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Magnesium in PDB 5l5a: Yeast 20S Proteasome with Human BETA5I (1-138; R57T)

Enzymatic activity of Yeast 20S Proteasome with Human BETA5I (1-138; R57T)

All present enzymatic activity of Yeast 20S Proteasome with Human BETA5I (1-138; R57T):
3.4.25.1;

Protein crystallography data

The structure of Yeast 20S Proteasome with Human BETA5I (1-138; R57T), PDB code: 5l5a 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 / 2.40
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 135.140, 301.150, 145.060, 90.00, 112.57, 90.00
R / Rfree (%) 20 / 21.9

Other elements in 5l5a:

The structure of Yeast 20S Proteasome with Human BETA5I (1-138; R57T) 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; R57T) (pdb code 5l5a). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 10 binding sites of Magnesium where determined in the Yeast 20S Proteasome with Human BETA5I (1-138; R57T), PDB code: 5l5a:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 10 in 5l5a

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Magnesium binding site 1 out of 10 in the Yeast 20S Proteasome with Human BETA5I (1-138; R57T)


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; R57T) within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:39.5
occ:1.00
 O G:MET125 2.1 40.3 1.0
O G:ARG122 2.2 36.1 1.0
O G:TYR119 2.3 31.9 1.0
O G:HOH428 2.5 39.0 1.0
OG1 G:THR8 2.6 38.8 1.0
CG2 G:THR8 3.3 37.6 1.0
C G:MET125 3.4 40.1 1.0
C G:ARG122 3.4 37.9 1.0
C G:TYR119 3.4 33.0 1.0
CB G:THR8 3.5 37.7 1.0
O G:ALA123 3.7 44.4 1.0
CA G:ALA123 3.8 39.3 1.0
C G:ALA123 3.9 41.3 1.0
N G:ALA123 4.1 38.2 1.0
N G:MET125 4.2 42.5 1.0
CA G:TYR119 4.2 32.6 1.0
N G:ARG126 4.3 36.5 1.0
CA G:MET125 4.3 43.6 1.0
CA G:ARG126 4.3 35.4 1.0
N G:THR120 4.4 33.3 1.0
N G:THR8 4.5 39.0 1.0
N G:ARG122 4.5 37.6 1.0
CA G:ARG122 4.5 40.3 1.0
CD G:PRO127 4.5 33.5 1.0
CA G:THR8 4.6 38.8 1.0
CA G:THR120 4.6 32.9 1.0
N G:TYR124 4.7 42.6 1.0
C G:THR120 4.7 33.5 1.0
CB G:MET125 4.7 48.9 1.0
CB G:TYR119 4.8 32.2 1.0
C G:ARG126 4.8 34.0 1.0
N G:GLN121 4.9 33.9 1.0
N G:PRO127 5.0 33.2 1.0

Magnesium binding site 2 out of 10 in 5l5a

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Magnesium binding site 2 out of 10 in the Yeast 20S Proteasome with Human BETA5I (1-138; R57T)


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; R57T) within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg301

b:57.8
occ:1.00
 O N:HOH331 2.0 41.8 1.0
O H:HOH402 2.2 50.4 1.0
O N:HOH326 2.5 45.4 1.0
OE1 H:GLN91 2.7 47.5 1.0
O N:HOH307 2.7 38.5 1.0
OD1 N:ASP51 3.4 35.6 1.0
CD H:GLN91 3.6 35.0 1.0
O H:HOH424 3.8 28.5 1.0
OD2 N:ASP51 3.9 37.9 1.0
NE2 H:GLN91 4.0 49.9 1.0
O N:ASN92 4.0 45.8 1.0
O H:HOH444 4.0 60.2 1.0
CG N:ASP51 4.1 34.9 1.0
O N:HOH304 4.2 36.3 1.0
ND1 H:HIS116 4.5 34.0 1.0
CG H:GLN91 4.9 44.8 1.0

Magnesium binding site 3 out of 10 in 5l5a

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Magnesium binding site 3 out of 10 in the Yeast 20S Proteasome with Human BETA5I (1-138; R57T)


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; R57T) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:51.1
occ:1.00
 O I:ASP177 2.4 37.2 1.0
O I:SER180 2.5 41.2 1.0
O I:HOH446 2.7 45.0 1.0
O I:ALA174 3.1 36.8 1.0
O Y:HOH418 3.3 39.4 1.0
OXT I:ASP204 3.6 44.1 1.0
C I:ASP177 3.6 36.2 1.0
C I:SER180 3.7 40.1 1.0
O I:ALA178 3.9 39.6 1.0
C I:ALA178 4.1 37.1 1.0
CA I:ALA178 4.1 36.6 1.0
C I:ALA174 4.2 37.4 1.0
N I:ALA178 4.3 35.5 1.0
O I:ASP204 4.3 42.1 1.0
N I:SER180 4.4 38.1 1.0
C I:ASP204 4.4 44.4 1.0
CD1 Y:ILE26 4.4 31.7 1.0
NH1 Y:ARG19 4.6 49.4 1.0
CA I:ASP175 4.6 39.3 1.0
N I:GLY181 4.7 39.7 1.0
CA I:SER180 4.7 39.3 1.0
N I:ASP177 4.7 36.4 1.0
CA I:GLY181 4.7 39.8 1.0
CA I:ASP177 4.7 36.5 1.0
NH2 Y:ARG19 4.8 49.3 1.0
N I:ASP175 4.9 38.7 1.0
N I:LEU179 4.9 36.5 1.0
C I:ASP175 5.0 39.0 1.0

Magnesium binding site 4 out of 10 in 5l5a

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Magnesium binding site 4 out of 10 in the Yeast 20S Proteasome with Human BETA5I (1-138; R57T)


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; R57T) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg302

b:41.2
occ:1.00
 O Y:ALA164 2.3 32.4 1.0
O Y:ASP167 2.3 39.0 1.0
O Y:SER170 2.3 42.2 1.0
O I:ASP204 2.4 42.1 1.0
O Y:HOH431 3.0 30.0 1.0
C I:ASP204 3.2 44.4 1.0
C Y:ASP167 3.4 40.0 1.0
C Y:ALA164 3.4 35.8 1.0
NH1 Y:ARG19 3.5 49.4 1.0
C Y:SER170 3.6 43.5 1.0
CA I:ASP204 3.7 44.3 1.0
CB I:ASP204 3.8 44.6 1.0
O Y:ALA168 3.8 42.7 1.0
CA Y:ALA168 3.9 42.5 1.0
C Y:ALA168 3.9 42.8 1.0
N Y:ALA168 4.1 40.4 1.0
CA Y:ALA164 4.1 38.4 1.0
N Y:SER170 4.1 42.6 1.0
OXT I:ASP204 4.2 44.1 1.0
CZ Y:ARG19 4.2 50.0 1.0
O Y:HIS165 4.3 42.1 1.0
CA Y:SER170 4.4 42.1 1.0
N Y:HIS165 4.5 37.5 1.0
C Y:HIS165 4.5 40.6 1.0
N Y:GLY171 4.5 44.5 1.0
NH2 Y:ARG19 4.5 49.3 1.0
CA Y:ASP167 4.6 39.8 1.0
N Y:ASP167 4.6 40.1 1.0
CA Y:GLY171 4.6 45.3 1.0
N Y:TYR169 4.7 43.4 1.0
O Y:ALA163 4.7 36.1 1.0
CA Y:HIS165 4.8 39.8 1.0
CG I:ASP204 4.8 45.0 1.0
CB Y:SER170 4.9 40.8 1.0
CB Y:ALA164 4.9 40.2 1.0

Magnesium binding site 5 out of 10 in 5l5a

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Magnesium binding site 5 out of 10 in the Yeast 20S Proteasome with Human BETA5I (1-138; R57T)


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; R57T) within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mg201

b:52.4
occ:1.00
 O J:HOH339 2.7 36.6 1.0
O J:THR124 3.0 33.2 1.0
OE1 J:GLN118 3.1 34.3 1.0
CG J:GLN118 3.5 31.9 1.0
O J:GLN118 3.6 30.9 1.0
N J:ASP120 3.6 30.4 1.0
CD J:GLN118 3.7 32.1 1.0
C J:GLN118 3.9 30.6 1.0
CB J:ASP120 4.0 32.4 1.0
CE1 J:HIS133 4.1 30.4 1.0
C J:THR124 4.1 33.3 1.0
CA J:ILE119 4.1 29.3 1.0
C J:ILE119 4.1 30.1 1.0
CG J:ASP120 4.1 33.0 1.0
OD2 J:ASP120 4.1 34.6 1.0
N J:ILE119 4.2 29.5 1.0
CB J:THR124 4.3 33.5 1.0
CB J:GLN118 4.3 31.0 1.0
CA J:ASP120 4.4 31.0 1.0
CG2 J:THR124 4.5 33.9 1.0
CA J:GLN118 4.8 30.9 1.0
OD1 J:ASP120 4.8 33.7 1.0
CA J:THR124 4.8 33.3 1.0
NE2 J:HIS133 4.8 30.0 1.0
ND1 J:HIS133 4.9 30.8 1.0
CG1 I:VAL35 4.9 42.4 1.0

Magnesium binding site 6 out of 10 in 5l5a

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Magnesium binding site 6 out of 10 in the Yeast 20S Proteasome with Human BETA5I (1-138; R57T)


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; R57T) within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg301

b:46.5
occ:1.00
 O K:ALA164 2.3 39.5 1.0
O K:ASP167 2.3 41.7 1.0
O W:ASP204 2.4 39.6 1.0
O K:SER170 2.4 40.7 1.0
C W:ASP204 3.1 42.0 1.0
C K:ASP167 3.4 41.4 1.0
C K:ALA164 3.4 38.2 1.0
NH1 K:ARG19 3.5 49.3 1.0
CA W:ASP204 3.5 43.0 1.0
C K:SER170 3.6 41.9 1.0
CB W:ASP204 3.7 43.5 1.0
O K:ALA168 3.8 39.2 1.0
CA K:ALA168 3.9 41.8 1.0
C K:ALA168 3.9 41.5 1.0
N K:ALA168 4.1 41.2 1.0
OXT W:ASP204 4.1 42.3 1.0
CA K:ALA164 4.1 39.3 1.0
N K:SER170 4.2 40.8 1.0
O K:HIS165 4.2 39.0 1.0
CZ K:ARG19 4.3 48.8 1.0
CA K:SER170 4.4 40.5 1.0
C K:HIS165 4.5 38.8 1.0
N K:HIS165 4.5 37.8 1.0
CA K:ASP167 4.6 40.2 1.0
N K:GLY171 4.6 43.5 1.0
N K:ASP167 4.6 40.8 1.0
NH2 K:ARG19 4.6 49.8 1.0
O K:ALA163 4.7 35.8 1.0
N K:TYR169 4.7 42.1 1.0
CA K:GLY171 4.7 44.6 1.0
CA K:HIS165 4.7 39.3 1.0
CG W:ASP204 4.7 43.1 1.0
CB K:SER170 4.9 39.8 1.0
CB K:ALA164 4.9 40.4 1.0
N W:ASP204 5.0 42.8 1.0

Magnesium binding site 7 out of 10 in 5l5a

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Magnesium binding site 7 out of 10 in the Yeast 20S Proteasome with Human BETA5I (1-138; R57T)


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; R57T) within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg302

b:64.7
occ:1.00
 O K:LEU82 2.8 46.8 1.0
O K:HOH434 2.9 50.2 1.0
C K:LEU82 3.6 47.9 1.0
CG K:MET86 3.7 47.2 1.0
CA K:LEU82 3.7 47.6 1.0
CB K:ASN85 3.9 57.0 1.0
N K:MET86 4.0 49.0 1.0
CB K:LEU82 4.1 44.3 1.0
CD2 K:LEU82 4.2 32.4 1.0
CE K:MET86 4.3 30.5 1.0
C K:ASN85 4.4 49.7 1.0
CA K:MET86 4.5 52.7 1.0
CB K:MET86 4.6 51.7 1.0
CA K:ASN85 4.7 54.2 1.0
CG K:LEU82 4.8 37.9 1.0
N K:LEU83 4.9 48.1 1.0
SD K:MET86 4.9 41.2 1.0
OD1 K:ASN85 5.0 55.9 1.0

Magnesium binding site 8 out of 10 in 5l5a

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Magnesium binding site 8 out of 10 in the Yeast 20S Proteasome with Human BETA5I (1-138; R57T)


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; R57T) within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg301

b:43.7
occ:1.00
 OXT L:ASP222 2.2 51.4 1.0
O V:ASP166 2.2 37.4 1.0
O V:ILE163 2.2 40.0 1.0
O V:SER169 2.2 44.1 1.0
C L:ASP222 3.1 53.7 1.0
C V:ASP166 3.2 38.4 1.0
C V:ILE163 3.3 41.4 1.0
C V:SER169 3.4 42.4 1.0
CA L:ASP222 3.8 53.7 1.0
NH1 V:ARG19 3.8 44.3 1.0
O V:GLY162 3.8 39.8 1.0
CA V:LEU167 3.9 39.7 1.0
N V:LEU167 3.9 38.6 1.0
O L:ASP222 4.0 58.3 1.0
CA V:ILE163 4.0 41.6 1.0
N V:ASP166 4.1 39.2 1.0
N V:SER169 4.2 40.3 1.0
CB L:ASP222 4.2 54.4 1.0
N V:GLY170 4.2 44.6 1.0
C V:LEU167 4.3 39.9 1.0
N V:TRP164 4.3 41.7 1.0
CA V:GLY170 4.3 46.2 1.0
CA V:ASP166 4.3 38.5 1.0
CA V:SER169 4.3 41.5 1.0
C V:TRP164 4.4 43.6 1.0
O V:LEU167 4.4 38.1 1.0
CZ V:ARG19 4.4 44.4 1.0
O V:TRP164 4.5 44.5 1.0
CA V:TRP164 4.5 43.3 1.0
NH2 V:ARG19 4.6 44.9 1.0
CB V:SER169 4.7 41.6 1.0
N V:ASN165 4.7 41.9 1.0
C V:GLY162 4.8 41.0 1.0
C V:ASN165 4.9 40.2 1.0
N V:ILE163 4.9 41.7 1.0
N V:GLY168 5.0 40.1 1.0

Magnesium binding site 9 out of 10 in 5l5a

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Magnesium binding site 9 out of 10 in the Yeast 20S Proteasome with Human BETA5I (1-138; R57T)


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; R57T) within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg201

b:38.6
occ:1.00
 O N:ILE163 2.5 36.6 1.0
O N:SER169 2.6 34.5 1.0
O N:ASP166 2.8 34.5 1.0
CD1 a:LEU34 3.6 40.9 1.0
C N:ILE163 3.6 36.7 1.0
C N:SER169 3.7 34.7 1.0
NH1 N:ARG19 3.7 37.1 1.0
C N:ASP166 3.8 34.1 1.0
CG2 N:ILE163 3.9 35.9 1.0
CA N:GLY167 4.1 34.5 1.0
CA N:ILE163 4.3 36.0 1.0
N N:GLY167 4.3 34.0 1.0
O N:GLY167 4.3 37.4 1.0
CZ N:ARG19 4.3 36.9 1.0
C N:GLY167 4.4 34.4 1.0
CA N:GLY170 4.4 36.5 1.0
N N:GLY170 4.5 35.4 1.0
NH2 N:ARG19 4.6 36.8 1.0
N N:SER169 4.7 34.6 1.0
N N:LYS164 4.7 38.5 1.0
CA N:SER169 4.7 34.0 1.0
CB N:ILE163 4.7 35.3 1.0
CG a:LEU34 4.7 40.4 1.0
N N:ASP166 4.9 34.0 1.0
C N:LYS164 4.9 39.8 1.0
CA N:ASP166 4.9 34.0 1.0
O N:LYS164 4.9 40.7 1.0
CA N:LYS164 5.0 40.2 1.0

Magnesium binding site 10 out of 10 in 5l5a

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Magnesium binding site 10 out of 10 in the Yeast 20S Proteasome with Human BETA5I (1-138; R57T)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Yeast 20S Proteasome with Human BETA5I (1-138; R57T) within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg301

b:61.0
occ:1.00
 O Z:HOH443 2.4 40.0 1.0
O Z:HIS195 2.5 41.4 1.0
O Z:VAL198 2.5 47.4 1.0
O Z:THR192 2.7 48.5 1.0
C Z:HIS195 3.5 41.8 1.0
CA Z:ILE196 3.6 41.4 1.0
O Z:ILE196 3.6 43.8 1.0
C Z:VAL198 3.7 45.8 1.0
C Z:THR192 3.7 50.2 1.0
C Z:ILE196 3.7 41.1 1.0
NH2 Z:ARG28 3.9 47.4 1.0
N Z:ILE196 4.0 41.0 1.0
CA Z:THR192 4.1 51.0 1.0
CG2 Z:THR192 4.1 53.0 1.0
N Z:VAL198 4.2 42.6 1.0
O Z:ASP222 4.2 55.1 1.0
NH2 H:ARG19 4.3 51.8 1.0
CA Z:VAL198 4.4 43.8 1.0
N Z:GLN197 4.6 40.0 1.0
CA Z:HIS195 4.7 42.2 1.0
N Z:HIS195 4.7 41.7 1.0
CB Z:THR192 4.7 51.4 1.0
N Z:GLY199 4.7 46.9 1.0
OD1 Z:ASP222 4.8 52.2 1.0
CB Z:VAL198 4.8 44.1 1.0
CA Z:GLY199 4.9 48.3 1.0
O Z:ALA191 4.9 49.5 1.0
N Z:GLU193 4.9 50.4 1.0
NH1 H:ARG19 4.9 49.3 1.0
CB Z:ILE196 4.9 40.3 1.0
CZ Z:ARG28 4.9 48.0 1.0
CZ H:ARG19 5.0 50.1 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 19:20:17 2024

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