Magnesium in PDB 8olr: Structure of Yeast 20S Proteasome in Complex with the Natural Product Beta-Lactone Inhibitor Cystargolide A

Enzymatic activity of Structure of Yeast 20S Proteasome in Complex with the Natural Product Beta-Lactone Inhibitor Cystargolide A

All present enzymatic activity of Structure of Yeast 20S Proteasome in Complex with the Natural Product Beta-Lactone Inhibitor Cystargolide A:
3.4.25.1;

Protein crystallography data

The structure of Structure of Yeast 20S Proteasome in Complex with the Natural Product Beta-Lactone Inhibitor Cystargolide A, PDB code: 8olr was solved by A.Illigmann, M.-T.Vielberg, M.Lakemeyer, F.Wolf, N.Staudt, T.Dema, P.Stange, I.Malik, S.Grond, S.A.Sieber, M.Groll, L.Kaysser, H.Broetz-Oesterhelt, 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 (°) 136.96, 302.05, 146.01, 90, 113.09, 90
R / Rfree (%) 18.2 / 20.8

Other elements in 8olr:

The structure of Structure of Yeast 20S Proteasome in Complex with the Natural Product Beta-Lactone Inhibitor Cystargolide A also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of Yeast 20S Proteasome in Complex with the Natural Product Beta-Lactone Inhibitor Cystargolide A (pdb code 8olr). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the Structure of Yeast 20S Proteasome in Complex with the Natural Product Beta-Lactone Inhibitor Cystargolide A, PDB code: 8olr:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 8olr

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Magnesium binding site 1 out of 7 in the Structure of Yeast 20S Proteasome in Complex with the Natural Product Beta-Lactone Inhibitor Cystargolide A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Yeast 20S Proteasome in Complex with the Natural Product Beta-Lactone Inhibitor Cystargolide A within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:74.6
occ:1.00
 O G:MET125 2.0 88.6 1.0
O G:TYR119 2.2 77.2 1.0
O G:ARG122 2.6 73.5 1.0
OG1 G:THR8 2.6 75.8 1.0
C G:MET125 3.3 84.6 1.0
CG2 G:THR8 3.3 69.8 1.0
C G:TYR119 3.5 71.9 1.0
CB G:THR8 3.5 72.4 1.0
C G:ARG122 3.7 75.5 1.0
O G:ALA123 3.8 85.4 1.0
CA G:ARG126 4.0 75.5 1.0
N G:ARG126 4.1 77.5 1.0
C G:ALA123 4.1 82.9 1.0
CA G:ALA123 4.1 78.3 1.0
CA G:TYR119 4.2 69.7 1.0
N G:ALA123 4.3 76.9 1.0
CA G:MET125 4.3 93.4 1.0
CD G:PRO127 4.4 75.2 1.0
N G:MET125 4.4 89.7 1.0
N G:THR120 4.5 70.8 1.0
N G:THR8 4.5 75.2 1.0
C G:ARG126 4.6 77.7 1.0
CA G:THR8 4.6 72.6 1.0
CA G:THR120 4.7 70.2 1.0
N G:PRO127 4.7 75.5 1.0
CB G:TYR119 4.8 68.3 1.0
CB G:MET125 4.8 103.3 1.0
C G:THR120 4.8 70.3 1.0
N G:ARG122 4.8 72.6 1.0
CA G:ARG122 4.9 76.6 1.0
N G:TYR124 5.0 86.5 1.0
CG G:PRO127 5.0 73.3 1.0

Magnesium binding site 2 out of 7 in 8olr

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Magnesium binding site 2 out of 7 in the Structure of Yeast 20S Proteasome in Complex with the Natural Product Beta-Lactone Inhibitor Cystargolide A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Yeast 20S Proteasome in Complex with the Natural Product Beta-Lactone Inhibitor Cystargolide A within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:77.6
occ:1.00
 O I:SER180 2.5 68.7 1.0
O I:ALA174 2.7 72.4 1.0
O I:ASP177 2.7 70.2 1.0
C I:ALA174 3.7 72.8 1.0
OXT I:ASP204 3.7 84.5 1.0
C I:SER180 3.7 68.6 1.0
C I:ASP177 3.9 70.9 1.0
CA I:ASP175 4.0 71.8 1.0
N I:ASP175 4.3 71.0 1.0
C I:ASP175 4.3 70.1 1.0
CA I:GLY181 4.4 67.9 1.0
O I:ASP175 4.4 73.0 1.0
N I:GLY181 4.5 66.4 1.0
OD1 I:ASP175 4.5 77.1 1.0
N I:ASP177 4.6 72.2 1.0
C I:ASP204 4.7 79.6 1.0
O I:ALA178 4.7 70.3 1.0
N I:SER180 4.7 64.6 1.0
CA I:SER180 4.8 65.9 1.0
N I:ALA178 4.8 67.5 1.0
C I:ALA178 4.8 68.0 1.0
CA I:ASP177 4.8 73.4 1.0
O I:ASP204 4.8 80.7 1.0
CA I:ALA174 4.8 71.2 1.0
CA I:ALA178 4.8 67.5 1.0

Magnesium binding site 3 out of 7 in 8olr

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Magnesium binding site 3 out of 7 in the Structure of Yeast 20S Proteasome in Complex with the Natural Product Beta-Lactone Inhibitor Cystargolide A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of Yeast 20S Proteasome in Complex with the Natural Product Beta-Lactone Inhibitor Cystargolide A within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg301

b:80.9
occ:1.00
 O K:ALA165 2.2 63.1 1.0
O K:ASP168 2.2 59.7 1.0
O W:ASP204 2.3 87.1 1.0
O K:SER171 3.0 66.1 1.0
C W:ASP204 3.1 90.2 1.0
C K:ASP168 3.2 61.5 1.0
C K:ALA165 3.4 65.4 1.0
CA W:ASP204 3.5 82.8 1.0
O K:HIS166 3.6 71.5 1.0
NH1 K:ARG19 3.8 77.8 1.0
CA K:ALA169 3.8 63.0 1.0
N K:ALA169 3.8 61.0 1.0
CB W:ASP204 4.0 83.2 1.0
C K:HIS166 4.0 68.8 1.0
OXT W:ASP204 4.0 100.0 1.0
C K:ALA169 4.1 65.8 1.0
N K:ASP168 4.2 66.7 1.0
O K:ALA169 4.2 69.1 1.0
C K:SER171 4.3 65.7 1.0
CA K:ASP168 4.3 63.2 1.0
N K:HIS166 4.3 67.5 1.0
CA K:ALA165 4.4 67.1 1.0
CA K:HIS166 4.4 70.4 1.0
C K:ARG167 4.6 69.9 1.0
N K:ARG167 4.7 68.6 1.0
O K:ALA164 4.7 68.8 1.0
N K:SER171 4.8 65.7 1.0
CZ K:ARG19 4.9 80.6 1.0
N W:ASP204 4.9 79.4 1.0
O K:ARG167 4.9 70.8 1.0
N K:TYR170 4.9 67.6 1.0

Magnesium binding site 4 out of 7 in 8olr

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Magnesium binding site 4 out of 7 in the Structure of Yeast 20S Proteasome in Complex with the Natural Product Beta-Lactone Inhibitor Cystargolide A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of Yeast 20S Proteasome in Complex with the Natural Product Beta-Lactone Inhibitor Cystargolide A within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg201

b:65.8
occ:1.00
 O N:ILE163 2.6 65.5 1.0
O N:SER169 2.6 70.6 1.0
O N:ASP166 2.9 63.1 1.0
NH1 N:ARG19 3.6 71.8 1.0
C N:ILE163 3.8 67.3 1.0
C N:SER169 3.8 67.0 1.0
CD1 a:LEU34 3.9 72.2 1.0
C N:ASP166 4.0 63.6 1.0
CG2 N:ILE163 4.0 64.9 1.0
CZ N:ARG19 4.2 70.8 1.0
CA N:GLY170 4.3 67.2 1.0
CA N:GLY167 4.3 63.2 1.0
CA N:ILE163 4.4 67.0 1.0
NH2 N:ARG19 4.4 68.0 1.0
N N:GLY170 4.5 66.0 1.0
O N:GLY167 4.5 60.9 1.0
N N:GLY167 4.5 62.8 1.0
C N:GLY167 4.6 62.7 1.0
N N:LYS164 4.8 71.7 1.0
CA N:SER169 4.8 63.8 1.0
CB N:ILE163 4.8 66.5 1.0
O N:LYS164 4.9 79.3 1.0
N N:SER169 4.9 65.7 1.0
C N:LYS164 5.0 73.7 1.0

Magnesium binding site 5 out of 7 in 8olr

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Magnesium binding site 5 out of 7 in the Structure of Yeast 20S Proteasome in Complex with the Natural Product Beta-Lactone Inhibitor Cystargolide A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of Yeast 20S Proteasome in Complex with the Natural Product Beta-Lactone Inhibitor Cystargolide A within 5.0Å range:
probe atom residue distance (Å) B Occ
W:Mg301

b:81.1
occ:1.00
 O W:ASP177 2.4 68.0 1.0
O W:ALA174 2.5 70.6 1.0
O W:SER180 2.5 75.2 1.0
C W:ASP177 3.6 68.1 1.0
C W:ALA174 3.6 70.8 1.0
C W:SER180 3.7 72.5 1.0
OXT W:ASP204 4.0 100.0 1.0
CA W:ASP175 4.0 76.2 1.0
N W:ASP175 4.2 73.5 1.0
C W:ASP175 4.3 73.6 1.0
N W:ASP177 4.3 71.7 1.0
O W:ASP175 4.4 71.2 1.0
N W:ALA178 4.5 64.8 1.0
O W:ALA178 4.5 68.3 1.0
CA W:ASP177 4.5 70.1 1.0
N W:GLY181 4.5 65.3 1.0
CA W:GLY181 4.5 66.0 1.0
N W:SER180 4.5 73.3 1.0
C W:ALA178 4.6 66.8 1.0
CA W:ALA178 4.6 64.2 1.0
OD1 W:ASP175 4.6 82.5 1.0
CA W:SER180 4.6 70.7 1.0
CA W:ALA174 4.7 68.5 1.0
C W:ASP204 4.9 90.2 1.0
N W:ARG176 4.9 74.3 1.0
O W:ASP204 5.0 87.1 1.0

Magnesium binding site 6 out of 7 in 8olr

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Magnesium binding site 6 out of 7 in the Structure of Yeast 20S Proteasome in Complex with the Natural Product Beta-Lactone Inhibitor Cystargolide A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure of Yeast 20S Proteasome in Complex with the Natural Product Beta-Lactone Inhibitor Cystargolide A within 5.0Å range:
probe atom residue distance (Å) B Occ
Y:Mg301

b:86.8
occ:1.00
 O Y:ASP168 2.2 65.5 1.0
O I:ASP204 2.2 80.7 1.0
O Y:ALA165 2.5 69.5 1.0
O Y:SER171 2.9 68.3 1.0
C I:ASP204 3.1 79.6 1.0
C Y:ASP168 3.1 63.8 1.0
NH1 Y:ARG19 3.5 72.6 1.0
CA Y:ALA169 3.6 65.0 1.0
N Y:ALA169 3.7 64.2 1.0
C Y:ALA165 3.7 65.1 1.0
CA I:ASP204 3.7 78.7 1.0
O Y:ALA169 3.8 65.2 1.0
C Y:ALA169 3.8 66.7 1.0
O Y:HIS166 3.9 64.8 1.0
OXT I:ASP204 4.0 84.5 1.0
C Y:SER171 4.2 66.2 1.0
CB I:ASP204 4.2 79.2 1.0
N Y:ASP168 4.3 65.4 1.0
CA Y:ASP168 4.3 63.4 1.0
C Y:HIS166 4.4 62.4 1.0
CA Y:ALA165 4.6 63.3 1.0
N Y:SER171 4.6 61.9 1.0
CZ Y:ARG19 4.6 74.0 1.0
N Y:HIS166 4.7 65.1 1.0
N Y:TYR170 4.7 65.8 1.0
C Y:ARG167 4.7 66.9 1.0
CA Y:HIS166 4.8 65.4 1.0
O Y:ALA164 4.9 65.7 1.0
CB Y:ALA169 4.9 65.8 1.0
CA Y:SER171 4.9 62.2 1.0
N Y:ARG167 5.0 62.4 1.0

Magnesium binding site 7 out of 7 in 8olr

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Magnesium binding site 7 out of 7 in the Structure of Yeast 20S Proteasome in Complex with the Natural Product Beta-Lactone Inhibitor Cystargolide A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Structure of Yeast 20S Proteasome in Complex with the Natural Product Beta-Lactone Inhibitor Cystargolide A within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg301

b:80.4
occ:1.00
 O Z:VAL198 2.6 75.9 1.0
O Z:THR192 2.7 74.7 1.0
O Z:HIS195 3.0 64.0 1.0
O Z:ASP222 3.4 90.4 1.0
NH2 Z:ARG28 3.7 82.4 1.0
C Z:THR192 3.8 76.8 1.0
C Z:VAL198 3.8 76.0 1.0
O Z:ILE196 3.8 76.8 1.0
CG2 Z:THR192 3.9 75.9 1.0
C Z:HIS195 4.0 66.1 1.0
CA Z:ILE196 4.0 70.3 1.0
C Z:ILE196 4.0 71.3 1.0
NH2 H:ARG19 4.1 84.9 1.0
OD1 Z:ASP222 4.1 95.5 1.0
CA Z:THR192 4.1 76.6 1.0
N Z:VAL198 4.4 71.7 1.0
N Z:ILE196 4.4 66.7 1.0
C Z:ASP222 4.6 95.6 1.0
CB Z:THR192 4.6 76.2 1.0
CA Z:VAL198 4.6 71.2 1.0
N Z:GLY199 4.7 75.0 1.0
CA Z:GLY199 4.8 76.5 1.0
CZ Z:ARG28 4.8 80.1 1.0
N Z:GLN197 4.9 70.1 1.0
N Z:GLU193 5.0 79.2 1.0

Reference:

A.Illigmann, M.T.Vielberg, M.Lakemeyer, F.Wolf, T.Dema, P.Stange, W.Kuttenlochner, E.Liebhart, A.Kulik, N.Staudt, I.Malik, S.Grond, S.A.Sieber, L.Kaysser, M.Groll, H.Brotz-Oesterhelt. Structure of Staphylococcus Aureus Clpp Bound to the Covalent Active Site Inhibitor Cystargolide A. Angew.Chem.Int.Ed.Engl. 14028 2023.
ISSN: ESSN 1521-3773
PubMed: 38029352
DOI: 10.1002/ANIE.202314028
Page generated: Fri Oct 4 14:52:41 2024

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