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Magnesium in PDB 4y84: Yeast 20S Proteasome in Complex with N3-A(4,4-F2P)Nll-Ep

Enzymatic activity of Yeast 20S Proteasome in Complex with N3-A(4,4-F2P)Nll-Ep

All present enzymatic activity of Yeast 20S Proteasome in Complex with N3-A(4,4-F2P)Nll-Ep:
3.4.25.1;

Protein crystallography data

The structure of Yeast 20S Proteasome in Complex with N3-A(4,4-F2P)Nll-Ep, PDB code: 4y84 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 / 2.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 136.950, 299.900, 145.790, 90.00, 113.00, 90.00
R / Rfree (%) 18.5 / 20.3

Other elements in 4y84:

The structure of Yeast 20S Proteasome in Complex with N3-A(4,4-F2P)Nll-Ep also contains other interesting chemical elements:

Fluorine (F) 12 atoms
Chlorine (Cl) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Yeast 20S Proteasome in Complex with N3-A(4,4-F2P)Nll-Ep (pdb code 4y84). 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-A(4,4-F2P)Nll-Ep, PDB code: 4y84:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 4y84

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Magnesium binding site 1 out of 7 in the Yeast 20S Proteasome in Complex with N3-A(4,4-F2P)Nll-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-A(4,4-F2P)Nll-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:64.5
occ:1.00
 O G:MET125 2.2 54.8 1.0
OG1 G:THR8 2.6 50.0 1.0
O G:TYR119 2.6 48.5 1.0
O G:ARG122 2.7 48.7 1.0
O G:ALA123 3.3 57.5 1.0
C G:MET125 3.4 56.0 1.0
CG2 G:THR8 3.4 51.6 1.0
CB G:THR8 3.6 49.7 1.0
C G:ALA123 3.7 54.6 1.0
C G:ARG122 3.7 49.4 1.0
CA G:ALA123 3.7 49.0 1.0
C G:TYR119 3.8 47.1 1.0
N G:MET125 4.1 51.7 1.0
N G:ALA123 4.2 47.2 1.0
N G:THR8 4.2 48.6 1.0
N G:ARG126 4.3 52.5 1.0
CA G:MET125 4.3 58.1 1.0
CA G:ARG126 4.4 48.0 1.0
CA G:THR8 4.5 49.5 1.0
CD G:PRO127 4.6 38.4 1.0
CA G:TYR119 4.6 46.6 1.0
N G:TYR124 4.6 58.6 1.0
CB G:MET125 4.8 67.0 1.0
N G:THR120 4.9 44.2 1.0
N G:ARG122 4.9 48.3 1.0
CA G:ARG122 5.0 51.9 1.0
C G:ARG126 5.0 46.6 1.0
C G:TYR124 5.0 53.4 1.0

Magnesium binding site 2 out of 7 in 4y84

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Magnesium binding site 2 out of 7 in the Yeast 20S Proteasome in Complex with N3-A(4,4-F2P)Nll-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-A(4,4-F2P)Nll-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:52.4
occ:1.00
 O I:ASP177 2.4 50.1 1.0
O I:SER180 2.6 58.3 1.0
O I:ALA174 2.6 53.0 1.0
O I:HOH405 3.4 54.2 1.0
C I:ASP177 3.6 51.1 1.0
C I:ALA174 3.7 55.0 1.0
C I:SER180 3.8 57.1 1.0
OXT I:ASP204 3.9 64.7 1.0
CA I:ASP175 4.1 55.9 1.0
N I:ASP175 4.3 58.4 1.0
CA I:ALA178 4.4 50.5 1.0
C I:ASP175 4.4 54.2 1.0
N I:ALA178 4.4 49.5 1.0
N I:ASP177 4.5 51.2 1.0
C I:ALA178 4.5 52.3 1.0
O I:ASP175 4.5 55.8 1.0
O I:ALA178 4.5 55.4 1.0
CA I:ASP177 4.6 53.3 1.0
N I:SER180 4.7 51.2 1.0
CA I:GLY181 4.7 54.2 1.0
N I:GLY181 4.7 56.5 1.0
OD1 I:ASP175 4.7 58.4 1.0
C I:ASP204 4.7 62.4 1.0
CA I:SER180 4.8 53.4 1.0
CA I:ALA174 4.8 51.4 1.0
O I:ASP204 4.8 75.2 1.0
NH2 Y:ARG19 4.9 74.0 1.0
NH1 Y:ARG19 4.9 74.7 1.0

Magnesium binding site 3 out of 7 in 4y84

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Magnesium binding site 3 out of 7 in the Yeast 20S Proteasome in Complex with N3-A(4,4-F2P)Nll-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-A(4,4-F2P)Nll-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg302

b:65.2
occ:1.00
 O Y:ASP168 2.2 57.0 1.0
O I:ASP204 2.4 75.2 1.0
O Y:ALA165 2.4 53.9 1.0
O Y:SER171 2.6 57.4 1.0
C Y:ASP168 3.1 51.6 1.0
C I:ASP204 3.2 62.4 1.0
CA Y:ALA169 3.5 45.5 1.0
C Y:ALA165 3.6 54.4 1.0
C Y:ALA169 3.6 46.5 1.0
N Y:ALA169 3.7 47.7 1.0
O Y:ALA169 3.7 47.3 1.0
CA I:ASP204 3.7 58.3 1.0
C Y:SER171 3.8 55.1 1.0
NH1 Y:ARG19 3.8 74.7 1.0
OXT I:ASP204 4.0 64.7 1.0
O Y:HIS166 4.1 52.3 1.0
CB I:ASP204 4.1 52.8 1.0
N Y:SER171 4.1 56.5 1.0
CA Y:ASP168 4.4 51.5 1.0
N Y:TYR170 4.4 48.9 1.0
C Y:HIS166 4.4 53.2 1.0
N Y:ASP168 4.4 53.0 1.0
CA Y:ALA165 4.4 53.4 1.0
CA Y:SER171 4.5 53.8 1.0
N Y:HIS166 4.5 54.2 1.0
CZ Y:ARG19 4.6 69.3 1.0
CA Y:HIS166 4.7 52.4 1.0
O Y:ALA164 4.7 55.8 1.0
N Y:GLY172 4.8 53.4 1.0
C Y:ARG167 4.8 52.9 1.0
CB Y:ALA169 4.9 46.6 1.0
NH2 Y:ARG19 4.9 74.0 1.0
CA Y:GLY172 4.9 51.3 1.0
CB Y:SER171 5.0 53.3 1.0

Magnesium binding site 4 out of 7 in 4y84

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Magnesium binding site 4 out of 7 in the Yeast 20S Proteasome in Complex with N3-A(4,4-F2P)Nll-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-A(4,4-F2P)Nll-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg301

b:63.4
occ:1.00
 O K:ASP168 2.2 54.2 1.0
O K:ALA165 2.3 54.0 1.0
O W:ASP204 2.4 61.5 1.0
O K:SER171 2.6 58.4 1.0
C W:ASP204 3.1 51.8 1.0
C K:ASP168 3.2 48.8 1.0
C K:ALA165 3.4 54.0 1.0
CA W:ASP204 3.6 51.5 1.0
CA K:ALA169 3.6 47.3 1.0
N K:ALA169 3.8 47.3 1.0
C K:ALA169 3.8 54.3 1.0
C K:SER171 3.8 58.3 1.0
O K:ALA169 3.8 54.9 1.0
NH1 K:ARG19 3.9 61.9 1.0
O K:HIS166 3.9 53.0 1.0
CB W:ASP204 4.0 51.0 1.0
OXT W:ASP204 4.0 60.1 1.0
N K:SER171 4.2 58.2 1.0
C K:HIS166 4.2 51.6 1.0
CA K:ALA165 4.3 53.4 1.0
N K:ASP168 4.4 46.2 1.0
CA K:ASP168 4.4 46.5 1.0
N K:HIS166 4.4 51.3 1.0
N K:TYR170 4.5 58.1 1.0
CA K:HIS166 4.5 51.5 1.0
CA K:SER171 4.6 56.4 1.0
O K:ALA164 4.6 54.5 1.0
CZ K:ARG19 4.7 63.2 1.0
N K:GLY172 4.8 55.5 1.0
C K:ARG167 4.8 45.5 1.0
N K:ARG167 4.9 48.4 1.0
CA K:GLY172 4.9 51.9 1.0
NH2 K:ARG19 5.0 69.1 1.0
N W:ASP204 5.0 46.9 1.0

Magnesium binding site 5 out of 7 in 4y84

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Magnesium binding site 5 out of 7 in the Yeast 20S Proteasome in Complex with N3-A(4,4-F2P)Nll-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-A(4,4-F2P)Nll-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg301

b:81.4
occ:1.00
 O V:ASP166 2.2 52.1 1.0
O V:ILE163 2.2 61.0 1.0
OXT L:ASP222 2.4 66.3 1.0
O V:SER169 2.8 58.3 1.0
C V:ASP166 3.1 54.6 1.0
C L:ASP222 3.1 71.3 1.0
C V:ILE163 3.3 60.5 1.0
O V:TRP164 3.6 62.5 1.0
CA L:ASP222 3.6 67.4 1.0
N V:ASP166 3.7 50.9 1.0
C V:TRP164 3.8 58.3 1.0
N V:LEU167 3.8 56.3 1.0
O L:ASP222 3.8 78.3 1.0
O V:GLY162 3.8 59.0 1.0
CA V:LEU167 3.9 53.7 1.0
CA V:ASP166 4.0 51.4 1.0
C V:SER169 4.0 52.6 1.0
N V:TRP164 4.1 56.7 1.0
CA V:TRP164 4.2 55.6 1.0
CA V:ILE163 4.2 62.5 1.0
N V:ASN165 4.3 55.9 1.0
CB L:ASP222 4.3 62.6 1.0
NH1 V:ARG19 4.4 68.5 1.0
C V:ASN165 4.4 51.3 1.0
C V:LEU167 4.6 48.9 1.0
N V:SER169 4.6 47.8 1.0
O L:ARG221 4.7 59.7 1.0
CD2 V:LEU167 4.7 47.9 1.0
C V:GLY162 4.8 57.5 1.0
CA V:ASN165 4.8 53.4 1.0
NH2 V:ARG19 4.8 69.8 1.0
CA V:SER169 4.8 48.3 1.0
CZ V:ARG19 4.9 69.0 1.0
CB V:ASP166 4.9 50.9 1.0
N L:ASP222 4.9 63.6 1.0
N V:GLY170 5.0 51.0 1.0
CA V:GLY170 5.0 52.4 1.0

Magnesium binding site 6 out of 7 in 4y84

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Magnesium binding site 6 out of 7 in the Yeast 20S Proteasome in Complex with N3-A(4,4-F2P)Nll-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-A(4,4-F2P)Nll-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg201

b:61.9
occ:1.00
 O N:SER169 2.5 49.8 1.0
O N:ILE163 2.5 48.5 1.0
O N:ASP166 2.7 57.1 1.0
C N:SER169 3.6 49.3 1.0
C N:ILE163 3.7 48.8 1.0
NH1 N:ARG19 3.7 57.1 1.0
C N:ASP166 3.8 50.5 1.0
CD1 a:LEU34 3.8 45.5 1.0
CG2 N:ILE163 3.8 40.3 1.0
CA N:GLY167 4.0 47.5 1.0
CA N:ILE163 4.3 47.4 1.0
O N:GLY167 4.3 51.3 1.0
C N:GLY167 4.3 48.8 1.0
N N:GLY167 4.3 48.2 1.0
CZ N:ARG19 4.4 54.3 1.0
CA N:GLY170 4.4 54.5 1.0
N N:SER169 4.4 45.4 1.0
N N:GLY170 4.5 51.3 1.0
CA N:SER169 4.6 44.2 1.0
NH2 N:ARG19 4.7 51.3 1.0
CB N:ILE163 4.7 45.7 1.0
N N:LYS164 4.7 50.8 1.0
O N:LYS164 4.9 54.6 1.0
CB N:SER169 4.9 39.8 1.0
C N:LYS164 5.0 53.6 1.0
CA N:ASP166 5.0 48.0 1.0
N N:ASP166 5.0 49.4 1.0

Magnesium binding site 7 out of 7 in 4y84

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Magnesium binding site 7 out of 7 in the Yeast 20S Proteasome in Complex with N3-A(4,4-F2P)Nll-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-A(4,4-F2P)Nll-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg301

b:60.7
occ:1.00
 O Z:HOH402 2.3 47.7 1.0
O Z:VAL198 2.4 53.9 1.0
O Z:THR192 2.4 58.1 1.0
O Z:HIS195 2.7 43.7 1.0
C Z:THR192 3.4 58.9 1.0
CG2 Z:THR192 3.5 46.2 1.0
C Z:VAL198 3.6 54.7 1.0
CA Z:THR192 3.7 54.6 1.0
C Z:HIS195 3.7 46.5 1.0
NH2 Z:ARG28 4.0 65.9 1.0
O Z:ASP222 4.0 61.1 1.0
O Z:ILE196 4.1 53.3 1.0
CA Z:ILE196 4.1 49.9 1.0
C Z:ILE196 4.2 50.4 1.0
CB Z:THR192 4.3 52.1 1.0
N Z:ILE196 4.4 47.8 1.0
N Z:VAL198 4.4 50.7 1.0
CA Z:VAL198 4.5 52.0 1.0
N Z:GLY199 4.6 54.9 1.0
OD1 Z:ASP222 4.6 62.2 1.0
CA Z:GLY199 4.6 56.6 1.0
N Z:GLU193 4.6 61.4 1.0
N Z:HIS195 4.7 50.4 1.0
NH2 H:ARG19 4.8 60.8 1.0
CA Z:HIS195 4.9 46.6 1.0
O Z:ALA191 4.9 48.2 1.0
CB Z:VAL198 4.9 55.0 1.0
C Z:ASP222 4.9 63.6 1.0
CZ Z:ARG28 5.0 64.7 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 22:52:53 2024

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