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Magnesium in PDB 5cgi: Yeast 20S Proteasome BETA5-G48C Mutant in Complex with Onx 0914

Enzymatic activity of Yeast 20S Proteasome BETA5-G48C Mutant in Complex with Onx 0914

All present enzymatic activity of Yeast 20S Proteasome BETA5-G48C Mutant in Complex with Onx 0914:
3.4.25.1;

Protein crystallography data

The structure of Yeast 20S Proteasome BETA5-G48C Mutant in Complex with Onx 0914, PDB code: 5cgi was solved by C.Dubiella, M.Groll, 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 (°) 136.190, 300.030, 145.040, 90.00, 112.96, 90.00
R / Rfree (%) 18.6 / 20.6

Other elements in 5cgi:

The structure of Yeast 20S Proteasome BETA5-G48C Mutant in Complex with Onx 0914 also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms
Sodium (Na) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Yeast 20S Proteasome BETA5-G48C Mutant in Complex with Onx 0914 (pdb code 5cgi). 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 BETA5-G48C Mutant in Complex with Onx 0914, PDB code: 5cgi:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 5cgi

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Magnesium binding site 1 out of 8 in the Yeast 20S Proteasome BETA5-G48C Mutant in Complex with Onx 0914


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 BETA5-G48C Mutant in Complex with Onx 0914 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:58.0
occ:1.00
 O G:MET125 2.4 51.3 1.0
OG1 G:THR8 2.6 46.3 1.0
O G:ARG122 2.9 45.8 1.0
O G:ALA123 3.0 50.1 1.0
O G:TYR119 3.2 38.7 1.0
CG2 G:THR8 3.3 48.1 1.0
CB G:THR8 3.5 47.5 1.0
C G:ALA123 3.5 50.1 1.0
C G:MET125 3.5 51.4 1.0
CA G:ALA123 3.6 48.2 1.0
N G:THR8 3.8 50.6 1.0
C G:ARG122 3.9 48.2 1.0
CA G:ARG126 4.2 47.1 1.0
N G:ALA123 4.2 47.1 1.0
N G:ARG126 4.2 48.3 1.0
CA G:THR8 4.3 48.8 1.0
N G:MET125 4.3 52.4 1.0
C G:TYR119 4.5 40.2 1.0
CA G:MET125 4.5 55.0 1.0
N G:TYR124 4.5 51.3 1.0
CD G:PRO127 4.7 45.6 1.0
CB G:ALA123 4.8 47.2 1.0
C G:ILE7 4.8 53.7 1.0
C G:TYR124 4.9 51.3 1.0
CA G:ILE7 5.0 54.1 1.0
C G:ARG126 5.0 47.5 1.0

Magnesium binding site 2 out of 8 in 5cgi

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Magnesium binding site 2 out of 8 in the Yeast 20S Proteasome BETA5-G48C Mutant in Complex with Onx 0914


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Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Yeast 20S Proteasome BETA5-G48C Mutant in Complex with Onx 0914 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:51.2
occ:1.00
 O I:ASP177 2.4 46.2 1.0
O I:SER180 2.4 49.4 1.0
O I:ALA174 2.7 51.1 1.0
C I:ASP177 3.6 45.8 1.0
C I:SER180 3.7 48.4 1.0
OXT I:ASP204 3.7 68.2 1.0
C I:ALA174 3.7 52.4 1.0
CA I:ASP175 4.1 53.0 1.0
O I:ALA178 4.3 48.4 1.0
CA I:ALA178 4.3 44.3 1.0
N I:ASP175 4.4 52.9 1.0
C I:ALA178 4.4 45.5 1.0
N I:ALA178 4.4 44.4 1.0
C I:ASP175 4.4 50.7 1.0
N I:ASP177 4.4 45.3 1.0
N I:SER180 4.5 45.1 1.0
CA I:GLY181 4.5 50.0 1.0
N I:GLY181 4.5 48.9 1.0
CA I:ASP177 4.6 46.3 1.0
O I:ASP175 4.6 52.5 1.0
CA I:SER180 4.6 46.8 1.0
C I:ASP204 4.7 69.5 1.0
O I:ASP204 4.8 72.7 1.0
CA I:ALA174 4.8 50.0 1.0
OD1 I:ASP175 4.8 59.3 1.0
NH1 Y:ARG19 4.9 68.0 1.0

Magnesium binding site 3 out of 8 in 5cgi

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Magnesium binding site 3 out of 8 in the Yeast 20S Proteasome BETA5-G48C Mutant in Complex with Onx 0914


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 BETA5-G48C Mutant in Complex with Onx 0914 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg302

b:53.6
occ:1.00
 O I:ASP204 2.2 72.7 1.0
O Y:ASP168 2.2 45.8 1.0
O Y:ALA165 2.6 48.3 1.0
O Y:SER171 2.8 48.1 1.0
C I:ASP204 3.1 69.5 1.0
C Y:ASP168 3.2 45.8 1.0
CA Y:ALA169 3.5 46.4 1.0
CA I:ASP204 3.6 66.3 1.0
C Y:ALA165 3.7 48.9 1.0
N Y:ALA169 3.7 45.9 1.0
C Y:ALA169 3.8 46.8 1.0
O Y:HIS166 3.8 45.7 1.0
O Y:ALA169 3.9 47.7 1.0
NH1 Y:ARG19 3.9 68.0 1.0
OXT I:ASP204 4.0 68.2 1.0
C Y:SER171 4.0 46.8 1.0
CB I:ASP204 4.1 65.8 1.0
C Y:HIS166 4.3 47.3 1.0
N Y:SER171 4.4 42.0 1.0
CA Y:ASP168 4.4 45.8 1.0
N Y:ASP168 4.5 46.7 1.0
CA Y:ALA165 4.6 49.0 1.0
CZ Y:ARG19 4.6 64.2 1.0
N Y:TYR170 4.6 46.9 1.0
N Y:HIS166 4.6 49.6 1.0
CA Y:HIS166 4.7 47.9 1.0
C Y:ARG167 4.7 47.5 1.0
O Y:ALA164 4.8 49.2 1.0
CA Y:SER171 4.8 42.4 1.0
CB Y:ALA169 4.8 46.1 1.0
NH2 Y:ARG19 4.8 68.1 1.0
O Y:ARG167 4.9 47.6 1.0
N Y:ARG167 5.0 46.8 1.0
N I:ASP204 5.0 63.0 1.0

Magnesium binding site 4 out of 8 in 5cgi

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Magnesium binding site 4 out of 8 in the Yeast 20S Proteasome BETA5-G48C Mutant in Complex with Onx 0914


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 BETA5-G48C Mutant in Complex with Onx 0914 within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg301

b:55.7
occ:1.00
 O K:ASP168 2.1 48.8 1.0
O W:ASP204 2.2 69.4 1.0
O K:ALA165 2.4 49.2 1.0
O K:SER171 2.8 48.6 1.0
C W:ASP204 3.1 63.4 1.0
C K:ASP168 3.2 48.6 1.0
C K:ALA165 3.5 49.4 1.0
CA W:ASP204 3.6 60.2 1.0
CA K:ALA169 3.6 49.8 1.0
O K:HIS166 3.7 47.4 1.0
N K:ALA169 3.8 49.6 1.0
C K:ALA169 3.9 51.2 1.0
C K:SER171 3.9 47.6 1.0
O K:ALA169 4.0 53.3 1.0
CB W:ASP204 4.0 59.3 1.0
OXT W:ASP204 4.1 67.7 1.0
C K:HIS166 4.1 47.4 1.0
NH1 K:ARG19 4.1 62.8 1.0
N K:ASP168 4.3 48.5 1.0
CA K:ASP168 4.3 47.3 1.0
N K:SER171 4.3 45.8 1.0
CA K:ALA165 4.4 50.8 1.0
N K:HIS166 4.4 48.3 1.0
CA K:HIS166 4.5 48.7 1.0
O K:ALA164 4.5 52.1 1.0
C K:ARG167 4.6 49.0 1.0
N K:TYR170 4.7 49.6 1.0
CA K:SER171 4.7 45.7 1.0
CZ K:ARG19 4.7 61.6 1.0
N K:ARG167 4.8 46.4 1.0
O K:ARG167 4.9 50.4 1.0
NH2 K:ARG19 4.9 66.7 1.0
N K:GLY172 4.9 49.3 1.0
N W:ASP204 5.0 59.0 1.0
CB K:ALA169 5.0 48.6 1.0

Magnesium binding site 5 out of 8 in 5cgi

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Magnesium binding site 5 out of 8 in the Yeast 20S Proteasome BETA5-G48C Mutant in Complex with Onx 0914


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 BETA5-G48C Mutant in Complex with Onx 0914 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg301

b:64.4
occ:1.00
 OXT L:ASP222 2.1 72.8 1.0
O V:ILE163 2.3 54.5 1.0
O V:ASP166 2.3 45.8 1.0
C L:ASP222 2.9 70.8 1.0
O V:SER169 3.1 48.3 1.0
C V:ASP166 3.2 49.5 1.0
C V:ILE163 3.4 55.9 1.0
O V:TRP164 3.4 53.6 1.0
CA L:ASP222 3.5 68.0 1.0
C V:TRP164 3.7 55.4 1.0
O L:ASP222 3.8 72.6 1.0
N V:ASP166 3.8 50.5 1.0
N V:LEU167 3.9 50.2 1.0
CA V:LEU167 3.9 51.3 1.0
O V:GLY162 4.0 55.8 1.0
CA V:TRP164 4.1 55.7 1.0
N V:TRP164 4.1 55.0 1.0
CA V:ASP166 4.1 49.6 1.0
N V:ASN165 4.2 54.6 1.0
C V:SER169 4.3 49.0 1.0
CB L:ASP222 4.3 65.7 1.0
CA V:ILE163 4.4 57.5 1.0
C V:ASN165 4.4 51.1 1.0
NH1 V:ARG19 4.4 65.0 1.0
O L:ARG221 4.5 65.3 1.0
C V:LEU167 4.6 50.3 1.0
CD2 V:LEU167 4.6 52.3 1.0
N L:ASP222 4.7 67.0 1.0
CA V:ASN165 4.8 53.7 1.0
O V:LEU167 4.9 53.2 1.0
N V:SER169 4.9 47.4 1.0
CD1 L:ILE35 4.9 58.6 1.0
C V:GLY162 5.0 56.0 1.0

Magnesium binding site 6 out of 8 in 5cgi

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Magnesium binding site 6 out of 8 in the Yeast 20S Proteasome BETA5-G48C Mutant in Complex with Onx 0914


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 BETA5-G48C Mutant in Complex with Onx 0914 within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg201

b:46.5
occ:1.00
 O N:SER169 2.6 48.0 1.0
O N:ILE163 2.8 49.2 1.0
O N:ASP166 3.1 49.0 1.0
NH1 N:ARG19 3.6 51.0 1.0
CD1 a:LEU34 3.7 54.6 1.0
C N:SER169 3.8 47.6 1.0
C N:ILE163 3.9 50.6 1.0
CG2 N:ILE163 4.0 50.4 1.0
CZ N:ARG19 4.2 50.8 1.0
C N:ASP166 4.2 48.6 1.0
CA N:GLY167 4.3 46.9 1.0
NH2 N:ARG19 4.3 50.0 1.0
CA N:GLY170 4.3 51.0 1.0
O N:GLY167 4.4 45.6 1.0
N N:GLY170 4.6 49.0 1.0
CA N:ILE163 4.6 50.0 1.0
C N:GLY167 4.6 46.0 1.0
N N:GLY167 4.7 46.6 1.0
N N:SER169 4.9 46.5 1.0
N N:LYS164 4.9 51.6 1.0
CA N:SER169 4.9 45.7 1.0
CB N:ILE163 5.0 50.1 1.0
O N:LYS164 5.0 55.5 1.0

Magnesium binding site 7 out of 8 in 5cgi

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Magnesium binding site 7 out of 8 in the Yeast 20S Proteasome BETA5-G48C Mutant in Complex with Onx 0914


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 BETA5-G48C Mutant in Complex with Onx 0914 within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Mg201

b:29.8
occ:1.00
 OE1 X:GLN118 3.6 46.6 1.0
O X:THR124 3.7 45.4 1.0
CB X:ASP120 3.8 39.8 1.0
CG X:ASP120 4.0 42.5 1.0
OD2 X:ASP120 4.0 44.8 1.0
N X:ASP120 4.1 38.0 1.0
CB X:THR124 4.3 42.4 1.0
CD X:GLN118 4.3 42.6 1.0
CG X:GLN118 4.4 41.7 1.0
CE1 X:HIS133 4.4 43.6 1.0
CG2 X:THR124 4.4 41.7 1.0
O X:GLN118 4.5 43.0 1.0
CA X:ASP120 4.5 37.9 1.0
OD1 X:ASP120 4.6 45.2 1.0
C X:THR124 4.7 44.5 1.0
CG1 W:VAL35 4.8 47.5 1.0
C X:ILE119 4.8 38.5 1.0
CD2 W:LEU28 4.9 48.5 1.0
C X:GLN118 4.9 40.8 1.0

Magnesium binding site 8 out of 8 in 5cgi

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Magnesium binding site 8 out of 8 in the Yeast 20S Proteasome BETA5-G48C Mutant in Complex with Onx 0914


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 BETA5-G48C Mutant in Complex with Onx 0914 within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg301

b:63.9
occ:1.00
 O Z:VAL198 2.5 49.8 1.0
O Z:THR192 2.6 55.6 1.0
O Z:HIS195 3.1 46.4 1.0
O Z:ASP222 3.5 68.9 1.0
CG2 Z:THR192 3.5 57.9 1.0
NH2 Z:ARG28 3.6 62.7 1.0
C Z:THR192 3.7 57.6 1.0
C Z:VAL198 3.8 51.2 1.0
CA Z:THR192 4.0 57.5 1.0
C Z:HIS195 4.1 48.2 1.0
OD1 Z:ASP222 4.2 65.4 1.0
O Z:ILE196 4.2 52.5 1.0
CA Z:ILE196 4.2 48.0 1.0
NH2 H:ARG19 4.3 65.6 1.0
CB Z:THR192 4.4 56.7 1.0
C Z:ILE196 4.4 48.7 1.0
C Z:ASP222 4.5 69.4 1.0
CA Z:GLY199 4.6 55.2 1.0
N Z:VAL198 4.6 48.5 1.0
N Z:GLY199 4.6 52.8 1.0
CZ Z:ARG28 4.6 61.7 1.0
N Z:ILE196 4.7 47.4 1.0
CA Z:VAL198 4.7 49.9 1.0
O Z:LYS220 4.8 61.5 1.0
N Z:GLU193 4.9 56.9 1.0
NH1 Z:ARG28 4.9 63.8 1.0

Reference:

C.Dubiella, R.Baur, H.Cui, E.M.Huber, M.Groll. Selective Inhibition of the Immunoproteasome By Structure-Based Targeting of A Non-Catalytic Cysteine. Angew.Chem.Int.Ed.Engl. V. 54 15888 2015.
ISSN: ESSN 1521-3773
PubMed: 26563572
DOI: 10.1002/ANIE.201506631
Page generated: Sun Sep 29 02:07:42 2024

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