human BETA5I (1-138;V31M) and Human BETA6 (97-111; 118-133):
3.4.25.1;

Protein crystallography data

The structure of Yeast 20S Proteasome with Human BETA5I (1-138;V31M) and Human BETA6 (97-111; 118-133), PDB code: 5l5r 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 (°) 133.830, 301.160, 144.980, 90.00, 112.67, 90.00
R / Rfree (%) 19.6 / 22.1

Other elements in 5l5r:

The structure of Yeast 20S Proteasome with Human BETA5I (1-138;V31M) and Human BETA6 (97-111; 118-133) 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;V31M) and Human BETA6 (97-111; 118-133) (pdb code 5l5r). 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;V31M) and Human BETA6 (97-111; 118-133), PDB code: 5l5r:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 5l5r

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Magnesium binding site 1 out of 8 in the Yeast 20S Proteasome with Human BETA5I (1-138;V31M) and Human BETA6 (97-111; 118-133)


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;V31M) and Human BETA6 (97-111; 118-133) within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:67.1
occ:1.00
 O G:MET125 2.1 62.2 1.0
O G:ARG122 2.4 57.3 1.0
O G:TYR119 2.5 52.8 1.0
OG1 G:THR8 2.5 62.3 1.0
CG2 G:THR8 3.2 58.6 1.0
C G:MET125 3.3 60.1 1.0
CB G:THR8 3.4 58.8 1.0
O G:ALA123 3.4 61.9 1.0
C G:ARG122 3.5 58.7 1.0
C G:TYR119 3.7 52.4 1.0
C G:ALA123 3.7 60.1 1.0
CA G:ALA123 3.7 59.5 1.0
N G:ALA123 4.0 58.6 1.0
N G:MET125 4.2 62.9 1.0
N G:ARG126 4.2 55.8 1.0
CA G:ARG126 4.2 54.8 1.0
N G:THR8 4.3 58.9 1.0
CA G:MET125 4.3 64.4 1.0
CA G:TYR119 4.4 51.5 1.0
CA G:THR8 4.5 58.9 1.0
CD G:PRO127 4.6 51.1 1.0
N G:TYR124 4.6 62.2 1.0
N G:THR120 4.7 52.4 1.0
CA G:ARG122 4.7 60.3 1.0
N G:ARG122 4.7 57.9 1.0
CB G:MET125 4.8 69.1 1.0
C G:ARG126 4.8 53.8 1.0
CA G:THR120 4.8 52.2 1.0
C G:THR120 4.9 53.4 1.0
C G:TYR124 5.0 61.6 1.0
CB G:TYR119 5.0 51.9 1.0

Magnesium binding site 2 out of 8 in 5l5r

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Magnesium binding site 2 out of 8 in the Yeast 20S Proteasome with Human BETA5I (1-138;V31M) and Human BETA6 (97-111; 118-133)


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;V31M) and Human BETA6 (97-111; 118-133) within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg301

b:51.7
occ:1.00
 OD1 N:ASP51 3.3 56.1 1.0
NE2 H:GLN91 3.4 55.8 1.0
OD2 N:ASP51 3.8 55.3 1.0
CG N:ASP51 4.0 41.8 1.0
O N:ASN92 4.2 60.2 1.0
CD H:GLN91 4.6 45.5 1.0
OG N:SER48 4.9 44.0 1.0
CG H:GLN91 4.9 55.3 1.0

Magnesium binding site 3 out of 8 in 5l5r

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Magnesium binding site 3 out of 8 in the Yeast 20S Proteasome with Human BETA5I (1-138;V31M) and Human BETA6 (97-111; 118-133)


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;V31M) and Human BETA6 (97-111; 118-133) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:63.9
occ:1.00
 O I:ASP177 2.5 57.5 1.0
O I:SER180 2.7 57.2 1.0
O I:ALA174 3.1 58.9 1.0
OXT I:ASP204 3.4 67.5 1.0
C I:ASP177 3.6 58.2 1.0
C I:SER180 4.0 59.5 1.0
CA I:ALA178 4.1 58.7 1.0
O I:ALA178 4.1 60.3 1.0
O I:ASP204 4.2 69.8 1.0
C I:ALA178 4.2 59.5 1.0
C I:ASP204 4.2 66.4 1.0
C I:ALA174 4.3 59.0 1.0
NH1 Y:ARG19 4.3 76.7 1.0
N I:ALA178 4.3 57.8 1.0
CD1 Y:ILE26 4.3 64.8 1.0
N I:SER180 4.6 58.9 1.0
NH2 Y:ARG19 4.6 72.3 1.0
CA I:ASP175 4.6 60.5 1.0
N I:ASP177 4.7 59.2 1.0
CA I:ASP177 4.8 58.8 1.0
CZ Y:ARG19 4.8 74.4 1.0
CA I:GLY181 4.8 61.6 1.0
N I:GLY181 4.8 60.3 1.0
CA I:SER180 4.9 60.0 1.0
N I:ASP175 4.9 58.7 1.0
C I:ASP175 5.0 58.4 1.0
N I:LEU179 5.0 58.9 1.0

Magnesium binding site 4 out of 8 in 5l5r

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Magnesium binding site 4 out of 8 in the Yeast 20S Proteasome with Human BETA5I (1-138;V31M) and Human BETA6 (97-111; 118-133)


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;V31M) and Human BETA6 (97-111; 118-133) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg302

b:52.0
occ:1.00
 O Y:ASP167 2.1 63.7 1.0
O Y:ALA164 2.3 60.0 1.0
O I:ASP204 2.4 69.8 1.0
O Y:SER170 2.7 55.5 1.0
C I:ASP204 3.2 66.4 1.0
C Y:ASP167 3.2 64.2 1.0
C Y:ALA164 3.5 58.1 1.0
CA I:ASP204 3.6 67.2 1.0
NH1 Y:ARG19 3.6 76.7 1.0
CA Y:ALA168 3.7 65.4 1.0
O Y:ALA168 3.8 66.2 1.0
N Y:ALA168 3.8 64.9 1.0
O Y:HIS165 3.9 55.2 1.0
C Y:ALA168 3.9 66.7 1.0
C Y:SER170 3.9 64.0 1.0
CB I:ASP204 3.9 68.3 1.0
OXT I:ASP204 4.1 67.5 1.0
C Y:HIS165 4.3 59.1 1.0
CA Y:ALA164 4.3 58.4 1.0
N Y:SER170 4.3 66.7 1.0
CA Y:ASP167 4.4 63.5 1.0
N Y:ASP167 4.4 62.1 1.0
CZ Y:ARG19 4.4 74.4 1.0
N Y:HIS165 4.4 57.6 1.0
CA Y:HIS165 4.6 58.7 1.0
CA Y:SER170 4.7 64.6 1.0
N Y:TYR169 4.7 67.6 1.0
NH2 Y:ARG19 4.7 72.3 1.0
O Y:ALA163 4.7 61.6 1.0
C Y:ARG166 4.8 61.0 1.0
N Y:GLY171 4.9 66.1 1.0
CG I:ASP204 4.9 70.8 1.0
N Y:ARG166 4.9 58.9 1.0

Magnesium binding site 5 out of 8 in 5l5r

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Magnesium binding site 5 out of 8 in the Yeast 20S Proteasome with Human BETA5I (1-138;V31M) and Human BETA6 (97-111; 118-133)


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;V31M) and Human BETA6 (97-111; 118-133) within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg301

b:45.9
occ:1.00
 O K:ASP167 2.2 64.4 1.0
O W:ASP204 2.2 72.5 1.0
O K:ALA164 2.4 59.1 1.0
O K:SER170 2.6 57.2 1.0
C W:ASP204 3.1 68.8 1.0
C K:ASP167 3.3 62.5 1.0
NH1 K:ARG19 3.5 69.9 1.0
CA W:ASP204 3.6 67.0 1.0
C K:ALA164 3.6 56.8 1.0
CA K:ALA168 3.7 62.6 1.0
O K:ALA168 3.7 59.7 1.0
C K:ALA168 3.8 62.1 1.0
C K:SER170 3.8 60.6 1.0
CB W:ASP204 3.9 66.5 1.0
N K:ALA168 3.9 63.2 1.0
OXT W:ASP204 4.0 74.2 1.0
O K:HIS165 4.0 57.8 1.0
CZ K:ARG19 4.2 68.8 1.0
N K:SER170 4.3 61.3 1.0
CA K:ALA164 4.3 58.2 1.0
C K:HIS165 4.4 57.5 1.0
CA K:ASP167 4.5 61.3 1.0
NH2 K:ARG19 4.5 69.5 1.0
N K:ASP167 4.5 60.7 1.0
N K:HIS165 4.6 55.6 1.0
CA K:SER170 4.6 61.2 1.0
N K:TYR169 4.6 62.9 1.0
CA K:HIS165 4.8 57.6 1.0
N K:GLY171 4.8 61.9 1.0
O K:ALA163 4.8 59.4 1.0
CG W:ASP204 4.8 66.9 1.0
CA K:GLY171 4.9 65.3 1.0
C K:ARG166 4.9 60.2 1.0
N W:ASP204 5.0 67.1 1.0

Magnesium binding site 6 out of 8 in 5l5r

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Magnesium binding site 6 out of 8 in the Yeast 20S Proteasome with Human BETA5I (1-138;V31M) and Human BETA6 (97-111; 118-133)


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;V31M) and Human BETA6 (97-111; 118-133) within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg301

b:67.1
occ:1.00
 OXT L:ASP222 1.9 85.9 1.0
O V:ASP166 2.0 54.6 1.0
O V:ILE163 2.1 55.4 1.0
O V:SER169 2.3 57.0 1.0
C L:ASP222 3.0 80.6 1.0
C V:ASP166 3.1 54.9 1.0
C V:ILE163 3.2 56.7 1.0
C V:SER169 3.5 57.0 1.0
CA L:ASP222 3.6 78.9 1.0
O V:GLY162 3.8 59.7 1.0
N V:LEU167 3.9 56.5 1.0
CA V:LEU167 3.9 54.9 1.0
NH1 V:ARG19 3.9 63.9 1.0
O L:ASP222 4.0 79.7 1.0
N V:ASP166 4.0 54.5 1.0
CA V:ILE163 4.0 56.8 1.0
O V:TRP164 4.1 59.6 1.0
CB L:ASP222 4.1 77.2 1.0
CA V:ASP166 4.1 53.9 1.0
C V:TRP164 4.2 58.2 1.0
N V:TRP164 4.2 56.8 1.0
C V:LEU167 4.3 54.1 1.0
N V:SER169 4.3 54.6 1.0
CA V:SER169 4.4 55.3 1.0
CA V:TRP164 4.4 58.5 1.0
N V:GLY170 4.4 58.4 1.0
CA V:GLY170 4.4 59.6 1.0
O V:LEU167 4.5 54.3 1.0
CZ V:ARG19 4.6 63.5 1.0
N V:ASN165 4.6 56.2 1.0
CB V:SER169 4.7 56.5 1.0
C V:ASN165 4.7 55.1 1.0
C V:GLY162 4.7 58.2 1.0
NH2 V:ARG19 4.8 68.5 1.0
N V:ILE163 4.9 56.9 1.0
CB V:ASP166 4.9 54.1 1.0
N V:GLY168 5.0 54.7 1.0
CG2 V:ILE163 5.0 57.4 1.0
N L:ASP222 5.0 74.4 1.0
O L:ARG221 5.0 70.2 1.0

Magnesium binding site 7 out of 8 in 5l5r

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Magnesium binding site 7 out of 8 in the Yeast 20S Proteasome with Human BETA5I (1-138;V31M) and Human BETA6 (97-111; 118-133)


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;V31M) and Human BETA6 (97-111; 118-133) within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg201

b:50.5
occ:1.00
 O N:ILE163 2.6 50.8 1.0
O N:SER169 2.8 48.2 1.0
O N:ASP166 3.2 53.2 1.0
CD1 a:LEU34 3.6 59.6 1.0
C N:ILE163 3.7 50.9 1.0
NH1 N:ARG19 3.8 49.5 1.0
CG2 N:ILE163 3.9 50.3 1.0
C N:SER169 3.9 48.2 1.0
C N:ASP166 4.2 49.9 1.0
CZ N:ARG19 4.2 49.8 1.0
NH2 N:ARG19 4.3 50.2 1.0
CA N:GLY167 4.4 48.4 1.0
CA N:GLY170 4.4 50.2 1.0
CA N:ILE163 4.4 50.3 1.0
O N:GLY167 4.6 48.9 1.0
N N:GLY170 4.6 47.7 1.0
N N:GLY167 4.7 49.8 1.0
C N:GLY167 4.7 47.2 1.0
N N:LYS164 4.7 51.8 1.0
CB N:ILE163 4.8 49.7 1.0
CG a:LEU34 4.9 59.6 1.0
O N:LYS164 4.9 60.2 1.0
C N:LYS164 4.9 55.6 1.0
CA N:LYS164 5.0 55.1 1.0

Magnesium binding site 8 out of 8 in 5l5r

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Magnesium binding site 8 out of 8 in the Yeast 20S Proteasome with Human BETA5I (1-138;V31M) and Human BETA6 (97-111; 118-133)


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;V31M) and Human BETA6 (97-111; 118-133) within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg301

b:66.8
occ:1.00
 O Z:VAL198 2.6 54.9 1.0
O Z:THR192 2.7 67.8 1.0
O Z:HIS195 2.9 55.0 1.0
O Z:ASP222 3.5 75.8 1.0
C Z:THR192 3.7 68.4 1.0
NH2 Z:ARG28 3.7 69.8 1.0
C Z:VAL198 3.8 61.1 1.0
CG2 Z:THR192 3.8 71.8 1.0
C Z:HIS195 3.8 61.2 1.0
O Z:ILE196 3.8 64.3 1.0
CA Z:ILE196 3.8 63.3 1.0
C Z:ILE196 4.0 62.9 1.0
NH2 H:ARG19 4.1 71.9 1.0
CA Z:THR192 4.1 70.0 1.0
N Z:ILE196 4.3 62.8 1.0
OD1 Z:ASP222 4.4 80.4 1.0
N Z:VAL198 4.5 62.2 1.0
CB Z:THR192 4.6 71.0 1.0
C Z:ASP222 4.6 83.2 1.0
CA Z:VAL198 4.7 62.9 1.0
N Z:GLY199 4.7 62.0 1.0
CA Z:GLY199 4.7 64.8 1.0
CZ Z:ARG28 4.8 68.9 1.0
CZ H:ARG19 4.9 71.3 1.0
N Z:GLU193 4.9 68.9 1.0
N Z:GLN197 4.9 63.2 1.0
NH1 H:ARG19 5.0 70.8 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 19:27:04 2024

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