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Magnesium in PDB 5bou: Yeast 20S Proteasome in Complex with A BETA1 / BETA2 Specific Non- Peptidic Sulfonamide Ligand

Enzymatic activity of Yeast 20S Proteasome in Complex with A BETA1 / BETA2 Specific Non- Peptidic Sulfonamide Ligand

All present enzymatic activity of Yeast 20S Proteasome in Complex with A BETA1 / BETA2 Specific Non- Peptidic Sulfonamide Ligand:
3.4.25.1;

Protein crystallography data

The structure of Yeast 20S Proteasome in Complex with A BETA1 / BETA2 Specific Non- Peptidic Sulfonamide Ligand, PDB code: 5bou was solved by P.Beck, M.Groll, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.00 / 2.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 135.840, 301.000, 146.300, 90.00, 113.27, 90.00
R / Rfree (%) 19.2 / 21.4

Other elements in 5bou:

The structure of Yeast 20S Proteasome in Complex with A BETA1 / BETA2 Specific Non- Peptidic Sulfonamide Ligand also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Yeast 20S Proteasome in Complex with A BETA1 / BETA2 Specific Non- Peptidic Sulfonamide Ligand (pdb code 5bou). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Yeast 20S Proteasome in Complex with A BETA1 / BETA2 Specific Non- Peptidic Sulfonamide Ligand, PDB code: 5bou:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 5bou

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Magnesium binding site 1 out of 8 in the Yeast 20S Proteasome in Complex with A BETA1 / BETA2 Specific Non- Peptidic Sulfonamide Ligand


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Yeast 20S Proteasome in Complex with A BETA1 / BETA2 Specific Non- Peptidic Sulfonamide Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:47.8
occ:1.00
 O G:MET125 2.2 44.1 1.0
O G:ARG122 2.3 41.6 1.0
O G:TYR119 2.3 39.4 1.0
OG1 G:THR8 2.6 41.4 1.0
CG2 G:THR8 3.3 42.3 1.0
C G:MET125 3.4 44.9 1.0
C G:ARG122 3.4 42.4 1.0
C G:TYR119 3.5 38.0 1.0
CB G:THR8 3.5 42.1 1.0
O G:ALA123 3.7 45.9 1.0
CA G:ALA123 3.9 42.9 1.0
C G:ALA123 3.9 44.0 1.0
N G:ALA123 4.1 42.2 1.0
N G:MET125 4.2 47.5 1.0
CA G:TYR119 4.3 37.6 1.0
N G:ARG126 4.3 41.8 1.0
CA G:MET125 4.3 49.0 1.0
CA G:ARG126 4.3 40.4 1.0
N G:THR8 4.4 43.7 1.0
N G:THR120 4.5 37.4 1.0
CD G:PRO127 4.5 37.9 1.0
N G:ARG122 4.5 41.3 1.0
CA G:ARG122 4.6 44.2 1.0
CA G:THR8 4.6 43.0 1.0
CA G:THR120 4.6 37.5 1.0
C G:THR120 4.7 37.8 1.0
CB G:MET125 4.7 53.5 1.0
N G:TYR124 4.8 45.1 1.0
O G:HOH419 4.8 46.4 1.0
C G:ARG126 4.8 38.6 1.0
CB G:TYR119 4.9 37.8 1.0
N G:GLN121 4.9 38.2 1.0
N G:PRO127 5.0 37.8 1.0

Magnesium binding site 2 out of 8 in 5bou

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Magnesium binding site 2 out of 8 in the Yeast 20S Proteasome in Complex with A BETA1 / BETA2 Specific Non- Peptidic Sulfonamide Ligand


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Yeast 20S Proteasome in Complex with A BETA1 / BETA2 Specific Non- Peptidic Sulfonamide Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:54.2
occ:1.00
 O I:SER180 2.4 46.6 1.0
O I:ASP177 2.5 44.2 1.0
O I:HOH423 2.7 50.1 1.0
O I:ALA174 2.8 41.4 1.0
C I:SER180 3.6 44.9 1.0
C I:ASP177 3.7 42.5 1.0
OXT I:ASP204 3.8 53.3 1.0
C I:ALA174 3.9 41.9 1.0
CA I:ASP175 4.2 45.3 1.0
O I:ALA178 4.2 48.0 1.0
C I:ALA178 4.4 44.4 1.0
CA I:ALA178 4.4 42.9 1.0
N I:SER180 4.4 43.9 1.0
N I:ASP175 4.5 43.5 1.0
N I:ALA178 4.5 41.6 1.0
CA I:GLY181 4.5 43.7 1.0
N I:GLY181 4.5 43.7 1.0
N I:ASP177 4.6 43.0 1.0
CA I:SER180 4.6 44.8 1.0
C I:ASP175 4.6 45.2 1.0
NH1 Y:ARG19 4.7 47.7 1.0
CA I:ASP177 4.7 42.4 1.0
C I:ASP204 4.7 50.5 1.0
O I:ASP204 4.7 50.5 1.0
OD1 I:ASP175 4.8 50.6 1.0
O I:ASP175 4.8 46.5 1.0
NH2 Y:ARG19 4.8 47.5 1.0
CA I:ALA174 5.0 40.4 1.0

Magnesium binding site 3 out of 8 in 5bou

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Magnesium binding site 3 out of 8 in the Yeast 20S Proteasome in Complex with A BETA1 / BETA2 Specific Non- Peptidic Sulfonamide Ligand


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Yeast 20S Proteasome in Complex with A BETA1 / BETA2 Specific Non- Peptidic Sulfonamide Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg302

b:44.0
occ:1.00
 O I:ASP204 2.2 50.5 1.0
O Y:ASP168 2.3 40.2 1.0
O Y:ALA165 2.4 38.9 1.0
O Y:SER171 2.4 41.1 1.0
C I:ASP204 3.2 50.5 1.0
C Y:ASP168 3.3 39.2 1.0
C Y:ALA165 3.5 38.6 1.0
NH1 Y:ARG19 3.6 47.7 1.0
C Y:SER171 3.6 40.9 1.0
O Y:ALA169 3.7 43.9 1.0
CA Y:ALA169 3.8 38.7 1.0
CA I:ASP204 3.8 49.0 1.0
C Y:ALA169 3.8 40.8 1.0
N Y:ALA169 4.0 38.9 1.0
CB I:ASP204 4.0 49.5 1.0
OXT I:ASP204 4.1 53.3 1.0
N Y:SER171 4.1 39.7 1.0
CA Y:ALA165 4.2 39.1 1.0
O Y:HIS166 4.3 39.7 1.0
CZ Y:ARG19 4.4 47.0 1.0
CA Y:SER171 4.4 39.8 1.0
N Y:ASP168 4.5 39.4 1.0
CA Y:ASP168 4.5 39.6 1.0
N Y:HIS166 4.5 38.7 1.0
C Y:HIS166 4.5 38.6 1.0
N Y:GLY172 4.6 41.1 1.0
N Y:TYR170 4.6 40.6 1.0
NH2 Y:ARG19 4.7 47.5 1.0
CA Y:GLY172 4.7 40.6 1.0
O Y:ALA164 4.7 39.2 1.0
CA Y:HIS166 4.8 38.2 1.0
CG I:ASP204 4.8 48.9 1.0
CB Y:SER171 4.9 40.0 1.0
CB Y:ALA165 5.0 39.5 1.0

Magnesium binding site 4 out of 8 in 5bou

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Magnesium binding site 4 out of 8 in the Yeast 20S Proteasome in Complex with A BETA1 / BETA2 Specific Non- Peptidic Sulfonamide Ligand


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Yeast 20S Proteasome in Complex with A BETA1 / BETA2 Specific Non- Peptidic Sulfonamide Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg301

b:45.0
occ:1.00
 O K:ASP168 2.2 42.3 1.0
O K:ALA165 2.2 41.5 1.0
O K:SER171 2.3 44.0 1.0
O W:ASP204 2.4 47.7 1.0
O K:HOH418 2.5 46.2 1.0
C W:ASP204 3.3 48.5 1.0
C K:ASP168 3.3 40.0 1.0
C K:ALA165 3.3 41.4 1.0
C K:SER171 3.5 43.0 1.0
NH1 K:ARG19 3.7 48.1 1.0
CA W:ASP204 3.8 48.0 1.0
CA K:ALA169 3.8 40.2 1.0
O K:ALA169 3.8 43.0 1.0
C K:ALA169 3.9 41.6 1.0
N K:ALA169 3.9 39.4 1.0
CA K:ALA165 4.0 41.6 1.0
CB W:ASP204 4.0 47.6 1.0
N K:SER171 4.0 41.9 1.0
OXT W:ASP204 4.2 50.3 1.0
CA K:SER171 4.3 41.5 1.0
O K:HIS166 4.3 41.2 1.0
N K:ASP168 4.4 39.1 1.0
CA K:ASP168 4.4 39.2 1.0
N K:HIS166 4.4 40.9 1.0
CZ K:ARG19 4.5 47.0 1.0
C K:HIS166 4.5 39.9 1.0
N K:GLY172 4.5 44.0 1.0
O K:ALA164 4.5 41.0 1.0
N K:TYR170 4.6 41.8 1.0
CA K:GLY172 4.6 44.5 1.0
CB K:SER171 4.7 41.1 1.0
CA K:HIS166 4.7 40.5 1.0
NH2 K:ARG19 4.8 48.3 1.0
CB K:ALA165 4.8 41.8 1.0
CG W:ASP204 4.9 47.4 1.0
C K:ARG167 4.9 39.8 1.0
N K:ARG167 5.0 39.5 1.0

Magnesium binding site 5 out of 8 in 5bou

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Magnesium binding site 5 out of 8 in the Yeast 20S Proteasome in Complex with A BETA1 / BETA2 Specific Non- Peptidic Sulfonamide Ligand


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Yeast 20S Proteasome in Complex with A BETA1 / BETA2 Specific Non- Peptidic Sulfonamide Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg301

b:59.3
occ:1.00
 O V:ASP166 2.1 44.4 1.0
OXT L:ASP222 2.2 58.7 1.0
O V:ILE163 2.2 45.2 1.0
O V:SER169 2.3 47.8 1.0
C L:ASP222 3.1 61.1 1.0
C V:ASP166 3.2 45.5 1.0
C V:ILE163 3.3 46.4 1.0
C V:SER169 3.4 48.1 1.0
CA L:ASP222 3.7 60.8 1.0
NH1 V:ARG19 3.8 52.4 1.0
O V:GLY162 3.8 45.5 1.0
CA V:LEU167 3.8 46.6 1.0
N V:LEU167 3.9 46.5 1.0
O L:ASP222 3.9 65.8 1.0
CA V:ILE163 4.1 46.6 1.0
N V:ASP166 4.1 45.4 1.0
C V:LEU167 4.2 46.9 1.0
N V:SER169 4.2 46.8 1.0
CB L:ASP222 4.2 61.0 1.0
CA V:ASP166 4.2 45.2 1.0
N V:TRP164 4.3 47.1 1.0
N V:GLY170 4.3 49.0 1.0
CA V:SER169 4.3 46.7 1.0
CA V:GLY170 4.4 51.2 1.0
C V:TRP164 4.4 49.0 1.0
O V:LEU167 4.4 47.2 1.0
O V:TRP164 4.5 51.6 1.0
CZ V:ARG19 4.5 51.5 1.0
CA V:TRP164 4.6 48.6 1.0
N V:ASN165 4.7 48.1 1.0
NH2 V:ARG19 4.7 53.3 1.0
CB V:SER169 4.7 46.5 1.0
C V:GLY162 4.8 46.0 1.0
C V:ASN165 4.9 45.4 1.0
N V:GLY168 4.9 47.0 1.0
N V:ILE163 4.9 46.6 1.0

Magnesium binding site 6 out of 8 in 5bou

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Magnesium binding site 6 out of 8 in the Yeast 20S Proteasome in Complex with A BETA1 / BETA2 Specific Non- Peptidic Sulfonamide Ligand


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Yeast 20S Proteasome in Complex with A BETA1 / BETA2 Specific Non- Peptidic Sulfonamide Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg201

b:50.6
occ:1.00
 O N:ILE163 2.6 41.7 1.0
O N:SER169 2.7 43.8 1.0
O N:ASP166 3.0 43.2 1.0
CD1 a:LEU34 3.6 46.9 1.0
C N:ILE163 3.7 41.5 1.0
NH1 N:ARG19 3.7 44.2 1.0
CG2 N:ILE163 3.8 40.0 1.0
C N:SER169 3.9 42.1 1.0
C N:ASP166 4.0 41.0 1.0
CZ N:ARG19 4.2 44.2 1.0
CA N:GLY167 4.3 40.2 1.0
NH2 N:ARG19 4.3 45.3 1.0
CA N:ILE163 4.4 40.4 1.0
CA N:GLY170 4.4 43.5 1.0
N N:GLY167 4.5 40.6 1.0
O N:GLY167 4.6 40.9 1.0
N N:GLY170 4.6 43.0 1.0
C N:GLY167 4.6 40.3 1.0
CB N:ILE163 4.7 39.8 1.0
N N:LYS164 4.7 43.0 1.0
N N:SER169 4.9 40.2 1.0
CA N:SER169 4.9 40.1 1.0
CG a:LEU34 4.9 46.6 1.0
C N:LYS164 5.0 44.6 1.0
O N:LYS164 5.0 44.3 1.0
CA N:LYS164 5.0 45.2 1.0

Magnesium binding site 7 out of 8 in 5bou

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Magnesium binding site 7 out of 8 in the Yeast 20S Proteasome in Complex with A BETA1 / BETA2 Specific Non- Peptidic Sulfonamide Ligand


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Yeast 20S Proteasome in Complex with A BETA1 / BETA2 Specific Non- Peptidic Sulfonamide Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
W:Mg301

b:56.0
occ:1.00
 O W:ASP177 2.2 45.4 1.0
O W:SER180 2.5 48.1 1.0
O W:ALA174 2.8 43.0 1.0
C W:ASP177 3.3 43.5 1.0
C W:SER180 3.7 45.3 1.0
O W:ALA178 3.9 43.3 1.0
C W:ALA174 4.0 43.1 1.0
CA W:ALA178 4.0 42.5 1.0
C W:ALA178 4.0 43.2 1.0
OXT W:ASP204 4.1 50.3 1.0
N W:ALA178 4.1 42.7 1.0
N W:SER180 4.2 45.3 1.0
N W:ASP177 4.3 43.8 1.0
O W:HOH410 4.3 40.3 1.0
CA W:ASP177 4.4 43.8 1.0
CA W:ASP175 4.4 46.6 1.0
NH1 K:ARG19 4.5 48.1 1.0
CA W:SER180 4.5 45.3 1.0
N W:ASP175 4.6 45.1 1.0
N W:GLY181 4.6 44.5 1.0
C W:ASP175 4.6 45.8 1.0
N W:LEU179 4.7 43.2 1.0
CA W:GLY181 4.8 44.5 1.0
O W:ASP204 4.8 47.7 1.0
NH2 K:ARG19 4.8 48.3 1.0
C W:ASP204 4.9 48.5 1.0
O W:ASP175 4.9 45.9 1.0
CB W:ASP177 5.0 45.1 1.0

Magnesium binding site 8 out of 8 in 5bou

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Magnesium binding site 8 out of 8 in the Yeast 20S Proteasome in Complex with A BETA1 / BETA2 Specific Non- Peptidic Sulfonamide Ligand


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Yeast 20S Proteasome in Complex with A BETA1 / BETA2 Specific Non- Peptidic Sulfonamide Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg301

b:56.0
occ:1.00
 O Z:HIS195 2.3 42.7 1.0
O Z:HOH416 2.4 35.2 1.0
O Z:THR192 2.5 52.8 1.0
O Z:VAL198 2.5 46.4 1.0
C Z:HIS195 3.4 44.5 1.0
C Z:THR192 3.5 53.7 1.0
CA Z:ILE196 3.7 43.8 1.0
C Z:VAL198 3.7 47.5 1.0
CA Z:THR192 3.9 52.8 1.0
C Z:ILE196 3.9 43.6 1.0
N Z:ILE196 3.9 43.7 1.0
O Z:ILE196 4.0 47.4 1.0
CG2 Z:THR192 4.0 54.4 1.0
NH2 Z:ARG28 4.1 51.7 1.0
N Z:VAL198 4.2 45.7 1.0
NH2 H:ARG19 4.4 57.9 1.0
O Z:ASP222 4.4 63.5 1.0
CA Z:VAL198 4.4 46.8 1.0
N Z:HIS195 4.5 45.9 1.0
CA Z:HIS195 4.5 44.5 1.0
CB Z:THR192 4.6 53.3 1.0
O Z:ALA191 4.6 49.3 1.0
N Z:GLN197 4.6 43.6 1.0
CB Z:VAL198 4.7 46.5 1.0
N Z:GLU193 4.7 54.2 1.0
N Z:GLY199 4.8 48.7 1.0
CA Z:GLY199 5.0 50.3 1.0
OD1 Z:ASP222 5.0 63.0 1.0

Reference:

P.Beck, M.Reboud-Ravaux, M.Groll. Identification of A Beta 1/ Beta 2-Specific Sulfonamide Proteasome Ligand By Crystallographic Screening. Angew.Chem.Int.Ed.Engl. V. 54 11275 2015.
ISSN: ESSN 1521-3773
PubMed: 26242779
DOI: 10.1002/ANIE.201505054
Page generated: Sun Sep 29 01:13:51 2024

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