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Magnesium in PDB 4ya2: Yeast 20S Proteasome BETA2-H116N Mutant in Complex with Ac-Lae-Ep

Enzymatic activity of Yeast 20S Proteasome BETA2-H116N Mutant in Complex with Ac-Lae-Ep

All present enzymatic activity of Yeast 20S Proteasome BETA2-H116N Mutant in Complex with Ac-Lae-Ep:
3.4.25.1;

Protein crystallography data

The structure of Yeast 20S Proteasome BETA2-H116N Mutant in Complex with Ac-Lae-Ep, PDB code: 4ya2 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 (°) 135.200, 300.040, 145.130, 90.00, 113.14, 90.00
R / Rfree (%) 18.4 / 20.5

Other elements in 4ya2:

The structure of Yeast 20S Proteasome BETA2-H116N Mutant in Complex with Ac-Lae-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 BETA2-H116N Mutant in Complex with Ac-Lae-Ep (pdb code 4ya2). 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 BETA2-H116N Mutant in Complex with Ac-Lae-Ep, PDB code: 4ya2:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 4ya2

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Magnesium binding site 1 out of 7 in the Yeast 20S Proteasome BETA2-H116N Mutant in Complex with Ac-Lae-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 BETA2-H116N Mutant in Complex with Ac-Lae-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:53.6
occ:1.00
 O G:MET125 2.3 46.9 1.0
O G:ARG122 2.6 50.4 1.0
OG1 G:THR8 2.7 43.0 1.0
O G:TYR119 2.9 39.8 1.0
O G:ALA123 3.1 49.9 1.0
CG2 G:THR8 3.2 44.7 1.0
C G:MET125 3.4 47.0 1.0
CB G:THR8 3.5 44.2 1.0
C G:ALA123 3.5 45.6 1.0
O G:HOH430 3.5 67.6 1.0
CA G:ALA123 3.6 44.5 1.0
C G:ARG122 3.7 47.4 1.0
N G:THR8 4.0 44.7 1.0
N G:ALA123 4.1 46.2 1.0
C G:TYR119 4.1 42.5 1.0
N G:MET125 4.1 45.7 1.0
N G:ARG126 4.3 46.1 1.0
CA G:MET125 4.4 47.3 1.0
CA G:THR8 4.4 44.8 1.0
CA G:ARG126 4.4 43.8 1.0
N G:TYR124 4.5 47.7 1.0
CD G:PRO127 4.6 35.1 1.0
CA G:TYR119 4.9 41.4 1.0
C G:TYR124 4.9 48.1 1.0
CB G:ALA123 4.9 42.7 1.0
CA G:ARG122 4.9 47.4 1.0
CB G:MET125 5.0 50.1 1.0
N G:ARG122 5.0 43.5 1.0

Magnesium binding site 2 out of 7 in 4ya2

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Magnesium binding site 2 out of 7 in the Yeast 20S Proteasome BETA2-H116N Mutant in Complex with Ac-Lae-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 BETA2-H116N Mutant in Complex with Ac-Lae-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg301

b:74.1
occ:1.00
 OE1 H:GLN91 2.8 65.1 1.0
O N:ASN92 2.8 45.2 1.0
O N:HOH311 3.1 44.0 1.0
C N:ASN92 3.8 44.6 1.0
CD H:GLN91 3.9 60.1 1.0
CA N:ASN92 4.3 44.0 1.0
OD1 N:ASP51 4.5 35.1 1.0
OD2 N:ASP51 4.5 34.4 1.0
CB N:ASN92 4.5 45.9 1.0
NE2 H:GLN91 4.5 60.3 1.0
N N:LEU93 4.9 42.8 1.0
CG N:ASP51 4.9 24.9 1.0

Magnesium binding site 3 out of 7 in 4ya2

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Magnesium binding site 3 out of 7 in the Yeast 20S Proteasome BETA2-H116N Mutant in Complex with Ac-Lae-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 BETA2-H116N Mutant in Complex with Ac-Lae-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:74.9
occ:1.00
 O I:SER180 2.7 55.9 1.0
O I:ASP177 2.7 44.6 1.0
O I:ALA174 2.8 47.7 1.0
O I:HOH412 3.6 38.6 1.0
OXT I:ASP204 3.7 61.1 1.0
C I:ALA174 3.8 49.4 1.0
C I:ASP177 3.8 47.5 1.0
C I:SER180 3.9 50.1 1.0
CA I:ASP175 4.0 53.6 1.0
N I:ASP175 4.3 51.5 1.0
C I:ASP175 4.4 55.4 1.0
O I:ALA178 4.5 47.0 1.0
O I:ASP175 4.5 59.9 1.0
OD1 I:ASP175 4.5 46.4 1.0
N I:ASP177 4.6 51.0 1.0
C I:ASP204 4.6 59.9 1.0
CA I:GLY181 4.6 46.3 1.0
CA I:ALA178 4.6 46.5 1.0
C I:ALA178 4.6 47.3 1.0
N I:ALA178 4.7 46.8 1.0
NH1 Y:ARG19 4.7 59.4 1.0
N I:GLY181 4.7 48.9 1.0
O I:ASP204 4.7 59.8 1.0
N I:SER180 4.8 46.0 1.0
CA I:ASP177 4.8 50.7 1.0
CA I:SER180 4.9 47.4 1.0
NH2 Y:ARG19 4.9 60.6 1.0
CA I:ALA174 4.9 45.0 1.0

Magnesium binding site 4 out of 7 in 4ya2

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Magnesium binding site 4 out of 7 in the Yeast 20S Proteasome BETA2-H116N Mutant in Complex with Ac-Lae-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 BETA2-H116N Mutant in Complex with Ac-Lae-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg302

b:50.6
occ:1.00
 O Y:ASP168 2.1 46.8 1.0
O I:ASP204 2.3 59.8 1.0
O Y:SER171 2.3 46.8 1.0
O Y:ALA165 2.6 44.5 1.0
O Y:HOH407 2.6 41.0 1.0
C Y:ASP168 3.2 41.4 1.0
C I:ASP204 3.3 59.9 1.0
O Y:ALA169 3.5 48.5 1.0
CA Y:ALA169 3.5 43.0 1.0
C Y:ALA169 3.5 45.6 1.0
C Y:SER171 3.5 46.5 1.0
C Y:ALA165 3.7 42.5 1.0
NH1 Y:ARG19 3.7 59.4 1.0
N Y:ALA169 3.7 41.6 1.0
CA I:ASP204 3.9 59.4 1.0
N Y:SER171 3.9 42.3 1.0
OXT I:ASP204 4.1 61.1 1.0
CB I:ASP204 4.2 59.8 1.0
CA Y:SER171 4.2 43.5 1.0
N Y:TYR170 4.2 48.2 1.0
CZ Y:ARG19 4.3 58.7 1.0
O Y:HIS166 4.3 44.0 1.0
CA Y:ALA165 4.4 42.1 1.0
CA Y:ASP168 4.4 41.0 1.0
N Y:ASP168 4.5 42.1 1.0
N Y:GLY172 4.5 48.0 1.0
NH2 Y:ARG19 4.6 60.6 1.0
C Y:HIS166 4.6 44.0 1.0
O Y:ALA164 4.6 42.1 1.0
N Y:HIS166 4.7 42.3 1.0
CB Y:SER171 4.7 42.4 1.0
CA Y:GLY172 4.7 49.9 1.0
C Y:TYR170 4.9 46.8 1.0
CB Y:ALA169 4.9 42.7 1.0
C Y:ARG167 4.9 44.2 1.0
CA Y:HIS166 4.9 43.6 1.0

Magnesium binding site 5 out of 7 in 4ya2

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Magnesium binding site 5 out of 7 in the Yeast 20S Proteasome BETA2-H116N Mutant in Complex with Ac-Lae-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 BETA2-H116N Mutant in Complex with Ac-Lae-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg301

b:56.3
occ:1.00
 O K:ASP168 2.1 45.9 1.0
O W:ASP204 2.2 56.3 1.0
O K:ALA165 2.5 47.6 1.0
O K:SER171 2.5 50.0 1.0
C W:ASP204 3.1 53.9 1.0
C K:ASP168 3.1 42.2 1.0
CA K:ALA169 3.5 42.1 1.0
O K:ALA169 3.6 47.4 1.0
C K:ALA165 3.6 46.2 1.0
C K:ALA169 3.6 45.6 1.0
C K:SER171 3.6 47.9 1.0
N K:ALA169 3.7 42.1 1.0
CA W:ASP204 3.7 51.3 1.0
NH1 K:ARG19 3.8 71.7 1.0
OXT W:ASP204 4.0 54.1 1.0
N K:SER171 4.0 47.2 1.0
CB W:ASP204 4.1 51.5 1.0
O K:HIS166 4.1 43.3 1.0
CA K:ALA165 4.3 49.9 1.0
CA K:ASP168 4.3 40.9 1.0
N K:TYR170 4.4 46.9 1.0
CA K:SER171 4.4 45.5 1.0
N K:ASP168 4.4 41.4 1.0
CZ K:ARG19 4.4 67.1 1.0
C K:HIS166 4.4 41.8 1.0
O K:ALA164 4.6 53.5 1.0
N K:HIS166 4.6 41.1 1.0
N K:GLY172 4.7 49.7 1.0
NH2 K:ARG19 4.7 65.7 1.0
CA K:HIS166 4.8 40.5 1.0
CB K:SER171 4.8 44.5 1.0
CA K:GLY172 4.8 50.7 1.0
C K:ARG167 4.8 42.0 1.0
CB K:ALA169 4.9 40.1 1.0

Magnesium binding site 6 out of 7 in 4ya2

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Magnesium binding site 6 out of 7 in the Yeast 20S Proteasome BETA2-H116N Mutant in Complex with Ac-Lae-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 BETA2-H116N Mutant in Complex with Ac-Lae-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg301

b:62.2
occ:1.00
 O V:ASP166 2.1 51.6 1.0
OXT L:ASP222 2.1 66.5 1.0
O V:SER169 2.2 48.6 1.0
O V:ILE163 2.2 41.0 1.0
C L:ASP222 3.1 65.0 1.0
C V:ASP166 3.1 51.2 1.0
C V:ILE163 3.3 45.4 1.0
C V:SER169 3.4 45.8 1.0
O V:GLY162 3.7 46.0 1.0
CA L:ASP222 3.8 59.8 1.0
NH1 V:ARG19 3.8 66.0 1.0
CA V:LEU167 3.9 49.4 1.0
N V:LEU167 3.9 51.5 1.0
O L:ASP222 4.0 73.2 1.0
CA V:ILE163 4.0 45.9 1.0
N V:ASP166 4.0 49.7 1.0
N V:SER169 4.2 44.0 1.0
CA V:ASP166 4.2 50.3 1.0
N V:TRP164 4.2 47.3 1.0
CB L:ASP222 4.2 59.2 1.0
C V:LEU167 4.3 48.4 1.0
CA V:SER169 4.3 42.7 1.0
N V:GLY170 4.3 47.3 1.0
CA V:GLY170 4.3 51.6 1.0
C V:TRP164 4.3 50.6 1.0
CZ V:ARG19 4.4 59.7 1.0
O V:LEU167 4.5 45.9 1.0
O V:TRP164 4.5 50.6 1.0
CA V:TRP164 4.5 48.5 1.0
N V:ASN165 4.6 50.6 1.0
NH2 V:ARG19 4.6 61.0 1.0
C V:GLY162 4.7 43.9 1.0
CB V:SER169 4.7 43.0 1.0
C V:ASN165 4.8 50.7 1.0
N V:ILE163 4.8 44.4 1.0
CB V:ASP166 4.9 50.8 1.0
N V:GLY168 4.9 47.5 1.0

Magnesium binding site 7 out of 7 in 4ya2

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Magnesium binding site 7 out of 7 in the Yeast 20S Proteasome BETA2-H116N Mutant in Complex with Ac-Lae-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 BETA2-H116N Mutant in Complex with Ac-Lae-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg201

b:52.7
occ:1.00
 O N:ILE163 2.6 42.5 1.0
O N:SER169 2.8 46.6 1.0
O N:ASP166 3.2 47.0 1.0
CD1 a:LEU34 3.6 44.1 1.0
NH1 N:ARG19 3.6 49.5 1.0
C N:ILE163 3.7 43.0 1.0
CG2 N:ILE163 3.9 38.5 1.0
C N:SER169 4.0 44.9 1.0
C N:ASP166 4.1 44.5 1.0
CA N:GLY167 4.2 42.9 1.0
O N:GLY167 4.4 40.9 1.0
CA N:ILE163 4.5 40.9 1.0
CZ N:ARG19 4.5 48.3 1.0
CA N:GLY170 4.5 45.6 1.0
N N:GLY167 4.6 42.7 1.0
C N:GLY167 4.6 41.5 1.0
N N:GLY170 4.7 44.6 1.0
N N:LYS164 4.8 45.1 1.0
NH2 N:ARG19 4.8 45.5 1.0
CG a:LEU34 4.8 44.6 1.0
O N:LYS164 4.8 50.5 1.0
CB N:ILE163 4.8 39.0 1.0
C N:LYS164 4.9 48.1 1.0
CA N:LYS164 4.9 47.1 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 23:05:57 2024

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