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Magnesium in PDB 4y78: Yeast 20S Proteasome in Complex with Ac-Lad-Ep

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

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

Protein crystallography data

The structure of Yeast 20S Proteasome in Complex with Ac-Lad-Ep, PDB code: 4y78 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 (°) 137.470, 300.130, 145.340, 90.00, 113.11, 90.00
R / Rfree (%) 19.5 / 21.9

Other elements in 4y78:

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

Chlorine (Cl) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Yeast 20S Proteasome in Complex with Ac-Lad-Ep (pdb code 4y78). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Yeast 20S Proteasome in Complex with Ac-Lad-Ep, PDB code: 4y78:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 4y78

Go back to Magnesium Binding Sites List in 4y78
Magnesium binding site 1 out of 8 in the Yeast 20S Proteasome in Complex with Ac-Lad-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-Lad-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:65.6
occ:1.00
 O G:MET125 2.5 65.9 1.0
OG1 G:THR8 2.5 57.7 1.0
O G:ARG122 2.7 59.0 1.0
O G:TYR119 3.0 58.8 1.0
O G:ALA123 3.1 67.8 1.0
CG2 G:THR8 3.3 63.7 1.0
CB G:THR8 3.5 61.5 1.0
C G:MET125 3.5 63.8 1.0
C G:ALA123 3.6 67.0 1.0
CA G:ALA123 3.6 63.0 1.0
C G:ARG122 3.7 61.6 1.0
N G:THR8 4.0 63.6 1.0
N G:ALA123 4.2 60.1 1.0
C G:TYR119 4.2 57.4 1.0
N G:MET125 4.3 64.9 1.0
N G:ARG126 4.3 60.2 1.0
CA G:ARG126 4.3 58.5 1.0
CA G:THR8 4.4 62.2 1.0
CA G:MET125 4.5 68.3 1.0
CD G:PRO127 4.6 57.0 1.0
N G:TYR124 4.6 69.3 1.0
CB G:ALA123 4.9 64.0 1.0
CA G:TYR119 5.0 56.9 1.0
C G:ARG126 5.0 57.8 1.0

Magnesium binding site 2 out of 8 in 4y78

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Magnesium binding site 2 out of 8 in the Yeast 20S Proteasome in Complex with Ac-Lad-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-Lad-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:73.2
occ:1.00
 O I:ASP177 2.5 57.4 1.0
O I:SER180 2.7 59.4 1.0
O I:ALA174 2.9 74.1 1.0
C I:ASP177 3.7 62.0 1.0
OXT I:ASP204 3.7 80.8 1.0
C I:ALA174 3.9 70.8 1.0
C I:SER180 3.9 61.2 1.0
CA I:ASP175 4.1 67.0 1.0
O I:ALA178 4.4 64.2 1.0
CA I:ALA178 4.4 61.1 1.0
C I:ASP175 4.4 62.0 1.0
N I:ASP175 4.4 69.8 1.0
N I:ALA178 4.5 61.9 1.0
C I:ALA178 4.5 62.9 1.0
O I:ASP175 4.5 56.4 1.0
N I:ASP177 4.5 58.9 1.0
C I:ASP204 4.6 78.4 1.0
NH1 Y:ARG19 4.6 69.8 1.0
O I:ASP204 4.6 78.6 1.0
CA I:ASP177 4.7 62.1 1.0
N I:SER180 4.7 61.0 1.0
CA I:GLY181 4.8 64.0 1.0
OD1 I:ASP175 4.8 72.6 1.0
N I:GLY181 4.8 61.9 1.0
NH2 Y:ARG19 4.8 68.6 1.0
CA I:SER180 4.9 62.0 1.0

Magnesium binding site 3 out of 8 in 4y78

Go back to Magnesium Binding Sites List in 4y78
Magnesium binding site 3 out of 8 in the Yeast 20S Proteasome in Complex with Ac-Lad-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-Lad-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg302

b:62.9
occ:1.00
 O I:ASP204 2.2 78.6 1.0
O Y:ASP168 2.4 55.7 1.0
O Y:ALA165 2.4 58.9 1.0
O Y:SER171 2.9 64.9 1.0
C I:ASP204 3.0 78.4 1.0
C Y:ASP168 3.3 59.4 1.0
CA I:ASP204 3.6 76.1 1.0
CA Y:ALA169 3.6 59.9 1.0
C Y:ALA165 3.6 60.1 1.0
O Y:ALA169 3.8 61.2 1.0
OXT I:ASP204 3.8 80.8 1.0
N Y:ALA169 3.8 60.8 1.0
C Y:ALA169 3.8 59.7 1.0
O Y:HIS166 3.8 57.3 1.0
C Y:SER171 4.0 62.9 1.0
CB I:ASP204 4.0 75.8 1.0
NH1 Y:ARG19 4.1 69.8 1.0
C Y:HIS166 4.2 59.1 1.0
N Y:SER171 4.5 62.1 1.0
N Y:HIS166 4.5 62.4 1.0
N Y:ASP168 4.5 63.2 1.0
CA Y:ASP168 4.5 60.4 1.0
CA Y:HIS166 4.5 60.2 1.0
CA Y:ALA165 4.5 60.1 1.0
CZ Y:ARG19 4.7 67.5 1.0
N Y:TYR170 4.7 60.7 1.0
C Y:ARG167 4.8 61.8 1.0
CA Y:SER171 4.8 59.1 1.0
O Y:ALA164 4.8 55.3 1.0
N Y:ARG167 4.9 58.1 1.0
NH2 Y:ARG19 4.9 68.6 1.0
N I:ASP204 4.9 75.4 1.0
CB Y:ALA169 4.9 60.0 1.0

Magnesium binding site 4 out of 8 in 4y78

Go back to Magnesium Binding Sites List in 4y78
Magnesium binding site 4 out of 8 in the Yeast 20S Proteasome in Complex with Ac-Lad-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-Lad-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg301

b:62.6
occ:1.00
 O K:ASP168 2.2 57.1 1.0
O W:ASP204 2.4 71.0 1.0
O K:ALA165 2.4 64.1 1.0
C W:ASP204 3.1 69.3 1.0
O K:SER171 3.1 65.2 1.0
C K:ASP168 3.1 59.9 1.0
CA K:ALA169 3.5 61.1 1.0
C K:ALA165 3.6 62.5 1.0
O K:HIS166 3.6 65.2 1.0
CA W:ASP204 3.6 68.4 1.0
N K:ALA169 3.6 60.4 1.0
OXT W:ASP204 3.8 75.0 1.0
C K:ALA169 3.8 65.8 1.0
O K:ALA169 3.9 71.0 1.0
C K:HIS166 4.0 63.3 1.0
CB W:ASP204 4.2 67.2 1.0
C K:SER171 4.2 65.2 1.0
N K:ASP168 4.3 60.5 1.0
CA K:ASP168 4.3 58.6 1.0
NH1 K:ARG19 4.4 66.0 1.0
CA K:HIS166 4.4 63.8 1.0
N K:HIS166 4.4 62.1 1.0
C K:ARG167 4.5 59.5 1.0
N K:SER171 4.6 64.1 1.0
CA K:ALA165 4.6 63.0 1.0
N K:ARG167 4.6 60.5 1.0
O K:ALA164 4.7 59.8 1.0
N K:TYR170 4.7 64.4 1.0
O K:ARG167 4.8 57.6 1.0
CB K:ALA169 4.8 59.4 1.0
CA K:SER171 4.9 62.4 1.0
N W:ASP204 4.9 67.8 1.0
CZ K:ARG19 5.0 68.1 1.0

Magnesium binding site 5 out of 8 in 4y78

Go back to Magnesium Binding Sites List in 4y78
Magnesium binding site 5 out of 8 in the Yeast 20S Proteasome in Complex with Ac-Lad-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-Lad-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg301

b:72.6
occ:1.00
 O V:ASP166 2.0 65.0 1.0
O V:ILE163 2.2 71.9 1.0
OXT L:ASP222 2.3 74.2 1.0
O V:SER169 2.7 64.4 1.0
C V:ASP166 3.0 63.1 1.0
C L:ASP222 3.1 76.5 1.0
C V:ILE163 3.2 68.4 1.0
O V:GLY162 3.6 59.4 1.0
N V:ASP166 3.7 63.5 1.0
CA L:ASP222 3.8 75.5 1.0
N V:LEU167 3.8 62.6 1.0
C V:SER169 3.8 61.9 1.0
C V:TRP164 3.9 68.3 1.0
O V:TRP164 3.9 72.8 1.0
O L:ASP222 3.9 87.9 1.0
CA V:LEU167 3.9 61.9 1.0
CA V:ASP166 4.0 61.2 1.0
N V:TRP164 4.1 64.9 1.0
CA V:ILE163 4.1 68.7 1.0
N V:ASN165 4.2 64.9 1.0
CA V:TRP164 4.2 66.6 1.0
NH1 V:ARG19 4.3 67.0 1.0
CB L:ASP222 4.4 72.4 1.0
C V:ASN165 4.4 62.7 1.0
C V:LEU167 4.5 61.6 1.0
N V:SER169 4.5 61.0 1.0
CA V:SER169 4.6 60.3 1.0
C V:GLY162 4.6 64.0 1.0
N V:GLY170 4.7 62.0 1.0
CA V:GLY170 4.8 65.1 1.0
CB V:ASP166 4.8 59.5 1.0
O V:LEU167 4.8 67.1 1.0
CA V:ASN165 4.8 63.2 1.0
CZ V:ARG19 4.8 65.2 1.0
N V:ILE163 4.9 66.3 1.0
CD2 V:LEU167 4.9 61.3 1.0
O L:ARG221 4.9 73.9 1.0
CB V:SER169 4.9 61.3 1.0
NH2 V:ARG19 5.0 69.0 1.0

Magnesium binding site 6 out of 8 in 4y78

Go back to Magnesium Binding Sites List in 4y78
Magnesium binding site 6 out of 8 in the Yeast 20S Proteasome in Complex with Ac-Lad-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-Lad-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg201

b:67.8
occ:1.00
 O N:SER169 2.6 57.0 1.0
O N:ILE163 2.9 51.9 1.0
O N:ASP166 2.9 59.5 1.0
CD1 a:LEU34 3.6 58.2 1.0
C N:SER169 3.8 54.8 1.0
NH1 N:ARG19 3.8 56.8 1.0
C N:ASP166 3.9 56.6 1.0
CA N:GLY167 4.0 54.8 1.0
C N:ILE163 4.1 54.7 1.0
O N:GLY167 4.2 57.8 1.0
CG2 N:ILE163 4.3 56.8 1.0
C N:GLY167 4.3 55.8 1.0
CZ N:ARG19 4.3 57.2 1.0
N N:GLY167 4.4 54.2 1.0
NH2 N:ARG19 4.4 60.4 1.0
CA N:GLY170 4.6 58.0 1.0
N N:GLY170 4.6 56.0 1.0
N N:SER169 4.7 52.6 1.0
CA N:ILE163 4.8 55.4 1.0
CA N:SER169 4.8 52.0 1.0
CG a:LEU34 4.9 59.1 1.0
O N:LYS164 5.0 55.9 1.0

Magnesium binding site 7 out of 8 in 4y78

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Magnesium binding site 7 out of 8 in the Yeast 20S Proteasome in Complex with Ac-Lad-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-Lad-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Mg101

b:30.0
occ:1.00
 SG H:CYS31 2.1 72.6 1.0
OD1 1:ASJ4 2.3 78.3 1.0
CG 1:ASJ4 3.0 73.1 1.0
OD2 1:ASJ4 3.0 86.9 1.0
CB H:CYS31 3.2 65.5 1.0
OG H:SER20 3.8 70.5 1.0
CG H:LYS33 4.2 61.5 1.0
CB H:SER20 4.2 65.2 1.0
CB 1:ASJ4 4.5 77.2 1.0
CA H:CYS31 4.5 63.6 1.0
CE H:LYS33 4.6 63.4 1.0
CB H:ALA49 4.6 55.7 1.0
O H:ALA32 4.6 56.6 1.0
C H:CYS31 4.6 60.7 1.0
N H:ALA32 4.7 56.4 1.0
CD H:LYS33 4.8 62.1 1.0
C H:ALA32 4.9 59.3 1.0

Magnesium binding site 8 out of 8 in 4y78

Go back to Magnesium Binding Sites List in 4y78
Magnesium binding site 8 out of 8 in the Yeast 20S Proteasome in Complex with Ac-Lad-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-Lad-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
4:Mg101

b:30.0
occ:1.00
 OD1 4:ASJ4 2.2 76.5 1.0
SG V:CYS31 2.3 77.6 1.0
CG 4:ASJ4 2.8 75.5 1.0
OD2 4:ASJ4 2.9 81.4 1.0
CB V:CYS31 3.4 74.5 1.0
OG V:SER20 3.8 75.4 1.0
CG V:LYS33 4.2 60.2 1.0
CB V:SER20 4.2 67.1 1.0
CB 4:ASJ4 4.4 79.0 1.0
CB V:ALA49 4.5 60.0 1.0
CE V:LYS33 4.6 59.9 1.0
O V:ALA32 4.7 68.7 1.0
CA V:CYS31 4.7 72.5 1.0
CD V:LYS33 4.8 59.5 1.0
C V:CYS31 4.8 72.2 1.0
N V:ALA32 4.8 69.5 1.0
C V:ALA32 4.9 67.5 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 22:51:50 2024

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