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Magnesium in PDB 5cgg: Yeast 20S Proteasome BETA5-G48C Mutant in Complex with Alpha- Chloroacetamide 1

Enzymatic activity of Yeast 20S Proteasome BETA5-G48C Mutant in Complex with Alpha- Chloroacetamide 1

All present enzymatic activity of Yeast 20S Proteasome BETA5-G48C Mutant in Complex with Alpha- Chloroacetamide 1:
3.4.25.1;

Protein crystallography data

The structure of Yeast 20S Proteasome BETA5-G48C Mutant in Complex with Alpha- Chloroacetamide 1, PDB code: 5cgg 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 / 2.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 134.440, 300.470, 144.740, 90.00, 113.00, 90.00
R / Rfree (%) 20.4 / 23.1

Other elements in 5cgg:

The structure of Yeast 20S Proteasome BETA5-G48C Mutant in Complex with Alpha- Chloroacetamide 1 also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Magnesium Binding Sites:

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

Magnesium binding site 1 out of 8 in 5cgg

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


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 Alpha- Chloroacetamide 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:42.4
occ:1.00
 O G:MET125 2.3 44.1 1.0
O G:ARG122 2.6 45.6 1.0
OG1 G:THR8 2.6 41.9 1.0
O G:TYR119 2.8 37.9 1.0
O G:ALA123 3.2 48.4 1.0
CG2 G:THR8 3.3 43.5 1.0
C G:MET125 3.4 45.9 1.0
CB G:THR8 3.5 43.4 1.0
C G:ALA123 3.6 47.4 1.0
C G:ARG122 3.7 46.6 1.0
CA G:ALA123 3.7 45.6 1.0
C G:TYR119 4.0 38.4 1.0
N G:THR8 4.1 48.2 1.0
N G:ALA123 4.1 44.4 1.0
CA G:ARG126 4.2 41.4 1.0
N G:ARG126 4.2 43.4 1.0
N G:MET125 4.2 49.5 1.0
CA G:THR8 4.4 45.5 1.0
CA G:MET125 4.4 50.8 1.0
N G:TYR124 4.6 49.5 1.0
CD G:PRO127 4.6 37.7 1.0
CA G:TYR119 4.7 37.6 1.0
C G:ARG126 4.8 41.0 1.0
C G:TYR124 4.9 50.8 1.0
N G:THR120 5.0 38.0 1.0
CA G:ARG122 5.0 49.1 1.0

Magnesium binding site 2 out of 8 in 5cgg

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Magnesium binding site 2 out of 8 in the Yeast 20S Proteasome BETA5-G48C Mutant in Complex with Alpha- Chloroacetamide 1


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 BETA5-G48C Mutant in Complex with Alpha- Chloroacetamide 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:61.5
occ:1.00
 O I:ASP177 2.4 47.1 1.0
O I:SER180 2.6 50.5 1.0
O I:ALA174 2.8 58.1 1.0
C I:ASP177 3.5 48.3 1.0
C I:SER180 3.8 48.9 1.0
C I:ALA174 3.9 54.1 1.0
O I:ALA178 4.1 56.2 1.0
CA I:ALA178 4.2 48.8 1.0
C I:ALA178 4.3 50.3 1.0
CA I:ASP175 4.3 54.5 1.0
N I:ALA178 4.3 47.4 1.0
N I:ASP177 4.5 47.4 1.0
C I:ASP175 4.5 51.5 1.0
C I:ASP204 4.5 71.3 1.0
O I:ASP204 4.5 72.5 1.0
O I:ASP175 4.5 51.9 1.0
N I:SER180 4.5 46.9 1.0
N I:ASP175 4.5 54.0 1.0
NH1 Y:ARG19 4.6 60.3 1.0
CA I:ASP177 4.6 48.8 1.0
CA I:GLY181 4.7 48.5 1.0
N I:GLY181 4.7 47.5 1.0
CA I:SER180 4.7 48.6 1.0
NH2 Y:ARG19 4.8 61.0 1.0

Magnesium binding site 3 out of 8 in 5cgg

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Magnesium binding site 3 out of 8 in the Yeast 20S Proteasome BETA5-G48C Mutant in Complex with Alpha- Chloroacetamide 1


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 Alpha- Chloroacetamide 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg302

b:42.8
occ:1.00
 O Y:ASP168 2.2 48.9 1.0
O I:ASP204 2.3 72.5 1.0
O Y:ALA165 2.5 42.1 1.0
O Y:SER171 2.8 43.7 1.0
C I:ASP204 3.2 71.3 1.0
C Y:ASP168 3.2 48.4 1.0
CA Y:ALA169 3.6 47.7 1.0
C Y:ALA165 3.6 44.8 1.0
CA I:ASP204 3.7 68.6 1.0
O Y:ALA169 3.7 45.0 1.0
O Y:HIS166 3.8 46.6 1.0
C Y:ALA169 3.8 46.5 1.0
N Y:ALA169 3.8 48.4 1.0
NH1 Y:ARG19 4.0 60.3 1.0
C Y:SER171 4.0 47.1 1.0
CB I:ASP204 4.1 68.3 1.0
C Y:HIS166 4.2 47.4 1.0
N Y:SER171 4.4 47.1 1.0
CA Y:ASP168 4.4 47.5 1.0
N Y:ASP168 4.5 48.5 1.0
CA Y:ALA165 4.5 45.5 1.0
CZ Y:ARG19 4.5 59.7 1.0
N Y:HIS166 4.5 46.5 1.0
CA Y:HIS166 4.6 46.8 1.0
N Y:TYR170 4.6 48.0 1.0
O Y:ALA164 4.7 43.4 1.0
C Y:ARG167 4.7 47.6 1.0
NH2 Y:ARG19 4.7 61.0 1.0
CA Y:SER171 4.8 46.2 1.0
N Y:ARG167 4.9 46.1 1.0
CB Y:ALA169 4.9 47.9 1.0
O Y:ARG167 5.0 46.4 1.0
N Y:GLY172 5.0 49.8 1.0

Magnesium binding site 4 out of 8 in 5cgg

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Magnesium binding site 4 out of 8 in the Yeast 20S Proteasome BETA5-G48C Mutant in Complex with Alpha- Chloroacetamide 1


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 Alpha- Chloroacetamide 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mg201

b:30.0
occ:1.00
 OE1 J:GLN118 3.4 35.8 1.0
CB J:ASP120 3.6 38.2 1.0
O J:THR124 3.8 42.5 1.0
N J:ASP120 3.9 35.1 1.0
CG J:ASP120 4.0 40.8 1.0
CE1 J:HIS133 4.1 39.0 1.0
OD2 J:ASP120 4.1 46.3 1.0
CD J:GLN118 4.2 34.9 1.0
CG J:GLN118 4.2 35.4 1.0
CA J:ASP120 4.4 36.5 1.0
O J:GLN118 4.4 34.4 1.0
CB J:THR124 4.5 39.5 1.0
CG2 J:THR124 4.6 39.7 1.0
C J:ILE119 4.7 34.5 1.0
OD1 J:ASP120 4.7 42.9 1.0
C J:GLN118 4.8 34.3 1.0
ND1 J:HIS133 4.8 38.9 1.0
C J:THR124 4.9 40.0 1.0
CG1 I:VAL35 4.9 55.2 1.0
CA J:ILE119 5.0 33.6 1.0
NE2 J:HIS133 5.0 38.9 1.0

Magnesium binding site 5 out of 8 in 5cgg

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Magnesium binding site 5 out of 8 in the Yeast 20S Proteasome BETA5-G48C Mutant in Complex with Alpha- Chloroacetamide 1


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 Alpha- Chloroacetamide 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg301

b:43.7
occ:1.00
 O K:ASP168 2.2 48.0 1.0
O W:ASP204 2.3 65.2 1.0
O K:ALA165 2.4 45.4 1.0
O K:SER171 2.8 45.1 1.0
C W:ASP204 3.2 60.3 1.0
C K:ASP168 3.3 46.5 1.0
C K:ALA165 3.5 45.4 1.0
CA W:ASP204 3.6 58.6 1.0
CA K:ALA169 3.7 47.4 1.0
O K:HIS166 3.7 46.4 1.0
N K:ALA169 3.9 47.3 1.0
O K:ALA169 3.9 50.9 1.0
C K:ALA169 3.9 48.5 1.0
C K:SER171 4.0 44.9 1.0
CB W:ASP204 4.0 58.7 1.0
NH1 K:ARG19 4.1 58.1 1.0
C K:HIS166 4.1 45.1 1.0
N K:HIS166 4.4 43.9 1.0
CA K:ALA165 4.4 45.9 1.0
N K:ASP168 4.4 45.1 1.0
N K:SER171 4.4 44.2 1.0
CA K:ASP168 4.4 45.1 1.0
CA K:HIS166 4.5 44.2 1.0
O K:ALA164 4.6 46.5 1.0
CZ K:ARG19 4.6 56.1 1.0
C K:ARG167 4.7 45.3 1.0
N K:TYR170 4.7 47.8 1.0
CA K:SER171 4.7 43.9 1.0
N K:ARG167 4.8 44.3 1.0
NH2 K:ARG19 4.8 58.4 1.0
O K:ARG167 4.9 43.6 1.0
N K:GLY172 5.0 45.7 1.0
N W:ASP204 5.0 58.0 1.0

Magnesium binding site 6 out of 8 in 5cgg

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Magnesium binding site 6 out of 8 in the Yeast 20S Proteasome BETA5-G48C Mutant in Complex with Alpha- Chloroacetamide 1


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 Alpha- Chloroacetamide 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg201

b:42.9
occ:1.00
 O N:SER169 2.5 42.1 1.0
O N:ILE163 2.6 45.0 1.0
O N:ASP166 2.9 43.9 1.0
NH1 N:ARG19 3.6 46.3 1.0
C N:ILE163 3.7 44.5 1.0
CD1 a:LEU34 3.7 48.4 1.0
C N:SER169 3.7 41.4 1.0
CG2 N:ILE163 3.9 41.8 1.0
C N:ASP166 4.0 43.5 1.0
CZ N:ARG19 4.2 44.5 1.0
CA N:GLY170 4.3 44.4 1.0
CA N:GLY167 4.3 44.0 1.0
CA N:ILE163 4.4 43.1 1.0
O N:GLY167 4.5 41.0 1.0
NH2 N:ARG19 4.5 44.1 1.0
N N:GLY170 4.5 43.2 1.0
N N:GLY167 4.6 43.8 1.0
C N:GLY167 4.6 43.0 1.0
N N:LYS164 4.7 44.5 1.0
CB N:ILE163 4.8 41.8 1.0
N N:SER169 4.8 40.0 1.0
CA N:SER169 4.8 39.2 1.0
O N:LYS164 4.8 49.3 1.0
C N:LYS164 4.9 46.7 1.0
CA N:LYS164 4.9 46.3 1.0
CG a:LEU34 4.9 48.9 1.0

Magnesium binding site 7 out of 8 in 5cgg

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Magnesium binding site 7 out of 8 in the Yeast 20S Proteasome BETA5-G48C Mutant in Complex with Alpha- Chloroacetamide 1


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 Alpha- Chloroacetamide 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Mg301

b:67.3
occ:1.00
 O V:ILE163 2.3 58.1 1.0
O V:ASP166 2.4 49.4 1.0
C L:ASP222 3.1 72.7 1.0
C V:ASP166 3.2 50.4 1.0
O V:SER169 3.2 48.5 1.0
O V:TRP164 3.3 58.1 1.0
C V:ILE163 3.4 58.6 1.0
C V:TRP164 3.6 56.0 1.0
CA L:ASP222 3.7 69.7 1.0
N V:LEU167 3.8 50.9 1.0
CA V:LEU167 3.9 50.7 1.0
N V:ASP166 3.9 49.5 1.0
O L:ASP222 3.9 69.8 1.0
CA V:TRP164 4.0 56.5 1.0
O V:GLY162 4.0 62.2 1.0
N V:TRP164 4.1 57.8 1.0
N V:ASN165 4.1 54.7 1.0
CA V:ASP166 4.2 49.5 1.0
C V:ASN165 4.3 51.4 1.0
O L:ARG221 4.4 58.9 1.0
C V:SER169 4.4 49.6 1.0
CA V:ILE163 4.4 58.1 1.0
CB L:ASP222 4.5 69.8 1.0
NH1 V:ARG19 4.5 59.7 1.0
C V:LEU167 4.6 50.0 1.0
CD2 V:LEU167 4.6 48.0 1.0
CA V:ASN165 4.7 53.1 1.0
CD1 L:ILE35 4.7 56.9 1.0
N L:ASP222 4.8 66.5 1.0
O V:LEU167 4.9 50.7 1.0
O V:ASN165 4.9 48.8 1.0

Magnesium binding site 8 out of 8 in 5cgg

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


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 Alpha- Chloroacetamide 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg301

b:52.2
occ:1.00
 O Z:VAL198 2.4 49.9 1.0
O Z:THR192 2.7 56.9 1.0
O Z:HIS195 2.8 42.0 1.0
NH2 Z:ARG28 3.5 63.2 1.0
O Z:ASP222 3.5 70.5 1.0
C Z:VAL198 3.6 51.9 1.0
CG2 Z:THR192 3.7 59.9 1.0
C Z:THR192 3.7 57.3 1.0
O Z:ILE196 3.8 55.0 1.0
C Z:HIS195 3.9 47.8 1.0
CA Z:ILE196 4.0 49.7 1.0
CA Z:THR192 4.0 57.8 1.0
C Z:ILE196 4.1 51.4 1.0
N Z:VAL198 4.4 49.8 1.0
N Z:ILE196 4.4 49.0 1.0
CB Z:THR192 4.5 58.3 1.0
CZ Z:ARG28 4.5 60.0 1.0
NH2 H:ARG19 4.5 57.6 1.0
OD1 Z:ASP222 4.5 73.9 1.0
N Z:GLY199 4.5 52.0 1.0
CA Z:VAL198 4.5 51.2 1.0
CA Z:GLY199 4.6 54.0 1.0
C Z:ASP222 4.6 74.6 1.0
NH1 Z:ARG28 4.8 60.0 1.0
N Z:GLU193 4.9 57.5 1.0
N Z:GLN197 5.0 50.4 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 02:06:15 2024

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