Chlorine 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:

Magnesium (Mg) 8 atoms

Chlorine Binding Sites:

The binding sites of Chlorine 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 Chlorine atom.
In total 2 binding sites of Chlorine 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 Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in 7o2l

Go back to Chlorine Binding Sites List in 7o2l
Chlorine binding site 1 out of 2 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 Chlorine with other atoms in the Cl 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:Cl302

b:72.9
occ:1.00
 OH H:TYR69 2.9 69.2 1.0
NH1 G:ARG111 3.2 78.5 1.0
OD1 G:ASN114 3.3 72.7 1.0
CE2 H:TYR69 3.6 70.7 1.0
CZ H:TYR69 3.6 70.7 1.0
CD G:ARG111 3.8 74.5 1.0
CB G:ASN114 3.8 71.0 1.0
CG G:ASN114 3.9 71.6 1.0
CZ G:ARG111 4.2 77.9 1.0
NE G:ARG111 4.4 76.5 1.0
CA G:ARG111 4.7 72.3 1.0
CD2 H:TYR69 4.8 71.1 1.0
OD2 A:ASP87 4.9 87.6 1.0
O G:ARG111 4.9 76.3 1.0
CE1 H:TYR69 4.9 71.3 1.0
O G:HOH404 5.0 66.1 1.0

Chlorine binding site 2 out of 2 in 7o2l

Go back to Chlorine Binding Sites List in 7o2l
Chlorine binding site 2 out of 2 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 Chlorine with other atoms in the Cl 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
U:Cl301

b:85.7
occ:1.00
 OH V:TYR69 2.9 81.1 1.0
NH1 U:ARG111 3.1 86.6 1.0
OD1 U:ASN114 3.2 85.1 1.0
CB U:ASN114 3.6 81.4 1.0
CE2 V:TYR69 3.6 79.0 1.0
CZ V:TYR69 3.7 79.6 1.0
CG U:ASN114 3.8 83.7 1.0
CD U:ARG111 3.9 83.4 1.0
CZ U:ARG111 4.2 85.3 1.0
NE U:ARG111 4.5 85.4 1.0
CA U:ARG111 4.8 79.2 1.0
O U:ARG111 4.8 78.5 1.0
OD2 O:ASP87 4.9 97.8 1.0
CD2 V:TYR69 4.9 79.5 1.0
CE1 V:TYR69 5.0 79.6 1.0
ND2 U:ASN114 5.0 81.9 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: Tue Jul 30 01:12:53 2024

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