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Magnesium in PDB 3oeu: Structure of Yeast 20S Open-Gate Proteasome with Compound 24

Enzymatic activity of Structure of Yeast 20S Open-Gate Proteasome with Compound 24

All present enzymatic activity of Structure of Yeast 20S Open-Gate Proteasome with Compound 24:
3.4.25.1;

Protein crystallography data

The structure of Structure of Yeast 20S Open-Gate Proteasome with Compound 24, PDB code: 3oeu was solved by M.D.Sintchak, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 136.774, 299.668, 145.301, 90.00, 113.22, 90.00
R / Rfree (%) 20.9 / 24.9

Other elements in 3oeu:

The structure of Structure of Yeast 20S Open-Gate Proteasome with Compound 24 also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of Yeast 20S Open-Gate Proteasome with Compound 24 (pdb code 3oeu). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 9 binding sites of Magnesium where determined in the Structure of Yeast 20S Open-Gate Proteasome with Compound 24, PDB code: 3oeu:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Magnesium binding site 1 out of 9 in 3oeu

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Magnesium binding site 1 out of 9 in the Structure of Yeast 20S Open-Gate Proteasome with Compound 24


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Yeast 20S Open-Gate Proteasome with Compound 24 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg242

b:0.3
occ:1.00
 O F:HOH655 1.8 44.6 1.0
O F:ALA164 2.9 45.6 1.0
SD F:MET150 3.3 41.4 1.0
OG1 F:THR165 3.3 48.8 1.0
CE F:MET150 3.3 40.8 1.0
CB F:THR165 3.4 48.2 1.0
CA F:THR165 3.7 47.7 1.0
OE2 F:GLU152 3.9 51.5 1.0
C F:ALA164 3.9 45.8 1.0
OE1 F:GLU152 4.0 50.5 1.0
N F:THR165 4.3 46.7 1.0
CD F:GLU152 4.4 50.3 1.0
CG F:MET150 4.6 40.1 1.0
NZ F:LYS173 4.6 57.2 1.0
CE F:LYS173 4.7 57.0 1.0
CG2 F:THR165 4.8 47.9 1.0
OG F:SER135 4.8 45.5 1.0
CB F:SER135 4.9 44.1 1.0
CD F:ARG169 4.9 54.7 1.0

Magnesium binding site 2 out of 9 in 3oeu

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Magnesium binding site 2 out of 9 in the Structure of Yeast 20S Open-Gate Proteasome with Compound 24


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Yeast 20S Open-Gate Proteasome with Compound 24 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg1

b:61.4
occ:1.00
 O G:HOH316 1.8 66.2 1.0
O G:TYR123 2.1 43.5 1.0
O G:ARG126 2.1 48.5 1.0
O G:MET129 2.3 50.2 1.0
OG1 G:THR13 2.8 49.5 1.0
C G:TYR123 3.1 43.5 1.0
C G:ARG126 3.3 48.8 1.0
C G:MET129 3.4 50.2 1.0
CG2 G:THR13 3.6 48.8 1.0
CB G:THR13 3.8 49.6 1.0
CA G:TYR123 3.8 43.2 1.0
N G:ARG126 4.1 47.3 1.0
N G:MET129 4.1 53.5 1.0
N G:ALA127 4.2 49.0 1.0
O G:ALA127 4.2 50.7 1.0
CA G:MET129 4.2 53.6 1.0
N G:THR124 4.2 44.2 1.0
C G:ALA127 4.2 50.8 1.0
CA G:ALA127 4.2 49.5 1.0
CB G:MET129 4.2 58.6 1.0
CA G:ARG126 4.3 49.1 1.0
N G:ARG130 4.5 45.8 1.0
CB G:TYR123 4.5 43.4 1.0
C G:THR124 4.5 44.1 1.0
CD G:PRO131 4.6 37.9 1.0
CA G:THR124 4.6 43.3 1.0
CA G:ARG130 4.6 42.2 1.0
N G:GLN125 4.6 43.8 1.0
O G:ILE122 4.7 41.9 1.0
N G:THR13 4.8 52.2 1.0
C G:GLN125 4.8 44.8 1.0
N G:TYR128 4.8 52.4 1.0
O G:THR124 4.9 44.2 1.0
CB G:ARG126 4.9 52.8 1.0
CA G:THR13 4.9 50.0 1.0
C G:ARG130 4.9 40.7 1.0
N G:PRO131 5.0 39.3 1.0

Magnesium binding site 3 out of 9 in 3oeu

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Magnesium binding site 3 out of 9 in the Structure of Yeast 20S Open-Gate Proteasome with Compound 24


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of Yeast 20S Open-Gate Proteasome with Compound 24 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg224

b:51.3
occ:1.00
 O H:SER169 2.2 45.8 1.0
O H:ILE163 2.2 41.1 1.0
O H:ASP166 2.4 43.5 1.0
O H:HOH249 2.4 54.0 1.0
OXT Z:ASP194 2.5 47.1 1.0
C Z:ASP194 3.2 47.6 1.0
C H:SER169 3.3 44.5 1.0
C H:ILE163 3.3 41.6 1.0
C H:ASP166 3.5 41.9 1.0
CA Z:ASP194 3.6 47.5 1.0
O H:GLY162 3.8 41.6 1.0
CB Z:ASP194 3.9 48.7 1.0
CA H:ILE163 3.9 41.7 1.0
NH1 H:ARG19 3.9 46.5 1.0
O Z:ASP194 4.0 47.0 1.0
N H:GLY170 4.1 45.3 1.0
CA H:GLY170 4.1 45.7 1.0
CA H:LEU167 4.1 42.6 1.0
CA H:SER169 4.2 43.8 1.0
N H:SER169 4.2 43.7 1.0
N H:LEU167 4.2 42.3 1.0
N H:TRP164 4.3 41.4 1.0
N H:ASP166 4.4 40.7 1.0
C H:LEU167 4.4 43.3 1.0
CZ H:ARG19 4.4 46.5 1.0
CA H:ASP166 4.5 41.4 1.0
NH2 H:ARG19 4.5 46.3 1.0
C H:TRP164 4.5 41.8 1.0
O H:LEU167 4.5 44.6 1.0
CB H:SER169 4.6 42.2 1.0
CA H:TRP164 4.6 41.3 1.0
O H:TRP164 4.7 42.9 1.0
C H:GLY162 4.7 41.5 1.0
CG Z:ASP194 4.8 49.7 1.0
N H:ILE163 4.8 40.7 1.0
N H:ASN165 4.8 40.5 1.0
CG2 H:ILE163 4.9 41.6 1.0

Magnesium binding site 4 out of 9 in 3oeu

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Magnesium binding site 4 out of 9 in the Structure of Yeast 20S Open-Gate Proteasome with Compound 24


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of Yeast 20S Open-Gate Proteasome with Compound 24 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg195

b:65.6
occ:1.00
 O I:HOH667 2.3 41.0 1.0
OG I:SER131 3.1 38.7 1.0
O I:HOH547 3.2 48.8 1.0
O I:GLY128 3.3 38.9 1.0
O I:THR129 3.9 39.2 1.0
C I:THR129 4.0 39.0 1.0
CA I:THR129 4.1 39.2 1.0
CB I:SER131 4.2 38.6 1.0
N I:SER131 4.3 39.2 1.0
C I:GLY128 4.3 38.4 1.0
N I:THR129 4.7 38.3 1.0
N I:ALA130 4.7 39.9 1.0
CA I:SER131 4.8 39.1 1.0
OD2 I:ASP132 4.8 46.7 1.0
N I:ASP132 5.0 39.9 1.0

Magnesium binding site 5 out of 9 in 3oeu

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Magnesium binding site 5 out of 9 in the Structure of Yeast 20S Open-Gate Proteasome with Compound 24


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of Yeast 20S Open-Gate Proteasome with Compound 24 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg196

b:64.2
occ:1.00
 O I:HOH871 1.5 58.2 1.0
O I:SER169 2.3 44.3 1.0
O I:ALA163 2.3 44.2 1.0
O I:ASP166 2.3 40.2 1.0
C I:SER169 3.2 43.1 1.0
C I:ALA163 3.3 42.7 1.0
C I:ASP166 3.5 39.8 1.0
N I:SER169 3.9 41.8 1.0
CA I:SER169 4.0 42.8 1.0
N I:GLY170 4.1 43.3 1.0
CA I:ASP164 4.1 44.9 1.0
N I:ASP164 4.1 44.0 1.0
CA I:GLY170 4.2 42.9 1.0
CA I:ALA163 4.2 41.4 1.0
CB I:SER169 4.3 43.1 1.0
N I:ASP166 4.3 40.0 1.0
CA I:ASP166 4.4 40.5 1.0
C I:ALA167 4.5 40.6 1.0
CB I:ALA163 4.5 40.5 1.0
N I:ALA167 4.5 38.9 1.0
C I:ASP164 4.6 44.9 1.0
OD2 I:ASP164 4.6 48.0 1.0
O I:ALA167 4.6 40.7 1.0
CA I:ALA167 4.6 39.1 1.0
CB I:ASP166 4.6 42.0 1.0
O I:HOH1147 4.7 36.5 1.0
OXT I:ASP194 4.8 40.8 1.0
N I:LEU168 4.9 41.1 1.0

Magnesium binding site 6 out of 9 in 3oeu

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Magnesium binding site 6 out of 9 in the Structure of Yeast 20S Open-Gate Proteasome with Compound 24


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure of Yeast 20S Open-Gate Proteasome with Compound 24 within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg212

b:79.9
occ:1.00
 O W:HOH204 1.5 58.0 1.0
O K:ALA163 2.0 40.0 1.0
O K:SER169 2.4 41.6 1.0
O K:ASP166 2.5 39.5 1.0
O W:ASP194 2.8 44.5 1.0
C K:ALA163 3.1 39.5 1.0
C K:SER169 3.3 40.9 1.0
C W:ASP194 3.5 44.8 1.0
C K:ASP166 3.6 38.9 1.0
CA W:ASP194 3.7 44.9 1.0
CA K:ALA163 3.7 39.7 1.0
CB W:ASP194 3.7 45.2 1.0
CA K:SER169 4.1 40.5 1.0
N K:SER169 4.1 40.7 1.0
N K:GLY170 4.1 41.4 1.0
N K:HIS164 4.2 39.0 1.0
NH1 K:ARG19 4.2 45.4 1.0
O K:HIS164 4.2 41.3 1.0
O K:ALA162 4.2 39.8 1.0
CA K:GLY170 4.2 42.1 1.0
O K:ALA167 4.3 39.4 1.0
C K:ALA167 4.3 39.2 1.0
C K:HIS164 4.3 40.9 1.0
CA K:ALA167 4.3 38.7 1.0
N K:ALA167 4.4 38.1 1.0
N K:ASP166 4.4 40.1 1.0
CB K:SER169 4.4 39.6 1.0
OXT W:ASP194 4.5 45.0 1.0
CA K:HIS164 4.5 39.6 1.0
CB K:ALA163 4.5 39.8 1.0
CA K:ASP166 4.6 39.0 1.0
CZ K:ARG19 4.6 45.5 1.0
CG W:ASP194 4.8 46.0 1.0
N K:ALA163 4.8 39.5 1.0
N K:TYR168 4.8 40.1 1.0
N K:ARG165 4.9 41.2 1.0
NH2 K:ARG19 4.9 45.9 1.0
C K:ALA162 5.0 39.2 1.0

Magnesium binding site 7 out of 9 in 3oeu

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Magnesium binding site 7 out of 9 in the Structure of Yeast 20S Open-Gate Proteasome with Compound 24


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Structure of Yeast 20S Open-Gate Proteasome with Compound 24 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg195

b:75.5
occ:1.00
 O L:HOH309 1.7 55.0 1.0
O L:HOH812 1.9 43.6 1.0
OE2 D:GLU105 2.1 38.2 1.0
OG L:SER78 2.5 43.1 1.0
OG L:SER75 2.6 42.8 1.0
CD D:GLU105 3.3 38.9 1.0
CB L:SER78 3.4 43.2 1.0
CB L:SER75 3.5 42.1 1.0
N L:SER75 3.7 42.9 1.0
OH L:TYR66 3.9 37.9 1.0
OE1 D:GLU105 4.1 38.9 1.0
CB D:GLU105 4.2 39.4 1.0
CA L:SER75 4.2 42.9 1.0
CG D:GLU105 4.2 38.8 1.0
OD1 L:ASN77 4.4 45.7 1.0
O L:LYS73 4.5 45.3 1.0
NZ L:LYS72 4.5 40.8 1.0
CE L:LYS72 4.6 40.7 1.0
O L:SER75 4.7 43.7 1.0
CA L:SER78 4.7 43.2 1.0
OE2 L:GLU106 4.8 63.7 1.0
C L:LEU74 4.8 43.8 1.0
O D:TYR103 4.8 39.7 1.0
N L:SER78 4.9 43.7 1.0
C L:SER75 4.9 43.6 1.0
CZ L:TYR66 4.9 37.6 1.0
CD1 L:LEU74 4.9 42.2 1.0
CA L:LEU74 5.0 43.8 1.0

Magnesium binding site 8 out of 9 in 3oeu

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Magnesium binding site 8 out of 9 in the Structure of Yeast 20S Open-Gate Proteasome with Compound 24


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Structure of Yeast 20S Open-Gate Proteasome with Compound 24 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg196

b:72.7
occ:1.00
 O L:HIS166 2.1 43.4 1.0
O L:HOH284 2.2 56.6 1.0
O L:THR163 2.2 50.1 1.0
O L:VAL169 2.9 48.4 1.0
C L:HIS166 3.1 43.8 1.0
C L:THR163 3.3 48.9 1.0
CA L:ILE167 3.7 44.8 1.0
CA L:THR163 3.7 47.6 1.0
N L:ILE167 3.8 44.0 1.0
C L:ILE167 4.0 46.0 1.0
N L:HIS166 4.0 45.5 1.0
C L:VAL169 4.1 47.1 1.0
O L:ILE167 4.1 47.2 1.0
CA L:HIS166 4.2 44.2 1.0
CG2 L:THR163 4.2 46.2 1.0
O L:ALA162 4.2 48.3 1.0
N L:VAL169 4.3 47.1 1.0
NH2 V:ARG19 4.3 50.1 1.0
N L:GLU164 4.4 48.9 1.0
NH2 L:ARG19 4.6 46.6 1.0
CB L:THR163 4.6 46.6 1.0
CA L:VAL169 4.6 46.8 1.0
C L:GLU164 4.6 48.8 1.0
N L:GLN168 4.7 46.4 1.0
N L:ARG165 4.8 47.4 1.0
CB L:VAL169 4.8 46.6 1.0
O L:ASP194 4.8 56.8 1.0
O L:GLU164 4.8 50.6 1.0
N L:THR163 4.8 47.7 1.0
CA L:GLU164 4.9 48.5 1.0
CZ V:ARG19 4.9 50.4 1.0
CB L:ILE167 5.0 44.3 1.0
C L:ALA162 5.0 48.0 1.0
C L:ARG165 5.0 46.6 1.0

Magnesium binding site 9 out of 9 in 3oeu

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Magnesium binding site 9 out of 9 in the Structure of Yeast 20S Open-Gate Proteasome with Compound 24


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Structure of Yeast 20S Open-Gate Proteasome with Compound 24 within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg188

b:68.1
occ:1.00
 O N:HOH202 1.6 43.3 1.0
O N:ASP166 2.1 41.5 1.0
O N:ILE163 2.3 38.0 1.0
O N:SER169 2.3 39.4 1.0
C N:ASP166 3.2 40.2 1.0
C N:SER169 3.2 38.2 1.0
C N:ILE163 3.3 39.1 1.0
CA N:ILE163 3.7 38.4 1.0
NH1 N:ARG19 3.7 38.5 1.0
CD1 1:LEU26 3.8 38.8 1.0
CG2 N:ILE163 3.8 35.9 1.0
N N:SER169 3.9 36.3 1.0
CA N:SER169 4.0 36.2 1.0
CA N:GLY167 4.0 37.4 1.0
N N:GLY167 4.0 39.0 1.0
CB N:SER169 4.1 34.4 1.0
C N:GLY167 4.1 38.0 1.0
N N:GLY170 4.2 38.3 1.0
O N:GLY167 4.2 38.2 1.0
N N:ASP166 4.3 41.1 1.0
CA N:ASP166 4.3 40.7 1.0
CB N:ILE163 4.3 37.1 1.0
CA N:GLY170 4.4 38.1 1.0
N N:LYS164 4.5 40.9 1.0
CZ N:ARG19 4.6 38.2 1.0
O N:ALA162 4.6 40.3 1.0
N N:SER168 4.8 37.2 1.0
CB N:ASP166 4.8 42.2 1.0
C N:LYS164 4.9 42.2 1.0
CG 1:LEU26 4.9 39.4 1.0
N N:ILE163 5.0 38.4 1.0

Reference:

C.Blackburn, C.Barrett, J.L.Blank, F.J.Bruzzese, N.Bump, L.R.Dick, P.Fleming, K.Garcia, P.Hales, Z.Hu, M.Jones, J.X.Liu, D.S.Sappal, M.D.Sintchak, C.Tsu, K.M.Gigstad. Optimization of A Series of Dipeptides with A P3 Threonine Residue As Non-Covalent Inhibitors of the Chymotrypsin-Like Activity of the Human 20S Proteasome. Bioorg.Med.Chem.Lett. V. 20 6581 2010.
ISSN: ISSN 0960-894X
PubMed: 20875739
DOI: 10.1016/J.BMCL.2010.09.032
Page generated: Thu Aug 15 08:18:45 2024

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