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Magnesium in PDB 6g8n: Yeast 20S Proteasome in Complex with Cystargolide B Derivative 2

Enzymatic activity of Yeast 20S Proteasome in Complex with Cystargolide B Derivative 2

All present enzymatic activity of Yeast 20S Proteasome in Complex with Cystargolide B Derivative 2:
3.4.25.1;

Protein crystallography data

The structure of Yeast 20S Proteasome in Complex with Cystargolide B Derivative 2, PDB code: 6g8n was solved by M.Groll, R.Tello-Aburto, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.00 / 3.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 136.220, 302.720, 143.970, 90.00, 112.82, 90.00
R / Rfree (%) 18.2 / 23.8

Other elements in 6g8n:

The structure of Yeast 20S Proteasome in Complex with Cystargolide B Derivative 2 also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Yeast 20S Proteasome in Complex with Cystargolide B Derivative 2 (pdb code 6g8n). 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 in Complex with Cystargolide B Derivative 2, PDB code: 6g8n:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 6g8n

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Magnesium binding site 1 out of 8 in the Yeast 20S Proteasome in Complex with Cystargolide B Derivative 2


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 in Complex with Cystargolide B Derivative 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:83.2
occ:1.00
 O G:MET125 2.1 79.8 1.0
OG1 G:THR8 2.7 66.5 1.0
O G:ARG122 2.8 67.0 1.0
O G:TYR119 2.8 62.6 1.0
CG2 G:THR8 3.2 71.3 1.0
O G:ALA123 3.2 82.3 1.0
C G:MET125 3.3 78.1 1.0
CB G:THR8 3.5 68.6 1.0
C G:ALA123 3.7 76.0 1.0
CA G:ALA123 3.8 70.6 1.0
C G:ARG122 3.9 68.0 1.0
CA G:ARG126 4.0 67.2 1.0
C G:TYR119 4.0 64.4 1.0
N G:ARG126 4.1 70.3 1.0
N G:THR8 4.1 73.0 1.0
N G:MET125 4.3 78.0 1.0
N G:ALA123 4.3 67.1 1.0
CA G:MET125 4.4 81.9 1.0
CD G:PRO127 4.4 66.3 1.0
CA G:THR8 4.4 70.7 1.0
C G:ARG126 4.6 65.8 1.0
N G:TYR124 4.7 75.6 1.0
CA G:TYR119 4.8 64.6 1.0
N G:PRO127 4.9 66.3 1.0
C G:TYR124 4.9 75.7 1.0
N G:THR120 5.0 64.1 1.0

Magnesium binding site 2 out of 8 in 6g8n

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Magnesium binding site 2 out of 8 in the Yeast 20S Proteasome in Complex with Cystargolide B Derivative 2


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 in Complex with Cystargolide B Derivative 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:96.6
occ:1.00
 O I:ALA174 3.1 69.2 1.0
OXT I:ASP204 3.1 0.1 1.0
O I:SER180 3.1 66.3 1.0
O I:ASP177 3.1 54.3 1.0
C I:ASP204 4.0 85.7 1.0
CA I:ASP175 4.0 73.0 1.0
C I:ALA174 4.0 69.2 1.0
O I:ASP204 4.2 83.9 1.0
C I:SER180 4.2 67.3 1.0
NH2 Y:ARG19 4.2 89.5 1.0
OD1 I:ASP175 4.3 74.5 1.0
C I:ASP177 4.3 66.2 1.0
O I:ASP175 4.4 86.5 1.0
N I:ASP175 4.4 70.9 1.0
CA I:GLY181 4.5 70.8 1.0
C I:ASP175 4.5 76.2 1.0
N I:GLY181 4.8 67.8 1.0
O I:ALA178 4.8 68.0 1.0
NH1 Y:ARG19 4.8 86.7 1.0
OD1 I:ASP204 4.8 86.2 1.0
CZ Y:ARG19 4.9 84.0 1.0

Magnesium binding site 3 out of 8 in 6g8n

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Magnesium binding site 3 out of 8 in the Yeast 20S Proteasome in Complex with Cystargolide B Derivative 2


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 in Complex with Cystargolide B Derivative 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg302

b:92.4
occ:1.00
 O K:ALA165 2.6 55.4 1.0
O K:ASP168 2.6 53.4 1.0
O W:ASP204 2.7 91.5 1.0
O K:HIS166 2.9 73.4 1.0
C W:ASP204 3.2 91.7 1.0
C K:ASP168 3.3 59.6 1.0
CA W:ASP204 3.5 82.5 1.0
C K:HIS166 3.6 66.1 1.0
CA K:ALA169 3.6 64.6 1.0
N K:ALA169 3.7 62.4 1.0
C K:ALA165 3.8 61.4 1.0
OXT W:ASP204 3.9 0.9 1.0
O K:SER171 3.9 60.9 1.0
C K:ARG167 4.1 61.8 1.0
O K:ARG167 4.1 63.9 1.0
N K:ASP168 4.1 59.8 1.0
CB W:ASP204 4.2 78.9 1.0
C K:ALA169 4.3 70.2 1.0
CA K:HIS166 4.3 64.2 1.0
CA K:ASP168 4.3 60.9 1.0
N K:ARG167 4.3 64.0 1.0
O K:ALA169 4.4 83.3 1.0
NH1 K:ARG19 4.4 83.6 1.0
N K:HIS166 4.5 60.8 1.0
NE1 W:TRP182 4.7 74.5 1.0
CA K:ARG167 4.7 60.3 1.0
N W:ASP204 4.8 80.7 1.0
CB K:ALA169 4.8 62.9 1.0
O K:ALA164 4.8 56.1 1.0
CA K:ALA165 4.9 63.6 1.0

Magnesium binding site 4 out of 8 in 6g8n

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Magnesium binding site 4 out of 8 in the Yeast 20S Proteasome in Complex with Cystargolide B Derivative 2


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 in Complex with Cystargolide B Derivative 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg202

b:55.9
occ:1.00
 O N:SER169 2.6 67.2 1.0
O N:ILE163 2.9 65.0 1.0
O N:ASP166 2.9 63.5 1.0
NH1 N:ARG19 3.4 74.4 1.0
CD1 a:LEU34 3.7 72.9 1.0
C N:SER169 3.7 65.4 1.0
CZ N:ARG19 3.9 72.9 1.0
NH2 N:ARG19 4.0 75.7 1.0
C N:ASP166 4.0 64.3 1.0
C N:ILE163 4.0 65.1 1.0
CG2 N:ILE163 4.0 65.7 1.0
CA N:GLY167 4.2 67.0 1.0
O N:GLY167 4.3 67.0 1.0
CA N:GLY170 4.4 67.9 1.0
C N:GLY167 4.5 66.5 1.0
N N:GLY167 4.5 65.2 1.0
N N:GLY170 4.5 67.0 1.0
CA N:ILE163 4.6 65.1 1.0
N N:SER169 4.8 62.5 1.0
CA N:SER169 4.8 62.8 1.0
NE N:ARG19 4.8 71.4 1.0
CB N:ILE163 4.9 64.7 1.0
CG a:LEU34 5.0 73.8 1.0

Magnesium binding site 5 out of 8 in 6g8n

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Magnesium binding site 5 out of 8 in the Yeast 20S Proteasome in Complex with Cystargolide B Derivative 2


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 in Complex with Cystargolide B Derivative 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Mg302

b:0.5
occ:1.00
 OXT L:ASP222 2.0 84.6 1.0
O V:ASP166 2.3 59.2 1.0
O V:ILE163 2.3 71.6 1.0
C L:ASP222 3.0 85.3 1.0
C V:ASP166 3.1 67.4 1.0
O V:SER169 3.3 60.0 1.0
O V:TRP164 3.3 61.6 1.0
C V:ILE163 3.5 71.0 1.0
CA L:ASP222 3.7 82.3 1.0
C V:TRP164 3.7 67.5 1.0
NH1 V:ARG19 3.7 87.2 1.0
N V:LEU167 3.7 67.0 1.0
CA V:LEU167 3.8 66.4 1.0
O L:ASP222 3.8 89.3 1.0
N V:ASP166 3.9 66.8 1.0
CA V:ASP166 4.1 67.0 1.0
O V:GLY162 4.1 73.1 1.0
CA V:TRP164 4.1 67.8 1.0
N V:TRP164 4.2 69.8 1.0
N V:ASN165 4.2 69.6 1.0
C V:ASN165 4.3 66.8 1.0
CD2 V:LEU167 4.4 63.5 1.0
CB L:ASP222 4.4 80.9 1.0
O L:ARG221 4.5 77.7 1.0
C V:LEU167 4.5 65.9 1.0
C V:SER169 4.5 66.4 1.0
CA V:ILE163 4.6 68.2 1.0
CA V:ASN165 4.7 69.1 1.0
CZ V:ARG19 4.8 82.0 1.0
O V:LEU167 4.8 55.5 1.0
O V:ASN165 4.8 67.2 1.0
NH2 V:ARG19 4.8 79.7 1.0
N L:ASP222 4.9 80.2 1.0
CB V:LEU167 4.9 65.2 1.0
CD1 L:ILE35 5.0 72.5 1.0

Magnesium binding site 6 out of 8 in 6g8n

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Magnesium binding site 6 out of 8 in the Yeast 20S Proteasome in Complex with Cystargolide B Derivative 2


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 in Complex with Cystargolide B Derivative 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
W:Mg301

b:84.8
occ:1.00
 O W:ASP177 2.9 61.7 1.0
O W:ALA174 2.9 66.3 1.0
O W:SER180 3.0 73.6 1.0
OXT W:ASP204 3.3 0.9 1.0
CA W:ASP175 3.9 77.4 1.0
C W:ALA174 3.9 72.4 1.0
C W:ASP177 4.0 69.3 1.0
NH2 K:ARG19 4.1 82.3 1.0
C W:SER180 4.1 72.8 1.0
C W:ASP204 4.2 91.7 1.0
O W:ASP175 4.3 87.8 1.0
O W:ASP204 4.3 91.5 1.0
C W:ASP175 4.3 79.5 1.0
N W:ASP175 4.3 77.5 1.0
OD1 W:ASP175 4.4 82.4 1.0
CA W:GLY181 4.6 69.8 1.0
O W:ALA178 4.6 74.2 1.0
NH1 K:ARG19 4.7 83.6 1.0
CA W:ALA178 4.8 68.7 1.0
CZ K:ARG19 4.8 79.4 1.0
N W:ASP177 4.8 74.0 1.0
N W:GLY181 4.8 69.6 1.0
N W:ALA178 4.8 67.4 1.0
C W:ALA178 4.9 68.9 1.0
OD1 W:ASP204 5.0 85.1 1.0

Magnesium binding site 7 out of 8 in 6g8n

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Magnesium binding site 7 out of 8 in the Yeast 20S Proteasome in Complex with Cystargolide B Derivative 2


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 in Complex with Cystargolide B Derivative 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
Y:Mg302

b:93.0
occ:1.00
 O I:ASP204 2.5 83.9 1.0
O Y:ASP168 2.7 59.2 1.0
O Y:ALA165 2.9 64.7 1.0
C I:ASP204 3.1 85.7 1.0
O Y:HIS166 3.2 64.7 1.0
C Y:ASP168 3.3 62.5 1.0
CA Y:ALA169 3.4 67.1 1.0
N Y:ALA169 3.6 66.7 1.0
CA I:ASP204 3.7 82.6 1.0
OXT I:ASP204 3.8 0.1 1.0
C Y:HIS166 4.0 63.3 1.0
O Y:SER171 4.0 80.5 1.0
C Y:ALA169 4.0 68.7 1.0
O Y:ALA169 4.1 67.1 1.0
C Y:ALA165 4.1 59.6 1.0
NH1 Y:ARG19 4.1 86.7 1.0
O Y:ARG167 4.3 57.5 1.0
C Y:ARG167 4.3 61.7 1.0
N Y:ASP168 4.3 60.2 1.0
CB I:ASP204 4.4 80.8 1.0
CA Y:ASP168 4.4 62.6 1.0
CB Y:ALA169 4.5 67.6 1.0
CA Y:HIS166 4.7 63.4 1.0
N Y:ARG167 4.7 63.9 1.0
NE1 I:TRP182 4.8 77.0 1.0
N Y:HIS166 4.8 59.5 1.0
CA Y:ARG167 4.9 62.8 1.0
N I:ASP204 4.9 81.8 1.0

Magnesium binding site 8 out of 8 in 6g8n

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Magnesium binding site 8 out of 8 in the Yeast 20S Proteasome in Complex with Cystargolide B Derivative 2


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 in Complex with Cystargolide B Derivative 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg301

b:62.0
occ:1.00
 O Z:VAL198 2.6 62.0 1.0
O Z:HIS195 2.8 67.3 1.0
O Z:THR192 2.8 77.0 1.0
O Z:ASP222 3.6 91.9 1.0
NH2 Z:ARG28 3.6 79.6 1.0
O Z:ILE196 3.7 68.5 1.0
CA Z:ILE196 3.8 66.0 1.0
C Z:VAL198 3.8 69.8 1.0
C Z:HIS195 3.8 66.8 1.0
NH2 H:ARG19 3.8 77.5 1.0
C Z:ILE196 3.9 64.0 1.0
C Z:THR192 3.9 75.3 1.0
CG2 Z:THR192 4.0 77.7 1.0
OD1 Z:ASP222 4.2 83.4 1.0
N Z:ILE196 4.3 64.1 1.0
CA Z:THR192 4.3 73.9 1.0
N Z:VAL198 4.4 65.9 1.0
C Z:ASP222 4.6 88.3 1.0
CZ Z:ARG28 4.6 71.7 1.0
CA Z:VAL198 4.7 66.8 1.0
N Z:GLY199 4.7 69.6 1.0
CB Z:THR192 4.8 76.3 1.0
CA Z:GLY199 4.8 70.2 1.0
N Z:GLN197 4.8 63.1 1.0
NH1 Z:ARG28 4.9 69.5 1.0

Reference:

D.Niroula, L.P.Hallada, C.Le Chapelain, S.K.Ganegamage, D.Dotson, S.Rogelj, M.Groll, R.Tello-Aburto. Design, Synthesis, and Evaluation of Cystargolide-Based Beta-Lactones As Potent Proteasome Inhibitors. Eur J Med Chem V. 157 962 2018.
ISSN: ISSN 1768-3254
PubMed: 30165344
DOI: 10.1016/J.EJMECH.2018.08.052
Page generated: Tue Oct 1 01:03:05 2024

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