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Magnesium in PDB 4y81: Yeast 20S Proteasome in Complex with Ac-Pay-Ep

Enzymatic activity of Yeast 20S Proteasome in Complex with Ac-Pay-Ep

All present enzymatic activity of Yeast 20S Proteasome in Complex with Ac-Pay-Ep:
3.4.25.1;

Protein crystallography data

The structure of Yeast 20S Proteasome in Complex with Ac-Pay-Ep, PDB code: 4y81 was solved by E.M.Huber, M.Groll, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.00 / 2.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 136.600, 299.890, 146.100, 90.00, 112.89, 90.00
R / Rfree (%) 20.4 / 23.4

Other elements in 4y81:

The structure of Yeast 20S Proteasome in Complex with Ac-Pay-Ep also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Yeast 20S Proteasome in Complex with Ac-Pay-Ep (pdb code 4y81). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 9 binding sites of Magnesium where determined in the Yeast 20S Proteasome in Complex with Ac-Pay-Ep, PDB code: 4y81:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Magnesium binding site 1 out of 9 in 4y81

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Magnesium binding site 1 out of 9 in the Yeast 20S Proteasome in Complex with Ac-Pay-Ep


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Yeast 20S Proteasome in Complex with Ac-Pay-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg301

b:30.0
occ:1.00
 O C:GLN115 2.7 33.6 1.0
N C:PHE127 2.8 37.7 1.0
O C:PRO150 3.0 43.6 1.0
CA C:PRO126 3.4 37.5 1.0
C C:GLN115 3.5 33.9 1.0
CB C:PRO126 3.5 37.5 1.0
C C:PRO126 3.6 36.9 1.0
CA C:GLN115 3.6 33.7 1.0
CD2 C:PHE127 3.7 37.9 1.0
CB C:PHE127 3.7 39.0 1.0
CA C:PHE127 3.7 39.1 1.0
CB C:GLN115 3.8 34.0 1.0
C C:PRO150 3.9 42.2 1.0
CG2 C:THR119 3.9 40.0 1.0
CB C:TYR118 4.0 37.5 1.0
CA C:PRO150 4.0 40.9 1.0
O C:PHE127 4.1 43.6 1.0
CG C:PHE127 4.1 38.5 1.0
CG C:GLN115 4.3 33.8 1.0
C C:PHE127 4.4 40.9 1.0
CB C:PRO150 4.4 40.7 1.0
C C:TYR118 4.7 37.9 1.0
N C:GLN116 4.7 35.5 1.0
CG C:PRO126 4.7 39.1 1.0
CE2 C:PHE127 4.8 39.9 1.0
O C:PRO126 4.8 35.0 1.0
CA C:TYR118 4.8 38.4 1.0
N C:PRO126 4.8 38.2 1.0
N C:THR119 4.9 39.5 1.0
O C:TYR118 4.9 38.5 1.0
NE2 C:GLN115 5.0 33.0 1.0

Magnesium binding site 2 out of 9 in 4y81

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Magnesium binding site 2 out of 9 in the Yeast 20S Proteasome in Complex with Ac-Pay-Ep


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Yeast 20S Proteasome in Complex with Ac-Pay-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:55.8
occ:1.00
 O G:MET125 2.4 47.0 1.0
OG1 G:THR8 2.8 36.1 1.0
O G:ARG122 2.8 38.5 1.0
O G:ALA123 3.0 39.4 1.0
O G:TYR119 3.1 31.9 1.0
CG2 G:THR8 3.3 39.9 1.0
C G:MET125 3.4 42.7 1.0
C G:ALA123 3.6 38.9 1.0
CB G:THR8 3.6 39.0 1.0
CA G:ALA123 3.7 40.2 1.0
C G:ARG122 3.9 40.5 1.0
N G:THR8 4.0 38.8 1.0
CA G:ARG126 4.2 37.5 1.0
N G:ARG126 4.2 39.3 1.0
N G:MET125 4.2 42.3 1.0
N G:ALA123 4.3 40.0 1.0
C G:TYR119 4.3 34.5 1.0
CA G:MET125 4.4 44.7 1.0
CA G:THR8 4.5 39.5 1.0
N G:TYR124 4.6 29.1 1.0
CD G:PRO127 4.6 35.4 1.0
C G:TYR124 4.9 41.5 1.0
C G:ARG126 4.9 37.4 1.0
CB G:ALA123 5.0 40.4 1.0

Magnesium binding site 3 out of 9 in 4y81

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Magnesium binding site 3 out of 9 in the Yeast 20S Proteasome in Complex with Ac-Pay-Ep


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Yeast 20S Proteasome in Complex with Ac-Pay-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:51.6
occ:1.00
 O I:ASP177 2.4 37.8 1.0
O I:ALA174 2.7 40.3 1.0
O I:SER180 2.8 38.6 1.0
O I:HOH418 3.3 36.9 1.0
C I:ASP177 3.5 36.8 1.0
C I:ALA174 3.7 42.0 1.0
CA I:ASP175 3.9 40.3 1.0
OXT I:ASP204 4.0 36.0 1.0
C I:SER180 4.0 37.8 1.0
C I:ASP175 4.2 39.0 1.0
O I:ASP175 4.2 38.4 1.0
N I:ASP175 4.2 42.0 1.0
N I:ASP177 4.3 32.7 1.0
N I:ALA178 4.4 36.1 1.0
CA I:ALA178 4.4 37.2 1.0
O I:ALA178 4.4 41.9 1.0
C I:ALA178 4.5 38.3 1.0
CA I:ASP177 4.5 36.1 1.0
O I:ASP204 4.7 36.7 1.0
NH1 Y:ARG19 4.7 48.1 1.0
N I:SER180 4.7 35.8 1.0
OD1 I:ASP175 4.7 44.5 1.0
C I:ASP204 4.7 34.4 1.0
NH2 Y:ARG19 4.8 41.1 1.0
CA I:GLY181 4.9 38.3 1.0
N I:GLY181 4.9 37.5 1.0
CA I:SER180 4.9 37.5 1.0
N I:ARG176 4.9 36.6 1.0
CA I:ALA174 4.9 41.7 1.0

Magnesium binding site 4 out of 9 in 4y81

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Magnesium binding site 4 out of 9 in the Yeast 20S Proteasome in Complex with Ac-Pay-Ep


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Yeast 20S Proteasome in Complex with Ac-Pay-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg302

b:31.7
occ:1.00
 O Y:ASP168 2.3 42.8 1.0
O I:ASP204 2.3 36.7 1.0
O Y:ALA165 2.6 35.8 1.0
O Y:SER171 2.6 42.4 1.0
O Y:HOH314 2.6 36.6 1.0
C I:ASP204 3.2 34.4 1.0
C Y:ASP168 3.3 38.2 1.0
CA Y:ALA169 3.5 36.9 1.0
O Y:ALA169 3.6 38.7 1.0
C Y:ALA169 3.7 37.9 1.0
C Y:ALA165 3.7 38.0 1.0
CA I:ASP204 3.8 39.6 1.0
C Y:SER171 3.8 40.5 1.0
N Y:ALA169 3.8 37.5 1.0
NH1 Y:ARG19 3.8 48.1 1.0
OXT I:ASP204 4.1 36.0 1.0
O Y:HIS166 4.1 38.3 1.0
CB I:ASP204 4.1 42.8 1.0
N Y:SER171 4.2 37.1 1.0
CZ Y:ARG19 4.4 45.0 1.0
C Y:HIS166 4.4 38.4 1.0
CA Y:ASP168 4.5 37.1 1.0
N Y:TYR170 4.5 37.1 1.0
CA Y:ALA165 4.5 38.8 1.0
CA Y:SER171 4.6 38.0 1.0
N Y:ASP168 4.6 37.1 1.0
NH2 Y:ARG19 4.6 41.1 1.0
N Y:HIS166 4.7 38.5 1.0
N Y:GLY172 4.8 42.2 1.0
CA Y:HIS166 4.8 37.4 1.0
O Y:ALA164 4.8 38.6 1.0
CA Y:GLY172 4.9 44.1 1.0
CB Y:ALA169 4.9 36.6 1.0
C Y:ARG167 4.9 37.2 1.0
O I:HOH405 5.0 31.3 1.0

Magnesium binding site 5 out of 9 in 4y81

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Magnesium binding site 5 out of 9 in the Yeast 20S Proteasome in Complex with Ac-Pay-Ep


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Yeast 20S Proteasome in Complex with Ac-Pay-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg301

b:50.1
occ:1.00
 O K:ASP168 2.2 41.8 1.0
O W:ASP204 2.3 34.6 1.0
O K:ALA165 2.5 39.2 1.0
O K:SER171 2.8 41.3 1.0
C W:ASP204 3.1 33.0 1.0
C K:ASP168 3.2 40.1 1.0
CA K:ALA169 3.5 39.9 1.0
C K:ALA165 3.7 40.3 1.0
CA W:ASP204 3.7 38.8 1.0
N K:ALA169 3.7 40.7 1.0
O K:ALA169 3.7 44.8 1.0
C K:ALA169 3.7 42.3 1.0
O K:HIS166 3.8 37.1 1.0
C K:SER171 4.0 39.3 1.0
OXT W:ASP204 4.0 41.6 1.0
CB W:ASP204 4.1 41.9 1.0
NH1 K:ARG19 4.1 47.4 1.0
C K:HIS166 4.2 37.5 1.0
N K:SER171 4.3 39.9 1.0
CA K:ASP168 4.4 38.1 1.0
N K:ASP168 4.4 39.9 1.0
N K:HIS166 4.5 39.4 1.0
CA K:ALA165 4.5 40.9 1.0
N K:TYR170 4.6 40.0 1.0
CA K:HIS166 4.6 38.7 1.0
CZ K:ARG19 4.7 46.5 1.0
O K:ALA164 4.7 40.7 1.0
C K:ARG167 4.7 41.0 1.0
CA K:SER171 4.7 38.3 1.0
CB K:ALA169 4.8 37.3 1.0
N K:ARG167 4.9 39.8 1.0
NH2 K:ARG19 4.9 51.4 1.0
O K:ARG167 4.9 42.1 1.0
N K:GLY172 5.0 40.5 1.0

Magnesium binding site 6 out of 9 in 4y81

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Magnesium binding site 6 out of 9 in the Yeast 20S Proteasome in Complex with Ac-Pay-Ep


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Yeast 20S Proteasome in Complex with Ac-Pay-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg301

b:56.1
occ:1.00
 O V:ASP166 2.3 46.2 1.0
O V:ILE163 2.4 50.5 1.0
OXT L:ASP222 2.4 53.6 1.0
C L:ASP222 3.1 55.2 1.0
C V:ASP166 3.1 47.2 1.0
O V:TRP164 3.3 48.9 1.0
O V:SER169 3.3 48.3 1.0
C V:ILE163 3.4 51.5 1.0
C V:TRP164 3.4 48.6 1.0
N V:ASP166 3.6 46.4 1.0
CA L:ASP222 3.7 54.8 1.0
O L:ASP222 3.8 61.2 1.0
N V:LEU167 3.8 48.3 1.0
N V:ASN165 3.9 47.2 1.0
CA V:TRP164 4.0 50.8 1.0
CA V:LEU167 4.0 47.6 1.0
O V:GLY162 4.0 46.5 1.0
CA V:ASP166 4.0 46.2 1.0
N V:TRP164 4.1 51.3 1.0
C V:ASN165 4.1 45.9 1.0
CA V:ASN165 4.4 45.4 1.0
O L:ARG221 4.5 54.9 1.0
CA V:ILE163 4.5 50.5 1.0
C V:SER169 4.5 47.1 1.0
CD2 V:LEU167 4.6 43.9 1.0
CB L:ASP222 4.6 55.7 1.0
O V:ASN165 4.7 46.8 1.0
C V:LEU167 4.7 47.0 1.0
NH1 V:ARG19 4.8 53.7 1.0
CD1 L:ILE35 4.8 47.5 1.0
N L:ASP222 4.9 53.1 1.0
C V:GLY162 5.0 48.1 1.0

Magnesium binding site 7 out of 9 in 4y81

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Magnesium binding site 7 out of 9 in the Yeast 20S Proteasome in Complex with Ac-Pay-Ep


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Yeast 20S Proteasome in Complex with Ac-Pay-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg201

b:40.9
occ:1.00
 O N:SER169 2.8 36.3 1.0
O N:ILE163 2.9 38.1 1.0
O N:ASP166 3.2 39.5 1.0
CD1 a:LEU34 3.5 41.6 1.0
NH1 N:ARG19 3.7 31.8 1.0
C N:SER169 4.0 34.1 1.0
C N:ILE163 4.1 38.4 1.0
C N:ASP166 4.2 34.8 1.0
CA N:GLY167 4.2 34.3 1.0
O a:HOH318 4.3 44.0 1.0
CG2 N:ILE163 4.3 38.5 1.0
CZ N:ARG19 4.3 30.3 1.0
O N:GLY167 4.4 36.4 1.0
NH2 N:ARG19 4.5 31.1 1.0
CA N:GLY170 4.6 37.4 1.0
C N:GLY167 4.6 33.9 1.0
N N:GLY167 4.6 31.7 1.0
N N:GLY170 4.8 35.2 1.0
CA N:ILE163 4.8 38.9 1.0
CG a:LEU34 4.9 42.1 1.0
O N:LYS164 5.0 39.6 1.0
N N:SER169 5.0 32.8 1.0

Magnesium binding site 8 out of 9 in 4y81

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Magnesium binding site 8 out of 9 in the Yeast 20S Proteasome in Complex with Ac-Pay-Ep


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Yeast 20S Proteasome in Complex with Ac-Pay-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Mg201

b:30.0
occ:1.00
 OE1 X:GLN118 3.5 39.8 1.0
O X:THR124 3.7 39.7 1.0
CB X:ASP120 3.8 35.0 1.0
N X:ASP120 3.9 33.7 1.0
CG X:GLN118 4.0 38.3 1.0
CE1 X:HIS133 4.0 39.3 1.0
CG X:ASP120 4.1 35.0 1.0
CD X:GLN118 4.1 39.2 1.0
OD2 X:ASP120 4.2 36.5 1.0
O X:GLN118 4.3 39.1 1.0
CB X:THR124 4.4 38.3 1.0
CA X:ASP120 4.5 33.5 1.0
C X:ILE119 4.5 34.8 1.0
C X:GLN118 4.6 38.8 1.0
CG2 X:THR124 4.7 38.4 1.0
C X:THR124 4.7 39.8 1.0
CA X:ILE119 4.7 34.7 1.0
OD1 X:ASP120 4.8 39.8 1.0
CG1 W:VAL35 4.8 41.9 1.0
CB X:GLN118 4.8 37.6 1.0
O X:HOH315 4.8 29.7 1.0
N X:ILE119 4.8 37.3 1.0
ND1 X:HIS133 4.8 38.5 1.0
NE2 X:HIS133 4.9 41.4 1.0

Magnesium binding site 9 out of 9 in 4y81

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Magnesium binding site 9 out of 9 in the Yeast 20S Proteasome in Complex with Ac-Pay-Ep


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Yeast 20S Proteasome in Complex with Ac-Pay-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg301

b:53.3
occ:1.00
 O Z:VAL198 2.4 47.5 1.0
O Z:THR192 2.8 48.0 1.0
O Z:HIS195 3.2 39.5 1.0
NH2 Z:ARG28 3.5 53.9 1.0
CG2 Z:THR192 3.5 51.7 1.0
O Z:ASP222 3.6 51.6 1.0
C Z:VAL198 3.6 46.8 1.0
C Z:THR192 3.7 49.0 1.0
O Z:ILE196 4.0 41.8 1.0
CA Z:THR192 4.0 49.2 1.0
C Z:HIS195 4.2 39.1 1.0
CA Z:ILE196 4.3 40.3 1.0
C Z:ILE196 4.3 40.4 1.0
OD1 Z:ASP222 4.3 55.9 1.0
CA Z:GLY199 4.4 46.0 1.0
CB Z:THR192 4.4 49.6 1.0
N Z:GLY199 4.4 45.6 1.0
NH2 H:ARG19 4.4 53.9 1.0
N Z:VAL198 4.5 43.4 1.0
CZ Z:ARG28 4.5 50.3 1.0
C Z:ASP222 4.5 52.8 1.0
CA Z:VAL198 4.6 43.6 1.0
NH1 Z:ARG28 4.7 51.0 1.0
N Z:ILE196 4.8 39.4 1.0
O Z:LYS220 4.8 50.7 1.0
N Z:GLU193 5.0 47.6 1.0

Reference:

E.M.Huber, G.De Bruin, W.Heinemeyer, G.Paniagua Soriano, H.S.Overkleeft, M.Groll. Systematic Analyses of Substrate Preferences of 20S Proteasomes Using Peptidic Epoxyketone Inhibitors. J.Am.Chem.Soc. V. 137 7835 2015.
ISSN: ESSN 1520-5126
PubMed: 26020686
DOI: 10.1021/JACS.5B03688
Page generated: Sat Sep 28 22:52:34 2024

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