Atomistry » Magnesium » PDB 7ny1-7o4g » 7o2l
Atomistry »
  Magnesium »
    PDB 7ny1-7o4g »
      7o2l »

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

Go back to Magnesium Binding Sites List in 7o2l
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 Apr 6 18:00:28 2023

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy