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Magnesium in PDB 3mg8: Structure of Yeast 20S Open-Gate Proteasome with Compound 16

Enzymatic activity of Structure of Yeast 20S Open-Gate Proteasome with Compound 16

All present enzymatic activity of Structure of Yeast 20S Open-Gate Proteasome with Compound 16:
3.4.25.1;

Protein crystallography data

The structure of Structure of Yeast 20S Open-Gate Proteasome with Compound 16, PDB code: 3mg8 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) 49.88 / 2.59
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 136.333, 299.185, 145.667, 90.00, 113.13, 90.00
R / Rfree (%) 22.4 / 25.2

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of Yeast 20S Open-Gate Proteasome with Compound 16 (pdb code 3mg8). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 10 binding sites of Magnesium where determined in the Structure of Yeast 20S Open-Gate Proteasome with Compound 16, PDB code: 3mg8:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 10 in 3mg8

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Magnesium binding site 1 out of 10 in the Structure of Yeast 20S Open-Gate Proteasome with Compound 16


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 16 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg242

b:68.0
occ:1.00
 O F:ALA164 2.5 37.5 1.0
C F:ALA164 3.6 37.4 1.0
CE F:LYS173 3.6 48.9 1.0
NZ F:LYS173 3.6 48.9 1.0
CA F:THR165 3.6 39.1 1.0
CE F:MET150 3.8 33.0 1.0
CD F:ARG169 3.8 44.6 1.0
OG1 F:THR165 3.9 40.4 1.0
CG F:ARG169 3.9 45.6 1.0
CB F:THR165 4.0 39.2 1.0
SD F:MET150 4.1 34.6 1.0
N F:THR165 4.1 38.2 1.0
CB F:ARG169 4.3 45.4 1.0
C F:THR165 4.8 39.5 1.0
CA F:ALA164 4.8 36.6 1.0
OE2 F:GLU152 4.9 42.4 1.0

Magnesium binding site 2 out of 10 in 3mg8

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Magnesium binding site 2 out of 10 in the Structure of Yeast 20S Open-Gate Proteasome with Compound 16


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 16 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg243

b:0.4
occ:1.00
 OG F:SER13 2.6 56.1 1.0
O G:ALA127 2.9 39.5 1.0
ND2 F:ASN127 3.2 46.1 1.0
CB F:ASN127 3.4 42.8 1.0
O G:TYR128 3.4 39.7 1.0
CB F:SER13 3.5 55.6 1.0
C G:TYR128 3.6 39.6 1.0
CG F:ASN127 3.6 44.5 1.0
CA G:TYR128 3.6 39.9 1.0
N F:ASN127 3.7 41.2 1.0
C G:ALA127 3.9 39.1 1.0
CG2 G:ILE12 4.1 44.8 1.0
CA F:ASN127 4.1 42.1 1.0
CE2 A:TYR8 4.2 67.0 1.0
N G:TYR128 4.3 39.5 1.0
N G:MET129 4.4 39.4 1.0
OD1 F:ASN127 4.7 47.5 1.0
C F:TYR126 4.8 40.2 1.0
CB G:TYR128 4.8 40.3 1.0
C G:MET129 4.8 37.5 1.0
CA F:SER13 4.9 55.3 1.0
O F:LEU125 4.9 36.9 1.0
OH A:TYR8 4.9 67.3 1.0
CA F:TYR126 4.9 39.1 1.0
O G:MET129 4.9 37.3 1.0

Magnesium binding site 3 out of 10 in 3mg8

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Magnesium binding site 3 out of 10 in the Structure of Yeast 20S Open-Gate Proteasome with Compound 16


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 16 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg241

b:39.0
occ:1.00
 O G:MET129 2.1 37.3 1.0
O G:TYR123 2.2 31.3 1.0
O G:ARG126 2.3 38.0 1.0
OG1 G:THR13 2.6 40.6 1.0
C G:MET129 3.3 37.5 1.0
C G:TYR123 3.3 31.4 1.0
CG2 G:THR13 3.4 39.9 1.0
C G:ARG126 3.6 37.8 1.0
CB G:THR13 3.6 40.8 1.0
O G:ALA127 4.0 39.5 1.0
CA G:TYR123 4.1 31.1 1.0
CA G:MET129 4.2 39.0 1.0
C G:ALA127 4.2 39.1 1.0
N G:MET129 4.2 39.4 1.0
N G:ARG130 4.2 35.8 1.0
CA G:ALA127 4.2 38.5 1.0
CA G:ARG130 4.3 34.3 1.0
N G:ALA127 4.3 38.1 1.0
N G:THR124 4.4 32.1 1.0
CB G:MET129 4.4 39.7 1.0
CD G:PRO131 4.4 32.2 1.0
N G:ARG126 4.5 36.6 1.0
N G:THR13 4.5 42.1 1.0
CA G:ARG126 4.6 37.8 1.0
C G:THR124 4.7 33.4 1.0
CB G:TYR123 4.7 30.8 1.0
CA G:THR124 4.7 32.8 1.0
C G:ARG130 4.7 33.4 1.0
CA G:THR13 4.7 40.7 1.0
N G:PRO131 4.8 32.4 1.0
N G:GLN125 4.8 33.9 1.0
N G:TYR128 5.0 39.5 1.0
O G:THR124 5.0 33.4 1.0

Magnesium binding site 4 out of 10 in 3mg8

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Magnesium binding site 4 out of 10 in the Structure of Yeast 20S Open-Gate Proteasome with Compound 16


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 16 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg224

b:44.5
occ:1.00
 O H:SER169 2.2 34.0 1.0
O H:ILE163 2.3 28.3 1.0
O H:ASP166 2.4 31.6 1.0
OXT Z:ASP194 2.7 38.3 1.0
C Z:ASP194 3.2 38.4 1.0
C H:ILE163 3.3 28.3 1.0
C H:SER169 3.4 33.4 1.0
C H:ASP166 3.4 31.1 1.0
CA Z:ASP194 3.6 38.2 1.0
O H:GLY162 3.8 28.3 1.0
CB Z:ASP194 3.9 38.5 1.0
CA H:ILE163 3.9 28.2 1.0
O Z:ASP194 4.0 38.5 1.0
NH1 H:ARG19 4.1 38.0 1.0
CA H:LEU167 4.1 31.2 1.0
N H:LEU167 4.1 31.1 1.0
N H:ASP166 4.2 30.5 1.0
N H:SER169 4.2 32.5 1.0
N H:GLY170 4.3 33.6 1.0
CA H:SER169 4.3 33.1 1.0
N H:TRP164 4.3 28.5 1.0
CA H:GLY170 4.3 33.8 1.0
CA H:ASP166 4.4 30.9 1.0
C H:LEU167 4.4 31.5 1.0
C H:TRP164 4.5 29.4 1.0
CZ H:ARG19 4.5 38.7 1.0
CA H:TRP164 4.6 29.1 1.0
CB H:SER169 4.6 32.7 1.0
N H:ASN165 4.6 29.3 1.0
NH2 H:ARG19 4.7 38.1 1.0
O H:LEU167 4.7 31.8 1.0
C H:GLY162 4.7 28.3 1.0
CG Z:ASP194 4.8 39.2 1.0
O H:TRP164 4.8 29.6 1.0
N H:ILE163 4.8 28.1 1.0
C H:ASN165 4.9 29.9 1.0
CG2 H:ILE163 5.0 27.6 1.0

Magnesium binding site 5 out of 10 in 3mg8

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Magnesium binding site 5 out of 10 in the Structure of Yeast 20S Open-Gate Proteasome with Compound 16


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 16 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg195

b:54.5
occ:1.00
 OG I:SER131 2.6 31.8 1.0
O I:GLY128 2.7 29.2 1.0
CB I:SER131 3.6 31.6 1.0
C I:GLY128 3.7 29.1 1.0
N I:SER131 4.3 31.3 1.0
CA I:THR129 4.4 30.0 1.0
N I:THR129 4.4 29.4 1.0
CA I:SER131 4.6 31.8 1.0
C I:THR129 4.6 30.2 1.0
N I:GLY128 4.6 29.2 1.0
CA I:GLY128 4.6 28.9 1.0
O I:THR129 4.8 30.3 1.0

Magnesium binding site 6 out of 10 in 3mg8

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Magnesium binding site 6 out of 10 in the Structure of Yeast 20S Open-Gate Proteasome with Compound 16


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 16 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg196

b:43.5
occ:1.00
 O I:ASP166 2.4 33.1 1.0
O I:SER169 2.5 34.1 1.0
O I:ALA163 2.6 33.5 1.0
C I:ASP166 3.5 33.2 1.0
C I:SER169 3.6 33.8 1.0
C I:ALA163 3.6 33.3 1.0
CA I:ASP164 4.2 34.1 1.0
N I:SER169 4.2 33.5 1.0
C I:ALA167 4.3 32.9 1.0
O I:ALA167 4.3 33.0 1.0
N I:ASP164 4.3 33.6 1.0
CA I:SER169 4.4 33.9 1.0
N I:ASP166 4.4 33.3 1.0
CA I:ALA167 4.4 32.8 1.0
N I:ALA167 4.4 32.9 1.0
C I:ASP164 4.5 34.0 1.0
CA I:ASP166 4.5 33.6 1.0
OXT I:ASP194 4.5 37.1 1.0
N I:GLY170 4.5 33.6 1.0
CA I:GLY170 4.6 33.3 1.0
O I:ASP164 4.6 34.1 1.0
CA I:ALA163 4.6 32.9 1.0
CB I:SER169 4.7 33.9 1.0
N I:LEU168 4.8 32.9 1.0
CB I:ALA163 4.9 32.6 1.0
OD2 I:ASP164 4.9 37.8 1.0
CB I:ASP166 5.0 33.8 1.0

Magnesium binding site 7 out of 10 in 3mg8

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Magnesium binding site 7 out of 10 in the Structure of Yeast 20S Open-Gate Proteasome with Compound 16


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 16 within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg212

b:39.5
occ:1.00
 O K:ASP166 2.3 30.0 1.0
O K:ALA163 2.3 29.5 1.0
O K:SER169 2.4 29.3 1.0
O W:ASP194 2.5 36.0 1.0
C W:ASP194 3.3 35.9 1.0
C K:ASP166 3.4 29.5 1.0
C K:ALA163 3.4 29.1 1.0
C K:SER169 3.5 29.4 1.0
CA W:ASP194 3.7 35.9 1.0
CB W:ASP194 3.9 35.9 1.0
NH1 K:ARG19 4.0 34.5 1.0
CA K:ALA167 4.0 29.0 1.0
O K:ALA167 4.1 29.1 1.0
C K:ALA167 4.1 29.1 1.0
CA K:ALA163 4.1 29.1 1.0
N K:ALA167 4.1 29.4 1.0
N K:SER169 4.2 29.2 1.0
OXT W:ASP194 4.2 35.9 1.0
CA K:SER169 4.3 29.2 1.0
N K:ASP166 4.3 29.0 1.0
O K:ALA162 4.4 29.8 1.0
N K:HIS164 4.4 28.6 1.0
O K:HIS164 4.4 28.8 1.0
C K:HIS164 4.5 28.8 1.0
CA K:ASP166 4.5 29.2 1.0
N K:GLY170 4.5 29.8 1.0
CZ K:ARG19 4.5 33.7 1.0
CA K:GLY170 4.6 30.0 1.0
CA K:HIS164 4.7 28.5 1.0
CB K:SER169 4.7 29.0 1.0
N K:TYR168 4.7 29.1 1.0
NH2 K:ARG19 4.8 35.2 1.0
CG W:ASP194 4.9 36.6 1.0
N K:ARG165 4.9 28.6 1.0
C K:ARG165 5.0 28.9 1.0

Magnesium binding site 8 out of 10 in 3mg8

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Magnesium binding site 8 out of 10 in the Structure of Yeast 20S Open-Gate Proteasome with Compound 16


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 16 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg195

b:48.4
occ:1.00
 OE2 D:GLU105 2.4 31.0 1.0
OG L:SER75 2.4 31.9 1.0
OG L:SER78 2.6 30.7 1.0
CB L:SER75 3.4 32.5 1.0
CB L:SER78 3.5 31.0 1.0
CD D:GLU105 3.5 32.0 1.0
N L:SER75 3.9 33.4 1.0
OD1 L:ASN77 4.0 34.1 1.0
CB D:GLU105 4.2 32.6 1.0
CA L:SER75 4.2 32.9 1.0
OE2 L:GLU106 4.3 51.7 1.0
OE1 D:GLU105 4.4 31.5 1.0
CG D:GLU105 4.4 32.6 1.0
OH L:TYR66 4.5 30.8 1.0
NZ L:LYS72 4.6 30.6 1.0
CA L:SER78 4.7 30.9 1.0
N L:SER78 4.7 31.2 1.0
CG L:ASN77 4.7 33.0 1.0
ND2 L:ASN77 4.7 33.2 1.0
O L:SER75 4.8 33.2 1.0
C L:SER75 4.8 33.0 1.0
CE L:LYS72 4.8 30.3 1.0
O L:LYS73 4.9 35.7 1.0
O D:TYR103 4.9 30.4 1.0

Magnesium binding site 9 out of 10 in 3mg8

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Magnesium binding site 9 out of 10 in the Structure of Yeast 20S Open-Gate Proteasome with Compound 16


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 16 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg196

b:50.6
occ:1.00
 O L:THR163 2.4 36.9 1.0
O L:VAL169 2.4 34.8 1.0
O L:HIS166 2.5 33.6 1.0
C L:THR163 3.4 36.8 1.0
C L:HIS166 3.6 33.7 1.0
C L:VAL169 3.6 34.8 1.0
CA L:THR163 3.7 36.5 1.0
CG2 L:THR163 3.8 35.9 1.0
NH2 L:ARG19 4.0 36.3 1.0
CA L:ILE167 4.0 33.3 1.0
C L:ILE167 4.2 33.6 1.0
N L:ILE167 4.2 33.5 1.0
O L:ILE167 4.3 33.7 1.0
N L:VAL169 4.3 34.6 1.0
CB L:THR163 4.4 36.5 1.0
O L:ASP194 4.4 46.9 1.0
CA L:VAL169 4.5 34.7 1.0
NH2 V:ARG19 4.5 41.6 1.0
N L:GLY170 4.6 34.9 1.0
N L:HIS166 4.6 34.6 1.0
N L:GLU164 4.6 36.7 1.0
O L:ALA162 4.6 36.9 1.0
CA L:HIS166 4.7 34.1 1.0
CA L:GLY170 4.7 35.0 1.0
OD1 L:ASP194 4.7 47.2 1.0
CB L:VAL169 4.9 34.8 1.0
N L:GLN168 4.9 33.9 1.0
N L:THR163 5.0 36.5 1.0

Magnesium binding site 10 out of 10 in 3mg8

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Magnesium binding site 10 out of 10 in the Structure of Yeast 20S Open-Gate Proteasome with Compound 16


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Structure of Yeast 20S Open-Gate Proteasome with Compound 16 within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg188

b:36.7
occ:1.00
 O N:SER169 2.4 28.1 1.0
O N:ILE163 2.4 29.0 1.0
O N:ASP166 2.6 29.0 1.0
C N:SER169 3.4 28.2 1.0
C N:ILE163 3.4 29.3 1.0
C N:ASP166 3.6 28.7 1.0
CD1 1:LEU26 3.6 30.6 1.0
CG2 N:ILE163 3.7 27.2 1.0
NH1 N:ARG19 3.7 29.3 1.0
CA N:ILE163 4.0 29.0 1.0
CA N:GLY167 4.2 28.5 1.0
N N:GLY170 4.3 28.1 1.0
CA N:GLY170 4.3 28.3 1.0
N N:SER169 4.3 27.9 1.0
CA N:SER169 4.3 27.9 1.0
N N:GLY167 4.3 28.6 1.0
CZ N:ARG19 4.4 28.5 1.0
CB N:ILE163 4.4 28.8 1.0
C N:GLY167 4.4 28.6 1.0
O N:GLY167 4.5 28.7 1.0
N N:LYS164 4.6 29.8 1.0
CB N:SER169 4.6 27.6 1.0
N N:ASP166 4.6 28.9 1.0
CA N:ASP166 4.7 28.8 1.0
NH2 N:ARG19 4.8 26.6 1.0
C N:LYS164 4.9 30.1 1.0
CG 1:LEU26 4.9 31.8 1.0
CA N:LYS164 5.0 30.2 1.0
O N:LYS164 5.0 30.4 1.0

Reference:

C.Blackburn, K.M.Gigstad, P.Hales, K.Garcia, M.Jones, F.J.Bruzzese, C.Barrett, J.X.Liu, T.A.Soucy, D.S.Sappal, N.Bump, E.J.Olhava, P.Fleming, L.R.Dick, C.Tsu, M.D.Sintchak, J.L.Blank. Characterization of A New Series of Non-Covalent Proteasome Inhibitors with Exquisite Potency and Selectivity For the 20S BETA5-Subunit. Biochem.J. V. 430 461 2010.
ISSN: ISSN 0264-6021
PubMed: 20632995
DOI: 10.1042/BJ20100383
Page generated: Wed Aug 14 19:17:01 2024

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