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Magnesium in PDB 5ltt: Yeast 20S Proteasome with Human BETA5I (1-138; R57T)in Complex with Pr-924

Enzymatic activity of Yeast 20S Proteasome with Human BETA5I (1-138; R57T)in Complex with Pr-924

All present enzymatic activity of Yeast 20S Proteasome with Human BETA5I (1-138; R57T)in Complex with Pr-924:
3.4.25.1;

Protein crystallography data

The structure of Yeast 20S Proteasome with Human BETA5I (1-138; R57T)in Complex with Pr-924, PDB code: 5ltt 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 / 2.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 135.850, 300.350, 145.580, 90.00, 113.36, 90.00
R / Rfree (%) 22.3 / 24.7

Other elements in 5ltt:

The structure of Yeast 20S Proteasome with Human BETA5I (1-138; R57T)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; R57T)in Complex with Pr-924 (pdb code 5ltt). 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; R57T)in Complex with Pr-924, PDB code: 5ltt:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 5ltt

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Magnesium binding site 1 out of 8 in the Yeast 20S Proteasome with Human BETA5I (1-138; R57T)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; R57T)in Complex with Pr-924 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:45.2
occ:1.00
 O G:MET125 2.1 42.0 1.0
O G:ARG122 2.5 41.6 1.0
OG1 G:THR8 2.7 41.0 1.0
O G:TYR119 2.7 35.2 1.0
CG2 G:THR8 3.2 43.2 1.0
C G:MET125 3.3 44.1 1.0
O G:ALA123 3.4 46.8 1.0
CB G:THR8 3.5 42.4 1.0
C G:ARG122 3.6 43.0 1.0
C G:ALA123 3.7 45.5 1.0
CA G:ALA123 3.8 44.0 1.0
C G:TYR119 3.9 36.0 1.0
N G:ARG126 4.2 42.1 1.0
CA G:ARG126 4.2 41.0 1.0
N G:ALA123 4.2 42.9 1.0
N G:MET125 4.2 45.7 1.0
N G:THR8 4.2 44.5 1.0
CA G:MET125 4.3 47.7 1.0
CD G:PRO127 4.5 36.9 1.0
CA G:THR8 4.5 43.4 1.0
N G:TYR124 4.6 47.2 1.0
CA G:TYR119 4.6 35.8 1.0
C G:ARG126 4.8 39.8 1.0
CA G:ARG122 4.9 44.5 1.0
CB G:MET125 4.9 51.2 1.0
N G:THR120 4.9 35.5 1.0
C G:TYR124 4.9 45.2 1.0
N G:ARG122 4.9 42.2 1.0
N G:PRO127 5.0 38.0 1.0

Magnesium binding site 2 out of 8 in 5ltt

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Magnesium binding site 2 out of 8 in the Yeast 20S Proteasome with Human BETA5I (1-138; R57T)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; R57T)in Complex with Pr-924 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:51.0
occ:1.00
 O I:ASP177 2.4 44.1 1.0
O I:SER180 2.4 41.0 1.0
O I:ALA174 2.8 44.7 1.0
OXT I:ASP204 3.5 49.1 1.0
C I:ASP177 3.6 44.1 1.0
C I:SER180 3.6 44.4 1.0
C I:ALA174 3.9 45.0 1.0
O I:ALA178 4.2 46.0 1.0
CD1 Y:ILE26 4.2 44.6 1.0
C I:ALA178 4.3 45.4 1.0
CA I:ALA178 4.3 43.8 1.0
N I:ALA178 4.4 43.0 1.0
N I:SER180 4.4 45.0 1.0
O I:ASP204 4.4 49.4 1.0
C I:ASP204 4.5 49.9 1.0
CA I:ASP175 4.5 47.9 1.0
CA I:GLY181 4.5 45.8 1.0
N I:GLY181 4.5 44.4 1.0
N I:ASP177 4.6 45.4 1.0
CA I:SER180 4.6 45.0 1.0
CA I:ASP177 4.6 44.8 1.0
N I:ASP175 4.7 45.8 1.0
NH1 Y:ARG19 4.8 57.0 1.0
NH2 Y:ARG19 4.9 56.8 1.0
C I:ASP175 4.9 48.0 1.0
OD1 I:ASP175 5.0 50.2 1.0
CA I:ALA174 5.0 43.3 1.0

Magnesium binding site 3 out of 8 in 5ltt

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Magnesium binding site 3 out of 8 in the Yeast 20S Proteasome with Human BETA5I (1-138; R57T)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; R57T)in Complex with Pr-924 within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mg201

b:49.5
occ:1.00
 OE1 J:GLN118 3.1 37.7 1.0
O J:THR124 3.3 39.1 1.0
N J:ASP120 3.7 35.4 1.0
CB J:ASP120 3.8 37.7 1.0
CG J:GLN118 3.9 35.2 1.0
CD J:GLN118 3.9 35.7 1.0
CG J:ASP120 4.0 40.1 1.0
O J:GLN118 4.0 36.2 1.0
OD2 J:ASP120 4.1 44.1 1.0
CE1 J:HIS133 4.2 36.6 1.0
CB J:THR124 4.2 39.2 1.0
C J:THR124 4.3 38.1 1.0
C J:GLN118 4.4 34.6 1.0
C J:ILE119 4.4 35.4 1.0
CA J:ASP120 4.4 36.3 1.0
CG2 J:THR124 4.4 38.9 1.0
CA J:ILE119 4.5 33.8 1.0
N J:ILE119 4.6 34.1 1.0
OD1 J:ASP120 4.6 43.2 1.0
CB J:GLN118 4.7 34.6 1.0
CG1 I:VAL35 4.8 49.8 1.0
ND1 J:HIS133 4.9 36.8 1.0
CA J:THR124 4.9 38.6 1.0

Magnesium binding site 4 out of 8 in 5ltt

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Magnesium binding site 4 out of 8 in the Yeast 20S Proteasome with Human BETA5I (1-138; R57T)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; R57T)in Complex with Pr-924 within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg302

b:50.8
occ:1.00
 O K:ASP167 2.2 44.9 1.0
O K:ALA164 2.3 43.8 1.0
O W:ASP204 2.4 56.0 1.0
O K:SER170 2.8 42.3 1.0
C W:ASP204 3.1 53.6 1.0
C K:ASP167 3.2 45.7 1.0
CA W:ASP204 3.5 54.4 1.0
C K:ALA164 3.5 43.2 1.0
NH1 K:ARG19 3.6 54.8 1.0
CA K:ALA168 3.6 45.4 1.0
O K:HIS165 3.7 46.8 1.0
N K:ALA168 3.8 45.8 1.0
CB W:ASP204 3.8 55.3 1.0
C K:ALA168 4.0 45.7 1.0
C K:SER170 4.0 44.0 1.0
O K:ALA168 4.0 45.4 1.0
OXT W:ASP204 4.1 53.7 1.0
C K:HIS165 4.1 44.7 1.0
N K:ASP167 4.3 47.8 1.0
CA K:ALA164 4.3 42.6 1.0
CA K:ASP167 4.3 45.4 1.0
N K:HIS165 4.4 43.6 1.0
N K:SER170 4.4 44.4 1.0
CA K:HIS165 4.5 44.6 1.0
CZ K:ARG19 4.6 54.4 1.0
C K:ARG166 4.6 47.9 1.0
O K:ALA163 4.7 43.1 1.0
N K:TYR169 4.7 45.2 1.0
CA K:SER170 4.8 43.7 1.0
N K:ARG166 4.8 44.8 1.0
N W:ASP204 4.8 53.6 1.0
CG W:ASP204 4.9 57.0 1.0
O K:ARG166 4.9 49.3 1.0
CB K:ALA168 5.0 45.1 1.0

Magnesium binding site 5 out of 8 in 5ltt

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Magnesium binding site 5 out of 8 in the Yeast 20S Proteasome with Human BETA5I (1-138; R57T)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; R57T)in Complex with Pr-924 within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg201

b:44.9
occ:1.00
 O N:ILE163 2.3 40.6 1.0
O N:SER169 2.6 39.5 1.0
O N:ASP166 2.9 38.4 1.0
C N:ILE163 3.5 39.6 1.0
CD1 a:LEU34 3.6 45.8 1.0
CG2 N:ILE163 3.7 38.1 1.0
C N:SER169 3.7 37.7 1.0
C N:ASP166 3.9 36.5 1.0
NH1 N:ARG19 4.0 41.0 1.0
CA N:ILE163 4.1 38.8 1.0
CA N:GLY167 4.2 36.5 1.0
CA N:GLY170 4.3 38.9 1.0
CZ N:ARG19 4.4 39.9 1.0
N N:GLY167 4.5 36.3 1.0
N N:GLY170 4.5 37.7 1.0
N N:LYS164 4.5 40.4 1.0
CB N:ILE163 4.5 37.9 1.0
O N:GLY167 4.6 35.1 1.0
NH2 N:ARG19 4.6 39.4 1.0
C N:GLY167 4.6 35.8 1.0
CA N:SER169 4.8 36.6 1.0
N N:SER169 4.8 37.2 1.0
CA N:LYS164 4.8 42.5 1.0
C N:LYS164 4.8 41.5 1.0
CG a:LEU34 4.9 46.5 1.0
O N:LYS164 4.9 42.3 1.0
N N:ASP166 4.9 35.8 1.0

Magnesium binding site 6 out of 8 in 5ltt

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Magnesium binding site 6 out of 8 in the Yeast 20S Proteasome with Human BETA5I (1-138; R57T)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; R57T)in Complex with Pr-924 within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Mg301

b:54.1
occ:1.00
 OXT L:ASP222 1.9 59.5 1.0
O V:ASP166 2.3 45.2 1.0
O V:ILE163 2.4 42.9 1.0
O V:SER169 2.4 48.9 1.0
C L:ASP222 2.9 63.7 1.0
C V:ASP166 3.3 45.4 1.0
C V:ILE163 3.5 45.0 1.0
NH1 V:ARG19 3.6 56.5 1.0
O L:ASP222 3.6 65.9 1.0
C V:SER169 3.6 48.1 1.0
CA L:ASP222 3.7 63.7 1.0
CA V:LEU167 3.7 45.9 1.0
N V:LEU167 3.8 45.3 1.0
C V:LEU167 4.1 45.8 1.0
O V:GLY162 4.2 46.2 1.0
CB L:ASP222 4.3 63.5 1.0
O V:TRP164 4.3 51.9 1.0
O V:LEU167 4.3 45.5 1.0
N V:ASP166 4.3 44.5 1.0
CA V:ILE163 4.3 46.9 1.0
CZ V:ARG19 4.4 53.9 1.0
C V:TRP164 4.4 49.7 1.0
CA V:ASP166 4.4 44.6 1.0
N V:SER169 4.4 45.7 1.0
N V:TRP164 4.5 46.2 1.0
CA V:GLY170 4.5 49.8 1.0
N V:GLY170 4.5 48.0 1.0
NH2 V:ARG19 4.6 54.8 1.0
CA V:SER169 4.6 47.3 1.0
CA V:TRP164 4.6 49.5 1.0
CD2 V:LEU167 4.7 46.5 1.0
N V:ASN165 4.9 49.9 1.0
O L:ARG221 4.9 55.9 1.0
N V:GLY168 4.9 47.7 1.0
N L:ASP222 4.9 61.6 1.0
CB V:LEU167 4.9 45.5 1.0

Magnesium binding site 7 out of 8 in 5ltt

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Magnesium binding site 7 out of 8 in the Yeast 20S Proteasome with Human BETA5I (1-138; R57T)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; R57T)in Complex with Pr-924 within 5.0Å range:
probe atom residue distance (Å) B Occ
Y:Mg302

b:46.5
occ:1.00
 O I:ASP204 2.2 49.4 1.0
O Y:ASP167 2.3 44.7 1.0
O Y:SER170 2.5 47.9 1.0
O Y:ALA164 2.6 39.2 1.0
NH1 Y:ARG19 3.0 57.0 1.0
C I:ASP204 3.1 49.9 1.0
C Y:ASP167 3.3 42.5 1.0
CA Y:ALA168 3.6 43.1 1.0
O Y:ALA168 3.6 42.3 1.0
CA I:ASP204 3.6 51.0 1.0
C Y:SER170 3.7 44.4 1.0
C Y:ALA168 3.7 42.5 1.0
C Y:ALA164 3.8 39.4 1.0
CB I:ASP204 3.8 50.9 1.0
N Y:ALA168 3.9 44.1 1.0
CZ Y:ARG19 4.1 55.7 1.0
OXT I:ASP204 4.1 49.1 1.0
N Y:SER170 4.1 41.4 1.0
O Y:HIS165 4.3 41.6 1.0
CA Y:SER170 4.5 42.0 1.0
N Y:TYR169 4.5 42.3 1.0
CA Y:ALA164 4.5 39.3 1.0
NH2 Y:ARG19 4.5 56.8 1.0
CA Y:ASP167 4.6 40.5 1.0
N Y:GLY171 4.7 45.1 1.0
N Y:ASP167 4.7 39.7 1.0
C Y:HIS165 4.7 40.6 1.0
CG I:ASP204 4.7 49.2 1.0
CA Y:GLY171 4.8 46.0 1.0
N Y:HIS165 4.8 40.9 1.0
CB Y:ALA168 4.9 44.0 1.0
O Y:ALA163 5.0 43.2 1.0
NE Y:ARG19 5.0 54.1 1.0

Magnesium binding site 8 out of 8 in 5ltt

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Magnesium binding site 8 out of 8 in the Yeast 20S Proteasome with Human BETA5I (1-138; R57T)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; R57T)in Complex with Pr-924 within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg301

b:55.6
occ:1.00
 O Z:VAL198 2.4 48.5 1.0
O Z:THR192 2.6 56.3 1.0
O Z:HIS195 2.8 45.4 1.0
C Z:THR192 3.6 58.3 1.0
C Z:VAL198 3.6 51.8 1.0
NH2 Z:ARG28 3.7 59.8 1.0
CG2 Z:THR192 3.7 60.4 1.0
C Z:HIS195 3.8 49.2 1.0
O Z:ASP222 3.8 63.6 1.0
CA Z:THR192 3.9 58.4 1.0
O Z:ILE196 4.0 50.7 1.0
CA Z:ILE196 4.0 50.0 1.0
C Z:ILE196 4.1 49.7 1.0
N Z:VAL198 4.4 50.3 1.0
NH2 H:ARG19 4.4 54.3 1.0
N Z:ILE196 4.4 48.9 1.0
OD1 Z:ASP222 4.4 64.9 1.0
CB Z:THR192 4.4 58.0 1.0
CA Z:VAL198 4.5 51.4 1.0
N Z:GLY199 4.5 53.1 1.0
CA Z:GLY199 4.6 53.7 1.0
CZ Z:ARG28 4.8 58.6 1.0
C Z:ASP222 4.8 64.6 1.0
N Z:GLU193 4.8 59.5 1.0
CB Z:VAL198 4.9 51.3 1.0
N Z:HIS195 5.0 50.6 1.0
N Z:GLN197 5.0 49.4 1.0
NH1 Z:ARG28 5.0 60.2 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 20:40:25 2024

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