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Magnesium in PDB 5l65: Yeast 20S Proteasome with Mouse BETA5I (1-138) and Mouse BETA6 (97- 111; 118-133) in Complex with Carfilzomib

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

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

Protein crystallography data

The structure of Yeast 20S Proteasome with Mouse BETA5I (1-138) and Mouse BETA6 (97- 111; 118-133) in Complex with Carfilzomib, PDB code: 5l65 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 (°) 135.500, 300.390, 145.490, 90.00, 112.77, 90.00
R / Rfree (%) 17.6 / 20.1

Other elements in 5l65:

The structure of Yeast 20S Proteasome with Mouse BETA5I (1-138) and Mouse BETA6 (97- 111; 118-133) in Complex with Carfilzomib 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 Mouse BETA5I (1-138) and Mouse BETA6 (97- 111; 118-133) in Complex with Carfilzomib (pdb code 5l65). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the Yeast 20S Proteasome with Mouse BETA5I (1-138) and Mouse BETA6 (97- 111; 118-133) in Complex with Carfilzomib, PDB code: 5l65:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 5l65

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


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 Mouse BETA5I (1-138) and Mouse BETA6 (97- 111; 118-133) in Complex with Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:57.3
occ:1.00
 O G:MET125 2.3 52.6 1.0
OG1 G:THR8 2.6 46.5 1.0
O G:ARG122 2.7 48.3 1.0
O G:TYR119 3.0 42.0 1.0
O G:ALA123 3.1 57.8 1.0
CG2 G:THR8 3.2 46.2 1.0
CB G:THR8 3.4 45.9 1.0
C G:MET125 3.4 50.9 1.0
C G:ALA123 3.5 52.5 1.0
CA G:ALA123 3.6 49.1 1.0
C G:ARG122 3.7 47.6 1.0
N G:THR8 3.9 49.5 1.0
N G:ALA123 4.1 46.8 1.0
C G:TYR119 4.2 41.4 1.0
N G:MET125 4.2 52.1 1.0
CA G:ARG126 4.2 45.0 1.0
N G:ARG126 4.2 46.9 1.0
CA G:THR8 4.3 47.2 1.0
CA G:MET125 4.4 54.3 1.0
N G:TYR124 4.5 51.6 1.0
CD G:PRO127 4.6 41.9 1.0
CB G:ALA123 4.9 49.2 1.0
C G:TYR124 4.9 51.1 1.0
C G:ARG126 5.0 44.1 1.0
C G:ILE7 5.0 51.9 1.0
CA G:TYR119 5.0 40.4 1.0

Magnesium binding site 2 out of 7 in 5l65

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Magnesium binding site 2 out of 7 in the Yeast 20S Proteasome with Mouse BETA5I (1-138) and Mouse BETA6 (97- 111; 118-133) in Complex with Carfilzomib


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 Mouse BETA5I (1-138) and Mouse BETA6 (97- 111; 118-133) in Complex with Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:57.6
occ:1.00
 O I:ASP177 2.5 55.9 1.0
O I:SER180 2.5 53.5 1.0
O I:ALA174 3.1 53.5 1.0
OXT I:ASP204 3.5 60.1 1.0
C I:ASP177 3.6 54.1 1.0
C I:SER180 3.8 52.3 1.0
O I:ALA178 4.1 57.4 1.0
CA I:ALA178 4.2 52.7 1.0
C I:ALA178 4.2 53.7 1.0
C I:ALA174 4.2 55.2 1.0
N I:ALA178 4.3 52.1 1.0
O I:ASP204 4.4 52.1 1.0
C I:ASP204 4.4 45.6 1.0
N I:SER180 4.4 49.9 1.0
CD1 Y:ILE26 4.5 53.8 1.0
CA I:GLY181 4.6 52.9 1.0
N I:GLY181 4.6 50.7 1.0
CA I:ASP175 4.6 57.6 1.0
N I:ASP177 4.7 56.0 1.0
CA I:SER180 4.7 52.0 1.0
CA I:ASP177 4.7 53.8 1.0
N I:ASP175 4.9 55.1 1.0
N I:LEU179 4.9 52.2 1.0
NH1 Y:ARG19 4.9 67.7 1.0
NH2 Y:ARG19 5.0 64.3 1.0
C I:ASP175 5.0 58.4 1.0

Magnesium binding site 3 out of 7 in 5l65

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Magnesium binding site 3 out of 7 in the Yeast 20S Proteasome with Mouse BETA5I (1-138) and Mouse BETA6 (97- 111; 118-133) in Complex with Carfilzomib


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 Mouse BETA5I (1-138) and Mouse BETA6 (97- 111; 118-133) in Complex with Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg302

b:55.7
occ:1.00
 O Y:ASP167 2.2 57.0 1.0
O I:ASP204 2.2 52.1 1.0
O Y:ALA164 2.4 52.4 1.0
O Y:SER170 2.7 54.7 1.0
C I:ASP204 3.1 45.6 1.0
C Y:ASP167 3.3 52.3 1.0
NH1 Y:ARG19 3.4 67.7 1.0
CA Y:ALA168 3.6 53.1 1.0
C Y:ALA164 3.6 48.8 1.0
CA I:ASP204 3.7 63.2 1.0
O Y:ALA168 3.8 56.3 1.0
C Y:ALA168 3.8 53.9 1.0
N Y:ALA168 3.8 52.6 1.0
C Y:SER170 3.9 53.6 1.0
CB I:ASP204 3.9 64.8 1.0
OXT I:ASP204 4.1 60.1 1.0
O Y:HIS165 4.1 48.7 1.0
N Y:SER170 4.3 51.5 1.0
CA Y:ALA164 4.4 48.3 1.0
C Y:HIS165 4.4 48.7 1.0
CZ Y:ARG19 4.4 65.5 1.0
CA Y:ASP167 4.5 51.2 1.0
N Y:ASP167 4.5 51.0 1.0
N Y:HIS165 4.6 49.4 1.0
N Y:TYR169 4.6 54.4 1.0
CA Y:SER170 4.7 51.2 1.0
CA Y:HIS165 4.7 48.6 1.0
C Y:ARG166 4.8 50.2 1.0
O Y:ALA163 4.8 47.9 1.0
NH2 Y:ARG19 4.9 64.3 1.0
N Y:GLY171 4.9 55.6 1.0
CB Y:ALA168 4.9 53.2 1.0
CG I:ASP204 4.9 66.3 1.0
CA Y:GLY171 5.0 55.0 1.0

Magnesium binding site 4 out of 7 in 5l65

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Magnesium binding site 4 out of 7 in the Yeast 20S Proteasome with Mouse BETA5I (1-138) and Mouse BETA6 (97- 111; 118-133) in Complex with Carfilzomib


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 Mouse BETA5I (1-138) and Mouse BETA6 (97- 111; 118-133) in Complex with Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mg201

b:53.0
occ:1.00
 OE1 J:GLN118 3.2 45.4 1.0
O J:THR124 3.3 44.8 1.0
CB J:ASP120 3.8 41.4 1.0
N J:ASP120 3.8 38.1 1.0
OD2 J:ASP120 3.9 50.3 1.0
CG J:ASP120 3.9 45.2 1.0
CD J:GLN118 4.1 39.7 1.0
CB J:THR124 4.1 44.0 1.0
CG J:GLN118 4.2 38.8 1.0
O J:GLN118 4.2 34.4 1.0
CE1 J:HIS133 4.2 41.1 1.0
CG2 J:THR124 4.3 44.1 1.0
C J:THR124 4.3 43.0 1.0
CA J:ASP120 4.4 39.3 1.0
C J:ILE119 4.5 37.5 1.0
OD1 J:ASP120 4.5 50.7 1.0
C J:GLN118 4.6 36.7 1.0
CA J:ILE119 4.7 36.5 1.0
N J:ILE119 4.8 36.0 1.0
CG1 I:VAL35 4.9 53.4 1.0
CA J:THR124 4.9 42.2 1.0
ND1 J:HIS133 4.9 40.2 1.0
CB J:GLN118 4.9 37.7 1.0

Magnesium binding site 5 out of 7 in 5l65

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Magnesium binding site 5 out of 7 in the Yeast 20S Proteasome with Mouse BETA5I (1-138) and Mouse BETA6 (97- 111; 118-133) in Complex with Carfilzomib


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 Mouse BETA5I (1-138) and Mouse BETA6 (97- 111; 118-133) in Complex with Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg302

b:59.9
occ:1.00
 O K:ALA164 2.2 48.4 1.0
O K:ASP167 2.2 56.5 1.0
O W:ASP204 2.4 67.8 1.0
O K:SER170 2.9 48.3 1.0
C W:ASP204 3.1 63.0 1.0
C K:ASP167 3.2 52.5 1.0
C K:ALA164 3.3 48.0 1.0
CA W:ASP204 3.6 60.2 1.0
CA K:ALA168 3.7 53.4 1.0
O K:HIS165 3.7 50.2 1.0
NH1 K:ARG19 3.7 65.7 1.0
N K:ALA168 3.9 52.8 1.0
CB W:ASP204 3.9 58.7 1.0
C K:HIS165 4.0 48.6 1.0
OXT W:ASP204 4.1 64.7 1.0
C K:ALA168 4.1 53.8 1.0
C K:SER170 4.1 50.9 1.0
O K:ALA168 4.1 53.9 1.0
CA K:ALA164 4.2 47.9 1.0
N K:HIS165 4.3 47.7 1.0
N K:ASP167 4.3 49.3 1.0
CA K:ASP167 4.4 50.3 1.0
CA K:HIS165 4.4 48.4 1.0
C K:ARG166 4.6 49.5 1.0
N K:SER170 4.6 51.0 1.0
O K:ALA163 4.6 50.6 1.0
N K:ARG166 4.7 48.0 1.0
CZ K:ARG19 4.8 63.3 1.0
O K:ARG166 4.8 51.1 1.0
CA K:SER170 4.9 50.4 1.0
N K:TYR169 4.9 53.9 1.0
N W:ASP204 4.9 60.4 1.0
CG W:ASP204 5.0 59.1 1.0

Magnesium binding site 6 out of 7 in 5l65

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Magnesium binding site 6 out of 7 in the Yeast 20S Proteasome with Mouse BETA5I (1-138) and Mouse BETA6 (97- 111; 118-133) in Complex with Carfilzomib


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 Mouse BETA5I (1-138) and Mouse BETA6 (97- 111; 118-133) in Complex with Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg202

b:51.7
occ:1.00
 O N:SER169 2.5 40.1 1.0
O N:ILE163 2.6 43.3 1.0
O N:ASP166 2.8 44.7 1.0
NH1 N:ARG19 3.6 50.3 1.0
CD1 a:LEU34 3.7 52.7 1.0
C N:SER169 3.7 41.3 1.0
C N:ILE163 3.8 43.7 1.0
C N:ASP166 3.9 42.9 1.0
CG2 N:ILE163 4.0 42.1 1.0
CA N:GLY167 4.1 44.9 1.0
CZ N:ARG19 4.2 47.9 1.0
CA N:GLY170 4.4 43.1 1.0
O N:GLY167 4.4 45.0 1.0
CA N:ILE163 4.4 42.4 1.0
C N:GLY167 4.4 45.2 1.0
N N:GLY167 4.4 42.1 1.0
NH2 N:ARG19 4.5 47.8 1.0
N N:GLY170 4.5 42.0 1.0
N N:SER169 4.7 42.7 1.0
CA N:SER169 4.8 40.9 1.0
N N:LYS164 4.8 44.6 1.0
CB N:ILE163 4.8 41.8 1.0
CG a:LEU34 4.9 51.9 1.0
O N:LYS164 5.0 46.8 1.0

Magnesium binding site 7 out of 7 in 5l65

Go back to Magnesium Binding Sites List in 5l65
Magnesium binding site 7 out of 7 in the Yeast 20S Proteasome with Mouse BETA5I (1-138) and Mouse BETA6 (97- 111; 118-133) in Complex with Carfilzomib


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 Mouse BETA5I (1-138) and Mouse BETA6 (97- 111; 118-133) in Complex with Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg301

b:70.1
occ:1.00
 O Z:VAL198 2.7 58.9 1.0
O Z:THR192 2.8 57.1 1.0
O Z:HIS195 3.0 48.0 1.0
O Z:ASP222 3.5 76.3 1.0
NH2 Z:ARG28 3.7 68.3 1.0
O Z:ILE196 3.8 52.1 1.0
CA Z:ILE196 3.9 55.1 1.0
C Z:THR192 3.9 61.8 1.0
C Z:VAL198 3.9 59.2 1.0
CG2 Z:THR192 4.0 63.3 1.0
C Z:HIS195 4.0 52.2 1.0
C Z:ILE196 4.0 53.7 1.0
NH2 H:ARG19 4.1 70.9 1.0
OD1 Z:ASP222 4.1 73.3 1.0
CA Z:THR192 4.3 62.6 1.0
N Z:ILE196 4.4 51.5 1.0
C Z:ASP222 4.5 75.3 1.0
N Z:VAL198 4.6 56.5 1.0
CZ Z:ARG28 4.7 64.9 1.0
NH1 H:ARG19 4.8 65.4 1.0
CB Z:THR192 4.8 61.1 1.0
CA Z:VAL198 4.8 57.6 1.0
CZ H:ARG19 4.8 65.0 1.0
N Z:GLY199 4.8 59.8 1.0
CA Z:GLY199 4.8 61.0 1.0
NH1 Z:ARG28 4.9 65.6 1.0
N Z:GLN197 5.0 54.0 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 19:38:53 2024

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