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Magnesium in PDB 1g65: Crystal Structure of Epoxomicin:20S Proteasome Reveals A Molecular Basis For Selectivity of Alpha,Beta-Epoxyketone Proteasome Inhibitors

Enzymatic activity of Crystal Structure of Epoxomicin:20S Proteasome Reveals A Molecular Basis For Selectivity of Alpha,Beta-Epoxyketone Proteasome Inhibitors

All present enzymatic activity of Crystal Structure of Epoxomicin:20S Proteasome Reveals A Molecular Basis For Selectivity of Alpha,Beta-Epoxyketone Proteasome Inhibitors:
3.4.25.1;

Protein crystallography data

The structure of Crystal Structure of Epoxomicin:20S Proteasome Reveals A Molecular Basis For Selectivity of Alpha,Beta-Epoxyketone Proteasome Inhibitors, PDB code: 1g65 was solved by M.Groll, K.B.Kim, N.Kairies, R.Huber, C.Crews, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.25
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 135.200, 300.200, 144.020, 90.00, 112.98, 90.00
R / Rfree (%) 28.3 / 33.6

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Epoxomicin:20S Proteasome Reveals A Molecular Basis For Selectivity of Alpha,Beta-Epoxyketone Proteasome Inhibitors (pdb code 1g65). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 10 binding sites of Magnesium where determined in the Crystal Structure of Epoxomicin:20S Proteasome Reveals A Molecular Basis For Selectivity of Alpha,Beta-Epoxyketone Proteasome Inhibitors, PDB code: 1g65:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 10 in 1g65

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Magnesium binding site 1 out of 10 in the Crystal Structure of Epoxomicin:20S Proteasome Reveals A Molecular Basis For Selectivity of Alpha,Beta-Epoxyketone Proteasome Inhibitors


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Epoxomicin:20S Proteasome Reveals A Molecular Basis For Selectivity of Alpha,Beta-Epoxyketone Proteasome Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg301

b:49.4
occ:1.00
 OE2 D:GLU105 2.1 22.4 1.0
O L:HOH311 2.2 31.5 1.0
O L:HOH307 2.2 43.1 1.0
O L:HOH312 2.3 39.5 1.0
OG L:SER75 2.7 30.5 1.0
OG L:SER78 2.8 28.2 1.0
CD D:GLU105 3.2 20.9 1.0
CB L:SER78 3.7 31.1 1.0
CB L:SER75 3.7 33.6 1.0
OH L:TYR66 3.8 19.0 1.0
OE1 D:GLU105 3.9 20.2 1.0
CB D:GLU105 3.9 26.9 1.0
N L:SER75 4.1 37.4 1.0
CG D:GLU105 4.1 20.8 1.0
NZ L:LYS72 4.4 43.0 1.0
CE L:LYS72 4.5 40.5 1.0
OE2 L:GLU106 4.6 70.4 1.0
CA L:SER75 4.6 33.6 1.0
OD1 L:ASN77 4.6 30.5 1.0
O L:LYS73 4.6 38.3 1.0
O L:HOH385 4.8 61.8 1.0
ND2 L:ASN77 4.9 30.2 1.0
O L:HOH426 4.9 77.9 1.0
O D:TYR103 4.9 21.1 1.0
CZ L:TYR66 5.0 17.4 1.0

Magnesium binding site 2 out of 10 in 1g65

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Magnesium binding site 2 out of 10 in the Crystal Structure of Epoxomicin:20S Proteasome Reveals A Molecular Basis For Selectivity of Alpha,Beta-Epoxyketone Proteasome Inhibitors


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Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Epoxomicin:20S Proteasome Reveals A Molecular Basis For Selectivity of Alpha,Beta-Epoxyketone Proteasome Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg301

b:53.4
occ:1.00
 OE2 F:GLU152 3.3 54.6 1.0
CD F:GLU152 4.2 50.6 1.0
O F:HOH445 4.3 50.8 1.0
CE F:MET150 4.4 49.4 1.0
NZ F:LYS173 4.5 74.2 1.0
O F:HOH427 4.6 38.9 1.0
OH F:TYR160 4.8 49.3 1.0
CG F:GLU152 4.9 45.8 1.0
O F:HOH468 4.9 33.3 1.0
OE1 F:GLU152 5.0 49.0 1.0
O F:HOH491 5.0 99.8 1.0

Magnesium binding site 3 out of 10 in 1g65

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Magnesium binding site 3 out of 10 in the Crystal Structure of Epoxomicin:20S Proteasome Reveals A Molecular Basis For Selectivity of Alpha,Beta-Epoxyketone Proteasome Inhibitors


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Epoxomicin:20S Proteasome Reveals A Molecular Basis For Selectivity of Alpha,Beta-Epoxyketone Proteasome Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg302

b:41.0
occ:1.00
 O F:HOH401 1.6 48.0 1.0
O F:HOH465 2.2 8.0 1.0
OD1 F:ASN127 2.8 38.2 1.0
O G:HOH456 3.0 53.1 1.0
O G:ALA127 3.1 40.5 1.0
OG F:SER13 3.3 41.8 1.0
OH A:TYR8 3.3 51.0 1.0
O G:HOH440 3.5 41.7 1.0
CG F:ASN127 3.8 37.5 1.0
O G:TYR128 4.0 40.8 1.0
CA G:TYR128 4.0 42.0 1.0
CZ A:TYR8 4.0 50.3 1.0
CE2 A:TYR8 4.1 51.9 1.0
C G:ALA127 4.1 37.0 1.0
C G:TYR128 4.1 39.4 1.0
CB F:ASN127 4.2 36.7 1.0
CG2 G:ILE12 4.3 29.0 1.0
N F:ASN127 4.5 31.6 1.0
N G:TYR128 4.5 39.2 1.0
CB F:SER13 4.5 34.6 1.0
O G:HOH407 4.7 26.2 1.0
ND2 F:ASN127 5.0 38.2 1.0
N G:MET129 5.0 38.1 1.0

Magnesium binding site 4 out of 10 in 1g65

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Magnesium binding site 4 out of 10 in the Crystal Structure of Epoxomicin:20S Proteasome Reveals A Molecular Basis For Selectivity of Alpha,Beta-Epoxyketone Proteasome Inhibitors


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Epoxomicin:20S Proteasome Reveals A Molecular Basis For Selectivity of Alpha,Beta-Epoxyketone Proteasome Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:24.0
occ:1.00
 O G:HOH407 2.1 26.2 1.0
O G:MET129 2.2 34.2 1.0
O G:ARG126 2.2 37.0 1.0
O G:TYR123 2.2 24.9 1.0
OG1 G:THR13 2.3 34.3 1.0
CG2 G:THR13 2.9 30.0 1.0
CB G:THR13 3.2 30.4 1.0
C G:ARG126 3.3 34.3 1.0
C G:MET129 3.4 35.4 1.0
C G:TYR123 3.4 24.8 1.0
O G:ALA127 3.6 40.5 1.0
C G:ALA127 3.8 37.0 1.0
CA G:ALA127 3.9 35.1 1.0
N G:ALA127 4.0 35.4 1.0
N G:MET129 4.0 38.1 1.0
N G:THR13 4.1 31.3 1.0
CA G:MET129 4.1 38.1 1.0
CA G:TYR123 4.1 26.4 1.0
N G:ARG126 4.2 30.5 1.0
CA G:THR13 4.3 30.4 1.0
CA G:ARG126 4.3 33.8 1.0
N G:ARG130 4.4 29.8 1.0
N G:THR124 4.4 24.8 1.0
O G:HOH440 4.5 41.7 1.0
CB G:MET129 4.5 43.3 1.0
O G:HOH465 4.6 37.7 1.0
CA G:ARG130 4.6 26.9 1.0
N G:TYR128 4.7 39.2 1.0
C G:THR124 4.7 29.1 1.0
CD G:PRO131 4.7 24.3 1.0
CB G:TYR123 4.7 29.8 1.0
CA G:THR124 4.8 29.0 1.0
N G:GLN125 4.8 27.5 1.0
C G:TYR128 4.9 39.4 1.0
C G:GLN125 5.0 26.1 1.0

Magnesium binding site 5 out of 10 in 1g65

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Magnesium binding site 5 out of 10 in the Crystal Structure of Epoxomicin:20S Proteasome Reveals A Molecular Basis For Selectivity of Alpha,Beta-Epoxyketone Proteasome Inhibitors


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Epoxomicin:20S Proteasome Reveals A Molecular Basis For Selectivity of Alpha,Beta-Epoxyketone Proteasome Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg301

b:34.6
occ:1.00
 OXT Z:ASP194 1.9 45.2 1.0
O H:ASP166 2.1 36.9 1.0
O H:ILE163 2.3 34.0 1.0
O H:HOH488 2.5 33.7 1.0
O H:SER169 2.6 29.7 1.0
C Z:ASP194 2.8 46.0 1.0
C H:ASP166 3.0 33.4 1.0
C H:ILE163 3.3 32.9 1.0
C H:SER169 3.5 29.4 1.0
CA Z:ASP194 3.6 44.0 1.0
O Z:ASP194 3.6 44.6 1.0
NH1 H:ARG19 3.7 29.3 1.0
N H:LEU167 3.7 34.0 1.0
CA H:LEU167 3.7 33.2 1.0
O H:GLY162 3.8 28.8 1.0
N H:ASP166 4.0 35.4 1.0
CA H:ILE163 4.1 29.6 1.0
CA H:ASP166 4.1 35.9 1.0
CB Z:ASP194 4.1 44.2 1.0
C H:LEU167 4.1 32.6 1.0
N H:SER169 4.2 31.9 1.0
CZ H:ARG19 4.3 31.9 1.0
N H:TRP164 4.3 33.6 1.0
CA H:SER169 4.3 28.6 1.0
O H:TRP164 4.3 33.7 1.0
N H:GLY170 4.4 29.9 1.0
O Z:HOH207 4.4 47.6 1.0
C H:TRP164 4.4 33.2 1.0
O H:LEU167 4.4 34.8 1.0
CA H:GLY170 4.4 33.6 1.0
NH2 H:ARG19 4.5 34.3 1.0
CA H:TRP164 4.6 32.7 1.0
CB H:SER169 4.6 25.5 1.0
C H:GLY162 4.8 26.2 1.0
N H:GLY168 4.8 30.3 1.0
N Z:ASP194 4.9 41.4 1.0
CB H:ASP166 4.9 34.5 1.0
CG2 H:ILE163 4.9 27.2 1.0
N H:ILE163 5.0 27.4 1.0
N H:ASN165 5.0 33.8 1.0

Magnesium binding site 6 out of 10 in 1g65

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Magnesium binding site 6 out of 10 in the Crystal Structure of Epoxomicin:20S Proteasome Reveals A Molecular Basis For Selectivity of Alpha,Beta-Epoxyketone Proteasome Inhibitors


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of Epoxomicin:20S Proteasome Reveals A Molecular Basis For Selectivity of Alpha,Beta-Epoxyketone Proteasome Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg201

b:45.7
occ:1.00
 OG I:SER131 2.2 30.2 1.0
O I:HOH327 2.5 32.1 1.0
O I:HOH364 2.5 44.6 1.0
O I:HOH368 2.6 49.4 1.0
O I:GLY128 2.8 29.0 1.0
CB I:SER131 3.3 24.2 1.0
O I:HOH328 3.4 41.4 1.0
C I:GLY128 4.0 30.1 1.0
O I:HOH392 4.2 43.6 1.0
N I:SER131 4.5 25.3 1.0
CA I:SER131 4.5 24.0 1.0
O I:HOH322 4.5 42.6 1.0
O I:HOH381 4.6 47.1 1.0
N I:GLY128 4.6 24.1 1.0
O H:HOH464 4.7 84.3 1.0
O I:HOH325 4.8 61.8 1.0
CA I:GLY128 4.9 29.8 1.0
O I:THR129 4.9 36.0 1.0
N I:THR129 4.9 29.4 1.0
CA I:THR129 4.9 29.9 1.0

Magnesium binding site 7 out of 10 in 1g65

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Magnesium binding site 7 out of 10 in the Crystal Structure of Epoxomicin:20S Proteasome Reveals A Molecular Basis For Selectivity of Alpha,Beta-Epoxyketone Proteasome Inhibitors


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of Epoxomicin:20S Proteasome Reveals A Molecular Basis For Selectivity of Alpha,Beta-Epoxyketone Proteasome Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg202

b:29.2
occ:1.00
 O I:ASP166 1.7 28.7 1.0
O I:ALA163 2.1 31.1 1.0
O I:HOH309 2.3 40.0 1.0
O I:HOH307 2.3 44.9 1.0
O I:SER169 2.8 32.6 1.0
C I:ASP166 2.9 28.6 1.0
C I:ALA163 3.2 33.3 1.0
N I:ASP166 3.6 30.2 1.0
C I:SER169 3.7 29.0 1.0
CA I:ASP166 3.7 28.5 1.0
N I:ALA167 3.9 27.7 1.0
CA I:ASP164 3.9 32.7 1.0
N I:ASP164 4.0 34.0 1.0
CA I:ALA167 4.1 26.1 1.0
C I:ASP164 4.1 31.8 1.0
CB I:ASP166 4.2 32.1 1.0
N I:SER169 4.2 28.1 1.0
C I:ALA167 4.2 29.3 1.0
CA I:ALA163 4.2 29.7 1.0
O I:ALA167 4.3 25.9 1.0
O I:ASP164 4.3 33.8 1.0
O Y:HOH301 4.4 53.4 1.0
CA I:SER169 4.4 26.4 1.0
N I:ARG165 4.5 30.0 1.0
N I:GLY170 4.6 28.1 1.0
CB I:ALA163 4.6 31.9 1.0
O I:HOH352 4.6 26.3 1.0
CB I:SER169 4.7 27.4 1.0
CA I:GLY170 4.7 28.1 1.0
OXT I:ASP194 4.7 37.5 1.0
O I:HOH355 4.8 40.5 1.0
C I:ARG165 4.8 29.5 1.0
OD2 I:ASP164 4.8 39.0 1.0
N I:LEU168 4.9 26.9 1.0

Magnesium binding site 8 out of 10 in 1g65

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Magnesium binding site 8 out of 10 in the Crystal Structure of Epoxomicin:20S Proteasome Reveals A Molecular Basis For Selectivity of Alpha,Beta-Epoxyketone Proteasome Inhibitors


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of Epoxomicin:20S Proteasome Reveals A Molecular Basis For Selectivity of Alpha,Beta-Epoxyketone Proteasome Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg301

b:40.3
occ:1.00
 O W:ASP194 2.1 40.0 1.0
O K:SER169 2.3 24.4 1.0
O K:ALA163 2.4 28.5 1.0
O K:ASP166 2.4 28.2 1.0
O K:HOH463 2.7 58.6 1.0
NH1 K:ARG19 3.1 46.7 1.0
C W:ASP194 3.3 37.8 1.0
C K:ASP166 3.4 25.8 1.0
C K:SER169 3.5 24.8 1.0
C K:ALA163 3.5 30.1 1.0
CA K:ALA167 3.6 28.8 1.0
C K:ALA167 3.6 29.4 1.0
O K:ALA167 3.6 28.3 1.0
CA W:ASP194 3.8 35.6 1.0
N K:SER169 3.9 27.4 1.0
N K:ALA167 4.0 27.8 1.0
CB W:ASP194 4.1 34.6 1.0
CZ K:ARG19 4.1 46.0 1.0
CA K:ALA163 4.2 27.8 1.0
O K:HIS164 4.3 26.5 1.0
CA K:SER169 4.3 23.3 1.0
OXT W:ASP194 4.3 38.9 1.0
N K:TYR168 4.4 28.2 1.0
N K:GLY170 4.5 27.6 1.0
O K:ALA162 4.5 27.4 1.0
N K:HIS164 4.5 27.3 1.0
CA K:GLY170 4.6 29.5 1.0
NH2 K:ARG19 4.6 46.5 1.0
C K:HIS164 4.6 25.5 1.0
CA K:ASP166 4.7 27.7 1.0
O W:HOH287 4.7 36.5 1.0
N K:ASP166 4.8 29.4 1.0
CA K:HIS164 4.8 25.3 1.0
CB K:SER169 4.8 25.0 1.0
O K:HOH459 4.8 35.0 1.0
C K:TYR168 4.9 28.6 1.0
CG W:ASP194 4.9 37.6 1.0
CB K:ALA167 4.9 31.3 1.0
NE K:ARG19 5.0 42.0 1.0

Magnesium binding site 9 out of 10 in 1g65

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Magnesium binding site 9 out of 10 in the Crystal Structure of Epoxomicin:20S Proteasome Reveals A Molecular Basis For Selectivity of Alpha,Beta-Epoxyketone Proteasome Inhibitors


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Crystal Structure of Epoxomicin:20S Proteasome Reveals A Molecular Basis For Selectivity of Alpha,Beta-Epoxyketone Proteasome Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg201

b:39.9
occ:1.00
 O L:HOH397 1.6 37.9 1.0
O L:HIS166 2.0 26.0 1.0
O L:HOH327 2.3 53.2 1.0
O L:THR163 2.3 31.5 1.0
O L:VAL169 2.5 32.4 1.0
C L:HIS166 3.1 25.1 1.0
C L:THR163 3.2 33.6 1.0
O L:HOH399 3.3 44.0 1.0
O L:HOH325 3.5 41.7 1.0
CG2 L:THR163 3.5 33.4 1.0
CA L:THR163 3.5 26.6 1.0
C L:VAL169 3.7 28.5 1.0
CA L:ILE167 3.8 28.4 1.0
N L:ILE167 3.9 26.8 1.0
NH2 L:ARG19 4.0 41.0 1.0
C L:ILE167 4.1 28.8 1.0
CB L:THR163 4.2 30.6 1.0
N L:HIS166 4.2 27.7 1.0
N L:VAL169 4.2 27.8 1.0
CA L:HIS166 4.2 23.5 1.0
O L:ILE167 4.4 30.6 1.0
CA L:VAL169 4.4 29.2 1.0
O L:ALA162 4.4 31.6 1.0
N L:GLU164 4.5 34.0 1.0
O L:ASP194 4.6 47.3 1.0
N L:GLN168 4.7 29.9 1.0
N L:GLY170 4.7 28.5 1.0
CB L:VAL169 4.7 22.0 1.0
N L:THR163 4.8 28.2 1.0
CA L:GLY170 4.8 32.1 1.0
OD1 L:ASP194 4.9 46.5 1.0
C L:GLU164 4.9 33.9 1.0
NH2 V:ARG19 4.9 32.1 1.0
CB L:HIS166 4.9 23.5 1.0

Magnesium binding site 10 out of 10 in 1g65

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Magnesium binding site 10 out of 10 in the Crystal Structure of Epoxomicin:20S Proteasome Reveals A Molecular Basis For Selectivity of Alpha,Beta-Epoxyketone Proteasome Inhibitors


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Crystal Structure of Epoxomicin:20S Proteasome Reveals A Molecular Basis For Selectivity of Alpha,Beta-Epoxyketone Proteasome Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg201

b:28.3
occ:1.00
 O N:ILE163 2.3 26.2 1.0
O N:ASP166 2.8 32.4 1.0
O N:SER169 2.8 30.6 1.0
O N:HOH336 3.3 62.2 1.0
NH1 N:ARG19 3.4 37.1 1.0
C N:ILE163 3.5 30.3 1.0
CD1 1:LEU26 3.6 25.0 1.0
C N:SER169 3.9 30.6 1.0
C N:ASP166 3.9 27.3 1.0
CG2 N:ILE163 3.9 25.6 1.0
CA N:GLY167 4.1 27.2 1.0
CA N:ILE163 4.3 28.8 1.0
O N:LYS164 4.4 31.1 1.0
CZ N:ARG19 4.4 33.7 1.0
N N:GLY167 4.5 26.3 1.0
CA N:GLY170 4.5 32.3 1.0
C N:GLY167 4.6 28.9 1.0
N N:LYS164 4.6 31.3 1.0
N N:GLY170 4.6 29.7 1.0
N N:SER169 4.7 31.9 1.0
C N:LYS164 4.7 31.7 1.0
O N:HOH382 4.7 53.7 1.0
CB N:ILE163 4.8 27.3 1.0
NH2 N:ARG19 4.8 36.4 1.0
CA N:SER169 4.8 28.4 1.0
O N:GLY167 4.8 31.2 1.0
CA N:LYS164 4.8 31.4 1.0
CG 1:LEU26 4.9 26.6 1.0

Reference:

M.Groll, K.B.Kim, N.Kairies, C.Crews. Crystal Structure of Epoxomicin:20S Proteasome Reveals A Molecular Basis For Selectivity of Alpha,Beta-Epoxyketone Proteasome Inhibitors J.Am.Chem.Soc. V. 122 1237 2000.
ISSN: ISSN 0002-7863
DOI: 10.1021/JA993588M
Page generated: Tue Aug 13 03:39:25 2024

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