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Chlorine in PDB 4qzz: Ycp in Complex with Omuralide

Enzymatic activity of Ycp in Complex with Omuralide

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

Protein crystallography data

The structure of Ycp in Complex with Omuralide, PDB code: 4qzz 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 / 2.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 135.960, 301.960, 145.050, 90.00, 113.14, 90.00
R / Rfree (%) 17.9 / 20.8

Other elements in 4qzz:

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

Magnesium (Mg) 7 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Ycp in Complex with Omuralide (pdb code 4qzz). 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 Omuralide, PDB code: 4qzz:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 4qzz

Go back to Chlorine Binding Sites List in 4qzz
Chlorine binding site 1 out of 4 in the Ycp in Complex with Omuralide


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 Omuralide within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Cl302

b:38.2
occ:1.00
OH H:TYR69 2.9 38.9 1.0
NH1 G:ARG111 3.0 36.7 1.0
OD1 G:ASN114 3.3 39.5 1.0
CD G:ARG111 3.6 35.2 1.0
CB G:ASN114 3.7 34.1 1.0
CZ H:TYR69 3.7 37.0 1.0
CE2 H:TYR69 3.8 36.6 1.0
CG G:ASN114 3.8 35.4 1.0
CZ G:ARG111 4.0 36.4 1.0
NE G:ARG111 4.2 36.2 1.0
CA G:ARG111 4.6 35.2 1.0
O G:ARG111 4.7 36.0 1.0
CG G:ARG111 4.9 34.3 1.0
CE1 H:TYR69 5.0 36.9 1.0
CB G:ARG111 5.0 34.5 1.0

Chlorine binding site 2 out of 4 in 4qzz

Go back to Chlorine Binding Sites List in 4qzz
Chlorine binding site 2 out of 4 in the Ycp in Complex with Omuralide


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 Omuralide within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Cl203

b:40.4
occ:1.00
NH1 N:ARG45 2.9 34.2 1.0
NH2 N:ARG45 3.0 34.0 1.0
NE2 N:GLN53 3.2 27.9 1.0
CZ N:ARG45 3.4 34.2 1.0
CG2 N:THR31 3.8 42.6 1.0
C15 N:SLA201 4.0 46.2 1.0
CB N:ALA49 4.0 30.7 1.0
CD N:GLN53 4.3 27.7 1.0
OD1 H:ASP120 4.5 58.6 1.0
CG N:GLN53 4.5 28.6 1.0
CA N:ALA49 4.6 31.6 1.0
NE N:ARG45 4.7 34.8 1.0
O N:ALA49 4.9 30.4 1.0
O H:THR119 4.9 38.5 1.0

Chlorine binding site 3 out of 4 in 4qzz

Go back to Chlorine Binding Sites List in 4qzz
Chlorine binding site 3 out of 4 in the Ycp in Complex with Omuralide


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 Omuralide within 5.0Å range:
probe atom residue distance (Å) B Occ
U:Cl301

b:45.4
occ:1.00
OH V:TYR69 2.9 44.4 1.0
NH1 U:ARG111 3.1 41.3 1.0
OD1 U:ASN114 3.3 47.8 1.0
CE2 V:TYR69 3.7 44.4 1.0
CZ V:TYR69 3.7 44.8 1.0
CB U:ASN114 3.7 41.0 1.0
CG U:ASN114 3.8 44.0 1.0
CD U:ARG111 3.8 39.9 1.0
CZ U:ARG111 4.2 41.2 1.0
NE U:ARG111 4.5 42.0 1.0
CA U:ARG111 4.8 38.4 1.0
ND2 U:ASN114 4.9 43.0 1.0
O U:ARG111 4.9 38.5 1.0
CD2 V:TYR69 4.9 43.5 1.0
CE1 V:TYR69 5.0 45.3 1.0
OD2 O:ASP87 5.0 49.4 1.0

Chlorine binding site 4 out of 4 in 4qzz

Go back to Chlorine Binding Sites List in 4qzz
Chlorine binding site 4 out of 4 in the Ycp in Complex with Omuralide


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 Omuralide within 5.0Å range:
probe atom residue distance (Å) B Occ
b:Cl202

b:41.0
occ:1.00
NH1 b:ARG45 3.0 38.0 1.0
NE2 b:GLN53 3.1 34.2 1.0
NH2 b:ARG45 3.1 37.0 1.0
CZ b:ARG45 3.5 37.1 1.0
CG2 b:THR31 3.8 43.3 1.0
CB b:ALA49 3.9 34.6 1.0
C15 b:SLA201 4.0 46.8 1.0
CD b:GLN53 4.2 34.3 1.0
OD1 V:ASP120 4.4 57.5 1.0
CG b:GLN53 4.5 34.1 1.0
CA b:ALA49 4.6 35.4 1.0
O V:THR119 4.8 41.5 1.0
NE b:ARG45 4.8 37.4 1.0
O b:ALA49 4.9 36.9 1.0

Reference:

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
Page generated: Fri Jul 26 01:01:41 2024

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