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Chlorine in PDB 6gop: Yeast 20S Proteasome in Complex with Homosalinosporamide A

Enzymatic activity of Yeast 20S Proteasome in Complex with Homosalinosporamide A

All present enzymatic activity of Yeast 20S Proteasome in Complex with Homosalinosporamide A:
3.4.25.1;

Protein crystallography data

The structure of Yeast 20S Proteasome in Complex with Homosalinosporamide A, PDB code: 6gop was solved by M.Groll, D.Romo, 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 (°) 135.040, 299.810, 144.410, 90.00, 112.56, 90.00
R / Rfree (%) 19.7 / 23.3

Other elements in 6gop:

The structure of Yeast 20S Proteasome in Complex with Homosalinosporamide A also contains other interesting chemical elements:

Magnesium (Mg) 7 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Yeast 20S Proteasome in Complex with Homosalinosporamide A (pdb code 6gop). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 10 binding sites of Chlorine where determined in the Yeast 20S Proteasome in Complex with Homosalinosporamide A, PDB code: 6gop:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 10 in 6gop

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Chlorine binding site 1 out of 10 in the Yeast 20S Proteasome in Complex with Homosalinosporamide A


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

b:32.6
occ:1.00
 OH H:TYR69 2.9 36.0 1.0
NH1 G:ARG111 3.1 33.6 1.0
OD1 G:ASN114 3.3 31.4 1.0
CD G:ARG111 3.6 32.4 1.0
CE2 H:TYR69 3.7 37.1 1.0
CZ H:TYR69 3.7 37.0 1.0
CB G:ASN114 3.7 32.7 1.0
CG G:ASN114 3.9 31.9 1.0
CZ G:ARG111 4.1 33.5 1.0
NE G:ARG111 4.3 33.3 1.0
CA G:ARG111 4.6 33.5 1.0
O G:ARG111 4.8 34.1 1.0
CG G:ARG111 4.9 32.0 1.0
CD2 H:TYR69 5.0 37.5 1.0
CE1 H:TYR69 5.0 36.6 1.0

Chlorine binding site 2 out of 10 in 6gop

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Chlorine binding site 2 out of 10 in the Yeast 20S Proteasome in Complex with Homosalinosporamide A


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 Homosalinosporamide A within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Cl301

b:57.3
occ:1.00
 CL H:F6K301 0.0 57.3 1.0
C21 H:F6K301 1.8 43.3 1.0
C1 H:F6K301 2.6 41.1 1.0
CB H:SER129 3.9 33.6 1.0
CE2 Z:TYR33 4.0 58.1 1.0
C2 H:F6K301 4.1 40.2 1.0
CZ Z:TYR33 4.3 56.4 1.0
O5 H:F6K301 4.3 44.1 1.0
OH Z:TYR33 4.4 55.6 1.0
OG H:SER129 4.4 34.2 1.0
CD2 Z:TYR33 4.5 54.4 1.0
CA H:SER129 4.9 34.9 1.0
CE1 Z:TYR33 5.0 56.5 1.0

Chlorine binding site 3 out of 10 in 6gop

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Chlorine binding site 3 out of 10 in the Yeast 20S Proteasome in Complex with Homosalinosporamide A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Yeast 20S Proteasome in Complex with Homosalinosporamide A within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Cl301

b:65.2
occ:1.00
 CL K:F6K301 0.0 65.2 1.0
C21 K:F6K301 1.7 40.2 1.0
C1 K:F6K301 2.4 38.6 1.0
C2 K:F6K301 3.8 38.0 1.0
CE2 K:TYR170 4.0 45.2 1.0
CD2 K:TYR170 4.1 43.3 1.0
O5 K:F6K301 4.3 40.3 1.0
O20 K:F6K301 4.6 35.8 1.0
CZ K:TYR170 4.8 45.8 1.0
C3 K:F6K301 4.8 38.0 1.0
C19 K:F6K301 4.9 36.9 1.0

Chlorine binding site 4 out of 10 in 6gop

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Chlorine binding site 4 out of 10 in the Yeast 20S Proteasome in Complex with Homosalinosporamide A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Yeast 20S Proteasome in Complex with Homosalinosporamide A within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Cl201

b:46.3
occ:1.00
 CL N:F6K201 0.0 46.3 1.0
C21 N:F6K201 1.8 41.2 1.0
C1 N:F6K201 2.8 40.3 1.0
C2 N:F6K201 3.2 40.2 1.0
O N:GLY23 3.6 42.6 1.0
N N:GLY23 3.6 44.6 1.0
CA N:GLY23 3.7 42.3 1.0
C N:GLY23 4.1 41.4 1.0
O N:THR21 4.5 41.6 1.0
OG1 N:THR21 4.6 45.0 1.0
C3 N:F6K201 4.7 40.7 1.0
C N:THR22 4.9 47.2 1.0

Chlorine binding site 5 out of 10 in 6gop

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Chlorine binding site 5 out of 10 in the Yeast 20S Proteasome in Complex with Homosalinosporamide A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Yeast 20S Proteasome in Complex with Homosalinosporamide A within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Cl203

b:39.7
occ:1.00
 NE2 N:GLN53 3.0 29.5 1.0
NH1 N:ARG45 3.2 34.1 1.0
NH2 N:ARG45 3.3 37.3 1.0
CZ N:ARG45 3.7 34.7 1.0
CG2 N:THR31 3.8 43.4 1.0
C13 N:F6K201 3.9 40.0 1.0
CD N:GLN53 4.1 29.1 1.0
OD1 H:ASP120 4.2 49.8 1.0
C12 N:F6K201 4.2 39.4 1.0
O H:THR119 4.3 39.6 1.0
CB N:ALA49 4.3 30.5 1.0
CG N:GLN53 4.5 29.9 1.0
C14 N:F6K201 4.6 40.4 1.0
O N:ASP32 4.7 45.8 1.0
CB a:TYR228 4.7 39.6 1.0
CD2 a:TYR228 4.8 36.4 1.0
CA N:ALA49 4.9 31.2 1.0
OG1 N:THR20 5.0 41.2 1.0

Chlorine binding site 6 out of 10 in 6gop

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Chlorine binding site 6 out of 10 in the Yeast 20S Proteasome in Complex with Homosalinosporamide A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Yeast 20S Proteasome in Complex with Homosalinosporamide A within 5.0Å range:
probe atom residue distance (Å) B Occ
U:Cl301

b:25.6
occ:1.00
 OH V:TYR69 3.0 36.3 1.0
NH1 U:ARG111 3.1 40.5 1.0
OD1 U:ASN114 3.4 42.3 1.0
CD U:ARG111 3.7 37.2 1.0
CE2 V:TYR69 3.7 38.7 1.0
CB U:ASN114 3.8 39.7 1.0
CZ V:TYR69 3.8 38.9 1.0
CG U:ASN114 4.0 41.7 1.0
CZ U:ARG111 4.1 39.5 1.0
NE U:ARG111 4.3 38.7 1.0
CA U:ARG111 4.7 36.0 1.0
O U:ARG111 4.9 33.9 1.0
CG U:ARG111 5.0 36.1 1.0

Chlorine binding site 7 out of 10 in 6gop

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Chlorine binding site 7 out of 10 in the Yeast 20S Proteasome in Complex with Homosalinosporamide A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Yeast 20S Proteasome in Complex with Homosalinosporamide A within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Cl301

b:55.5
occ:1.00
 CL V:F6K301 0.0 55.5 1.0
C21 V:F6K301 1.8 41.6 1.0
C1 V:F6K301 2.6 39.1 1.0
CB V:SER129 3.8 29.3 1.0
CE2 L:TYR33 4.0 55.8 1.0
C2 V:F6K301 4.1 38.1 1.0
CZ L:TYR33 4.2 56.6 1.0
OG V:SER129 4.3 31.9 1.0
O5 V:F6K301 4.3 40.6 1.0
OH L:TYR33 4.4 56.1 1.0
CD2 L:TYR33 4.5 52.6 1.0
CA V:SER129 4.9 30.4 1.0
CE1 L:TYR33 5.0 56.9 1.0

Chlorine binding site 8 out of 10 in 6gop

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Chlorine binding site 8 out of 10 in the Yeast 20S Proteasome in Complex with Homosalinosporamide A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Yeast 20S Proteasome in Complex with Homosalinosporamide A within 5.0Å range:
probe atom residue distance (Å) B Occ
Y:Cl301

b:68.3
occ:1.00
 CL Y:F6K301 0.0 68.3 1.0
C21 Y:F6K301 1.7 41.4 1.0
C1 Y:F6K301 2.3 39.9 1.0
C2 Y:F6K301 3.7 39.2 1.0
CE2 Y:TYR170 3.9 45.5 1.0
CD2 Y:TYR170 4.0 43.7 1.0
O5 Y:F6K301 4.2 41.5 1.0
O20 Y:F6K301 4.6 36.8 1.0
C3 Y:F6K301 4.7 39.2 1.0
CZ Y:TYR170 4.7 43.8 1.0
C19 Y:F6K301 4.9 38.2 1.0
CG Y:TYR170 4.9 42.5 1.0
C4 Y:F6K301 5.0 39.2 1.0
CB Y:SER131 5.0 33.6 1.0

Chlorine binding site 9 out of 10 in 6gop

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Chlorine binding site 9 out of 10 in the Yeast 20S Proteasome in Complex with Homosalinosporamide A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of Yeast 20S Proteasome in Complex with Homosalinosporamide A within 5.0Å range:
probe atom residue distance (Å) B Occ
b:Cl201

b:44.8
occ:1.00
 CL b:F6K201 0.0 44.8 1.0
C21 b:F6K201 1.8 41.1 1.0
C1 b:F6K201 2.8 40.7 1.0
C2 b:F6K201 3.2 40.3 1.0
O b:HOH303 3.3 35.1 1.0
O b:GLY23 3.6 41.0 1.0
N b:GLY23 3.7 48.8 1.0
CA b:GLY23 3.7 44.5 1.0
C b:GLY23 4.1 42.2 1.0
O b:THR21 4.5 46.5 1.0
OG1 b:THR21 4.6 45.8 1.0
C3 b:F6K201 4.7 39.9 1.0
C b:THR22 4.9 51.9 1.0
O20 b:F6K201 5.0 37.0 1.0

Chlorine binding site 10 out of 10 in 6gop

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Chlorine binding site 10 out of 10 in the Yeast 20S Proteasome in Complex with Homosalinosporamide A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 10 of Yeast 20S Proteasome in Complex with Homosalinosporamide A within 5.0Å range:
probe atom residue distance (Å) B Occ
b:Cl202

b:40.2
occ:1.00
 NE2 b:GLN53 3.1 33.8 1.0
NH1 b:ARG45 3.3 36.8 1.0
NH2 b:ARG45 3.3 38.3 1.0
CZ b:ARG45 3.7 37.0 1.0
CG2 b:THR31 3.8 41.6 1.0
C13 b:F6K201 3.9 39.8 1.0
OD1 V:ASP120 4.2 53.8 1.0
CD b:GLN53 4.2 33.0 1.0
O V:THR119 4.3 39.6 1.0
C12 b:F6K201 4.3 40.4 1.0
CB b:ALA49 4.4 33.8 1.0
CG b:GLN53 4.5 33.5 1.0
O b:ASP32 4.6 44.6 1.0
C14 b:F6K201 4.7 40.2 1.0
CB M:TYR228 4.7 49.3 1.0
CD2 M:TYR228 4.7 45.6 1.0
CA b:ALA49 5.0 34.9 1.0
OG1 b:THR20 5.0 37.1 1.0

Reference:

M.Groll, H.Nguyen, S.Vellalath, D.Romo. (-)-Homosalinosporamide A and Its Mode of Proteasome Inhibition: An X-Ray Crystallographic Study. Mar Drugs V. 16 2018.
ISSN: ISSN 1660-3397
PubMed: 30029468
DOI: 10.3390/MD16070240
Page generated: Sun Jul 28 00:05:26 2024

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