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Magnesium in PDB 4ya3: Yeast 20S Proteasome BETA2-H116N Mutant in Complex with Ac-Pae-Ep

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

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

Protein crystallography data

The structure of Yeast 20S Proteasome BETA2-H116N Mutant in Complex with Ac-Pae-Ep, PDB code: 4ya3 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 (°) 137.500, 301.360, 145.840, 90.00, 113.25, 90.00
R / Rfree (%) 20.2 / 22

Other elements in 4ya3:

The structure of Yeast 20S Proteasome BETA2-H116N Mutant in Complex with Ac-Pae-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-Pae-Ep (pdb code 4ya3). 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-Pae-Ep, PDB code: 4ya3:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 4ya3

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

b:51.9
occ:1.00
 O G:MET125 2.0 51.2 1.0
O G:ARG122 2.7 49.0 1.0
OG1 G:THR8 2.7 44.5 1.0
O G:TYR119 2.8 45.5 1.0
C G:MET125 3.2 51.7 1.0
CG2 G:THR8 3.3 47.6 1.0
O G:ALA123 3.4 50.7 1.0
CB G:THR8 3.6 47.1 1.0
C G:ALA123 3.8 49.9 1.0
C G:ARG122 3.8 47.5 1.0
CA G:ALA123 3.8 48.1 1.0
C G:TYR119 4.0 42.6 1.0
N G:ARG126 4.0 47.9 1.0
CA G:ARG126 4.0 45.8 1.0
N G:MET125 4.1 53.5 1.0
N G:THR8 4.2 50.1 1.0
CA G:MET125 4.2 55.3 1.0
N G:ALA123 4.3 47.3 1.0
CD G:PRO127 4.4 43.6 1.0
CA G:THR8 4.6 48.2 1.0
N G:TYR124 4.7 50.7 1.0
C G:ARG126 4.7 43.9 1.0
CA G:TYR119 4.7 42.2 1.0
CB G:MET125 4.8 60.0 1.0
N G:PRO127 4.9 44.0 1.0
C G:TYR124 4.9 52.2 1.0

Magnesium binding site 2 out of 7 in 4ya3

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

b:67.5
occ:1.00
 O I:ASP177 2.7 46.8 1.0
O I:SER180 2.8 56.0 1.0
O I:ALA174 3.2 51.0 1.0
OXT I:ASP204 3.6 59.1 1.0
C I:ASP177 3.8 48.2 1.0
C I:SER180 4.0 52.6 1.0
O I:ASP204 4.2 58.0 1.0
O I:ALA178 4.2 52.6 1.0
C I:ALA174 4.2 50.8 1.0
C I:ASP204 4.3 57.5 1.0
NH1 Y:ARG19 4.3 55.9 1.0
CA I:ALA178 4.4 48.4 1.0
CA I:ASP175 4.4 53.0 1.0
NH2 Y:ARG19 4.4 58.1 1.0
C I:ALA178 4.4 50.7 1.0
N I:ALA178 4.5 47.4 1.0
C I:ASP175 4.7 54.2 1.0
O I:ASP175 4.7 58.9 1.0
N I:ASP177 4.7 49.4 1.0
N I:SER180 4.7 50.2 1.0
CZ Y:ARG19 4.8 56.5 1.0
N I:ASP175 4.8 51.1 1.0
CA I:GLY181 4.8 50.7 1.0
N I:GLY181 4.9 51.1 1.0
CA I:ASP177 4.9 48.8 1.0
CA I:SER180 4.9 51.8 1.0
OD1 I:ASP175 5.0 56.1 1.0

Magnesium binding site 3 out of 7 in 4ya3

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

b:49.2
occ:1.00
 O K:ALA165 2.3 50.7 1.0
O K:ASP168 2.4 49.5 1.0
O W:ASP204 2.4 56.4 1.0
O K:HOH406 2.5 40.0 1.0
O K:SER171 2.6 46.9 1.0
C W:ASP204 3.1 56.8 1.0
C K:ASP168 3.4 47.8 1.0
C K:ALA165 3.5 49.2 1.0
CA W:ASP204 3.6 56.7 1.0
NH1 K:ARG19 3.7 58.6 1.0
CA K:ALA169 3.8 48.0 1.0
C K:SER171 3.8 50.3 1.0
O K:ALA169 3.8 51.2 1.0
CB W:ASP204 3.9 56.1 1.0
C K:ALA169 3.9 49.2 1.0
OXT W:ASP204 4.0 54.7 1.0
N K:ALA169 4.0 47.7 1.0
O K:HIS166 4.2 51.5 1.0
CA K:ALA165 4.2 49.9 1.0
N K:SER171 4.3 50.2 1.0
C K:HIS166 4.4 48.8 1.0
N K:HIS166 4.5 48.1 1.0
CZ K:ARG19 4.5 56.8 1.0
N K:ASP168 4.5 47.2 1.0
CA K:ASP168 4.6 46.8 1.0
CA K:SER171 4.6 49.8 1.0
CA K:HIS166 4.7 48.6 1.0
O K:ALA164 4.7 50.4 1.0
N K:TYR170 4.7 50.1 1.0
N K:GLY172 4.8 50.6 1.0
NH2 K:ARG19 4.8 58.5 1.0
CG W:ASP204 4.8 55.7 1.0
CA K:GLY172 4.9 52.9 1.0
C K:ARG167 4.9 46.8 1.0
N K:ARG167 5.0 46.9 1.0

Magnesium binding site 4 out of 7 in 4ya3

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Magnesium binding site 4 out of 7 in the Yeast 20S Proteasome BETA2-H116N Mutant in Complex with Ac-Pae-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-Pae-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg201

b:53.9
occ:1.00
 O N:SER169 2.8 45.6 1.0
O N:ILE163 3.2 44.9 1.0
O N:ASP166 3.4 48.2 1.0
NH1 N:ARG19 3.5 46.7 1.0
CD1 a:LEU34 3.6 50.4 1.0
C N:SER169 4.0 44.4 1.0
CZ N:ARG19 4.1 46.4 1.0
CA N:GLY167 4.1 42.4 1.0
NH2 N:ARG19 4.2 48.9 1.0
O N:GLY167 4.2 45.1 1.0
CG2 N:ILE163 4.3 42.6 1.0
C N:ASP166 4.3 43.6 1.0
C N:ILE163 4.3 44.4 1.0
C N:GLY167 4.4 42.5 1.0
CA N:GLY170 4.5 44.8 1.0
N N:GLY167 4.6 42.5 1.0
N N:GLY170 4.7 44.4 1.0
CG a:LEU34 4.9 50.5 1.0
CA N:ILE163 4.9 43.1 1.0
N N:SER169 5.0 42.0 1.0

Magnesium binding site 5 out of 7 in 4ya3

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

b:67.9
occ:1.00
 O V:ASP166 2.2 46.9 1.0
O V:ILE163 2.2 50.3 1.0
OXT L:ASP222 2.2 64.2 1.0
O V:SER169 2.2 49.3 1.0
O V:HOH408 2.7 43.6 1.0
C L:ASP222 3.2 66.0 1.0
C V:ASP166 3.2 48.2 1.0
C V:ILE163 3.3 49.9 1.0
C V:SER169 3.4 48.2 1.0
O V:GLY162 3.8 46.2 1.0
CA L:ASP222 3.8 67.0 1.0
CA V:LEU167 3.9 49.5 1.0
N V:LEU167 3.9 49.1 1.0
NH1 V:ARG19 4.0 57.7 1.0
CA V:ILE163 4.0 49.1 1.0
N V:ASP166 4.1 49.5 1.0
O L:ASP222 4.1 68.0 1.0
N V:SER169 4.2 47.1 1.0
CA V:ASP166 4.2 48.2 1.0
CB L:ASP222 4.2 67.2 1.0
N V:TRP164 4.2 51.4 1.0
CA V:SER169 4.3 47.7 1.0
N V:GLY170 4.3 49.3 1.0
C V:TRP164 4.3 52.1 1.0
C V:LEU167 4.3 49.7 1.0
CA V:GLY170 4.4 53.0 1.0
O V:TRP164 4.5 52.4 1.0
CA V:TRP164 4.5 51.9 1.0
O V:LEU167 4.5 52.1 1.0
CZ V:ARG19 4.5 56.2 1.0
N V:ASN165 4.6 51.3 1.0
CB V:SER169 4.6 47.6 1.0
C V:GLY162 4.7 47.9 1.0
C V:ASN165 4.8 49.9 1.0
NH2 V:ARG19 4.8 59.6 1.0
N V:ILE163 4.9 48.7 1.0
CB V:ASP166 5.0 48.1 1.0
N V:GLY168 5.0 48.3 1.0

Magnesium binding site 6 out of 7 in 4ya3

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

b:53.2
occ:1.00
 O Y:ASP168 2.3 47.1 1.0
O I:ASP204 2.4 58.0 1.0
O Y:SER171 2.5 51.6 1.0
O Y:ALA165 2.6 49.8 1.0
C I:ASP204 3.2 57.5 1.0
C Y:ASP168 3.3 47.1 1.0
NH1 Y:ARG19 3.4 55.9 1.0
O Y:ALA169 3.5 48.2 1.0
CA Y:ALA169 3.6 46.7 1.0
C Y:ALA169 3.6 47.3 1.0
C Y:SER171 3.7 48.8 1.0
C Y:ALA165 3.8 46.6 1.0
CA I:ASP204 3.8 57.2 1.0
N Y:ALA169 3.9 47.1 1.0
OXT I:ASP204 4.1 59.1 1.0
CB I:ASP204 4.1 57.6 1.0
N Y:SER171 4.1 46.8 1.0
CZ Y:ARG19 4.3 56.5 1.0
O Y:HIS166 4.4 46.3 1.0
CA Y:ALA165 4.4 47.1 1.0
N Y:TYR170 4.5 47.5 1.0
CA Y:SER171 4.5 47.3 1.0
CA Y:ASP168 4.6 47.2 1.0
N Y:ASP168 4.7 48.2 1.0
C Y:HIS166 4.7 45.9 1.0
NH2 Y:ARG19 4.7 58.1 1.0
N Y:GLY172 4.7 48.6 1.0
N Y:HIS166 4.8 46.6 1.0
O Y:ALA164 4.9 45.0 1.0
CA Y:GLY172 4.9 48.5 1.0
CB Y:ALA169 5.0 46.3 1.0
CG I:ASP204 5.0 58.0 1.0

Magnesium binding site 7 out of 7 in 4ya3

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

b:60.7
occ:1.00
 O Z:VAL198 2.6 53.2 1.0
O Z:THR192 2.7 58.7 1.0
O Z:HIS195 3.0 44.9 1.0
C Z:THR192 3.7 58.6 1.0
C Z:VAL198 3.8 53.3 1.0
O Z:ASP222 3.8 70.7 1.0
CG2 Z:THR192 3.8 60.9 1.0
NH2 Z:ARG28 3.9 58.0 1.0
O Z:ILE196 4.0 52.2 1.0
C Z:HIS195 4.0 49.6 1.0
CA Z:THR192 4.1 58.9 1.0
CA Z:ILE196 4.1 50.6 1.0
NH2 H:ARG19 4.2 62.3 1.0
C Z:ILE196 4.2 50.5 1.0
OD1 Z:ASP222 4.4 64.0 1.0
N Z:VAL198 4.5 50.1 1.0
N Z:ILE196 4.5 49.8 1.0
CB Z:THR192 4.6 59.7 1.0
CA Z:VAL198 4.6 52.4 1.0
C Z:ASP222 4.7 70.3 1.0
N Z:GLY199 4.7 53.3 1.0
CA Z:GLY199 4.7 54.8 1.0
CZ Z:ARG28 4.8 57.3 1.0
N Z:GLU193 4.9 59.6 1.0
CZ H:ARG19 4.9 59.3 1.0
NH1 H:ARG19 5.0 59.3 1.0
NH1 Z:ARG28 5.0 59.0 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 23:05:58 2024

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