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Magnesium in PDB 4y8g: Yeast 20S Proteasome in Complex with N3-Apnll-Ep

Enzymatic activity of Yeast 20S Proteasome in Complex with N3-Apnll-Ep

All present enzymatic activity of Yeast 20S Proteasome in Complex with N3-Apnll-Ep:
3.4.25.1;

Protein crystallography data

The structure of Yeast 20S Proteasome in Complex with N3-Apnll-Ep, PDB code: 4y8g 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 / 2.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 136.230, 300.480, 145.710, 90.00, 113.18, 90.00
R / Rfree (%) 19.2 / 20.8

Other elements in 4y8g:

The structure of Yeast 20S Proteasome in Complex with N3-Apnll-Ep also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Yeast 20S Proteasome in Complex with N3-Apnll-Ep (pdb code 4y8g). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the Yeast 20S Proteasome in Complex with N3-Apnll-Ep, PDB code: 4y8g:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 4y8g

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Magnesium binding site 1 out of 7 in the Yeast 20S Proteasome in Complex with N3-Apnll-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 N3-Apnll-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:55.2
occ:1.00
 O G:MET125 2.2 50.8 1.0
O G:ARG122 2.5 49.0 1.0
O G:TYR119 2.6 45.6 1.0
OG1 G:THR8 2.6 47.5 1.0
O G:ALA123 3.3 55.8 1.0
C G:MET125 3.4 53.4 1.0
CG2 G:THR8 3.5 50.1 1.0
C G:ARG122 3.5 48.7 1.0
C G:ALA123 3.6 53.0 1.0
CB G:THR8 3.6 48.9 1.0
CA G:ALA123 3.6 49.6 1.0
C G:TYR119 3.8 44.4 1.0
N G:ALA123 4.0 47.9 1.0
N G:MET125 4.1 53.0 1.0
N G:THR8 4.3 48.6 1.0
CA G:MET125 4.3 56.6 1.0
N G:ARG126 4.4 49.0 1.0
CA G:ARG126 4.5 45.4 1.0
CA G:TYR119 4.5 44.4 1.0
N G:TYR124 4.5 55.8 1.0
CA G:THR8 4.6 49.2 1.0
CD G:PRO127 4.7 37.4 1.0
N G:ARG122 4.8 48.7 1.0
N G:THR120 4.8 43.3 1.0
CA G:ARG122 4.8 51.6 1.0
CB G:MET125 4.8 64.0 1.0
C G:THR120 4.9 44.1 1.0
CA G:THR120 4.9 43.0 1.0
CB G:ALA123 4.9 47.9 1.0
C G:TYR124 5.0 52.4 1.0

Magnesium binding site 2 out of 7 in 4y8g

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Magnesium binding site 2 out of 7 in the Yeast 20S Proteasome in Complex with N3-Apnll-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 N3-Apnll-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:56.8
occ:1.00
 O I:SER180 2.5 54.5 1.0
O I:ASP177 2.6 50.3 1.0
O I:ALA174 2.6 50.5 1.0
C I:ALA174 3.7 51.5 1.0
C I:SER180 3.7 53.4 1.0
C I:ASP177 3.8 50.3 1.0
OXT I:ASP204 3.8 60.9 1.0
CA I:ASP175 4.1 54.5 1.0
N I:ASP175 4.3 53.8 1.0
CA I:GLY181 4.5 51.6 1.0
CA I:ALA178 4.5 48.8 1.0
C I:ASP175 4.5 52.8 1.0
N I:GLY181 4.5 51.9 1.0
O I:ALA178 4.5 50.5 1.0
C I:ALA178 4.6 49.6 1.0
N I:SER180 4.6 49.5 1.0
N I:ALA178 4.6 49.1 1.0
N I:ASP177 4.6 50.1 1.0
O I:ASP175 4.7 54.2 1.0
CA I:SER180 4.7 51.7 1.0
OD1 I:ASP175 4.7 57.3 1.0
C I:ASP204 4.7 57.5 1.0
CA I:ALA174 4.7 49.5 1.0
CA I:ASP177 4.8 51.2 1.0
O I:ASP204 4.8 63.0 1.0
CB I:ALA174 4.9 50.6 1.0
NH2 Y:ARG19 5.0 69.2 1.0

Magnesium binding site 3 out of 7 in 4y8g

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Magnesium binding site 3 out of 7 in the Yeast 20S Proteasome in Complex with N3-Apnll-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 N3-Apnll-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg302

b:55.8
occ:1.00
 O Y:ASP168 2.2 50.6 1.0
O I:ASP204 2.3 63.0 1.0
O Y:ALA165 2.4 47.1 1.0
O Y:SER171 2.5 50.7 1.0
C I:ASP204 3.1 57.5 1.0
C Y:ASP168 3.2 47.1 1.0
CA Y:ALA169 3.5 42.6 1.0
C Y:ALA165 3.6 50.0 1.0
CA I:ASP204 3.7 58.0 1.0
C Y:ALA169 3.7 43.0 1.0
O Y:ALA169 3.7 43.5 1.0
C Y:SER171 3.7 50.8 1.0
NH1 Y:ARG19 3.8 70.5 1.0
N Y:ALA169 3.8 43.7 1.0
OXT I:ASP204 4.0 60.9 1.0
CB I:ASP204 4.0 56.3 1.0
O Y:HIS166 4.1 50.3 1.0
N Y:SER171 4.1 51.5 1.0
C Y:HIS166 4.4 48.6 1.0
CA Y:ALA165 4.4 50.3 1.0
CA Y:ASP168 4.4 47.5 1.0
N Y:TYR170 4.4 45.4 1.0
N Y:ASP168 4.5 49.4 1.0
CZ Y:ARG19 4.5 66.3 1.0
CA Y:SER171 4.5 50.1 1.0
N Y:HIS166 4.5 49.0 1.0
CA Y:HIS166 4.7 48.5 1.0
O Y:ALA164 4.7 48.8 1.0
N Y:GLY172 4.7 50.3 1.0
NH2 Y:ARG19 4.8 69.2 1.0
CA Y:GLY172 4.9 49.9 1.0
C Y:ARG167 4.9 49.0 1.0
CB Y:ALA169 4.9 42.8 1.0

Magnesium binding site 4 out of 7 in 4y8g

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Magnesium binding site 4 out of 7 in the Yeast 20S Proteasome in Complex with N3-Apnll-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 N3-Apnll-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg301

b:58.2
occ:1.00
 O K:ASP168 2.2 48.5 1.0
O K:ALA165 2.3 48.7 1.0
O W:ASP204 2.4 56.5 1.0
O K:SER171 2.5 53.6 1.0
C W:ASP204 3.1 47.6 1.0
C K:ASP168 3.2 45.7 1.0
C K:ALA165 3.5 50.4 1.0
CA W:ASP204 3.6 51.0 1.0
CA K:ALA169 3.6 44.6 1.0
C K:SER171 3.7 53.7 1.0
C K:ALA169 3.7 48.5 1.0
O K:ALA169 3.8 47.4 1.0
N K:ALA169 3.8 44.3 1.0
CB W:ASP204 3.9 52.5 1.0
O K:HIS166 4.1 47.1 1.0
OXT W:ASP204 4.1 53.8 1.0
N K:SER171 4.1 53.7 1.0
NH1 K:ARG19 4.2 62.2 1.0
CA K:ALA165 4.3 50.2 1.0
C K:HIS166 4.4 47.5 1.0
CA K:ASP168 4.4 44.6 1.0
CA K:SER171 4.4 53.0 1.0
N K:HIS166 4.4 49.3 1.0
N K:ASP168 4.5 44.6 1.0
N K:TYR170 4.5 52.7 1.0
CA K:HIS166 4.6 48.5 1.0
O K:ALA164 4.6 51.1 1.0
CZ K:ARG19 4.6 61.4 1.0
N K:GLY172 4.7 53.3 1.0
NH2 K:ARG19 4.7 66.1 1.0
CA K:GLY172 4.8 52.0 1.0
C K:ARG167 4.9 44.3 1.0
CB K:SER171 4.9 51.1 1.0
N W:ASP204 5.0 49.1 1.0

Magnesium binding site 5 out of 7 in 4y8g

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Magnesium binding site 5 out of 7 in the Yeast 20S Proteasome in Complex with N3-Apnll-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 N3-Apnll-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg301

b:67.3
occ:1.00
 O V:ASP166 2.1 49.6 1.0
O V:ILE163 2.3 55.8 1.0
OXT L:ASP222 2.3 69.4 1.0
O V:SER169 2.6 51.4 1.0
C L:ASP222 3.0 70.5 1.0
C V:ASP166 3.1 50.9 1.0
C V:ILE163 3.3 57.0 1.0
CA L:ASP222 3.6 66.8 1.0
C V:SER169 3.8 48.7 1.0
N V:LEU167 3.8 51.0 1.0
N V:ASP166 3.8 49.4 1.0
O V:GLY162 3.8 52.4 1.0
O V:TRP164 3.9 58.8 1.0
O L:ASP222 3.9 79.4 1.0
CA V:LEU167 3.9 49.6 1.0
C V:TRP164 4.0 55.7 1.0
CA V:ASP166 4.1 49.5 1.0
NH1 V:ARG19 4.1 67.4 1.0
N V:TRP164 4.2 54.3 1.0
CA V:ILE163 4.2 59.9 1.0
CB L:ASP222 4.3 64.0 1.0
CA V:TRP164 4.3 54.6 1.0
N V:SER169 4.4 44.9 1.0
C V:LEU167 4.4 46.0 1.0
N V:ASN165 4.4 54.2 1.0
C V:ASN165 4.6 50.3 1.0
CA V:SER169 4.6 45.0 1.0
NH2 V:ARG19 4.7 66.5 1.0
CZ V:ARG19 4.7 65.5 1.0
O L:ARG221 4.7 59.0 1.0
N V:GLY170 4.7 48.7 1.0
CA V:GLY170 4.8 50.8 1.0
CD2 V:LEU167 4.8 47.3 1.0
C V:GLY162 4.8 54.3 1.0
O V:LEU167 4.8 45.0 1.0
CB V:ASP166 4.9 48.4 1.0
N L:ASP222 4.9 64.0 1.0
N V:GLY168 5.0 43.2 1.0

Magnesium binding site 6 out of 7 in 4y8g

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Magnesium binding site 6 out of 7 in the Yeast 20S Proteasome in Complex with N3-Apnll-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 N3-Apnll-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg201

b:52.5
occ:1.00
 O N:SER169 2.4 47.0 1.0
O N:ILE163 2.5 43.1 1.0
O N:ASP166 2.7 50.7 1.0
C N:ILE163 3.6 45.6 1.0
C N:SER169 3.6 44.2 1.0
NH1 N:ARG19 3.7 53.7 1.0
CG2 N:ILE163 3.8 39.2 1.0
C N:ASP166 3.8 46.9 1.0
CD1 a:LEU34 3.8 43.8 1.0
CA N:GLY167 4.1 45.2 1.0
CA N:ILE163 4.2 44.0 1.0
O N:GLY167 4.4 45.2 1.0
CA N:GLY170 4.4 49.8 1.0
CZ N:ARG19 4.4 50.6 1.0
N N:GLY167 4.4 45.2 1.0
C N:GLY167 4.4 44.7 1.0
N N:GLY170 4.4 47.1 1.0
N N:SER169 4.5 41.4 1.0
CA N:SER169 4.6 40.4 1.0
NH2 N:ARG19 4.6 47.9 1.0
CB N:ILE163 4.6 42.4 1.0
N N:LYS164 4.7 47.6 1.0
O N:LYS164 4.9 49.0 1.0
C N:LYS164 4.9 50.3 1.0
CB N:SER169 5.0 37.3 1.0
CA N:LYS164 5.0 50.4 1.0
CA N:ASP166 5.0 46.2 1.0
N N:ASP166 5.0 46.9 1.0

Magnesium binding site 7 out of 7 in 4y8g

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Magnesium binding site 7 out of 7 in the Yeast 20S Proteasome in Complex with N3-Apnll-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 N3-Apnll-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg301

b:56.5
occ:1.00
 O Z:HOH403 2.3 44.2 1.0
O Z:VAL198 2.4 53.5 1.0
O Z:HIS195 2.5 42.9 1.0
O Z:THR192 2.5 52.9 1.0
C Z:THR192 3.5 55.0 1.0
C Z:HIS195 3.6 44.0 1.0
C Z:VAL198 3.6 52.5 1.0
CG2 Z:THR192 3.7 47.3 1.0
CA Z:THR192 3.8 52.7 1.0
CA Z:ILE196 3.9 46.9 1.0
O Z:ILE196 3.9 49.6 1.0
NH2 Z:ARG28 3.9 63.4 1.0
C Z:ILE196 4.0 46.8 1.0
O Z:ASP222 4.1 66.0 1.0
N Z:ILE196 4.2 45.1 1.0
N Z:VAL198 4.2 48.7 1.0
CB Z:THR192 4.4 50.1 1.0
CA Z:VAL198 4.4 50.7 1.0
N Z:GLY199 4.5 53.3 1.0
N Z:HIS195 4.7 46.2 1.0
CA Z:GLY199 4.7 53.9 1.0
OD1 Z:ASP222 4.7 58.6 1.0
CA Z:HIS195 4.7 44.5 1.0
N Z:GLU193 4.7 57.0 1.0
NH2 H:ARG19 4.8 59.0 1.0
O Z:ALA191 4.8 51.0 1.0
CB Z:VAL198 4.8 52.7 1.0
N Z:GLN197 4.9 45.3 1.0
CZ Z:ARG28 5.0 63.4 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 22:56:54 2024

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