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Magnesium in PDB 6g7f: Yeast 20S Proteasome in Complex with Cystargolide B

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

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

Protein crystallography data

The structure of Yeast 20S Proteasome in Complex with Cystargolide B, PDB code: 6g7f 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 / 2.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 134.740, 301.970, 143.620, 90.00, 112.95, 90.00
R / Rfree (%) 18.8 / 21.4

Other elements in 6g7f:

The structure of Yeast 20S Proteasome in Complex with Cystargolide B 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 (pdb code 6g7f). 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, PDB code: 6g7f:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 6g7f

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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:62.4
occ:1.00
 O G:MET125 2.2 65.1 1.0
OG1 G:THR8 2.6 60.9 1.0
O G:ARG122 2.7 59.9 1.0
O G:TYR119 2.9 54.2 1.0
CG2 G:THR8 3.2 62.5 1.0
O G:ALA123 3.2 67.7 1.0
C G:MET125 3.3 65.9 1.0
CB G:THR8 3.4 61.0 1.0
C G:ALA123 3.6 66.5 1.0
CA G:ALA123 3.7 64.1 1.0
C G:ARG122 3.8 61.2 1.0
N G:THR8 4.0 62.7 1.0
N G:ARG126 4.1 60.4 1.0
CA G:ARG126 4.1 58.7 1.0
C G:TYR119 4.1 53.9 1.0
N G:ALA123 4.2 61.6 1.0
N G:MET125 4.2 68.5 1.0
CA G:THR8 4.3 61.9 1.0
CA G:MET125 4.4 70.9 1.0
CD G:PRO127 4.5 56.1 1.0
N G:TYR124 4.6 68.5 1.0
C G:ARG126 4.8 56.9 1.0
C G:TYR124 4.9 66.9 1.0
CA G:TYR119 4.9 53.1 1.0
CB G:ALA123 5.0 64.9 1.0

Magnesium binding site 2 out of 8 in 6g7f

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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:88.3
occ:1.00
 O I:SER180 2.7 64.6 1.0
O I:ASP177 2.7 57.1 1.0
O I:ALA174 3.0 62.2 1.0
OXT I:ASP204 3.4 89.8 1.0
C I:ASP177 3.9 59.2 1.0
C I:SER180 3.9 64.0 1.0
C I:ALA174 4.1 63.0 1.0
O I:ASP204 4.2 86.7 1.0
CA I:ASP175 4.3 66.9 1.0
C I:ASP204 4.3 80.8 1.0
NH1 Y:ARG19 4.3 73.6 1.0
O I:ALA178 4.4 59.5 1.0
CA I:ALA178 4.5 59.5 1.0
C I:ALA178 4.6 59.0 1.0
O I:ASP175 4.6 75.1 1.0
C I:ASP175 4.6 68.7 1.0
NH2 Y:ARG19 4.6 70.0 1.0
N I:ASP175 4.6 65.1 1.0
N I:ALA178 4.6 58.0 1.0
CA I:GLY181 4.7 64.3 1.0
N I:ASP177 4.7 62.0 1.0
N I:GLY181 4.8 64.5 1.0
N I:SER180 4.8 59.5 1.0
OD1 I:ASP175 4.8 64.0 1.0
CZ Y:ARG19 4.9 70.4 1.0
CA I:ASP177 4.9 61.4 1.0
CA I:SER180 4.9 62.3 1.0

Magnesium binding site 3 out of 8 in 6g7f

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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg302

b:59.8
occ:1.00
 O K:ALA165 2.2 54.2 1.0
O W:ASP204 2.4 83.4 1.0
O K:ASP168 2.4 48.8 1.0
O K:SER171 2.9 57.4 1.0
C W:ASP204 3.1 81.9 1.0
C K:ASP168 3.3 51.1 1.0
C K:ALA165 3.4 55.0 1.0
CA W:ASP204 3.5 74.7 1.0
O K:HIS166 3.6 60.1 1.0
CA K:ALA169 3.7 55.8 1.0
CB W:ASP204 3.8 72.4 1.0
N K:ALA169 3.9 53.2 1.0
NH1 K:ARG19 3.9 72.9 1.0
O K:ALA169 3.9 61.1 1.0
C K:ALA169 4.0 58.5 1.0
C K:HIS166 4.1 58.5 1.0
OXT W:ASP204 4.1 87.0 1.0
C K:SER171 4.1 55.8 1.0
CA K:ALA165 4.3 56.7 1.0
N K:ASP168 4.3 52.0 1.0
N K:HIS166 4.4 54.5 1.0
CA K:ASP168 4.4 52.0 1.0
CA K:HIS166 4.5 57.5 1.0
C K:ARG167 4.6 54.4 1.0
N K:SER171 4.6 52.2 1.0
O K:ALA164 4.6 54.4 1.0
N K:ARG167 4.7 57.5 1.0
CZ K:ARG19 4.8 70.2 1.0
O K:ARG167 4.8 54.5 1.0
N K:TYR170 4.9 58.3 1.0
N W:ASP204 4.9 72.8 1.0
CA K:SER171 4.9 53.2 1.0
CG W:ASP204 4.9 71.6 1.0

Magnesium binding site 4 out of 8 in 6g7f

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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg202

b:54.3
occ:1.00
 O N:SER169 2.7 49.6 1.0
O N:ILE163 2.8 53.2 1.0
O N:ASP166 3.1 53.8 1.0
NH1 N:ARG19 3.5 56.7 1.0
CD1 a:LEU34 3.6 65.6 1.0
C N:SER169 3.9 49.4 1.0
C N:ILE163 3.9 55.6 1.0
CG2 N:ILE163 3.9 55.3 1.0
CZ N:ARG19 4.1 55.4 1.0
C N:ASP166 4.1 52.9 1.0
NH2 N:ARG19 4.1 56.9 1.0
CA N:GLY167 4.3 53.6 1.0
CA N:GLY170 4.4 53.6 1.0
CA N:ILE163 4.5 55.6 1.0
O N:GLY167 4.6 49.3 1.0
N N:GLY170 4.6 51.4 1.0
N N:GLY167 4.6 54.0 1.0
C N:GLY167 4.7 50.9 1.0
CB N:ILE163 4.8 55.4 1.0
N N:LYS164 4.9 57.2 1.0
CG a:LEU34 4.9 65.0 1.0
CA N:SER169 4.9 48.3 1.0
O N:LYS164 5.0 64.0 1.0
N N:SER169 5.0 47.4 1.0

Magnesium binding site 5 out of 8 in 6g7f

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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Mg302

b:93.1
occ:1.00
 OXT L:ASP222 2.4 84.3 1.0
O V:ASP166 2.8 54.0 1.0
O V:ILE163 2.9 54.2 1.0
O V:TRP164 3.0 62.4 1.0
C L:ASP222 3.1 82.3 1.0
C V:ASP166 3.2 56.9 1.0
C V:TRP164 3.5 61.8 1.0
N V:LEU167 3.7 55.4 1.0
O L:ASP222 3.7 79.4 1.0
CA V:LEU167 3.7 55.1 1.0
CD2 V:LEU167 3.7 57.5 1.0
N V:ASP166 3.8 58.2 1.0
CA L:ASP222 3.9 78.7 1.0
C V:ILE163 4.0 60.3 1.0
CD1 L:ILE35 4.0 66.4 1.0
C V:ASN165 4.1 58.6 1.0
O V:SER169 4.1 53.4 1.0
O L:ARG221 4.1 72.4 1.0
CA V:ASP166 4.1 58.2 1.0
N V:ASN165 4.2 61.1 1.0
CA V:TRP164 4.2 63.1 1.0
O V:ASN165 4.5 58.7 1.0
CA V:ASN165 4.5 60.4 1.0
N V:TRP164 4.6 62.1 1.0
CG V:LEU167 4.6 56.9 1.0
O V:GLY162 4.6 58.8 1.0
CB V:LEU167 4.7 56.4 1.0
C V:LEU167 4.8 52.0 1.0
NH1 V:ARG19 4.8 73.1 1.0
N L:ASP222 4.9 75.3 1.0
NH1 L:ARG28 4.9 74.4 1.0
C L:ARG221 4.9 73.8 1.0
CG1 L:ILE35 4.9 64.4 1.0
CB L:ASP222 4.9 76.0 1.0

Magnesium binding site 6 out of 8 in 6g7f

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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
W:Mg301

b:76.9
occ:1.00
 O W:ASP177 2.7 56.6 1.0
O W:SER180 2.7 64.5 1.0
O W:ALA174 2.8 60.5 1.0
OXT W:ASP204 3.7 87.0 1.0
C W:ASP177 3.8 59.4 1.0
C W:ALA174 3.8 61.9 1.0
C W:SER180 3.9 62.0 1.0
CA W:ASP175 4.0 66.0 1.0
N W:ASP175 4.3 64.9 1.0
C W:ASP175 4.4 64.4 1.0
O W:ASP175 4.4 65.1 1.0
N W:ASP177 4.5 62.7 1.0
NH1 K:ARG19 4.5 72.9 1.0
O W:ALA178 4.5 60.1 1.0
O W:ASP204 4.5 83.4 1.0
C W:ASP204 4.5 81.9 1.0
CA W:ALA178 4.6 59.6 1.0
N W:ALA178 4.6 59.5 1.0
C W:ALA178 4.6 58.9 1.0
OD1 W:ASP175 4.7 76.1 1.0
CA W:GLY181 4.7 60.8 1.0
N W:GLY181 4.7 60.0 1.0
CA W:ASP177 4.7 61.5 1.0
N W:SER180 4.7 61.6 1.0
NH2 K:ARG19 4.8 73.5 1.0
CA W:SER180 4.9 62.1 1.0
CA W:ALA174 5.0 58.5 1.0

Magnesium binding site 7 out of 8 in 6g7f

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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
Y:Mg302

b:76.0
occ:1.00
 O Y:ASP168 2.3 57.2 1.0
O Y:ALA165 2.4 61.3 1.0
O I:ASP204 2.4 86.7 1.0
O Y:SER171 3.0 56.8 1.0
C Y:ASP168 3.2 57.1 1.0
C I:ASP204 3.2 80.8 1.0
CA Y:ALA169 3.6 57.2 1.0
C Y:ALA165 3.6 60.1 1.0
O Y:HIS166 3.7 57.4 1.0
CA I:ASP204 3.7 74.4 1.0
N Y:ALA169 3.7 58.3 1.0
O Y:ALA169 3.8 54.6 1.0
C Y:ALA169 3.9 56.2 1.0
NH1 Y:ARG19 3.9 73.6 1.0
CB I:ASP204 4.0 73.6 1.0
C Y:HIS166 4.1 56.6 1.0
OXT I:ASP204 4.1 89.8 1.0
C Y:SER171 4.2 56.8 1.0
N Y:ASP168 4.3 58.3 1.0
CA Y:ASP168 4.3 56.4 1.0
CA Y:ALA165 4.4 58.1 1.0
N Y:HIS166 4.5 59.1 1.0
C Y:ARG167 4.5 58.4 1.0
CA Y:HIS166 4.6 57.1 1.0
N Y:SER171 4.6 53.8 1.0
O Y:ALA164 4.7 58.9 1.0
N Y:ARG167 4.8 55.7 1.0
N Y:TYR170 4.8 55.8 1.0
O Y:ARG167 4.8 58.5 1.0
CZ Y:ARG19 4.8 70.4 1.0
CB Y:ALA169 4.9 57.3 1.0
CA Y:SER171 4.9 55.0 1.0

Magnesium binding site 8 out of 8 in 6g7f

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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg301

b:79.1
occ:1.00
 O Z:VAL198 2.7 59.4 1.0
O Z:HIS195 2.8 51.8 1.0
O Z:THR192 2.9 70.6 1.0
O Z:ASP222 3.6 87.5 1.0
NH2 Z:ARG28 3.6 67.1 1.0
O Z:ILE196 3.6 64.2 1.0
CA Z:ILE196 3.7 59.9 1.0
C Z:HIS195 3.7 56.2 1.0
C Z:ILE196 3.8 60.5 1.0
C Z:VAL198 3.9 59.6 1.0
C Z:THR192 3.9 71.7 1.0
CG2 Z:THR192 4.1 72.0 1.0
N Z:ILE196 4.1 57.5 1.0
NH2 H:ARG19 4.2 74.1 1.0
CA Z:THR192 4.3 70.5 1.0
N Z:VAL198 4.4 61.3 1.0
OD1 Z:ASP222 4.4 74.6 1.0
C Z:ASP222 4.6 86.4 1.0
CZ Z:ARG28 4.6 66.6 1.0
CA Z:VAL198 4.7 61.4 1.0
N Z:GLN197 4.7 59.4 1.0
CB Z:THR192 4.8 69.4 1.0
N Z:GLY199 4.9 58.4 1.0
NH1 H:ARG19 4.9 73.7 1.0
CZ H:ARG19 4.9 71.5 1.0
NH1 Z:ARG28 4.9 67.5 1.0
CB Z:ILE196 4.9 59.6 1.0
CA Z:GLY199 5.0 60.0 1.0
CA Z:HIS195 5.0 57.3 1.0
N Z:HIS195 5.0 58.1 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 01:02:02 2024

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