Chlorine in PDB 4qvl: Ycp in Complex with Bortezomib

All present enzymatic activity of Ycp in Complex with Bortezomib:
3.4.25.1;

The structure of Ycp in Complex with Bortezomib, PDB code: 4qvl was solved by E.M.Huber, W.Heinemeyer, M.Groll, 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 (°)	134.910, 300.210, 144.760, 90.00, 112.85, 90.00
R / Rfree (%)	18.7 / 21.5

The structure of Ycp in Complex with Bortezomib also contains other interesting chemical elements:

Magnesium

(Mg)

8 atoms

The binding sites of Chlorine atom in the Ycp in Complex with Bortezomib (pdb code 4qvl). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Ycp in Complex with Bortezomib, PDB code: 4qvl:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the Ycp in Complex with Bortezomib


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Ycp in Complex with Bortezomib within 5.0Å range: probe atom residue distance (Å) B Occ G:Cl302 b:44.0 occ:1.00 OH H:TYR69 2.8 42.0 1.0 NH1 G:ARG111 3.0 47.3 1.0 OD1 G:ASN114 3.2 47.8 1.0 CD G:ARG111 3.6 46.3 1.0 CZ H:TYR69 3.7 43.8 1.0 CB G:ASN114 3.7 45.1 1.0 CE2 H:TYR69 3.7 44.2 1.0 CG G:ASN114 3.8 46.3 1.0 CZ G:ARG111 4.1 46.9 1.0 NE G:ARG111 4.2 47.1 1.0 CA G:ARG111 4.6 46.3 1.0 O G:ARG111 4.7 49.5 1.0 CG G:ARG111 4.9 46.1 1.0 CE1 H:TYR69 5.0 44.4 1.0 OD2 A:ASP87 5.0 55.4 1.0

Chlorine binding site 2 out of 4 in the Ycp in Complex with Bortezomib


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Ycp in Complex with Bortezomib within 5.0Å range: probe atom residue distance (Å) B Occ N:Cl203 b:45.7 occ:1.00 NH2 N:ARG45 2.9 44.5 1.0 NE2 N:GLN53 3.1 37.6 1.0 NH1 N:ARG45 3.3 47.1 1.0 CZ N:ARG45 3.5 45.3 1.0 CG2 N:THR31 3.7 49.2 1.0 C25 N:BO2201 4.0 37.5 1.0 CB N:ALA49 4.2 41.6 1.0 CD N:GLN53 4.2 36.9 1.0 C24 N:BO2201 4.3 37.7 1.0 OD1 H:ASP120 4.3 75.9 1.0 CG N:GLN53 4.4 37.7 1.0 O H:THR119 4.7 49.7 1.0 CB a:TYR228 4.7 46.5 1.0 C23 N:BO2201 4.8 37.7 1.0 O N:ASP32 4.8 47.2 1.0 CA N:ALA49 4.8 42.0 1.0 NE N:ARG45 4.9 45.0 1.0 O N:ALA49 4.9 41.6 1.0 CD2 a:TYR228 4.9 42.8 1.0

Chlorine binding site 3 out of 4 in the Ycp in Complex with Bortezomib


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Ycp in Complex with Bortezomib within 5.0Å range: probe atom residue distance (Å) B Occ U:Cl301 b:48.9 occ:1.00 OH V:TYR69 3.0 45.6 1.0 NH1 U:ARG111 3.0 53.3 1.0 OD1 U:ASN114 3.2 57.1 1.0 CD U:ARG111 3.7 49.6 1.0 CB U:ASN114 3.7 48.2 1.0 CE2 V:TYR69 3.8 47.6 1.0 CZ V:TYR69 3.8 48.4 1.0 CG U:ASN114 3.8 52.4 1.0 CZ U:ARG111 4.1 52.3 1.0 NE U:ARG111 4.3 52.4 1.0 CA U:ARG111 4.7 47.5 1.0 O U:ARG111 4.8 45.8 1.0 OD2 O:ASP87 4.9 60.6 1.0

Chlorine binding site 4 out of 4 in the Ycp in Complex with Bortezomib


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Ycp in Complex with Bortezomib within 5.0Å range: probe atom residue distance (Å) B Occ b:Cl202 b:45.5 occ:1.00 NH2 b:ARG45 3.0 42.8 1.0 NE2 b:GLN53 3.0 39.3 1.0 NH1 b:ARG45 3.4 48.1 1.0 CZ b:ARG45 3.6 44.8 1.0 CG2 b:THR31 3.7 48.0 1.0 CD b:GLN53 4.1 38.7 1.0 C25 b:BO2201 4.2 43.2 1.0 OD1 V:ASP120 4.2 63.9 1.0 CB b:ALA49 4.2 43.1 1.0 CG b:GLN53 4.4 40.2 1.0 C24 b:BO2201 4.5 43.7 1.0 O V:THR119 4.5 46.1 1.0 CB M:TYR228 4.6 50.6 1.0 CA b:ALA49 4.8 43.8 1.0 O b:ASP32 4.9 51.2 1.0 CD2 M:TYR228 4.9 45.0 1.0 O b:ALA49 4.9 45.8 1.0 NE b:ARG45 4.9 45.1 1.0 C23 b:BO2201 4.9 43.5 1.0

E.M.Huber, W.Heinemeyer, M.Groll. Bortezomib-Resistant Mutant Proteasomes: Structural and Biochemical Evaluation with Carfilzomib and Onx 0914. Structure 2015.
ISSN: ISSN 0969-2126
PubMed: 25599643
DOI: 10.1016/J.STR.2014.11.019