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Chlorine in PDB 4r00: Ycp BETA5-C52F Mutant in Complex with Omuralide

Enzymatic activity of Ycp BETA5-C52F Mutant in Complex with Omuralide

All present enzymatic activity of Ycp BETA5-C52F Mutant in Complex with Omuralide:
3.4.25.1;

Protein crystallography data

The structure of Ycp BETA5-C52F Mutant in Complex with Omuralide, PDB code: 4r00 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 (°) 136.250, 301.240, 144.330, 90.00, 113.16, 90.00
R / Rfree (%) 18.4 / 21

Other elements in 4r00:

The structure of Ycp BETA5-C52F Mutant in Complex with Omuralide also contains other interesting chemical elements:

Magnesium (Mg) 8 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Ycp BETA5-C52F Mutant in Complex with Omuralide (pdb code 4r00). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 5 binding sites of Chlorine where determined in the Ycp BETA5-C52F Mutant in Complex with Omuralide, PDB code: 4r00:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in 4r00

Go back to Chlorine Binding Sites List in 4r00
Chlorine binding site 1 out of 5 in the Ycp BETA5-C52F Mutant 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 BETA5-C52F Mutant in Complex with Omuralide within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Cl302

b:39.3
occ:1.00
 OH H:TYR69 2.9 39.8 1.0
NH1 G:ARG111 3.0 38.4 1.0
OD1 G:ASN114 3.4 42.9 1.0
CD G:ARG111 3.6 37.2 1.0
CE2 H:TYR69 3.7 37.9 1.0
CZ H:TYR69 3.7 37.9 1.0
CB G:ASN114 3.8 37.5 1.0
CG G:ASN114 4.0 38.8 1.0
CZ G:ARG111 4.0 38.4 1.0
NE G:ARG111 4.2 38.5 1.0
CA G:ARG111 4.6 37.4 1.0
O G:ARG111 4.8 41.1 1.0
CG G:ARG111 4.9 36.1 1.0
CD2 H:TYR69 4.9 37.5 1.0
CE1 H:TYR69 5.0 37.2 1.0

Chlorine binding site 2 out of 5 in 4r00

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Chlorine binding site 2 out of 5 in the Ycp BETA5-C52F Mutant 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 BETA5-C52F Mutant in Complex with Omuralide within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Cl303

b:63.4
occ:1.00
 O K:ILE82 2.9 35.1 1.0
CB K:ASN85 3.6 35.5 1.0
C K:ILE82 3.7 35.5 1.0
CA K:ILE82 3.7 36.6 1.0
N K:LEU86 3.9 33.3 1.0
CG2 K:ILE82 4.0 35.7 1.0
C K:ASN85 4.2 34.2 1.0
CB K:ILE82 4.4 36.5 1.0
CA K:LEU86 4.4 33.1 1.0
CB K:LEU86 4.4 32.9 1.0
CA K:ASN85 4.5 34.6 1.0
O K:LYS81 4.6 35.4 1.0
CH2 K:TRP58 4.6 35.2 1.0
CG K:ASN85 4.7 36.1 1.0
OD1 K:ASN85 4.7 38.2 1.0
CG1 K:ILE82 4.7 37.3 1.0
O K:ASN85 4.9 35.0 1.0
N K:ILE82 4.9 37.5 1.0
N K:ASN85 5.0 34.0 1.0

Chlorine binding site 3 out of 5 in 4r00

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Chlorine binding site 3 out of 5 in the Ycp BETA5-C52F Mutant 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 BETA5-C52F Mutant in Complex with Omuralide within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Cl203

b:36.4
occ:1.00
 NH2 N:ARG45 3.1 37.5 1.0
NH1 N:ARG45 3.1 35.1 1.0
NE2 N:GLN53 3.2 31.5 1.0
CZ N:ARG45 3.5 36.4 1.0
CG2 N:THR31 3.9 43.8 1.0
CB N:ALA49 3.9 33.8 1.0
C15 N:SLA201 3.9 46.0 1.0
CD N:GLN53 4.3 31.1 1.0
OD1 H:ASP120 4.4 62.2 1.0
CG N:GLN53 4.5 31.4 1.0
CA N:ALA49 4.5 34.4 1.0
O H:THR119 4.8 41.2 1.0
NE N:ARG45 4.9 37.0 1.0
O N:ALA49 4.9 33.4 1.0

Chlorine binding site 4 out of 5 in 4r00

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Chlorine binding site 4 out of 5 in the Ycp BETA5-C52F Mutant 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 BETA5-C52F Mutant in Complex with Omuralide within 5.0Å range:
probe atom residue distance (Å) B Occ
U:Cl301

b:40.5
occ:1.00
 OH V:TYR69 3.0 48.0 1.0
NH1 U:ARG111 3.0 44.5 1.0
OD1 U:ASN114 3.2 49.1 1.0
CB U:ASN114 3.6 43.1 1.0
CE2 V:TYR69 3.7 47.3 1.0
CD U:ARG111 3.7 41.6 1.0
CG U:ASN114 3.8 45.9 1.0
CZ V:TYR69 3.8 47.9 1.0
CZ U:ARG111 4.1 44.1 1.0
NE U:ARG111 4.4 43.7 1.0
CA U:ARG111 4.7 40.8 1.0
O U:ARG111 4.8 41.5 1.0
ND2 U:ASN114 5.0 45.8 1.0

Chlorine binding site 5 out of 5 in 4r00

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Chlorine binding site 5 out of 5 in the Ycp BETA5-C52F Mutant in Complex with Omuralide


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Ycp BETA5-C52F Mutant in Complex with Omuralide within 5.0Å range:
probe atom residue distance (Å) B Occ
b:Cl202

b:40.1
occ:1.00
 NH2 b:ARG45 3.0 37.4 1.0
NH1 b:ARG45 3.1 39.0 1.0
NE2 b:GLN53 3.3 35.1 1.0
CZ b:ARG45 3.5 38.0 1.0
CG2 b:THR31 3.9 45.8 1.0
CB b:ALA49 3.9 37.5 1.0
C15 b:SLA201 3.9 46.1 1.0
CD b:GLN53 4.3 34.5 1.0
OD1 V:ASP120 4.5 57.0 1.0
CA b:ALA49 4.5 38.6 1.0
CG b:GLN53 4.5 35.2 1.0
NE b:ARG45 4.8 38.1 1.0
O b:ALA49 4.9 37.0 1.0
O V:THR119 4.9 41.0 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 01:01:39 2024

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