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Magnesium in PDB 3sdk: Structure of Yeast 20S Open-Gate Proteasome with Compound 34

Enzymatic activity of Structure of Yeast 20S Open-Gate Proteasome with Compound 34

All present enzymatic activity of Structure of Yeast 20S Open-Gate Proteasome with Compound 34:
3.4.25.1;

Protein crystallography data

The structure of Structure of Yeast 20S Open-Gate Proteasome with Compound 34, PDB code: 3sdk 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 / 2.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 136.121, 299.404, 146.236, 90.00, 112.92, 90.00
R / Rfree (%) 22.3 / 25.9

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of Yeast 20S Open-Gate Proteasome with Compound 34 (pdb code 3sdk). 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 34, PDB code: 3sdk:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 10 in 3sdk

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Magnesium binding site 1 out of 10 in the Structure of Yeast 20S Open-Gate Proteasome with Compound 34


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 34 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg301

b:62.0
occ:1.00
 O F:ALA164 2.7 47.8 1.0
NZ F:LYS173 3.5 62.6 1.0
CE F:LYS173 3.7 62.0 1.0
CE F:MET150 3.7 42.2 1.0
CD F:ARG169 3.7 54.6 1.0
CA F:THR165 3.7 49.2 1.0
C F:ALA164 3.8 47.7 1.0
CG F:ARG169 3.8 54.8 1.0
CB F:THR165 3.9 49.3 1.0
OG1 F:THR165 3.9 50.5 1.0
SD F:MET150 4.1 43.1 1.0
N F:THR165 4.2 48.5 1.0
CB F:ARG169 4.4 54.0 1.0
OE2 F:GLU152 4.8 49.5 1.0
NE F:ARG169 4.9 54.5 1.0
C F:THR165 4.9 49.7 1.0

Magnesium binding site 2 out of 10 in 3sdk

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Magnesium binding site 2 out of 10 in the Structure of Yeast 20S Open-Gate Proteasome with Compound 34


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 34 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg302

b:0.1
occ:1.00
 OG F:SER13 2.4 63.6 1.0
O G:ALA127 3.0 45.9 1.0
CB F:ASN127 3.3 49.8 1.0
ND2 F:ASN127 3.3 54.3 1.0
CB F:SER13 3.4 63.3 1.0
O G:TYR128 3.7 46.5 1.0
CG F:ASN127 3.7 52.3 1.0
C G:TYR128 3.7 46.5 1.0
CA G:TYR128 3.7 46.7 1.0
N F:ASN127 3.8 47.9 1.0
CG2 G:ILE12 4.0 54.8 1.0
C G:ALA127 4.0 45.5 1.0
CA F:ASN127 4.1 49.1 1.0
CE2 A:TYR8 4.2 76.7 1.0
N G:TYR128 4.4 46.0 1.0
N G:MET129 4.5 46.2 1.0
O F:SER13 4.5 62.6 1.0
OH A:TYR8 4.7 77.4 1.0
CA F:SER13 4.7 63.1 1.0
C F:TYR126 4.8 47.0 1.0
OD1 F:ASN127 4.9 55.0 1.0
CB G:TYR128 4.9 47.2 1.0
C G:MET129 4.9 44.4 1.0
CZ A:TYR8 4.9 77.0 1.0
C F:SER13 4.9 62.0 1.0

Magnesium binding site 3 out of 10 in 3sdk

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Magnesium binding site 3 out of 10 in the Structure of Yeast 20S Open-Gate Proteasome with Compound 34


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 34 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:59.9
occ:1.00
 O G:MET129 2.2 44.1 1.0
OG1 G:THR13 2.3 51.5 1.0
O G:ARG126 2.4 44.1 1.0
O G:TYR123 2.5 38.6 1.0
C G:MET129 3.4 44.4 1.0
CB G:THR13 3.5 51.0 1.0
C G:ARG126 3.6 44.1 1.0
CG2 G:THR13 3.6 50.7 1.0
O G:ALA127 3.7 45.9 1.0
C G:TYR123 3.7 38.7 1.0
C G:ALA127 4.0 45.5 1.0
CA G:ALA127 4.1 45.0 1.0
N G:THR13 4.2 52.3 1.0
N G:MET129 4.2 46.2 1.0
N G:ALA127 4.3 44.4 1.0
CA G:MET129 4.3 45.9 1.0
N G:ARG130 4.3 42.6 1.0
CA G:ARG130 4.4 41.1 1.0
CA G:TYR123 4.5 38.4 1.0
CA G:THR13 4.5 50.9 1.0
CD G:PRO131 4.5 39.3 1.0
N G:ARG126 4.6 43.0 1.0
CB G:MET129 4.7 46.8 1.0
N G:THR124 4.7 39.2 1.0
CA G:ARG126 4.7 44.3 1.0
N G:TYR128 4.8 46.0 1.0
C G:THR124 4.9 40.4 1.0
C G:ARG130 4.9 40.5 1.0
CA G:THR124 4.9 39.8 1.0
CB G:TYR123 5.0 38.5 1.0

Magnesium binding site 4 out of 10 in 3sdk

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Magnesium binding site 4 out of 10 in the Structure of Yeast 20S Open-Gate Proteasome with Compound 34


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 34 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg301

b:66.6
occ:1.00
 O H:ILE163 2.3 40.3 1.0
O H:ASP166 2.3 42.9 1.0
O H:SER169 2.4 43.1 1.0
OXT Z:ASP194 2.6 51.8 1.0
C H:ILE163 3.2 40.2 1.0
C H:ASP166 3.3 42.5 1.0
C Z:ASP194 3.4 51.9 1.0
C H:SER169 3.5 42.9 1.0
O H:GLY162 3.7 40.3 1.0
CA Z:ASP194 3.9 51.8 1.0
CA H:ILE163 3.9 40.1 1.0
N H:ASP166 4.0 41.7 1.0
CA H:LEU167 4.1 42.5 1.0
N H:LEU167 4.1 42.5 1.0
N H:TRP164 4.1 40.2 1.0
CA H:ASP166 4.2 42.4 1.0
N H:SER169 4.2 42.8 1.0
CB Z:ASP194 4.2 52.1 1.0
NH1 H:ARG19 4.3 47.9 1.0
O Z:ASP194 4.3 51.9 1.0
N H:GLY170 4.3 43.2 1.0
CA H:SER169 4.3 42.7 1.0
C H:TRP164 4.3 40.1 1.0
CA H:GLY170 4.4 43.5 1.0
C H:LEU167 4.4 43.0 1.0
CA H:TRP164 4.5 40.0 1.0
N H:ASN165 4.5 40.2 1.0
C H:GLY162 4.6 40.1 1.0
O H:LEU167 4.6 43.3 1.0
CZ H:ARG19 4.6 48.2 1.0
CB H:SER169 4.6 42.3 1.0
NH2 H:ARG19 4.7 47.8 1.0
O H:TRP164 4.7 40.2 1.0
N H:ILE163 4.8 40.0 1.0
C H:ASN165 4.8 40.9 1.0
CB H:ASP166 5.0 42.6 1.0
N H:GLY168 5.0 43.1 1.0
CG2 H:ILE163 5.0 40.0 1.0

Magnesium binding site 5 out of 10 in 3sdk

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Magnesium binding site 5 out of 10 in the Structure of Yeast 20S Open-Gate Proteasome with Compound 34


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 34 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg201

b:58.3
occ:1.00
 O I:GLY128 2.6 38.8 1.0
OG I:SER131 2.6 41.4 1.0
C I:GLY128 3.6 38.6 1.0
CB I:SER131 3.7 40.5 1.0
CA I:THR129 4.1 39.3 1.0
N I:SER131 4.2 40.4 1.0
N I:THR129 4.3 39.1 1.0
C I:THR129 4.3 39.7 1.0
O I:THR129 4.5 40.2 1.0
CA I:SER131 4.6 40.6 1.0
CA I:GLY128 4.7 38.2 1.0
N I:GLY128 4.7 37.6 1.0
N I:ALA130 4.8 39.8 1.0

Magnesium binding site 6 out of 10 in 3sdk

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Magnesium binding site 6 out of 10 in the Structure of Yeast 20S Open-Gate Proteasome with Compound 34


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 34 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg202

b:57.7
occ:1.00
 O I:ALA163 2.5 44.4 1.0
O I:ASP166 2.6 43.1 1.0
O I:SER169 2.8 44.3 1.0
C I:ALA163 3.4 44.4 1.0
C I:SER169 3.7 44.2 1.0
C I:ASP166 3.8 43.4 1.0
CA I:ASP164 3.8 45.0 1.0
N I:ASP164 4.0 44.8 1.0
OXT I:ASP194 4.2 49.6 1.0
OD2 I:ASP164 4.2 47.3 1.0
C I:ASP164 4.3 45.0 1.0
CA I:GLY170 4.3 43.9 1.0
N I:GLY170 4.3 44.2 1.0
N I:ASP166 4.4 44.1 1.0
CA I:ALA163 4.5 43.9 1.0
O I:ASP164 4.5 45.4 1.0
N I:SER169 4.5 43.9 1.0
CA I:SER169 4.6 44.2 1.0
CA I:ASP166 4.6 43.8 1.0
CB I:ALA163 4.7 43.7 1.0
N I:ALA167 4.7 43.1 1.0
C I:ALA167 4.8 43.0 1.0
O I:ALA167 4.8 43.2 1.0
CA I:ALA167 4.8 42.9 1.0
CB I:SER169 4.9 44.4 1.0
N I:ARG165 4.9 44.6 1.0
CB I:ASP164 5.0 44.9 1.0

Magnesium binding site 7 out of 10 in 3sdk

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Magnesium binding site 7 out of 10 in the Structure of Yeast 20S Open-Gate Proteasome with Compound 34


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 34 within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg301

b:53.1
occ:1.00
 O K:ASP166 2.3 41.2 1.0
O W:ASP194 2.4 48.7 1.0
O K:ALA163 2.4 40.9 1.0
O K:SER169 2.5 40.4 1.0
C W:ASP194 3.3 48.3 1.0
C K:ASP166 3.3 40.6 1.0
C K:ALA163 3.4 40.5 1.0
C K:SER169 3.7 40.3 1.0
NH1 K:ARG19 3.7 45.0 1.0
CA K:ALA167 3.8 40.2 1.0
CA W:ASP194 3.9 47.9 1.0
C K:ALA167 3.9 40.3 1.0
N K:ALA167 4.0 40.4 1.0
O K:ALA167 4.0 39.8 1.0
O K:HIS164 4.0 40.6 1.0
CA K:ALA163 4.1 40.4 1.0
CB W:ASP194 4.1 47.7 1.0
OXT W:ASP194 4.2 48.5 1.0
N K:SER169 4.2 40.3 1.0
N K:ASP166 4.3 40.5 1.0
C K:HIS164 4.3 40.4 1.0
CA K:ASP166 4.4 40.7 1.0
O K:ALA162 4.4 40.3 1.0
N K:HIS164 4.4 40.2 1.0
CA K:SER169 4.4 40.1 1.0
CZ K:ARG19 4.6 44.6 1.0
N K:TYR168 4.6 40.3 1.0
CA K:HIS164 4.6 40.3 1.0
N K:GLY170 4.7 40.7 1.0
CB K:SER169 4.8 39.8 1.0
CA K:GLY170 4.8 40.8 1.0
C K:ARG165 4.9 40.3 1.0
NH2 K:ARG19 5.0 45.7 1.0
N K:ARG165 5.0 40.1 1.0

Magnesium binding site 8 out of 10 in 3sdk

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Magnesium binding site 8 out of 10 in the Structure of Yeast 20S Open-Gate Proteasome with Compound 34


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 34 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg201

b:56.7
occ:1.00
 OG L:SER75 2.4 38.9 1.0
OE2 D:GLU105 2.6 37.3 1.0
OG L:SER78 2.9 37.2 1.0
CB L:SER75 3.4 39.5 1.0
CD D:GLU105 3.7 38.0 1.0
OE2 L:GLU106 3.8 57.6 1.0
OD1 L:ASN77 3.8 41.6 1.0
CB L:SER78 3.9 37.7 1.0
CB D:GLU105 3.9 39.8 1.0
N L:SER75 4.3 40.8 1.0
CG D:GLU105 4.4 38.9 1.0
CA L:SER75 4.4 40.1 1.0
ND2 L:ASN77 4.5 40.2 1.0
CG L:ASN77 4.5 40.8 1.0
CD L:GLU106 4.6 57.1 1.0
OE1 L:GLU106 4.7 57.7 1.0
OE1 D:GLU105 4.7 39.2 1.0
NZ L:LYS72 4.7 37.6 1.0
OH L:TYR66 4.9 33.6 1.0
N L:SER78 4.9 38.2 1.0
CE L:LYS72 4.9 38.8 1.0
CA L:SER78 5.0 37.6 1.0

Magnesium binding site 9 out of 10 in 3sdk

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Magnesium binding site 9 out of 10 in the Structure of Yeast 20S Open-Gate Proteasome with Compound 34


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 34 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg202

b:54.2
occ:1.00
 O L:HIS166 2.4 43.0 1.0
O L:VAL169 2.5 45.0 1.0
O L:THR163 2.6 47.5 1.0
C L:HIS166 3.5 43.0 1.0
C L:THR163 3.6 47.3 1.0
C L:VAL169 3.7 44.9 1.0
CA L:ILE167 3.8 42.8 1.0
CG2 L:THR163 3.8 46.6 1.0
CA L:THR163 3.9 47.3 1.0
O L:ILE167 3.9 43.4 1.0
NH2 L:ARG19 3.9 47.0 1.0
C L:ILE167 4.0 43.2 1.0
N L:ILE167 4.1 42.8 1.0
O L:ASP194 4.2 60.0 1.0
N L:VAL169 4.3 44.4 1.0
NH2 V:ARG19 4.5 51.9 1.0
CB L:THR163 4.5 47.2 1.0
CA L:VAL169 4.5 44.7 1.0
OD1 L:ASP194 4.7 62.6 1.0
N L:GLY170 4.7 45.1 1.0
N L:HIS166 4.7 43.6 1.0
CA L:HIS166 4.7 43.0 1.0
N L:GLN168 4.7 43.6 1.0
CA L:GLY170 4.8 45.4 1.0
N L:GLU164 4.8 47.0 1.0
O L:ALA162 4.8 47.8 1.0
CB L:VAL169 4.9 44.7 1.0

Magnesium binding site 10 out of 10 in 3sdk

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Magnesium binding site 10 out of 10 in the Structure of Yeast 20S Open-Gate Proteasome with Compound 34


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 34 within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg201

b:47.1
occ:1.00
 O N:ILE163 2.3 38.7 1.0
O N:SER169 2.5 37.4 1.0
O N:ASP166 2.6 39.9 1.0
C N:ILE163 3.5 38.9 1.0
C N:SER169 3.5 37.0 1.0
C N:ASP166 3.7 39.7 1.0
CD1 1:LEU26 3.7 39.6 1.0
CG2 N:ILE163 3.8 37.3 1.0
NH1 N:ARG19 3.9 37.3 1.0
CA N:GLY167 4.0 38.9 1.0
CA N:ILE163 4.1 38.5 1.0
N N:GLY167 4.3 39.2 1.0
CA N:GLY170 4.3 36.6 1.0
N N:GLY170 4.3 36.8 1.0
C N:GLY167 4.4 39.0 1.0
CA N:SER169 4.4 37.0 1.0
O N:GLY167 4.4 39.4 1.0
CZ N:ARG19 4.4 37.1 1.0
N N:SER169 4.4 37.5 1.0
CB N:ILE163 4.5 38.2 1.0
N N:LYS164 4.6 39.5 1.0
CB N:SER169 4.6 36.7 1.0
NH2 N:ARG19 4.7 36.3 1.0
N N:ASP166 4.7 40.1 1.0
CA N:ASP166 4.8 40.1 1.0
CG 1:LEU26 4.8 40.6 1.0
C N:LYS164 4.9 40.2 1.0
O N:LYS164 4.9 40.4 1.0
CA N:LYS164 4.9 40.0 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 10:51:39 2024

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