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Magnesium in PDB 4y9z: Yeast 20S Proteasome BETA2-H116E Mutant in Complex with Ac-Lae-Ep

Enzymatic activity of Yeast 20S Proteasome BETA2-H116E Mutant in Complex with Ac-Lae-Ep

All present enzymatic activity of Yeast 20S Proteasome BETA2-H116E Mutant in Complex with Ac-Lae-Ep:
3.4.25.1;

Protein crystallography data

The structure of Yeast 20S Proteasome BETA2-H116E Mutant in Complex with Ac-Lae-Ep, PDB code: 4y9z 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 (°) 135.350, 299.220, 145.140, 90.00, 113.20, 90.00
R / Rfree (%) 19.5 / 21.8

Other elements in 4y9z:

The structure of Yeast 20S Proteasome BETA2-H116E 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-H116E Mutant in Complex with Ac-Lae-Ep (pdb code 4y9z). 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-H116E Mutant in Complex with Ac-Lae-Ep, PDB code: 4y9z:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 4y9z

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Magnesium binding site 1 out of 7 in the Yeast 20S Proteasome BETA2-H116E 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-H116E Mutant in Complex with Ac-Lae-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:65.0
occ:1.00
 O G:MET125 2.3 55.5 1.0
O G:ARG122 2.5 52.1 1.0
OG1 G:THR8 2.6 49.1 1.0
O G:TYR119 2.7 51.5 1.0
CG2 G:THR8 3.3 54.4 1.0
O G:ALA123 3.4 56.7 1.0
C G:MET125 3.4 53.4 1.0
CB G:THR8 3.5 52.7 1.0
C G:ARG122 3.7 52.0 1.0
C G:ALA123 3.7 54.5 1.0
CA G:ALA123 3.8 53.0 1.0
C G:TYR119 3.9 48.5 1.0
N G:ALA123 4.2 52.4 1.0
N G:ARG126 4.2 50.2 1.0
N G:THR8 4.2 51.8 1.0
CA G:ARG126 4.2 48.9 1.0
N G:MET125 4.2 55.6 1.0
CA G:MET125 4.4 57.3 1.0
CD G:PRO127 4.5 46.6 1.0
CA G:THR8 4.5 53.3 1.0
CA G:TYR119 4.6 47.3 1.0
N G:TYR124 4.7 56.1 1.0
C G:ARG126 4.8 48.3 1.0
N G:THR120 4.9 47.2 1.0
CA G:ARG122 4.9 53.9 1.0
N G:PRO127 5.0 46.3 1.0
N G:ARG122 5.0 52.9 1.0
CB G:MET125 5.0 61.5 1.0

Magnesium binding site 2 out of 7 in 4y9z

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Magnesium binding site 2 out of 7 in the Yeast 20S Proteasome BETA2-H116E 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-H116E Mutant in Complex with Ac-Lae-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg301

b:64.7
occ:1.00
 OE1 H:GLN91 2.4 61.9 1.0
O N:ASN92 3.3 50.5 1.0
CD H:GLN91 3.5 56.8 1.0
OD1 N:ASP51 3.5 46.4 1.0
OD2 N:ASP51 3.8 54.2 1.0
NE2 H:GLN91 3.9 56.6 1.0
CG N:ASP51 4.1 45.9 1.0
C N:ASN92 4.4 52.5 1.0
CG H:GLN91 4.8 54.4 1.0

Magnesium binding site 3 out of 7 in 4y9z

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Magnesium binding site 3 out of 7 in the Yeast 20S Proteasome BETA2-H116E 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-H116E Mutant in Complex with Ac-Lae-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:70.0
occ:1.00
 O I:ASP177 2.7 58.2 1.0
O I:SER180 2.8 56.0 1.0
O I:ALA174 2.9 54.4 1.0
OXT I:ASP204 3.6 74.3 1.0
C I:ASP177 3.8 55.8 1.0
C I:ALA174 4.0 60.2 1.0
C I:SER180 4.0 55.7 1.0
CA I:ASP175 4.1 61.2 1.0
O I:ALA178 4.3 61.3 1.0
C I:ASP204 4.4 70.1 1.0
C I:ASP175 4.5 59.4 1.0
N I:ASP175 4.5 60.5 1.0
CA I:ALA178 4.5 55.4 1.0
O I:ASP204 4.5 69.1 1.0
C I:ALA178 4.5 57.1 1.0
NH1 Y:ARG19 4.5 65.1 1.0
O I:ASP175 4.6 60.0 1.0
N I:ALA178 4.6 54.8 1.0
OD1 I:ASP175 4.6 65.2 1.0
N I:ASP177 4.7 56.0 1.0
NH2 Y:ARG19 4.7 65.5 1.0
CA I:GLY181 4.8 56.2 1.0
N I:SER180 4.8 54.3 1.0
CA I:ASP177 4.9 56.0 1.0
N I:GLY181 4.9 55.4 1.0
CA I:SER180 5.0 54.7 1.0

Magnesium binding site 4 out of 7 in 4y9z

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Magnesium binding site 4 out of 7 in the Yeast 20S Proteasome BETA2-H116E 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-H116E Mutant in Complex with Ac-Lae-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg302

b:63.5
occ:1.00
 O Y:ASP168 2.2 59.4 1.0
O I:ASP204 2.3 69.1 1.0
O Y:ALA165 2.4 53.5 1.0
O Y:SER171 2.7 59.0 1.0
C I:ASP204 3.1 70.1 1.0
C Y:ASP168 3.2 55.4 1.0
CA Y:ALA169 3.5 55.0 1.0
C Y:ALA165 3.5 55.8 1.0
O Y:ALA169 3.7 55.3 1.0
C Y:ALA169 3.7 54.4 1.0
CA I:ASP204 3.7 67.9 1.0
N Y:ALA169 3.7 55.4 1.0
C Y:SER171 3.8 57.6 1.0
OXT I:ASP204 4.0 74.3 1.0
NH1 Y:ARG19 4.1 65.1 1.0
O Y:HIS166 4.1 56.0 1.0
CB I:ASP204 4.1 67.6 1.0
N Y:SER171 4.2 55.9 1.0
C Y:HIS166 4.3 55.7 1.0
CA Y:ASP168 4.4 53.8 1.0
N Y:ASP168 4.4 54.9 1.0
CA Y:ALA165 4.4 57.1 1.0
N Y:HIS166 4.5 56.4 1.0
N Y:TYR170 4.5 53.7 1.0
CA Y:SER171 4.5 55.8 1.0
CZ Y:ARG19 4.6 63.7 1.0
CA Y:HIS166 4.6 55.7 1.0
O Y:ALA164 4.6 54.4 1.0
NH2 Y:ARG19 4.8 65.5 1.0
C Y:ARG167 4.8 54.9 1.0
N Y:GLY172 4.8 59.0 1.0
CB Y:ALA169 4.9 55.9 1.0
CB Y:SER171 4.9 54.3 1.0
N Y:ARG167 4.9 53.6 1.0
CA Y:GLY172 4.9 61.3 1.0

Magnesium binding site 5 out of 7 in 4y9z

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Magnesium binding site 5 out of 7 in the Yeast 20S Proteasome BETA2-H116E 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-H116E Mutant in Complex with Ac-Lae-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg301

b:77.3
occ:1.00
 O K:ASP168 2.1 58.2 1.0
O K:ALA165 2.2 59.1 1.0
O W:ASP204 2.4 64.7 1.0
O K:SER171 2.8 55.9 1.0
C W:ASP204 3.1 61.6 1.0
C K:ASP168 3.1 53.3 1.0
C K:ALA165 3.3 56.8 1.0
CA W:ASP204 3.6 59.3 1.0
CA K:ALA169 3.6 52.5 1.0
N K:ALA169 3.8 52.2 1.0
O K:HIS166 3.8 58.6 1.0
C K:ALA169 3.9 54.2 1.0
C K:SER171 3.9 55.8 1.0
O K:ALA169 3.9 57.1 1.0
OXT W:ASP204 4.0 62.7 1.0
CB W:ASP204 4.0 59.1 1.0
C K:HIS166 4.0 56.2 1.0
N K:ASP168 4.2 54.8 1.0
CA K:ALA165 4.2 56.4 1.0
N K:HIS166 4.2 56.2 1.0
CA K:ASP168 4.3 52.7 1.0
NH1 K:ARG19 4.3 58.8 1.0
N K:SER171 4.4 52.7 1.0
CA K:HIS166 4.4 56.4 1.0
O K:ALA164 4.4 59.4 1.0
C K:ARG167 4.6 54.2 1.0
CA K:SER171 4.6 53.8 1.0
N K:ARG167 4.6 54.9 1.0
N K:TYR170 4.7 53.3 1.0
CZ K:ARG19 4.8 59.2 1.0
N K:GLY172 4.9 56.7 1.0
CB K:SER171 4.9 53.5 1.0
O K:ARG167 4.9 53.4 1.0
NH2 K:ARG19 5.0 61.2 1.0
N W:ASP204 5.0 59.6 1.0
CA K:GLY172 5.0 58.2 1.0

Magnesium binding site 6 out of 7 in 4y9z

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Magnesium binding site 6 out of 7 in the Yeast 20S Proteasome BETA2-H116E 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-H116E Mutant in Complex with Ac-Lae-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg301

b:65.0
occ:1.00
 O V:ASP166 2.1 55.2 1.0
O V:ILE163 2.2 58.7 1.0
OXT L:ASP222 2.2 62.2 1.0
O V:SER169 2.6 57.0 1.0
C L:ASP222 3.0 64.5 1.0
C V:ASP166 3.1 54.3 1.0
C V:ILE163 3.3 58.8 1.0
CA L:ASP222 3.6 65.0 1.0
O V:GLY162 3.7 58.4 1.0
C V:SER169 3.8 55.4 1.0
O L:ASP222 3.8 68.5 1.0
N V:LEU167 3.8 53.9 1.0
N V:ASP166 3.8 54.1 1.0
CA V:LEU167 3.9 52.9 1.0
C V:TRP164 4.0 59.1 1.0
O V:TRP164 4.0 58.7 1.0
CA V:ASP166 4.1 54.1 1.0
N V:TRP164 4.1 59.5 1.0
CA V:ILE163 4.2 58.9 1.0
NH1 V:ARG19 4.2 58.8 1.0
CB L:ASP222 4.2 64.5 1.0
CA V:TRP164 4.3 59.7 1.0
N V:ASN165 4.3 58.5 1.0
C V:LEU167 4.4 52.9 1.0
N V:SER169 4.5 54.0 1.0
C V:ASN165 4.5 54.8 1.0
CA V:SER169 4.6 53.7 1.0
N V:GLY170 4.7 55.7 1.0
CA V:GLY170 4.7 57.0 1.0
O V:LEU167 4.7 51.8 1.0
CZ V:ARG19 4.7 58.0 1.0
C V:GLY162 4.7 58.4 1.0
O L:ARG221 4.8 67.6 1.0
NH2 V:ARG19 4.8 60.8 1.0
CD2 V:LEU167 4.9 52.5 1.0
N L:ASP222 4.9 65.4 1.0
CB V:ASP166 4.9 54.0 1.0
CA V:ASN165 4.9 56.3 1.0
CB V:SER169 5.0 54.7 1.0
N V:ILE163 5.0 58.4 1.0

Magnesium binding site 7 out of 7 in 4y9z

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Magnesium binding site 7 out of 7 in the Yeast 20S Proteasome BETA2-H116E 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-H116E Mutant in Complex with Ac-Lae-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg201

b:56.6
occ:1.00
 O N:ILE163 2.5 49.8 1.0
O N:SER169 2.6 48.3 1.0
O N:ASP166 3.0 53.8 1.0
CD1 a:LEU34 3.6 48.6 1.0
C N:ILE163 3.6 49.6 1.0
C N:SER169 3.7 45.9 1.0
NH1 N:ARG19 3.7 49.0 1.0
CG2 N:ILE163 3.8 48.3 1.0
C N:ASP166 4.0 48.2 1.0
CA N:GLY167 4.3 46.0 1.0
CA N:ILE163 4.3 48.5 1.0
O N:GLY167 4.4 47.9 1.0
CZ N:ARG19 4.4 47.7 1.0
CA N:GLY170 4.4 47.0 1.0
N N:GLY170 4.5 45.2 1.0
C N:GLY167 4.5 46.1 1.0
N N:GLY167 4.6 46.6 1.0
NH2 N:ARG19 4.6 46.3 1.0
N N:LYS164 4.7 51.2 1.0
CB N:ILE163 4.7 48.0 1.0
CA N:SER169 4.7 43.8 1.0
N N:SER169 4.7 43.5 1.0
O N:LYS164 4.9 56.6 1.0
C N:LYS164 4.9 52.1 1.0
CA N:LYS164 4.9 52.7 1.0
CG a:LEU34 4.9 49.8 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 23:05:49 2024

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