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Magnesium in PDB 1ryp: Crystal Structure of the 20S Proteasome From Yeast at 2.4 Angstroms Resolution

Enzymatic activity of Crystal Structure of the 20S Proteasome From Yeast at 2.4 Angstroms Resolution

All present enzymatic activity of Crystal Structure of the 20S Proteasome From Yeast at 2.4 Angstroms Resolution:
3.4.99.46;

Protein crystallography data

The structure of Crystal Structure of the 20S Proteasome From Yeast at 2.4 Angstroms Resolution, PDB code: 1ryp was solved by M.Groll, L.Ditzel, J.Loewe, D.Stock, M.Bochtler, H.D.Bartunik, R.Huber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 135.490, 300.700, 144.420, 90.00, 112.89, 90.00
R / Rfree (%) 28.6 / 33

Magnesium Binding Sites:

Pages:

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

Binding sites:

The binding sites of Magnesium atom in the Crystal Structure of the 20S Proteasome From Yeast at 2.4 Angstroms Resolution (pdb code 1ryp). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 20 binding sites of Magnesium where determined in the Crystal Structure of the 20S Proteasome From Yeast at 2.4 Angstroms Resolution, PDB code: 1ryp:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 20 in 1ryp

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Magnesium binding site 1 out of 20 in the Crystal Structure of the 20S Proteasome From Yeast at 2.4 Angstroms Resolution


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 the 20S Proteasome From Yeast at 2.4 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1

b:29.6
occ:1.00
 O A:MET134 2.0 27.2 1.0
O A:TYR128 2.2 24.3 1.0
O A:ARG131 2.4 24.3 1.0
O A:HOH260 2.4 25.3 1.0
OG1 A:THR17 2.6 29.8 1.0
C A:MET134 3.2 28.0 1.0
C A:TYR128 3.3 23.9 1.0
C A:ARG131 3.4 25.5 1.0
CG2 A:THR17 3.4 23.4 1.0
CB A:THR17 3.6 22.3 1.0
CA A:ALA132 3.9 23.8 1.0
C A:ALA132 4.0 27.1 1.0
N A:MET134 4.0 30.0 1.0
N A:ALA132 4.0 28.0 1.0
O A:ALA132 4.1 30.4 1.0
CA A:TYR128 4.1 24.0 1.0
CA A:MET134 4.1 32.7 1.0
N A:ARG135 4.2 29.0 1.0
N A:THR129 4.3 22.4 1.0
CA A:ARG135 4.4 26.6 1.0
N A:THR17 4.4 27.9 1.0
CB A:MET134 4.4 38.2 1.0
N A:ARG131 4.5 25.6 1.0
CA A:ARG131 4.5 24.3 1.0
CD A:PRO136 4.6 17.6 1.0
CA A:THR17 4.6 22.5 1.0
N A:TYR133 4.6 31.4 1.0
C A:THR129 4.7 27.3 1.0
CA A:THR129 4.7 24.9 1.0
CB A:TYR128 4.7 21.9 1.0
O A:HOH325 4.8 35.4 1.0
O A:HOH297 4.9 34.4 1.0
C A:TYR133 4.9 25.8 1.0
C A:ARG135 4.9 26.1 1.0
N A:GLN130 4.9 27.3 1.0
O A:THR129 5.0 27.8 1.0

Magnesium binding site 2 out of 20 in 1ryp

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Magnesium binding site 2 out of 20 in the Crystal Structure of the 20S Proteasome From Yeast at 2.4 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of the 20S Proteasome From Yeast at 2.4 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg253

b:55.1
occ:1.00
 O A:HOH313 2.4 41.8 1.0
O G:HOH249 2.6 40.6 1.0
O A:ALA132 2.9 30.4 1.0
OD1 G:ASN126 3.1 40.0 1.0
OH B:TYR5 3.2 33.6 1.0
O A:TYR133 3.5 28.2 1.0
CE1 B:TYR5 3.6 29.6 1.0
CA A:TYR133 3.7 30.6 1.0
O G:HOH310 3.7 36.4 1.0
CG G:ASN126 3.8 33.1 1.0
CZ B:TYR5 3.8 28.3 1.0
OG G:SER12 3.8 27.1 1.0
C A:TYR133 3.8 25.8 1.0
C A:ALA132 3.9 27.1 1.0
N A:TYR133 4.3 31.4 1.0
N G:ASN126 4.3 24.5 1.0
CB G:ASN126 4.4 32.0 1.0
O A:HOH297 4.4 34.4 1.0
ND2 G:ASN126 4.6 41.7 1.0
CG2 A:ILE16 4.6 23.0 1.0
N A:MET134 4.8 30.0 1.0
CD1 B:TYR5 4.8 31.0 1.0
CB A:TYR133 4.8 31.4 1.0
O A:HOH260 4.8 25.3 1.0
CE2 B:TYR5 5.0 27.3 1.0

Magnesium binding site 3 out of 20 in 1ryp

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Magnesium binding site 3 out of 20 in the Crystal Structure of the 20S Proteasome From Yeast at 2.4 Angstroms Resolution


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 the 20S Proteasome From Yeast at 2.4 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg2

b:34.2
occ:1.00
 O M:HOH220 2.1 51.9 1.0
O M:HOH226 2.1 30.9 1.0
OE1 E:GLU105 2.3 28.9 1.0
OG M:SER76 2.4 32.1 1.0
O M:HOH227 2.5 43.0 1.0
OG M:SER79 2.6 27.6 1.0
CD E:GLU105 3.4 18.2 1.0
CB M:SER76 3.6 29.1 1.0
CB M:SER79 3.6 24.5 1.0
CB E:GLU105 3.8 23.9 1.0
CG E:GLU105 4.2 21.1 1.0
N M:SER76 4.2 24.9 1.0
OD1 M:ASN78 4.2 25.4 1.0
OE2 E:GLU105 4.3 23.5 1.0
OE2 M:GLU107 4.4 58.8 1.0
OH M:TYR66 4.4 28.6 1.0
CA M:SER76 4.5 27.1 1.0
O M:HOH294 4.5 45.8 1.0
ND2 M:ASN78 4.6 24.9 1.0
CG M:ASN78 4.8 27.1 1.0
CA M:SER79 4.8 24.2 1.0
O E:TYR103 4.8 25.0 1.0
CD M:GLU107 4.8 53.6 1.0
O E:HOH320 4.8 42.1 1.0
CE M:LYS73 4.8 22.1 1.0
OE1 M:GLU107 4.9 58.4 1.0
N M:SER79 4.9 27.4 1.0
NZ M:LYS73 4.9 25.7 1.0
O M:LYS74 4.9 29.2 1.0

Magnesium binding site 4 out of 20 in 1ryp

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Magnesium binding site 4 out of 20 in the Crystal Structure of the 20S Proteasome From Yeast at 2.4 Angstroms Resolution


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 the 20S Proteasome From Yeast at 2.4 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg248

b:78.9
occ:1.00
 O G:HOH291 3.7 33.2 1.0
NZ G:LYS172 3.9 52.9 1.0
OE2 G:GLU151 4.2 43.2 1.0
CD G:GLU151 4.5 35.6 1.0
O G:HOH336 4.6 47.9 1.0
OE1 G:GLU151 4.7 40.2 1.0

Magnesium binding site 5 out of 20 in 1ryp

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Magnesium binding site 5 out of 20 in the Crystal Structure of the 20S Proteasome From Yeast at 2.4 Angstroms Resolution


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 the 20S Proteasome From Yeast at 2.4 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg197

b:27.1
occ:1.00
 O H:ILE163 2.4 22.1 1.0
O H:SER169 2.4 24.5 1.0
O H:ASP166 2.7 29.0 1.0
C H:ILE163 3.5 23.0 1.0
C H:SER169 3.6 22.2 1.0
CD1 2:LEU26 3.6 21.1 1.0
O 2:HOH301 3.7 37.6 1.0
C H:ASP166 3.8 17.5 1.0
NH1 H:ARG19 3.8 27.4 1.0
CG2 H:ILE163 3.8 17.5 1.0
CA H:GLY167 4.1 15.4 1.0
CA H:ILE163 4.2 17.1 1.0
CA H:GLY170 4.3 17.1 1.0
N H:GLY167 4.4 17.6 1.0
CZ H:ARG19 4.4 25.2 1.0
N H:GLY170 4.4 20.6 1.0
C H:GLY167 4.4 18.7 1.0
O H:GLY167 4.4 25.3 1.0
O H:LYS164 4.5 27.8 1.0
N H:SER169 4.5 25.2 1.0
CA H:SER169 4.6 20.2 1.0
N H:LYS164 4.6 23.9 1.0
CB H:ILE163 4.7 15.9 1.0
NH2 H:ARG19 4.7 21.8 1.0
C H:LYS164 4.7 23.5 1.0
N H:ASP166 4.8 22.4 1.0
O H:HOH321 4.8 38.5 1.0
CA H:ASP166 4.8 18.7 1.0
O 2:HOH307 4.8 45.5 1.0
CB H:SER169 4.8 20.9 1.0
CG 2:LEU26 4.9 19.8 1.0
CA H:LYS164 4.9 23.0 1.0

Magnesium binding site 6 out of 20 in 1ryp

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Magnesium binding site 6 out of 20 in the Crystal Structure of the 20S Proteasome From Yeast at 2.4 Angstroms Resolution


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 the 20S Proteasome From Yeast at 2.4 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg223

b:24.9
occ:1.00
 O I:ASP166 2.0 26.7 1.0
OXT 1:ASP213 2.1 34.7 1.0
O I:ILE163 2.2 31.6 1.0
O 1:HOH324 2.2 30.1 1.0
O I:SER169 2.4 25.8 1.0
C 1:ASP213 3.0 36.0 1.0
C I:ASP166 3.2 21.2 1.0
C I:ILE163 3.3 25.0 1.0
C I:SER169 3.5 20.8 1.0
CA 1:ASP213 3.5 33.0 1.0
NH1 I:ARG19 3.7 27.7 1.0
O I:GLY162 3.8 24.2 1.0
CA I:LEU167 3.9 21.9 1.0
N I:ASP166 3.9 27.6 1.0
O 1:ASP213 3.9 43.1 1.0
N I:LEU167 3.9 21.4 1.0
CB 1:ASP213 4.0 26.9 1.0
CA I:ILE163 4.0 21.3 1.0
CA I:ASP166 4.2 22.5 1.0
N I:SER169 4.2 23.9 1.0
N I:TRP164 4.2 25.9 1.0
C I:TRP164 4.3 25.2 1.0
C I:LEU167 4.3 22.5 1.0
CA I:GLY170 4.3 23.7 1.0
O I:TRP164 4.3 31.4 1.0
N I:GLY170 4.3 22.3 1.0
O 1:HOH245 4.3 56.9 1.0
CA I:SER169 4.4 17.1 1.0
CZ I:ARG19 4.4 21.9 1.0
CA I:TRP164 4.5 22.8 1.0
O I:LEU167 4.6 24.5 1.0
NH2 I:ARG19 4.6 27.2 1.0
CB I:SER169 4.7 15.5 1.0
N I:ASN165 4.7 23.7 1.0
C I:GLY162 4.8 19.9 1.0
C I:ASN165 4.8 27.8 1.0
CB I:ASP166 4.9 25.6 1.0
N 1:ASP213 4.9 30.4 1.0
N I:GLY168 4.9 24.7 1.0
O 1:ARG212 4.9 27.2 1.0
N I:ILE163 4.9 20.9 1.0
CD2 I:LEU167 4.9 21.3 1.0
CG 1:ASP213 5.0 29.6 1.0

Magnesium binding site 7 out of 20 in 1ryp

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Magnesium binding site 7 out of 20 in the Crystal Structure of the 20S Proteasome From Yeast at 2.4 Angstroms Resolution


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 the 20S Proteasome From Yeast at 2.4 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mg197

b:52.4
occ:1.00
 O J:HOH266 2.2 34.2 1.0
OG J:SER134 2.5 28.0 1.0
O J:HOH225 2.5 36.6 1.0
O J:GLY131 3.0 28.1 1.0
O J:HOH226 3.6 38.8 1.0
CB J:SER134 3.6 21.2 1.0
O J:HOH293 3.8 56.3 1.0
C J:GLY131 4.2 21.7 1.0
O J:HOH269 4.2 41.8 1.0
O J:HOH284 4.2 42.6 1.0
O J:HOH223 4.3 36.5 1.0
N J:SER134 4.7 21.4 1.0
CA J:SER134 4.8 18.5 1.0
N J:GLY131 4.8 20.6 1.0
CA J:THR132 4.9 23.0 1.0
N J:THR132 5.0 24.1 1.0

Magnesium binding site 8 out of 20 in 1ryp

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Magnesium binding site 8 out of 20 in the Crystal Structure of the 20S Proteasome From Yeast at 2.4 Angstroms Resolution


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 the 20S Proteasome From Yeast at 2.4 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mg198

b:32.5
occ:1.00
 O J:HOH206 2.0 35.5 1.0
O J:ALA166 2.2 27.4 1.0
O J:ASP169 2.3 23.9 1.0
O J:SER172 2.4 30.8 1.0
O J:HOH204 2.5 29.2 1.0
C J:ALA166 3.3 22.0 1.0
C J:SER172 3.4 24.0 1.0
C J:ASP169 3.4 20.4 1.0
O J:HOH203 3.8 43.4 1.0
CA J:ASP167 3.9 22.1 1.0
N J:ASP167 4.0 28.1 1.0
N J:ASP169 4.1 24.0 1.0
N J:SER172 4.1 26.1 1.0
C J:ASP167 4.2 22.4 1.0
CA J:SER172 4.2 23.8 1.0
CA J:ASP169 4.3 21.3 1.0
N J:GLY173 4.3 23.7 1.0
CA J:GLY173 4.4 24.4 1.0
CA J:ALA166 4.4 20.2 1.0
O J:HOH255 4.4 25.0 1.0
N J:ALA170 4.4 22.7 1.0
OXT J:ASP196 4.5 31.3 1.0
O J:ALA170 4.5 28.2 1.0
CA J:ALA170 4.5 24.3 1.0
C J:ALA170 4.5 27.0 1.0
O J:ASP167 4.6 28.1 1.0
CB J:SER172 4.6 24.4 1.0
CB J:ALA166 4.6 23.6 1.0
OD1 J:ASP167 4.6 30.9 1.0
O J:HOH258 4.6 44.3 1.0
CB J:ASP169 4.7 22.4 1.0
N J:ARG168 4.7 25.1 1.0

Magnesium binding site 9 out of 20 in 1ryp

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Magnesium binding site 9 out of 20 in the Crystal Structure of the 20S Proteasome From Yeast at 2.4 Angstroms Resolution


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 the 20S Proteasome From Yeast at 2.4 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg213

b:29.4
occ:1.00
 O X:ASP196 2.1 36.1 1.0
O L:ALA165 2.2 28.7 1.0
O L:ASP168 2.3 30.6 1.0
O L:HOH280 2.5 27.8 1.0
O L:SER171 2.6 27.9 1.0
C X:ASP196 3.0 34.8 1.0
C L:ALA165 3.3 24.8 1.0
C L:ASP168 3.3 23.5 1.0
CA X:ASP196 3.4 30.2 1.0
NH1 L:ARG19 3.7 30.8 1.0
CB X:ASP196 3.8 23.9 1.0
C L:SER171 3.8 25.5 1.0
CA L:ALA169 3.8 20.2 1.0
N L:ALA169 4.0 22.2 1.0
O L:HIS166 4.0 29.5 1.0
CA L:ALA165 4.0 23.3 1.0
C L:ALA169 4.0 20.6 1.0
OXT X:ASP196 4.1 34.5 1.0
O L:ALA169 4.1 23.7 1.0
N L:SER171 4.3 25.6 1.0
C L:HIS166 4.3 23.0 1.0
N L:ASP168 4.3 24.6 1.0
N L:HIS166 4.4 23.6 1.0
O X:HOH284 4.4 39.6 1.0
CA L:ASP168 4.4 20.9 1.0
O L:ALA164 4.6 28.4 1.0
CZ L:ARG19 4.6 29.8 1.0
CA L:SER171 4.6 23.8 1.0
CA L:HIS166 4.6 22.0 1.0
N L:TYR170 4.7 25.7 1.0
N L:GLY172 4.7 27.2 1.0
CG X:ASP196 4.7 24.4 1.0
CA L:GLY172 4.8 24.8 1.0
CB L:ALA165 4.8 24.3 1.0
N X:ASP196 4.8 25.7 1.0
C L:ARG167 4.9 25.3 1.0
NH2 L:ARG19 4.9 29.4 1.0
N L:ARG167 4.9 23.1 1.0
O X:HOH231 5.0 28.8 1.0

Magnesium binding site 10 out of 20 in 1ryp

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Magnesium binding site 10 out of 20 in the Crystal Structure of the 20S Proteasome From Yeast at 2.4 Angstroms Resolution


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 the 20S Proteasome From Yeast at 2.4 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Mg214

b:33.8
occ:1.00
 O M:HOH303 1.7 54.0 1.0
O M:HOH242 2.2 30.9 1.0
O M:VAL189 2.2 30.8 1.0
O M:HIS186 2.3 22.0 1.0
O M:THR183 2.6 31.8 1.0
O M:HOH305 3.4 41.3 1.0
C M:VAL189 3.4 26.2 1.0
C M:HIS186 3.4 19.4 1.0
C M:THR183 3.4 28.3 1.0
CG2 M:THR183 3.6 26.2 1.0
CA M:THR183 3.6 27.1 1.0
O M:HOH240 3.8 36.0 1.0
CA M:ILE187 3.8 21.4 1.0
NH1 M:ARG19 3.9 26.9 1.0
C M:ILE187 4.0 20.9 1.0
N M:VAL189 4.0 27.2 1.0
O M:ILE187 4.1 23.9 1.0
N M:ILE187 4.1 22.9 1.0
CA M:VAL189 4.2 23.6 1.0
CB M:THR183 4.2 26.3 1.0
O M:ASP213 4.3 45.3 1.0
N M:GLY190 4.4 22.8 1.0
N M:HIS186 4.5 23.9 1.0
CA M:HIS186 4.6 19.8 1.0
CA M:GLY190 4.6 17.4 1.0
N M:GLN188 4.6 25.8 1.0
CB M:VAL189 4.6 23.0 1.0
O M:ALA182 4.6 35.1 1.0
N M:GLU184 4.7 30.4 1.0
OD1 M:ASP213 4.8 39.6 1.0
NH2 W:ARG19 4.8 21.5 1.0
N M:THR183 4.9 28.5 1.0
OG1 M:THR183 4.9 28.9 1.0
C M:GLN188 5.0 23.8 1.0
CZ M:ARG19 5.0 24.7 1.0

Reference:

M.Groll, L.Ditzel, J.Lowe, D.Stock, M.Bochtler, H.D.Bartunik, R.Huber. Structure of 20S Proteasome From Yeast at 2.4 A Resolution. Nature V. 386 463 1997.
ISSN: ISSN 0028-0836
PubMed: 9087403
DOI: 10.1038/386463A0
Page generated: Tue Aug 13 13:10:00 2024

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