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Magnesium in PDB 5l5b: Yeast 20S Proteasome with Human BETA5I (1-138) and Human BETA6 (97- 111; 118-133)

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

All present enzymatic activity of Yeast 20S Proteasome with Human BETA5I (1-138) 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) and Human BETA6 (97- 111; 118-133), PDB code: 5l5b 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 / 2.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 134.050, 301.900, 144.450, 90.00, 112.61, 90.00
R / Rfree (%) 18.7 / 21.1

Other elements in 5l5b:

The structure of Yeast 20S Proteasome with Human BETA5I (1-138) and Human BETA6 (97- 111; 118-133) also contains other interesting chemical elements:

Chlorine (Cl) 4 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) (pdb code 5l5b). 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), PDB code: 5l5b:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Magnesium binding site 1 out of 9 in 5l5b

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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)


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

b:59.6
occ:1.00
 O G:MET125 2.1 50.1 1.0
O G:ARG122 2.4 48.5 1.0
O G:TYR119 2.6 43.1 1.0
OG1 G:THR8 2.6 48.2 1.0
CG2 G:THR8 3.2 47.8 1.0
C G:MET125 3.3 49.2 1.0
O G:ALA123 3.4 55.7 1.0
C G:ARG122 3.5 48.2 1.0
CB G:THR8 3.5 47.7 1.0
C G:ALA123 3.7 51.2 1.0
CA G:ALA123 3.7 49.0 1.0
C G:TYR119 3.8 41.5 1.0
N G:ALA123 4.0 48.0 1.0
N G:MET125 4.1 52.3 1.0
N G:ARG126 4.2 46.0 1.0
CA G:ARG126 4.2 44.8 1.0
N G:THR8 4.3 49.3 1.0
CA G:MET125 4.3 53.3 1.0
CA G:THR8 4.5 48.7 1.0
CA G:TYR119 4.5 41.2 1.0
N G:TYR124 4.6 52.2 1.0
CD G:PRO127 4.6 42.2 1.0
CA G:ARG122 4.7 49.4 1.0
N G:ARG122 4.8 46.7 1.0
N G:THR120 4.8 41.0 1.0
CB G:MET125 4.8 57.5 1.0
C G:ARG126 4.9 42.6 1.0
CA G:THR120 4.9 41.8 1.0
C G:TYR124 4.9 51.1 1.0
C G:THR120 5.0 42.8 1.0

Magnesium binding site 2 out of 9 in 5l5b

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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)


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) within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg301

b:55.5
occ:1.00
 OE1 H:GLN91 3.0 48.7 1.0
OD1 N:ASP51 3.3 46.9 1.0
CD H:GLN91 3.8 35.4 1.0
OD2 N:ASP51 3.8 45.0 1.0
O N:ASN92 3.9 49.6 1.0
NE2 H:GLN91 3.9 51.4 1.0
CG N:ASP51 4.0 41.7 1.0
C N:ASN92 5.0 50.5 1.0

Magnesium binding site 3 out of 9 in 5l5b

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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)


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

b:54.0
occ:1.00
 O I:ASP177 2.3 46.5 1.0
O I:SER180 2.6 51.4 1.0
O I:ALA174 3.0 46.8 1.0
C I:ASP177 3.5 46.3 1.0
OXT I:ASP204 3.6 53.4 1.0
C I:SER180 3.8 49.4 1.0
O I:ALA178 4.0 50.2 1.0
CA I:ALA178 4.1 45.7 1.0
C I:ALA178 4.1 47.1 1.0
C I:ALA174 4.1 46.0 1.0
N I:ALA178 4.2 45.7 1.0
CD1 Y:ILE26 4.3 43.8 1.0
O I:ASP204 4.4 52.6 1.0
N I:SER180 4.4 47.7 1.0
C I:ASP204 4.5 53.0 1.0
NH1 Y:ARG19 4.5 60.1 1.0
N I:ASP177 4.6 45.9 1.0
CA I:ASP175 4.6 48.3 1.0
CA I:ASP177 4.6 45.4 1.0
CA I:SER180 4.7 48.5 1.0
N I:GLY181 4.8 48.8 1.0
CA I:GLY181 4.8 49.2 1.0
NH2 Y:ARG19 4.8 57.7 1.0
N I:ASP175 4.8 46.9 1.0
N I:LEU179 4.8 46.4 1.0
C I:ASP175 4.9 48.8 1.0

Magnesium binding site 4 out of 9 in 5l5b

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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)


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

b:49.6
occ:1.00
 O Y:ASP167 2.1 52.5 1.0
O Y:ALA164 2.3 47.8 1.0
O I:ASP204 2.5 52.6 1.0
O Y:SER170 2.5 45.4 1.0
C Y:ASP167 3.2 49.6 1.0
C I:ASP204 3.2 53.0 1.0
C Y:ALA164 3.5 46.3 1.0
NH1 Y:ARG19 3.5 60.1 1.0
CA Y:ALA168 3.6 50.1 1.0
C Y:SER170 3.7 50.8 1.0
O Y:ALA168 3.7 52.0 1.0
CA I:ASP204 3.7 55.0 1.0
C Y:ALA168 3.8 51.4 1.0
N Y:ALA168 3.8 49.3 1.0
CB I:ASP204 4.0 55.7 1.0
O Y:HIS165 4.1 49.0 1.0
OXT I:ASP204 4.1 53.4 1.0
N Y:SER170 4.2 51.2 1.0
CA Y:ALA164 4.2 46.5 1.0
CZ Y:ARG19 4.3 59.2 1.0
CA Y:ASP167 4.4 48.8 1.0
C Y:HIS165 4.4 48.4 1.0
N Y:ASP167 4.4 49.6 1.0
CA Y:SER170 4.5 50.2 1.0
N Y:HIS165 4.5 46.6 1.0
N Y:TYR169 4.5 52.0 1.0
O Y:ALA163 4.6 47.4 1.0
NH2 Y:ARG19 4.7 57.7 1.0
N Y:GLY171 4.7 52.3 1.0
CA Y:HIS165 4.7 47.8 1.0
C Y:ARG166 4.8 49.2 1.0
CA Y:GLY171 4.9 52.8 1.0
CB Y:SER170 4.9 49.6 1.0

Magnesium binding site 5 out of 9 in 5l5b

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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)


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

b:65.4
occ:1.00
 O J:THR124 2.9 44.1 1.0
OE1 J:GLN118 3.2 42.2 1.0
N J:ASP120 3.6 38.7 1.0
O J:GLN118 3.7 38.4 1.0
CG J:GLN118 3.7 40.3 1.0
CD J:GLN118 3.8 40.5 1.0
CB J:ASP120 4.0 41.0 1.0
C J:THR124 4.0 42.5 1.0
C J:GLN118 4.0 39.0 1.0
CG J:ASP120 4.1 43.5 1.0
OD2 J:ASP120 4.1 47.9 1.0
CB J:THR124 4.1 42.6 1.0
CE1 J:HIS133 4.2 40.8 1.0
C J:ILE119 4.2 38.2 1.0
CA J:ILE119 4.2 37.9 1.0
N J:ILE119 4.3 38.1 1.0
CG2 J:THR124 4.3 42.1 1.0
CA J:ASP120 4.4 39.9 1.0
CB J:GLN118 4.4 39.5 1.0
OD1 J:ASP120 4.7 49.8 1.0
CA J:THR124 4.7 41.9 1.0
CA J:GLN118 4.9 39.2 1.0
CG1 I:VAL35 4.9 52.9 1.0
NE2 J:HIS133 5.0 40.1 1.0
ND1 J:HIS133 5.0 41.4 1.0
N J:LYS125 5.0 42.1 1.0

Magnesium binding site 6 out of 9 in 5l5b

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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)


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) within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg301

b:47.3
occ:1.00
 O K:ASP167 2.1 54.3 1.0
O K:ALA164 2.3 49.1 1.0
O W:ASP204 2.4 53.2 1.0
O K:SER170 2.4 52.1 1.0
C W:ASP204 3.2 53.8 1.0
C K:ASP167 3.3 50.6 1.0
C K:ALA164 3.5 47.4 1.0
NH1 K:ARG19 3.5 59.5 1.0
C K:SER170 3.6 51.1 1.0
CA W:ASP204 3.6 53.7 1.0
CA K:ALA168 3.7 50.5 1.0
O K:ALA168 3.7 49.6 1.0
C K:ALA168 3.8 50.3 1.0
N K:ALA168 3.9 50.3 1.0
CB W:ASP204 3.9 54.3 1.0
OXT W:ASP204 4.1 55.9 1.0
N K:SER170 4.1 49.9 1.0
O K:HIS165 4.1 50.1 1.0
CA K:ALA164 4.2 48.1 1.0
CZ K:ARG19 4.3 58.1 1.0
CA K:SER170 4.4 49.5 1.0
CA K:ASP167 4.4 49.3 1.0
C K:HIS165 4.5 48.0 1.0
N K:ASP167 4.5 49.6 1.0
N K:HIS165 4.5 46.8 1.0
N K:TYR169 4.6 51.7 1.0
NH2 K:ARG19 4.6 58.6 1.0
O K:ALA163 4.6 47.3 1.0
N K:GLY171 4.6 52.2 1.0
CA K:HIS165 4.8 48.0 1.0
CA K:GLY171 4.8 53.3 1.0
CB K:SER170 4.9 48.6 1.0
CG W:ASP204 4.9 54.2 1.0
C K:ARG166 4.9 49.8 1.0

Magnesium binding site 7 out of 9 in 5l5b

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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)


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

b:61.0
occ:1.00
 OXT L:ASP222 2.0 78.7 1.0
O V:ASP166 2.1 42.9 1.0
O V:ILE163 2.1 46.8 1.0
O V:SER169 2.3 49.4 1.0
C L:ASP222 3.0 73.2 1.0
C V:ASP166 3.1 44.7 1.0
C V:ILE163 3.2 47.5 1.0
C V:SER169 3.4 48.9 1.0
CA L:ASP222 3.7 70.5 1.0
O V:GLY162 3.8 46.1 1.0
CA V:LEU167 3.8 45.5 1.0
N V:LEU167 3.8 45.6 1.0
NH1 V:ARG19 3.9 52.9 1.0
O L:ASP222 4.0 76.5 1.0
N V:ASP166 4.0 45.6 1.0
CA V:ILE163 4.0 47.1 1.0
CA V:ASP166 4.1 44.2 1.0
CB L:ASP222 4.2 68.9 1.0
N V:SER169 4.2 45.7 1.0
N V:TRP164 4.2 48.6 1.0
C V:LEU167 4.2 44.7 1.0
C V:TRP164 4.2 49.4 1.0
O V:TRP164 4.3 51.8 1.0
CA V:SER169 4.3 46.4 1.0
N V:GLY170 4.4 49.7 1.0
CA V:GLY170 4.4 51.0 1.0
CA V:TRP164 4.5 49.5 1.0
O V:LEU167 4.5 44.7 1.0
CZ V:ARG19 4.5 52.4 1.0
N V:ASN165 4.6 47.4 1.0
CB V:SER169 4.7 47.0 1.0
C V:GLY162 4.7 46.9 1.0
C V:ASN165 4.8 46.7 1.0
NH2 V:ARG19 4.8 54.8 1.0
N V:ILE163 4.9 47.3 1.0
N V:GLY168 4.9 45.3 1.0
CB V:ASP166 4.9 44.5 1.0
O L:ARG221 5.0 60.2 1.0

Magnesium binding site 8 out of 9 in 5l5b

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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)


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

b:50.7
occ:1.00
 O N:SER169 2.6 40.0 1.0
O N:ILE163 2.7 43.1 1.0
O N:ASP166 3.0 41.2 1.0
CD1 a:LEU34 3.5 47.9 1.0
NH1 N:ARG19 3.6 43.0 1.0
C N:ILE163 3.8 42.5 1.0
C N:SER169 3.8 40.3 1.0
C N:ASP166 4.0 40.3 1.0
CG2 N:ILE163 4.0 42.0 1.0
CA N:GLY167 4.1 40.0 1.0
CZ N:ARG19 4.2 42.1 1.0
O N:GLY167 4.3 40.0 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 42.0 1.0
N N:GLY167 4.5 39.9 1.0
C N:GLY167 4.5 39.5 1.0
N N:GLY170 4.6 40.8 1.0
CG a:LEU34 4.8 47.2 1.0
N N:SER169 4.8 40.8 1.0
CB N:ILE163 4.8 41.5 1.0
CA N:SER169 4.9 39.9 1.0
N N:LYS164 4.9 42.9 1.0
O N:LYS164 5.0 50.7 1.0

Magnesium binding site 9 out of 9 in 5l5b

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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)


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) within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg301

b:72.8
occ:1.00
 O Z:VAL198 2.7 50.0 1.0
O Z:THR192 2.7 57.1 1.0
O Z:HIS195 2.9 48.5 1.0
O Z:ASP222 3.6 77.3 1.0
C Z:THR192 3.8 59.6 1.0
NH2 Z:ARG28 3.8 60.2 1.0
C Z:HIS195 3.8 52.2 1.0
CA Z:ILE196 3.8 54.7 1.0
O Z:ILE196 3.8 59.4 1.0
C Z:VAL198 3.9 54.8 1.0
CG2 Z:THR192 3.9 62.6 1.0
C Z:ILE196 4.0 54.3 1.0
NH2 H:ARG19 4.1 60.6 1.0
CA Z:THR192 4.2 61.6 1.0
N Z:ILE196 4.2 53.7 1.0
OD1 Z:ASP222 4.3 69.9 1.0
N Z:VAL198 4.5 53.1 1.0
C Z:ASP222 4.6 75.0 1.0
CB Z:THR192 4.7 61.2 1.0
CA Z:VAL198 4.7 55.3 1.0
N Z:GLY199 4.8 55.5 1.0
CZ H:ARG19 4.8 57.3 1.0
CA Z:GLY199 4.8 57.4 1.0
NH1 H:ARG19 4.9 57.5 1.0
CZ Z:ARG28 4.9 60.4 1.0
N Z:GLN197 4.9 52.8 1.0
N Z:GLU193 5.0 58.8 1.0
N Z:HIS195 5.0 53.7 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 19:20:32 2024

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