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Sodium in PDB 7b12: Human Immunoproteasome 20S Particle in Complex with [2-(3- Ethylphenyl)-1-[(2S)-3-Phenyl-2-[(Pyrazin-2-Yl) Formamido]Propanamido]Ethyl]Boronic Acid

Enzymatic activity of Human Immunoproteasome 20S Particle in Complex with [2-(3- Ethylphenyl)-1-[(2S)-3-Phenyl-2-[(Pyrazin-2-Yl) Formamido]Propanamido]Ethyl]Boronic Acid

All present enzymatic activity of Human Immunoproteasome 20S Particle in Complex with [2-(3- Ethylphenyl)-1-[(2S)-3-Phenyl-2-[(Pyrazin-2-Yl) Formamido]Propanamido]Ethyl]Boronic Acid:
3.4.25.1;

Protein crystallography data

The structure of Human Immunoproteasome 20S Particle in Complex with [2-(3- Ethylphenyl)-1-[(2S)-3-Phenyl-2-[(Pyrazin-2-Yl) Formamido]Propanamido]Ethyl]Boronic Acid, PDB code: 7b12 was solved by D.Musil, M.Klein, S.Crosignani, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 107.89 / 2.43
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 118.995, 201.736, 161.932, 90, 106.83, 90
R / Rfree (%) 18 / 22.5

Sodium Binding Sites:

The binding sites of Sodium atom in the Human Immunoproteasome 20S Particle in Complex with [2-(3- Ethylphenyl)-1-[(2S)-3-Phenyl-2-[(Pyrazin-2-Yl) Formamido]Propanamido]Ethyl]Boronic Acid (pdb code 7b12). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the Human Immunoproteasome 20S Particle in Complex with [2-(3- Ethylphenyl)-1-[(2S)-3-Phenyl-2-[(Pyrazin-2-Yl) Formamido]Propanamido]Ethyl]Boronic Acid, PDB code: 7b12:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in 7b12

Go back to Sodium Binding Sites List in 7b12
Sodium binding site 1 out of 6 in the Human Immunoproteasome 20S Particle in Complex with [2-(3- Ethylphenyl)-1-[(2S)-3-Phenyl-2-[(Pyrazin-2-Yl) Formamido]Propanamido]Ethyl]Boronic Acid


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Human Immunoproteasome 20S Particle in Complex with [2-(3- Ethylphenyl)-1-[(2S)-3-Phenyl-2-[(Pyrazin-2-Yl) Formamido]Propanamido]Ethyl]Boronic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na301

b:42.1
occ:1.00
 O A:ASN128 2.2 41.5 1.0
O A:MET131 2.3 50.3 1.0
O A:TYR125 2.4 45.7 1.0
O A:HOH414 2.5 39.6 1.0
OG1 A:THR14 2.5 55.1 1.0
C A:ASN128 3.3 42.6 1.0
CG2 A:THR14 3.4 53.3 1.0
CB A:THR14 3.5 53.4 1.0
C A:MET131 3.6 50.4 1.0
CA A:ALA129 3.6 45.8 1.0
C A:TYR125 3.6 45.5 1.0
C A:ALA129 3.9 48.5 1.0
N A:ALA129 3.9 44.1 1.0
O A:ALA129 3.9 49.3 1.0
N A:MET131 4.2 50.5 1.0
O G:HOH306 4.2 30.5 1.0
N A:THR14 4.2 52.6 1.0
CA A:TYR125 4.4 45.6 1.0
CA A:MET131 4.5 50.6 1.0
SD A:MET131 4.5 53.0 1.0
CA A:THR14 4.5 52.1 1.0
N A:ARG132 4.5 49.8 1.0
CA A:ASN128 4.5 42.9 1.0
N A:ASN128 4.5 43.3 1.0
CA A:ARG132 4.5 49.5 1.0
N A:THR126 4.6 45.0 1.0
N A:GLU130 4.7 49.2 1.0
C A:THR126 4.9 43.9 1.0
CB A:ALA129 4.9 45.2 1.0
CD A:PRO133 4.9 48.6 1.0
CG A:MET131 4.9 52.1 1.0
CA A:THR126 5.0 44.9 1.0

Sodium binding site 2 out of 6 in 7b12

Go back to Sodium Binding Sites List in 7b12
Sodium binding site 2 out of 6 in the Human Immunoproteasome 20S Particle in Complex with [2-(3- Ethylphenyl)-1-[(2S)-3-Phenyl-2-[(Pyrazin-2-Yl) Formamido]Propanamido]Ethyl]Boronic Acid


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Human Immunoproteasome 20S Particle in Complex with [2-(3- Ethylphenyl)-1-[(2S)-3-Phenyl-2-[(Pyrazin-2-Yl) Formamido]Propanamido]Ethyl]Boronic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Na302

b:30.4
occ:1.00
 O L:SER170 2.2 44.0 1.0
O L:THR164 2.2 40.7 1.0
O X:ASP205 2.2 46.0 1.0
O L:ASP167 2.3 38.2 1.0
O L:HOH416 2.5 23.6 1.0
C X:ASP205 3.2 45.8 1.0
C L:ASP167 3.3 37.6 1.0
C L:THR164 3.4 40.0 1.0
C L:SER170 3.4 42.9 1.0
NH1 L:ARG19 3.4 48.7 1.0
CA L:SER168 3.7 40.0 1.0
CA X:ASP205 3.7 45.0 1.0
N L:SER168 3.9 38.1 1.0
CA L:THR164 3.9 39.9 1.0
C L:SER168 3.9 40.6 1.0
CB X:ASP205 4.0 44.6 1.0
N L:SER170 4.0 42.2 1.0
O L:SER168 4.0 41.0 1.0
OXT X:ASP205 4.1 46.8 1.0
CA L:SER170 4.2 42.8 1.0
CZ L:ARG19 4.2 46.8 1.0
N L:GLY171 4.4 42.4 1.0
CB L:THR164 4.4 41.1 1.0
CA L:ASP167 4.4 36.1 1.0
N L:HIS165 4.5 39.1 1.0
N L:ASP167 4.5 35.9 1.0
CA L:GLY171 4.6 43.3 1.0
N L:TYR169 4.6 41.2 1.0
NH2 L:ARG19 4.6 45.4 1.0
O L:HIS165 4.6 40.4 1.0
CB L:SER170 4.6 43.4 1.0
C L:HIS165 4.8 38.8 1.0
CA L:HIS165 4.9 38.1 1.0
O L:ALA163 5.0 40.0 1.0
O L:HOH405 5.0 45.3 1.0
CB L:SER168 5.0 43.6 1.0
CG X:ASP205 5.0 45.1 1.0

Sodium binding site 3 out of 6 in 7b12

Go back to Sodium Binding Sites List in 7b12
Sodium binding site 3 out of 6 in the Human Immunoproteasome 20S Particle in Complex with [2-(3- Ethylphenyl)-1-[(2S)-3-Phenyl-2-[(Pyrazin-2-Yl) Formamido]Propanamido]Ethyl]Boronic Acid


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Human Immunoproteasome 20S Particle in Complex with [2-(3- Ethylphenyl)-1-[(2S)-3-Phenyl-2-[(Pyrazin-2-Yl) Formamido]Propanamido]Ethyl]Boronic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Na301

b:33.2
occ:1.00
 O O:ASN128 2.2 41.2 1.0
O O:TYR125 2.2 37.4 1.0
O O:MET131 2.3 38.7 1.0
O O:HOH413 2.3 41.7 1.0
OG1 O:THR14 2.6 40.5 1.0
CG2 O:THR14 3.4 40.0 1.0
C O:ASN128 3.4 41.0 1.0
C O:TYR125 3.4 36.7 1.0
C O:MET131 3.5 39.0 1.0
CB O:THR14 3.5 40.2 1.0
CA O:ALA129 3.8 40.7 1.0
C O:ALA129 4.0 40.4 1.0
N O:ALA129 4.0 40.9 1.0
O O:ALA129 4.1 40.8 1.0
N O:MET131 4.2 40.0 1.0
CA O:TYR125 4.2 35.6 1.0
SD O:MET131 4.3 45.1 1.0
N O:THR14 4.4 41.5 1.0
CA O:MET131 4.4 39.3 1.0
N O:THR126 4.4 36.8 1.0
N O:ARG132 4.4 38.9 1.0
N O:ASN128 4.5 39.9 1.0
CA O:ARG132 4.5 38.8 1.0
CA O:ASN128 4.5 40.6 1.0
CA O:THR14 4.6 40.9 1.0
N O:GLU130 4.8 40.1 1.0
CD O:PRO133 4.8 37.9 1.0
CA O:THR126 4.8 37.7 1.0
C O:THR126 4.8 38.1 1.0
CG O:MET131 4.8 41.6 1.0
CB O:TYR125 4.9 35.2 1.0
C O:ARG132 4.9 38.7 1.0
N O:GLN127 5.0 38.3 1.0

Sodium binding site 4 out of 6 in 7b12

Go back to Sodium Binding Sites List in 7b12
Sodium binding site 4 out of 6 in the Human Immunoproteasome 20S Particle in Complex with [2-(3- Ethylphenyl)-1-[(2S)-3-Phenyl-2-[(Pyrazin-2-Yl) Formamido]Propanamido]Ethyl]Boronic Acid


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Human Immunoproteasome 20S Particle in Complex with [2-(3- Ethylphenyl)-1-[(2S)-3-Phenyl-2-[(Pyrazin-2-Yl) Formamido]Propanamido]Ethyl]Boronic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Na302

b:47.5
occ:1.00
 O Z:SER170 2.2 44.6 1.0
O Z:THR164 2.2 41.0 1.0
O Z:ASP167 2.2 41.1 1.0
O J:ASP205 2.3 45.6 1.0
C Z:ASP167 3.2 39.4 1.0
C J:ASP205 3.3 45.5 1.0
C Z:THR164 3.4 40.0 1.0
C Z:SER170 3.4 43.6 1.0
NH1 Z:ARG19 3.5 44.4 1.0
CA Z:SER168 3.6 40.4 1.0
N Z:SER168 3.8 39.5 1.0
CA J:ASP205 3.9 45.2 1.0
C Z:SER168 3.9 41.4 1.0
CA Z:THR164 3.9 39.2 1.0
N Z:SER170 4.0 42.2 1.0
CB J:ASP205 4.0 44.9 1.0
O Z:SER168 4.1 41.0 1.0
CA Z:SER170 4.2 42.5 1.0
OXT J:ASP205 4.3 45.7 1.0
CZ Z:ARG19 4.3 45.2 1.0
CA Z:ASP167 4.4 37.7 1.0
N Z:ASP167 4.4 37.1 1.0
N Z:GLY171 4.4 43.7 1.0
N Z:HIS165 4.5 38.6 1.0
CB Z:THR164 4.5 38.5 1.0
O Z:HIS165 4.5 38.7 1.0
N Z:TYR169 4.6 42.2 1.0
CB Z:SER170 4.6 42.5 1.0
CA Z:GLY171 4.6 44.8 1.0
C Z:HIS165 4.6 37.4 1.0
NH2 Z:ARG19 4.8 44.2 1.0
O Z:ALA163 4.9 40.0 1.0
CA Z:HIS165 4.9 37.4 1.0
CB Z:SER168 4.9 41.6 1.0

Sodium binding site 5 out of 6 in 7b12

Go back to Sodium Binding Sites List in 7b12
Sodium binding site 5 out of 6 in the Human Immunoproteasome 20S Particle in Complex with [2-(3- Ethylphenyl)-1-[(2S)-3-Phenyl-2-[(Pyrazin-2-Yl) Formamido]Propanamido]Ethyl]Boronic Acid


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Human Immunoproteasome 20S Particle in Complex with [2-(3- Ethylphenyl)-1-[(2S)-3-Phenyl-2-[(Pyrazin-2-Yl) Formamido]Propanamido]Ethyl]Boronic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
i:Na302

b:47.8
occ:1.00
 O i:SER169 2.2 37.3 1.0
O i:ILE163 2.2 38.8 1.0
O i:ASP166 2.5 32.0 1.0
OXT 1:ASP213 2.6 50.0 1.0
CB 1:ASP213 3.3 45.2 1.0
C 1:ASP213 3.3 48.0 1.0
CA 1:ASP213 3.4 46.4 1.0
C i:SER169 3.5 37.5 1.0
C i:ILE163 3.5 37.5 1.0
C i:ASP166 3.5 32.0 1.0
NH1 i:ARG19 4.1 54.1 1.0
CA i:LEU167 4.1 33.2 1.0
N i:LEU167 4.2 32.5 1.0
N i:GLY170 4.3 38.6 1.0
CZ i:ARG19 4.3 53.4 1.0
O i:LEU164 4.3 34.9 1.0
CA i:GLY170 4.3 40.2 1.0
CA i:LEU164 4.3 34.9 1.0
NH2 i:ARG19 4.3 54.4 1.0
C i:LEU164 4.3 35.0 1.0
CG 1:ASP213 4.4 45.1 1.0
N i:LEU164 4.4 35.6 1.0
N i:ASP166 4.4 33.6 1.0
CA i:ILE163 4.4 36.9 1.0
CA i:SER169 4.4 35.9 1.0
N i:SER169 4.4 35.5 1.0
C i:LEU167 4.5 34.2 1.0
O i:LEU167 4.5 34.6 1.0
O 1:ASP213 4.5 48.5 1.0
O i:GLY162 4.5 37.4 1.0
CA i:ASP166 4.6 31.8 1.0
CB i:SER169 4.8 36.0 1.0
N 1:ASP213 4.8 46.2 1.0
OD2 1:ASP213 4.9 46.2 1.0
N i:GLY165 4.9 35.1 1.0
CG2 i:ILE163 5.0 36.4 1.0

Sodium binding site 6 out of 6 in 7b12

Go back to Sodium Binding Sites List in 7b12
Sodium binding site 6 out of 6 in the Human Immunoproteasome 20S Particle in Complex with [2-(3- Ethylphenyl)-1-[(2S)-3-Phenyl-2-[(Pyrazin-2-Yl) Formamido]Propanamido]Ethyl]Boronic Acid


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Human Immunoproteasome 20S Particle in Complex with [2-(3- Ethylphenyl)-1-[(2S)-3-Phenyl-2-[(Pyrazin-2-Yl) Formamido]Propanamido]Ethyl]Boronic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
w:Na302

b:60.7
occ:1.00
 O w:ILE163 2.2 36.7 1.0
O w:ASP166 2.4 35.3 1.0
O w:SER169 2.6 36.2 1.0
OXT M:ASP213 2.9 52.1 1.0
C w:ASP166 3.4 35.5 1.0
C w:ILE163 3.4 36.9 1.0
CA M:ASP213 3.5 49.8 1.0
CB M:ASP213 3.5 49.9 1.0
C M:ASP213 3.6 50.5 1.0
O w:LEU164 3.7 40.5 1.0
C w:SER169 3.8 36.2 1.0
C w:LEU164 3.9 39.3 1.0
N w:ASP166 4.0 36.4 1.0
N w:LEU167 4.1 35.3 1.0
CA w:LEU167 4.1 35.0 1.0
CA w:LEU164 4.1 37.8 1.0
N w:LEU164 4.2 36.9 1.0
CA w:ASP166 4.3 35.6 1.0
NH1 w:ARG19 4.4 47.0 1.0
O w:GLY162 4.4 37.8 1.0
CA w:ILE163 4.5 37.0 1.0
N w:GLY165 4.5 38.9 1.0
C w:LEU167 4.6 34.6 1.0
CG M:ASP213 4.7 52.2 1.0
N w:GLY170 4.7 37.6 1.0
N w:SER169 4.7 34.5 1.0
CA w:GLY170 4.7 38.7 1.0
O w:LEU167 4.7 34.8 1.0
NH2 w:ARG19 4.7 49.6 1.0
CA w:SER169 4.7 34.7 1.0
O M:ASP213 4.7 50.4 1.0
C w:GLY165 4.7 38.2 1.0
CZ w:ARG19 4.7 48.6 1.0
N M:ASP213 4.9 49.9 1.0
CB w:SER169 5.0 35.4 1.0

Reference:

D.Musil, M.Klein. Human Immunoproteasome 20S Particle in Complex with [2-(3-Ethylphenyl)-1-[(2S)-3-Phenyl-2-[(Pyrazin-2-Yl) Formamido]Propanamido]Ethyl]Boronic Acid To Be Published.
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