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Magnesium in PDB 7o2l: Yeast 20S Proteasome in Complex with the Covalently Bound Inhibitor B- Lactone (2R,3S)-3-Isopropyl-4-Oxo-2-Oxetane-Carboxylate (Ioc)

Enzymatic activity of Yeast 20S Proteasome in Complex with the Covalently Bound Inhibitor B- Lactone (2R,3S)-3-Isopropyl-4-Oxo-2-Oxetane-Carboxylate (Ioc)

All present enzymatic activity of Yeast 20S Proteasome in Complex with the Covalently Bound Inhibitor B- Lactone (2R,3S)-3-Isopropyl-4-Oxo-2-Oxetane-Carboxylate (Ioc):
3.4.25.1;

Protein crystallography data

The structure of Yeast 20S Proteasome in Complex with the Covalently Bound Inhibitor B- Lactone (2R,3S)-3-Isopropyl-4-Oxo-2-Oxetane-Carboxylate (Ioc), PDB code: 7o2l was solved by Y.M.Shi, M.Hirschmann, Y.N.Shi, A.Shabbir, D.Abebew, N.J.Tobias, P.Gruen, J.J.Crames, L.Poeschel, W.Kuttenlochner, C.Richter, J.Herrmann, R.Mueller, A.Thanwisai, S.J.Pidot, T.P.Stinear, M.Groll, Y.Kim, H.Bode, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 3.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 135.12, 301.5, 144.25, 90, 112.93, 90
R / Rfree (%) 17.8 / 21.6

Other elements in 7o2l:

The structure of Yeast 20S Proteasome in Complex with the Covalently Bound Inhibitor B- Lactone (2R,3S)-3-Isopropyl-4-Oxo-2-Oxetane-Carboxylate (Ioc) 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 the Covalently Bound Inhibitor B- Lactone (2R,3S)-3-Isopropyl-4-Oxo-2-Oxetane-Carboxylate (Ioc) (pdb code 7o2l). 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 the Covalently Bound Inhibitor B- Lactone (2R,3S)-3-Isopropyl-4-Oxo-2-Oxetane-Carboxylate (Ioc), PDB code: 7o2l:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 7o2l

Go back to Magnesium Binding Sites List in 7o2l
Magnesium binding site 1 out of 8 in the Yeast 20S Proteasome in Complex with the Covalently Bound Inhibitor B- Lactone (2R,3S)-3-Isopropyl-4-Oxo-2-Oxetane-Carboxylate (Ioc)


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 the Covalently Bound Inhibitor B- Lactone (2R,3S)-3-Isopropyl-4-Oxo-2-Oxetane-Carboxylate (Ioc) within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:86.9
occ:1.00
 O G:MET125 2.2 91.4 1.0
OG1 G:THR8 2.6 81.4 1.0
O G:ARG122 2.9 88.7 1.0
O G:TYR119 3.1 74.6 1.0
O G:ALA123 3.1 97.8 1.0
CG2 G:THR8 3.2 82.7 1.0
C G:MET125 3.3 90.6 1.0
CB G:THR8 3.4 81.5 1.0
C G:ALA123 3.6 94.9 1.0
CA G:ALA123 3.7 92.0 1.0
N G:THR8 3.9 84.6 1.0
C G:ARG122 3.9 87.5 1.0
CA G:ARG126 4.0 83.7 1.0
N G:ARG126 4.0 86.0 1.0
N G:ALA123 4.2 89.9 1.0
N G:MET125 4.3 96.5 1.0
CA G:THR8 4.3 82.8 1.0
C G:TYR119 4.3 75.0 1.0
CA G:MET125 4.4 97.7 1.0
CD G:PRO127 4.4 82.0 1.0
N G:TYR124 4.6 96.5 1.0
C G:ARG126 4.8 82.0 1.0
C G:ILE7 4.9 88.1 1.0
C G:TYR124 5.0 95.6 1.0
N G:PRO127 5.0 81.2 1.0
CB G:ALA123 5.0 92.6 1.0

Magnesium binding site 2 out of 8 in 7o2l

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Magnesium binding site 2 out of 8 in the Yeast 20S Proteasome in Complex with the Covalently Bound Inhibitor B- Lactone (2R,3S)-3-Isopropyl-4-Oxo-2-Oxetane-Carboxylate (Ioc)


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 the Covalently Bound Inhibitor B- Lactone (2R,3S)-3-Isopropyl-4-Oxo-2-Oxetane-Carboxylate (Ioc) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:98.6
occ:1.00
 O I:SER180 2.7 82.2 1.0
O I:ASP177 2.9 81.0 1.0
O I:ALA174 2.9 86.3 1.0
OXT I:ASP204 3.3 112.3 1.0
C I:SER180 3.9 80.7 1.0
C I:ALA174 4.0 86.9 1.0
C I:ASP177 4.1 82.8 1.0
CA I:ASP175 4.1 88.2 1.0
O I:ASP204 4.1 106.8 1.0
C I:ASP204 4.1 106.9 1.0
NH2 Y:ARG19 4.2 103.7 1.0
O I:ALA178 4.4 82.7 1.0
N I:ASP175 4.4 87.6 1.0
CA I:GLY181 4.5 81.8 1.0
C I:ASP175 4.5 87.3 1.0
OD1 I:ASP175 4.5 89.8 1.0
O I:ASP175 4.6 89.1 1.0
N I:GLY181 4.6 80.2 1.0
NH1 Y:ARG19 4.6 107.5 1.0
C I:ALA178 4.7 82.7 1.0
CA I:ALA178 4.8 83.0 1.0
CZ Y:ARG19 4.8 103.9 1.0
N I:ALA178 4.8 81.2 1.0
N I:ASP177 4.9 84.6 1.0
N I:SER180 4.9 78.1 1.0
CA I:SER180 5.0 78.5 1.0

Magnesium binding site 3 out of 8 in 7o2l

Go back to Magnesium Binding Sites List in 7o2l
Magnesium binding site 3 out of 8 in the Yeast 20S Proteasome in Complex with the Covalently Bound Inhibitor B- Lactone (2R,3S)-3-Isopropyl-4-Oxo-2-Oxetane-Carboxylate (Ioc)


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 the Covalently Bound Inhibitor B- Lactone (2R,3S)-3-Isopropyl-4-Oxo-2-Oxetane-Carboxylate (Ioc) within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg902

b:85.1
occ:1.00
 O K:ALA165 2.3 81.9 1.0
O K:ASP168 2.3 77.5 1.0
O W:ASP204 2.6 113.9 1.0
O K:SER171 3.0 83.0 1.0
C W:ASP204 3.1 111.2 1.0
C K:ASP168 3.3 80.8 1.0
CA W:ASP204 3.4 105.6 1.0
C K:ALA165 3.5 83.0 1.0
O K:HIS166 3.5 88.0 1.0
NH1 K:ARG19 3.7 99.7 1.0
CA K:ALA169 3.8 83.4 1.0
CB W:ASP204 3.8 106.7 1.0
N K:ALA169 3.9 81.4 1.0
C K:HIS166 4.0 86.3 1.0
OXT W:ASP204 4.1 117.1 1.0
O K:ALA169 4.1 85.4 1.0
C K:ALA169 4.1 84.4 1.0
C K:SER171 4.2 81.3 1.0
N K:HIS166 4.3 83.3 1.0
CA K:ALA165 4.4 83.5 1.0
N K:ASP168 4.4 83.4 1.0
C K:ARG167 4.4 84.4 1.0
CA K:HIS166 4.5 86.7 1.0
CA K:ASP168 4.5 82.0 1.0
O K:ARG167 4.5 81.6 1.0
N K:ARG167 4.6 86.4 1.0
O K:ALA164 4.6 83.8 1.0
CZ K:ARG19 4.7 99.2 1.0
N K:SER171 4.8 82.1 1.0
N W:ASP204 4.8 101.4 1.0
N K:TYR170 4.9 84.0 1.0
CG W:ASP204 5.0 103.5 1.0

Magnesium binding site 4 out of 8 in 7o2l

Go back to Magnesium Binding Sites List in 7o2l
Magnesium binding site 4 out of 8 in the Yeast 20S Proteasome in Complex with the Covalently Bound Inhibitor B- Lactone (2R,3S)-3-Isopropyl-4-Oxo-2-Oxetane-Carboxylate (Ioc)


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 the Covalently Bound Inhibitor B- Lactone (2R,3S)-3-Isopropyl-4-Oxo-2-Oxetane-Carboxylate (Ioc) within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg902

b:66.8
occ:1.00
 O N:ILE163 2.7 77.9 1.0
O N:SER169 2.8 81.2 1.0
O N:ASP166 3.3 75.6 1.0
NH1 N:ARG19 3.5 86.5 1.0
CD1 a:LEU34 3.7 88.1 1.0
C N:ILE163 3.8 78.5 1.0
CG2 N:ILE163 3.8 78.7 1.0
C N:SER169 4.0 78.5 1.0
CZ N:ARG19 4.1 85.1 1.0
NH2 N:ARG19 4.2 87.5 1.0
CA N:GLY170 4.3 80.3 1.0
C N:ASP166 4.4 77.1 1.0
CA N:ILE163 4.5 77.8 1.0
N N:GLY170 4.6 78.5 1.0
CA N:GLY167 4.7 77.6 1.0
O N:GLY167 4.8 75.7 1.0
CB N:ILE163 4.8 78.0 1.0
N N:LYS164 4.8 80.4 1.0
O N:LYS164 4.9 84.8 1.0
C N:GLY167 5.0 76.3 1.0
N N:GLY167 5.0 77.2 1.0
C N:LYS164 5.0 82.6 1.0

Magnesium binding site 5 out of 8 in 7o2l

Go back to Magnesium Binding Sites List in 7o2l
Magnesium binding site 5 out of 8 in the Yeast 20S Proteasome in Complex with the Covalently Bound Inhibitor B- Lactone (2R,3S)-3-Isopropyl-4-Oxo-2-Oxetane-Carboxylate (Ioc)


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 the Covalently Bound Inhibitor B- Lactone (2R,3S)-3-Isopropyl-4-Oxo-2-Oxetane-Carboxylate (Ioc) within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Mg902

b:100.6
occ:1.00
 OXT L:ASP222 2.4 105.8 1.0
O V:ASP166 2.6 81.6 1.0
O V:ILE163 2.9 77.5 1.0
O V:TRP164 3.0 83.5 1.0
C L:ASP222 3.1 104.4 1.0
C V:ASP166 3.2 84.5 1.0
C V:TRP164 3.5 83.5 1.0
O L:ASP222 3.6 104.6 1.0
N V:LEU167 3.7 84.4 1.0
O V:SER169 3.8 78.8 1.0
CA V:LEU167 3.8 84.1 1.0
N V:ASP166 3.8 83.8 1.0
CA L:ASP222 3.8 102.4 1.0
C V:ILE163 3.9 82.3 1.0
CD2 V:LEU167 4.0 79.9 1.0
N V:ASN165 4.1 82.9 1.0
CD1 L:ILE35 4.1 89.3 1.0
C V:ASN165 4.1 84.9 1.0
O L:ARG221 4.1 95.7 1.0
CA V:ASP166 4.1 83.5 1.0
CA V:TRP164 4.2 83.4 1.0
N V:TRP164 4.4 83.3 1.0
CA V:ASN165 4.5 83.1 1.0
NH1 V:ARG19 4.6 101.1 1.0
O V:GLY162 4.6 77.8 1.0
C V:LEU167 4.6 84.3 1.0
O V:ASN165 4.7 86.0 1.0
N L:ASP222 4.8 101.2 1.0
NH1 L:ARG28 4.8 99.3 1.0
C L:ARG221 4.8 98.7 1.0
O V:LEU167 4.9 85.8 1.0
CB L:ASP222 4.9 100.2 1.0
CB V:LEU167 4.9 82.4 1.0
CG V:LEU167 5.0 80.7 1.0

Magnesium binding site 6 out of 8 in 7o2l

Go back to Magnesium Binding Sites List in 7o2l
Magnesium binding site 6 out of 8 in the Yeast 20S Proteasome in Complex with the Covalently Bound Inhibitor B- Lactone (2R,3S)-3-Isopropyl-4-Oxo-2-Oxetane-Carboxylate (Ioc)


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 the Covalently Bound Inhibitor B- Lactone (2R,3S)-3-Isopropyl-4-Oxo-2-Oxetane-Carboxylate (Ioc) within 5.0Å range:
probe atom residue distance (Å) B Occ
W:Mg301

b:90.5
occ:1.00
 O W:ASP177 2.7 88.2 1.0
O W:ALA174 2.7 85.6 1.0
O W:SER180 2.8 91.3 1.0
OXT W:ASP204 3.6 117.1 1.0
C W:ALA174 3.8 88.8 1.0
C W:ASP177 3.8 89.9 1.0
C W:SER180 3.9 90.1 1.0
CA W:ASP175 4.0 93.9 1.0
NH2 K:ARG19 4.3 101.8 1.0
O W:ASP204 4.3 113.9 1.0
N W:ASP175 4.3 91.2 1.0
C W:ASP175 4.3 92.9 1.0
C W:ASP204 4.4 111.2 1.0
O W:ALA178 4.4 89.4 1.0
O W:ASP175 4.4 93.5 1.0
OD1 W:ASP175 4.6 100.1 1.0
CA W:ALA178 4.6 88.9 1.0
N W:ASP177 4.6 90.0 1.0
N W:ALA178 4.6 89.4 1.0
CA W:GLY181 4.6 86.9 1.0
C W:ALA178 4.7 88.7 1.0
NH1 K:ARG19 4.7 99.7 1.0
N W:GLY181 4.7 87.6 1.0
CZ K:ARG19 4.8 99.2 1.0
CA W:ASP177 4.8 89.7 1.0
N W:SER180 4.8 88.2 1.0
CA W:SER180 4.9 88.1 1.0

Magnesium binding site 7 out of 8 in 7o2l

Go back to Magnesium Binding Sites List in 7o2l
Magnesium binding site 7 out of 8 in the Yeast 20S Proteasome in Complex with the Covalently Bound Inhibitor B- Lactone (2R,3S)-3-Isopropyl-4-Oxo-2-Oxetane-Carboxylate (Ioc)


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 the Covalently Bound Inhibitor B- Lactone (2R,3S)-3-Isopropyl-4-Oxo-2-Oxetane-Carboxylate (Ioc) within 5.0Å range:
probe atom residue distance (Å) B Occ
Y:Mg902

b:103.9
occ:1.00
 O I:ASP204 2.4 106.8 1.0
O Y:ASP168 2.5 77.0 1.0
O Y:ALA165 2.8 83.8 1.0
C I:ASP204 3.1 106.9 1.0
C Y:ASP168 3.3 80.3 1.0
CA Y:ALA169 3.4 80.6 1.0
O Y:SER171 3.5 82.3 1.0
O Y:HIS166 3.5 81.9 1.0
CA I:ASP204 3.6 103.3 1.0
N Y:ALA169 3.6 80.7 1.0
NH1 Y:ARG19 3.7 107.5 1.0
OXT I:ASP204 3.9 112.3 1.0
O Y:ALA169 3.9 80.4 1.0
C Y:ALA169 3.9 80.2 1.0
C Y:ALA165 4.0 82.3 1.0
C Y:HIS166 4.1 81.9 1.0
CB I:ASP204 4.2 103.1 1.0
O Y:ARG167 4.2 82.4 1.0
C Y:ARG167 4.4 84.0 1.0
N Y:ASP168 4.4 83.0 1.0
CA Y:ASP168 4.5 81.5 1.0
CB Y:ALA169 4.6 81.7 1.0
C Y:SER171 4.7 81.5 1.0
CA Y:HIS166 4.8 82.6 1.0
N Y:ARG167 4.8 81.6 1.0
N Y:HIS166 4.8 82.2 1.0
CZ Y:ARG19 4.8 103.9 1.0
N Y:TYR170 4.8 77.1 1.0
N I:ASP204 4.9 101.2 1.0
CA Y:ALA165 5.0 82.1 1.0
O I:ALA178 5.0 82.7 1.0

Magnesium binding site 8 out of 8 in 7o2l

Go back to Magnesium Binding Sites List in 7o2l
Magnesium binding site 8 out of 8 in the Yeast 20S Proteasome in Complex with the Covalently Bound Inhibitor B- Lactone (2R,3S)-3-Isopropyl-4-Oxo-2-Oxetane-Carboxylate (Ioc)


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 the Covalently Bound Inhibitor B- Lactone (2R,3S)-3-Isopropyl-4-Oxo-2-Oxetane-Carboxylate (Ioc) within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg301

b:96.2
occ:1.00
 O Z:HOH401 2.3 80.1 1.0
O Z:VAL198 2.4 93.7 1.0
O Z:ASP222 3.1 113.8 1.0
O Z:THR192 3.2 98.1 1.0
NH2 Z:ARG28 3.3 98.8 1.0
CG2 Z:THR192 3.5 97.6 1.0
C Z:VAL198 3.6 92.2 1.0
O Z:HIS195 3.7 80.7 1.0
OD1 Z:ASP222 3.8 105.1 1.0
O Z:LYS220 4.0 95.8 1.0
CZ Z:ARG28 4.0 97.4 1.0
CA Z:GLY199 4.1 92.6 1.0
NH1 Z:ARG28 4.1 100.0 1.0
C Z:THR192 4.1 96.1 1.0
O Z:ILE196 4.1 93.5 1.0
C Z:ASP222 4.2 110.2 1.0
N Z:GLY199 4.2 90.5 1.0
CA Z:THR192 4.3 96.2 1.0
NH2 H:ARG19 4.4 121.0 1.0
CB Z:THR192 4.5 95.8 1.0
C Z:ILE196 4.6 91.1 1.0
CA Z:ILE196 4.7 90.6 1.0
N Z:VAL198 4.7 89.5 1.0
CA Z:VAL198 4.7 88.7 1.0
C Z:HIS195 4.8 86.9 1.0
CG Z:ASP222 4.8 105.8 1.0
OXT Z:ASP222 4.9 108.5 1.0
N Z:ASP222 4.9 108.0 1.0
C Z:LYS220 4.9 98.1 1.0

Reference:

Y.M.Shi, M.Hirschmann, Y.N.Shi, S.Ahmed, D.Abebew, N.J.Tobias, P.Grun, J.J.Crames, L.Poschel, W.Kuttenlochner, C.Richter, J.Herrmann, R.Muller, A.Thanwisai, S.J.Pidot, T.P.Stinear, M.Groll, Y.Kim, H.B.Bode. Global Analysis of Biosynthetic Gene Clusters Reveals Conserved and Unique Natural Products in Entomopathogenic Nematode-Symbiotic Bacteria. Nat.Chem. V. 14 701 2022.
ISSN: ESSN 1755-4349
PubMed: 35469007
DOI: 10.1038/S41557-022-00923-2
Page generated: Thu Oct 3 02:32:12 2024

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