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

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

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

Protein crystallography data

The structure of Structure of Yeast 20S Open-Gate Proteasome with Compound 20, PDB code: 3sdi 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) 30.00 / 2.65
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 136.600, 299.450, 145.483, 90.00, 113.17, 90.00
R / Rfree (%) 21.9 / 25.3

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20;

Binding sites:

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

Magnesium binding site 1 out of 20 in 3sdi

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


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

b:74.5
occ:1.00
 NZ F:LYS173 3.3 59.6 1.0
CE F:LYS173 4.8 58.3 1.0

Magnesium binding site 2 out of 20 in 3sdi

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


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

b:0.9
occ:1.00
 OG F:SER13 2.5 78.3 1.0
OD1 F:ASN127 2.6 57.1 1.0
O G:TYR128 3.0 44.1 1.0
CG F:ASN127 3.3 52.8 1.0
O G:ALA127 3.4 43.2 1.0
C G:TYR128 3.4 44.1 1.0
N F:ASN127 3.5 47.8 1.0
CB F:SER13 3.6 78.0 1.0
CB F:ASN127 3.6 50.0 1.0
CA G:TYR128 3.6 44.7 1.0
CA F:ASN127 4.1 48.9 1.0
N G:MET129 4.3 43.5 1.0
C G:ALA127 4.3 43.0 1.0
C F:TYR126 4.3 46.4 1.0
CA F:TYR126 4.4 44.7 1.0
ND2 F:ASN127 4.4 54.6 1.0
N G:TYR128 4.5 43.9 1.0
O F:LEU125 4.5 41.9 1.0
CE2 A:TYR8 4.6 66.3 1.0
CB G:TYR128 4.6 45.6 1.0
CG2 G:ILE12 4.7 48.2 1.0
C G:MET129 4.7 41.6 1.0
CA F:SER13 4.9 77.6 1.0
N G:ARG130 4.9 39.5 1.0
CA G:MET129 4.9 43.2 1.0

Magnesium binding site 3 out of 20 in 3sdi

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


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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 20 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg9001

b:45.4
occ:1.00
 O G:MET129 2.1 41.4 1.0
O G:TYR123 2.3 34.9 1.0
O G:ARG126 2.3 41.3 1.0
OG1 G:THR13 2.5 45.2 1.0
C G:MET129 3.3 41.6 1.0
C G:TYR123 3.4 35.0 1.0
C G:ARG126 3.5 41.3 1.0
CG2 G:THR13 3.6 44.1 1.0
CB G:THR13 3.6 45.1 1.0
O G:ALA127 4.0 43.2 1.0
N G:MET129 4.1 43.5 1.0
C G:ALA127 4.1 43.0 1.0
CA G:MET129 4.1 43.2 1.0
CA G:TYR123 4.2 34.9 1.0
CA G:ALA127 4.2 42.5 1.0
N G:ALA127 4.3 41.7 1.0
N G:ARG130 4.3 39.5 1.0
CB G:MET129 4.4 44.0 1.0
CA G:ARG130 4.4 37.5 1.0
N G:ARG126 4.4 40.3 1.0
N G:THR124 4.5 35.7 1.0
CD G:PRO131 4.5 35.5 1.0
CA G:ARG126 4.5 41.4 1.0
N G:THR13 4.5 46.2 1.0
CA G:THR13 4.7 45.0 1.0
C G:THR124 4.7 36.8 1.0
N G:TYR128 4.8 43.9 1.0
CB G:TYR123 4.8 35.0 1.0
CA G:THR124 4.8 36.1 1.0
N G:GLN125 4.8 37.4 1.0
C G:ARG130 4.8 36.7 1.0
N G:PRO131 4.9 35.6 1.0

Magnesium binding site 4 out of 20 in 3sdi

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


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

b:47.6
occ:1.00
 O H:ILE163 2.0 33.9 1.0
O H:SER169 2.2 36.0 1.0
O H:ASP166 2.4 35.3 1.0
OXT Z:ASP194 2.4 48.0 1.0
C H:ILE163 3.1 33.9 1.0
C H:SER169 3.3 35.9 1.0
C Z:ASP194 3.4 48.1 1.0
C H:ASP166 3.5 35.1 1.0
CA Z:ASP194 3.7 47.6 1.0
O H:GLY162 3.7 33.8 1.0
CA H:ILE163 3.8 33.9 1.0
CB Z:ASP194 3.9 47.7 1.0
N H:GLY170 4.1 36.6 1.0
CA H:GLY170 4.1 37.3 1.0
NH1 H:ARG19 4.1 44.0 1.0
N H:TRP164 4.2 34.2 1.0
N H:SER169 4.2 34.9 1.0
CA H:SER169 4.2 35.3 1.0
N H:ASP166 4.2 35.0 1.0
N H:LEU167 4.3 35.0 1.0
CA H:LEU167 4.3 35.1 1.0
C H:TRP164 4.4 34.3 1.0
CA H:ASP166 4.4 35.2 1.0
O Z:ASP194 4.5 48.6 1.0
CA H:TRP164 4.5 33.9 1.0
C H:LEU167 4.5 35.1 1.0
CZ H:ARG19 4.5 44.2 1.0
O H:TRP164 4.5 35.0 1.0
CB H:SER169 4.6 34.6 1.0
C H:GLY162 4.6 33.8 1.0
NH2 H:ARG19 4.6 44.7 1.0
CG2 H:ILE163 4.7 33.6 1.0
N H:ILE163 4.7 33.7 1.0
N H:ASN165 4.7 34.3 1.0
O H:LEU167 4.7 35.2 1.0
CB H:ILE163 4.8 33.9 1.0
CG Z:ASP194 4.9 48.3 1.0

Magnesium binding site 5 out of 20 in 3sdi

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


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

b:46.2
occ:1.00
 OG I:SER131 2.6 37.0 1.0
O I:GLY128 3.2 32.6 1.0
CB I:SER131 3.7 35.6 1.0
C I:GLY128 4.3 32.5 1.0
N I:GLY128 4.8 31.3 1.0
CA I:SER131 4.9 35.9 1.0
N I:SER131 4.9 35.3 1.0

Magnesium binding site 6 out of 20 in 3sdi

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


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

b:50.3
occ:1.00
 O I:ASP166 2.5 37.6 1.0
O I:ALA163 2.6 37.0 1.0
O I:SER169 2.8 39.4 1.0
C I:ALA163 3.5 36.8 1.0
C I:ASP166 3.7 37.7 1.0
C I:SER169 3.7 39.0 1.0
CA I:ASP164 3.8 37.9 1.0
N I:ASP164 4.0 37.4 1.0
C I:ASP164 4.1 37.8 1.0
O I:ASP164 4.2 38.1 1.0
N I:ASP166 4.3 37.8 1.0
OD2 I:ASP164 4.3 41.6 1.0
OXT I:ASP194 4.4 42.9 1.0
N I:SER169 4.5 37.9 1.0
CA I:ASP166 4.5 38.1 1.0
N I:GLY170 4.5 39.0 1.0
CA I:ALA163 4.5 36.3 1.0
CA I:SER169 4.5 38.8 1.0
CA I:GLY170 4.5 38.8 1.0
N I:ALA167 4.7 37.0 1.0
CB I:ALA163 4.7 35.8 1.0
CA I:ALA167 4.8 36.7 1.0
CB I:SER169 4.8 39.0 1.0
C I:ALA167 4.8 36.9 1.0
N I:ARG165 4.9 37.5 1.0
CB I:ASP166 4.9 38.9 1.0
O I:ALA167 4.9 37.1 1.0
O I:ASP194 4.9 42.8 1.0

Magnesium binding site 7 out of 20 in 3sdi

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


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

b:50.9
occ:1.00
 O K:ASP166 2.3 35.1 1.0
O K:ALA163 2.4 33.0 1.0
O W:ASP194 2.5 41.1 1.0
O K:SER169 2.7 34.4 1.0
C W:ASP194 3.3 41.1 1.0
C K:ASP166 3.4 34.9 1.0
C K:ALA163 3.5 32.6 1.0
CA W:ASP194 3.7 40.8 1.0
C K:SER169 3.7 34.1 1.0
NH1 K:ARG19 3.9 38.1 1.0
CA K:ALA167 3.9 34.4 1.0
O K:ALA167 3.9 34.2 1.0
CB W:ASP194 3.9 40.7 1.0
C K:ALA167 4.0 34.4 1.0
N K:ALA167 4.1 34.6 1.0
O K:HIS164 4.2 33.0 1.0
CA K:ALA163 4.2 32.4 1.0
N K:SER169 4.3 34.0 1.0
OXT W:ASP194 4.3 41.5 1.0
C K:HIS164 4.4 33.2 1.0
CZ K:ARG19 4.5 38.0 1.0
N K:HIS164 4.5 32.5 1.0
N K:ASP166 4.5 34.9 1.0
CA K:SER169 4.5 33.7 1.0
CA K:ASP166 4.5 34.9 1.0
O K:ALA162 4.7 32.8 1.0
N K:GLY170 4.7 34.6 1.0
CA K:HIS164 4.7 32.6 1.0
NH2 K:ARG19 4.7 39.7 1.0
N K:TYR168 4.7 34.4 1.0
CA K:GLY170 4.8 34.9 1.0
CB K:SER169 4.9 33.6 1.0
CG W:ASP194 4.9 42.3 1.0
C K:ARG165 4.9 34.5 1.0

Magnesium binding site 8 out of 20 in 3sdi

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


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

b:52.1
occ:1.00
 OE2 D:GLU105 2.4 29.9 1.0
OG L:SER75 2.7 35.1 1.0
OG L:SER78 2.9 31.4 1.0
CB L:SER78 3.5 32.3 1.0
CB L:SER75 3.5 34.4 1.0
CD D:GLU105 3.5 31.8 1.0
N L:SER75 3.5 35.8 1.0
OH L:TYR66 3.7 29.1 1.0
CA L:SER75 4.1 35.1 1.0
O L:LYS73 4.2 39.7 1.0
OE1 D:GLU105 4.2 32.6 1.0
NZ L:LYS72 4.3 31.0 1.0
CE L:LYS72 4.3 30.9 1.0
CB D:GLU105 4.5 34.9 1.0
CG D:GLU105 4.6 33.8 1.0
C L:LEU74 4.6 36.6 1.0
CA L:LEU74 4.7 37.1 1.0
OD1 L:ASN77 4.7 37.2 1.0
CZ L:TYR66 4.8 27.1 1.0
O L:SER75 4.9 34.8 1.0
CD1 L:LEU74 4.9 35.8 1.0
CA L:SER78 4.9 32.2 1.0
C L:SER75 4.9 35.3 1.0

Magnesium binding site 9 out of 20 in 3sdi

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


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

b:46.4
occ:1.00
 O L:VAL169 2.5 39.4 1.0
O L:THR163 2.5 41.8 1.0
O L:HIS166 2.7 36.3 1.0
C L:THR163 3.5 41.5 1.0
CG2 L:THR163 3.6 41.1 1.0
C L:VAL169 3.7 38.9 1.0
C L:HIS166 3.8 36.8 1.0
CA L:THR163 3.8 41.2 1.0
NH2 L:ARG19 3.9 39.7 1.0
CA L:ILE167 4.1 37.0 1.0
O L:ILE167 4.1 37.2 1.0
NH2 V:ARG19 4.1 46.6 1.0
C L:ILE167 4.3 37.3 1.0
OD1 L:ASP194 4.3 55.3 1.0
CB L:THR163 4.4 41.2 1.0
N L:ILE167 4.4 36.9 1.0
N L:VAL169 4.5 38.3 1.0
O L:ASP194 4.5 53.3 1.0
CA L:VAL169 4.6 38.6 1.0
N L:GLY170 4.6 39.3 1.0
CA L:GLY170 4.7 39.6 1.0
N L:GLU164 4.8 41.2 1.0
N L:HIS166 4.8 38.3 1.0
O L:ALA162 4.8 40.2 1.0
CZ V:ARG19 4.9 46.7 1.0
OXT L:ASP194 4.9 52.9 1.0
C L:ASP194 4.9 52.8 1.0
CA L:HIS166 4.9 37.2 1.0
NH1 V:ARG19 5.0 47.0 1.0

Magnesium binding site 10 out of 20 in 3sdi

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


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

b:41.6
occ:1.00
 O N:SER169 2.5 32.2 1.0
O N:ILE163 2.6 31.0 1.0
O N:ASP166 2.8 32.9 1.0
NH1 N:ARG19 3.3 33.4 1.0
CD1 1:LEU25 3.6 31.0 1.0
C N:SER169 3.7 32.0 1.0
C N:ILE163 3.8 31.4 1.0
C N:ASP166 3.9 32.4 1.0
CG2 N:ILE163 4.0 28.8 1.0
CZ N:ARG19 4.1 32.7 1.0
CA N:GLY167 4.1 32.2 1.0
CA N:GLY170 4.3 31.8 1.0
NH2 N:ARG19 4.4 30.4 1.0
CA N:ILE163 4.4 31.1 1.0
N N:GLY170 4.5 31.8 1.0
O N:GLY167 4.5 32.8 1.0
C N:GLY167 4.5 32.7 1.0
N N:GLY167 4.5 32.0 1.0
N N:SER169 4.7 32.0 1.0
CA N:SER169 4.7 31.6 1.0
CB N:ILE163 4.8 30.8 1.0
N N:LYS164 4.8 31.8 1.0
CG 1:LEU25 4.9 32.9 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 10:51:38 2024

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