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Chlorine in PDB 5lf1: Human 20S Proteasome Complex with Dihydroeponemycin at 2.0 Angstrom

Enzymatic activity of Human 20S Proteasome Complex with Dihydroeponemycin at 2.0 Angstrom

All present enzymatic activity of Human 20S Proteasome Complex with Dihydroeponemycin at 2.0 Angstrom:
3.4.25.1;

Protein crystallography data

The structure of Human 20S Proteasome Complex with Dihydroeponemycin at 2.0 Angstrom, PDB code: 5lf1 was solved by J.Schrader, F.Henneberg, R.Mata, K.Tittmann, T.R.Schneider, H.Stark, G.Bourenkov, A.Chari, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 171.09 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 113.890, 203.490, 316.040, 90.00, 90.00, 90.00
R / Rfree (%) 17.8 / 21.3

Other elements in 5lf1:

The structure of Human 20S Proteasome Complex with Dihydroeponemycin at 2.0 Angstrom also contains other interesting chemical elements:

Magnesium (Mg) 10 atoms
Potassium (K) 6 atoms

Chlorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 50; Page 6, Binding sites: 51 - 56;

Binding sites:

The binding sites of Chlorine atom in the Human 20S Proteasome Complex with Dihydroeponemycin at 2.0 Angstrom (pdb code 5lf1). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 56 binding sites of Chlorine where determined in the Human 20S Proteasome Complex with Dihydroeponemycin at 2.0 Angstrom, PDB code: 5lf1:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 56 in 5lf1

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Chlorine binding site 1 out of 56 in the Human 20S Proteasome Complex with Dihydroeponemycin at 2.0 Angstrom


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Human 20S Proteasome Complex with Dihydroeponemycin at 2.0 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl301

b:52.1
occ:1.00
 O A:HOH449 2.8 64.8 1.0
O C:HOH430 2.9 47.5 1.0
N A:SER6 3.1 35.2 1.0
NH2 C:ARG5 3.7 60.0 1.0
CD2 A:PHE7 3.7 33.8 1.0
CB A:SER6 3.8 38.0 1.0
CE2 A:PHE7 3.9 34.1 1.0
CA A:TYR5 3.9 36.5 1.0
C A:TYR5 4.0 35.3 1.0
CA A:SER6 4.0 35.9 1.0
N B:SER2 4.2 47.3 1.0
O A:GLY4 4.3 48.6 1.0
OG A:SER6 4.4 41.5 1.0
N A:PHE7 4.5 34.1 1.0
CD1 C:TYR3 4.5 41.0 1.0
CB A:TYR5 4.6 35.4 1.0
CZ C:ARG5 4.6 58.6 1.0
C A:SER6 4.7 35.2 1.0
CE1 C:TYR3 4.9 41.2 1.0
CD2 A:TYR5 4.9 36.1 1.0
NH1 C:ARG5 4.9 62.1 1.0
CG A:PHE7 4.9 33.3 1.0
N A:TYR5 5.0 39.8 1.0

Chlorine binding site 2 out of 56 in 5lf1

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Chlorine binding site 2 out of 56 in the Human 20S Proteasome Complex with Dihydroeponemycin at 2.0 Angstrom


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Human 20S Proteasome Complex with Dihydroeponemycin at 2.0 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl302

b:64.4
occ:1.00
 N A:ARG219 3.4 46.4 1.0
CA A:ARG218 3.9 46.2 1.0
CB A:ARG219 4.1 47.7 1.0
C A:ARG218 4.1 46.2 1.0
CZ A:ARG219 4.2 46.1 1.0
CB A:ARG218 4.2 48.5 1.0
NH2 A:ARG219 4.3 47.6 1.0
CA A:ARG219 4.3 47.9 1.0
CG A:ARG219 4.4 47.5 1.0
CG A:PRO66 4.4 38.2 1.0
NH1 A:ARG219 4.5 44.4 1.0
NE A:ARG219 4.5 47.5 1.0
CD A:PRO66 4.6 37.8 1.0
CB A:PRO66 4.7 38.0 1.0
CE2 A:PHE217 4.9 42.1 1.0
O A:ARG219 4.9 51.2 1.0
O A:PHE217 4.9 44.8 1.0

Chlorine binding site 3 out of 56 in 5lf1

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Chlorine binding site 3 out of 56 in the Human 20S Proteasome Complex with Dihydroeponemycin at 2.0 Angstrom


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Human 20S Proteasome Complex with Dihydroeponemycin at 2.0 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl303

b:50.2
occ:1.00
 O H:HOH495 3.1 48.2 1.0
NH2 A:ARG90 3.1 31.1 1.0
O G:HOH408 3.2 50.4 1.0
O A:HOH445 3.5 45.9 1.0
ND1 A:HIS87 3.6 47.1 1.0
CA A:HIS87 3.7 35.5 1.0
CB A:HIS87 3.8 37.5 1.0
CD A:ARG90 3.8 31.7 1.0
NZ G:LYS116 3.8 51.3 1.0
CG A:HIS87 4.1 42.3 1.0
OG H:SER69 4.1 45.4 1.0
CZ A:ARG90 4.2 31.5 1.0
N A:HIS87 4.2 33.2 1.0
O A:HOH468 4.3 52.8 1.0
CB H:SER69 4.3 40.7 1.0
NE A:ARG90 4.4 32.1 1.0
CG1 A:VAL86 4.5 32.2 1.0
CA H:SER69 4.6 40.0 1.0
CE1 A:HIS87 4.7 46.6 1.0
C A:VAL86 4.7 32.8 1.0
CE G:LYS116 4.8 46.2 1.0
O A:VAL86 4.8 31.1 1.0
O A:HOH463 4.9 45.3 1.0
CG A:ARG90 4.9 32.6 1.0
C A:HIS87 5.0 34.6 1.0

Chlorine binding site 4 out of 56 in 5lf1

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Chlorine binding site 4 out of 56 in the Human 20S Proteasome Complex with Dihydroeponemycin at 2.0 Angstrom


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Human 20S Proteasome Complex with Dihydroeponemycin at 2.0 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl304

b:57.2
occ:1.00
 O A:HOH446 2.8 34.0 1.0
O A:HOH487 3.2 51.5 1.0
CG2 A:THR68 3.8 40.3 1.0
CB A:THR68 4.0 41.4 1.0
NE2 A:GLN94 4.0 38.2 1.0
NZ A:LYS69 4.1 58.2 1.0
CD2 A:TYR97 4.2 39.2 1.0
CA A:PRO103 4.2 40.1 1.0
CB A:PRO103 4.2 41.0 1.0
CG A:TYR97 4.4 38.0 1.0
CB A:TYR97 4.4 36.5 1.0
OE2 H:GLU64 4.5 50.5 1.0
CG A:PRO103 4.7 42.6 1.0
OE1 H:GLU64 4.8 47.5 1.0
CE2 A:TYR97 4.9 41.2 1.0
O A:ALA93 4.9 33.1 1.0
CA A:THR68 4.9 40.7 1.0
CE1 A:HIS70 4.9 46.3 1.0
CD A:GLN94 5.0 36.9 1.0
OG1 A:THR68 5.0 43.2 1.0
N A:ILE104 5.0 37.0 1.0

Chlorine binding site 5 out of 56 in 5lf1

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Chlorine binding site 5 out of 56 in the Human 20S Proteasome Complex with Dihydroeponemycin at 2.0 Angstrom


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Human 20S Proteasome Complex with Dihydroeponemycin at 2.0 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl301

b:41.3
occ:1.00
 O B:HOH490 2.8 48.6 1.0
CL B:CL302 2.9 57.3 1.0
O I:HOH544 3.1 48.0 1.0
NE2 B:GLN95 3.3 37.0 1.0
N B:GLU70 3.3 47.0 1.0
CB B:ASN69 3.7 42.4 1.0
CA B:ASN69 3.9 42.8 1.0
CB B:GLU70 4.0 52.7 1.0
ND2 I:ASN71 4.1 37.1 1.0
C B:ASN69 4.1 45.0 1.0
OE1 B:GLU70 4.2 59.9 1.0
CA B:GLU70 4.2 49.1 1.0
CD2 B:LEU98 4.4 41.5 1.0
CG I:ASN71 4.4 37.7 1.0
CD B:GLN95 4.4 37.5 1.0
OE1 B:GLN95 4.7 38.8 1.0
CG B:ASN69 4.7 44.4 1.0
O I:HOH494 4.8 45.1 1.0
CB I:ASN71 4.8 37.6 1.0
OD1 I:ASN71 4.9 38.4 1.0
CD B:GLU70 4.9 62.5 1.0
O B:HOH428 5.0 33.9 1.0

Chlorine binding site 6 out of 56 in 5lf1

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Chlorine binding site 6 out of 56 in the Human 20S Proteasome Complex with Dihydroeponemycin at 2.0 Angstrom


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Human 20S Proteasome Complex with Dihydroeponemycin at 2.0 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl302

b:57.3
occ:1.00
 O B:HOH462 2.8 36.7 1.0
CL B:CL301 2.9 41.3 1.0
CD2 B:LEU98 3.7 41.5 1.0
ND2 B:ASN69 3.8 45.3 1.0
CB B:PRO104 3.9 41.6 1.0
CA B:PRO104 3.9 40.6 1.0
CB B:ASN69 3.9 42.4 1.0
O I:HOH544 4.0 48.0 1.0
CG B:ASN69 4.1 44.4 1.0
N B:GLU70 4.4 47.0 1.0
NE2 B:GLN95 4.4 37.0 1.0
CG B:LEU98 4.4 40.3 1.0
CD1 B:LEU98 4.5 39.3 1.0
CB B:LEU98 4.5 38.8 1.0
N B:PRO104 4.7 41.1 1.0
CB B:GLU70 4.7 52.7 1.0
N B:ILE105 4.8 39.5 1.0
CG B:PRO104 4.9 42.8 1.0
C B:PRO104 4.9 39.3 1.0

Chlorine binding site 7 out of 56 in 5lf1

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Chlorine binding site 7 out of 56 in the Human 20S Proteasome Complex with Dihydroeponemycin at 2.0 Angstrom


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Human 20S Proteasome Complex with Dihydroeponemycin at 2.0 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl301

b:60.7
occ:1.00
 O C:HOH425 3.2 58.3 1.0
N C:GLY162 3.2 52.0 1.0
CA C:ILE161 3.7 51.4 1.0
O C:HOH444 3.8 58.8 1.0
C C:ILE161 3.9 52.1 1.0
CB C:ILE161 3.9 49.9 1.0
CG1 C:VAL26 4.0 48.6 1.0
O C:GLY162 4.1 55.8 1.0
CB C:ALA165 4.2 61.4 1.0
CA C:GLY162 4.2 52.7 1.0
CG2 C:ILE161 4.2 49.2 1.0
CG C:LYS27 4.5 62.3 1.0
C C:GLY162 4.6 55.4 1.0
O C:ALA160 4.9 53.4 1.0
CB C:VAL26 5.0 48.4 1.0
N C:ILE161 5.0 52.0 1.0

Chlorine binding site 8 out of 56 in 5lf1

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Chlorine binding site 8 out of 56 in the Human 20S Proteasome Complex with Dihydroeponemycin at 2.0 Angstrom


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Human 20S Proteasome Complex with Dihydroeponemycin at 2.0 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl302

b:71.2
occ:1.00
 O C:HOH435 2.8 50.0 1.0
NH2 C:ARG117 3.4 55.9 1.0
NH2 C:ARG86 3.5 54.1 1.0
NE C:ARG117 3.6 52.5 1.0
CD1 C:LEU114 3.7 40.5 1.0
NH1 C:ARG86 3.8 53.5 1.0
O C:HOH455 3.9 65.5 1.0
CZ C:ARG117 4.0 54.0 1.0
CZ C:ARG86 4.1 53.8 1.0
CE1 C:TYR118 4.1 37.8 1.0
NH1 C:ARG124 4.4 59.6 1.0
CD C:ARG117 4.7 50.6 1.0
NH2 C:ARG124 4.8 61.5 1.0
OH C:TYR118 4.9 39.8 1.0
CD1 C:TYR118 4.9 36.9 1.0

Chlorine binding site 9 out of 56 in 5lf1

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Chlorine binding site 9 out of 56 in the Human 20S Proteasome Complex with Dihydroeponemycin at 2.0 Angstrom


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of Human 20S Proteasome Complex with Dihydroeponemycin at 2.0 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl301

b:69.0
occ:1.00
 O D:HOH409 3.2 47.4 1.0
N D:GLY171 3.2 50.0 1.0
OG D:SER174 3.4 59.3 1.0
O D:HOH410 3.6 77.5 1.0
CG2 D:ILE31 3.6 51.0 1.0
CA D:ILE170 3.7 50.9 1.0
C D:ILE170 3.9 51.1 1.0
CB D:ILE170 4.0 50.4 1.0
O D:GLY171 4.1 52.6 1.0
NZ D:LYS32 4.1 63.9 1.0
CE D:LYS32 4.1 62.5 1.0
CB D:SER174 4.2 59.4 1.0
CA D:GLY171 4.2 50.9 1.0
CG2 D:ILE170 4.3 50.3 1.0
CB D:ILE31 4.5 50.4 1.0
C D:GLY171 4.6 52.0 1.0
O D:ALA169 4.7 52.8 1.0
N D:ILE170 4.9 51.6 1.0

Chlorine binding site 10 out of 56 in 5lf1

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Chlorine binding site 10 out of 56 in the Human 20S Proteasome Complex with Dihydroeponemycin at 2.0 Angstrom


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 10 of Human 20S Proteasome Complex with Dihydroeponemycin at 2.0 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl301

b:61.5
occ:1.00
 N E:GLY162 2.9 37.8 1.0
O E:HOH522 3.1 51.1 1.0
O E:HOH430 3.4 79.4 1.0
OG E:SER165 3.6 40.4 1.0
CA E:ILE161 3.6 37.1 1.0
O E:GLY162 3.7 40.5 1.0
C E:ILE161 3.7 37.6 1.0
CA E:GLY162 3.8 39.0 1.0
CG E:LYS30 3.8 50.3 1.0
CB E:ILE161 3.9 37.1 1.0
CA E:LYS30 4.0 46.9 1.0
CG2 E:VAL29 4.0 39.8 1.0
O E:HOH464 4.0 55.4 1.0
C3 E:6V1148 4.0 64.8 1.0
C E:GLY162 4.1 40.7 1.0
C6 E:6V1148 4.2 65.3 1.0
N E:LYS30 4.3 44.5 1.0
CG2 E:ILE161 4.3 37.1 1.0
CB E:LYS30 4.4 48.5 1.0
NH1 E:ARG169 4.5 39.3 1.0
C E:VAL29 4.6 42.8 1.0
O E:VAL29 4.6 44.0 1.0
CB E:SER165 4.7 41.2 1.0
CD E:LYS30 4.9 54.7 1.0
N E:ILE161 4.9 37.1 1.0
O E:ILE161 5.0 37.9 1.0

Reference:

J.Schrader, F.Henneberg, R.A.Mata, K.Tittmann, T.R.Schneider, H.Stark, G.Bourenkov, A.Chari. The Inhibition Mechanism of Human 20S Proteasomes Enables Next-Generation Inhibitor Design. Science V. 353 594 2016.
ISSN: ESSN 1095-9203
PubMed: 27493187
DOI: 10.1126/SCIENCE.AAF8993
Page generated: Fri Jul 26 11:35:21 2024

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