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Magnesium in PDB 4ya7: Yeast 20S Proteasome BETA2-H114D Mutant in Complex with Ac-Lae-Ep

Enzymatic activity of Yeast 20S Proteasome BETA2-H114D Mutant in Complex with Ac-Lae-Ep

All present enzymatic activity of Yeast 20S Proteasome BETA2-H114D Mutant in Complex with Ac-Lae-Ep:
3.4.25.1;

Protein crystallography data

The structure of Yeast 20S Proteasome BETA2-H114D Mutant in Complex with Ac-Lae-Ep, PDB code: 4ya7 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 (°) 135.020, 299.940, 144.880, 90.00, 113.00, 90.00
R / Rfree (%) 21.5 / 23.7

Other elements in 4ya7:

The structure of Yeast 20S Proteasome BETA2-H114D 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-H114D Mutant in Complex with Ac-Lae-Ep (pdb code 4ya7). 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-H114D Mutant in Complex with Ac-Lae-Ep, PDB code: 4ya7:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 4ya7

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Magnesium binding site 1 out of 7 in the Yeast 20S Proteasome BETA2-H114D 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-H114D Mutant in Complex with Ac-Lae-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:42.6
occ:1.00
 O G:ARG122 2.3 39.9 1.0
O G:MET125 2.3 41.4 1.0
O G:HOH422 2.4 42.2 1.0
O G:TYR119 2.5 36.6 1.0
OG1 G:THR8 2.5 39.7 1.0
CG2 G:THR8 3.3 41.5 1.0
C G:ARG122 3.4 39.7 1.0
C G:MET125 3.5 39.4 1.0
CB G:THR8 3.5 40.5 1.0
O G:ALA123 3.5 40.5 1.0
C G:TYR119 3.6 35.0 1.0
CA G:ALA123 3.7 39.7 1.0
C G:ALA123 3.8 40.4 1.0
N G:ALA123 4.0 39.3 1.0
N G:MET125 4.2 41.8 1.0
N G:ARG126 4.3 37.2 1.0
N G:THR8 4.4 41.0 1.0
CA G:MET125 4.4 42.8 1.0
CA G:ARG126 4.4 35.5 1.0
CA G:TYR119 4.4 34.0 1.0
CA G:THR8 4.6 41.1 1.0
CD G:PRO127 4.6 33.4 1.0
CA G:ARG122 4.6 40.5 1.0
N G:ARG122 4.6 38.5 1.0
N G:THR120 4.7 34.5 1.0
N G:TYR124 4.7 42.1 1.0
CA G:THR120 4.8 34.2 1.0
C G:THR120 4.9 35.1 1.0
CB G:MET125 4.9 46.9 1.0
C G:ARG126 4.9 35.0 1.0
CB G:TYR119 4.9 34.1 1.0

Magnesium binding site 2 out of 7 in 4ya7

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Magnesium binding site 2 out of 7 in the Yeast 20S Proteasome BETA2-H114D 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-H114D Mutant in Complex with Ac-Lae-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg301

b:62.0
occ:1.00
 OE1 H:GLN91 2.4 42.8 1.0
O N:HOH312 3.0 35.6 1.0
CD H:GLN91 3.5 42.1 1.0
O N:ASN92 3.7 37.9 1.0
OD1 N:ASP51 3.9 30.9 1.0
NE2 H:GLN91 4.0 43.5 1.0
OD2 N:ASP51 4.2 31.0 1.0
O H:HOH414 4.2 27.9 1.0
CG N:ASP51 4.5 29.7 1.0
O N:HOH324 4.6 38.9 1.0
C N:ASN92 4.7 37.2 1.0
CG H:GLN91 4.7 39.3 1.0

Magnesium binding site 3 out of 7 in 4ya7

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Magnesium binding site 3 out of 7 in the Yeast 20S Proteasome BETA2-H114D 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-H114D Mutant in Complex with Ac-Lae-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:54.2
occ:1.00
 O I:HOH426 2.5 54.0 1.0
O I:SER180 2.5 39.4 1.0
O I:ALA174 2.5 43.4 1.0
O I:ASP177 2.6 39.6 1.0
O I:HOH418 3.5 44.0 1.0
C I:ALA174 3.5 44.0 1.0
C I:SER180 3.7 39.4 1.0
C I:ASP177 3.8 39.4 1.0
CA I:ASP175 3.8 45.2 1.0
OXT I:ASP204 4.0 48.8 1.0
O I:HOH402 4.1 44.4 1.0
N I:ASP175 4.1 44.2 1.0
C I:ASP175 4.3 43.8 1.0
OD1 I:ASP175 4.4 48.6 1.0
N I:ASP177 4.5 39.8 1.0
CA I:GLY181 4.5 40.2 1.0
O I:ASP175 4.5 44.6 1.0
N I:GLY181 4.6 39.0 1.0
O I:ALA178 4.6 40.5 1.0
N I:SER180 4.6 39.1 1.0
CA I:ALA174 4.6 43.4 1.0
N I:ALA178 4.7 38.8 1.0
CA I:ALA178 4.7 39.3 1.0
CA I:ASP177 4.7 40.0 1.0
C I:ALA178 4.7 40.1 1.0
CA I:SER180 4.7 39.5 1.0
CB I:ALA174 4.8 43.8 1.0
C I:ASP204 4.9 51.2 1.0
N I:ARG176 5.0 41.7 1.0

Magnesium binding site 4 out of 7 in 4ya7

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Magnesium binding site 4 out of 7 in the Yeast 20S Proteasome BETA2-H114D 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-H114D Mutant in Complex with Ac-Lae-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg302

b:56.1
occ:1.00
 O Y:ASP168 2.2 40.3 1.0
O I:ASP204 2.3 52.1 1.0
O Y:SER171 2.4 44.4 1.0
O Y:ALA165 2.5 41.2 1.0
C I:ASP204 3.1 51.2 1.0
C Y:ASP168 3.2 38.3 1.0
O Y:ALA169 3.5 40.5 1.0
CA Y:ALA169 3.5 38.6 1.0
C Y:SER171 3.5 41.8 1.0
C Y:ALA169 3.6 39.1 1.0
C Y:ALA165 3.6 40.4 1.0
CA I:ASP204 3.8 51.4 1.0
N Y:ALA169 3.8 38.7 1.0
NH1 Y:ARG19 3.8 47.8 1.0
OXT I:ASP204 4.0 48.8 1.0
N Y:SER171 4.0 38.7 1.0
CB I:ASP204 4.1 52.6 1.0
CZ Y:ARG19 4.3 46.7 1.0
CA Y:SER171 4.3 39.9 1.0
N Y:TYR170 4.4 39.0 1.0
CA Y:ALA165 4.4 40.8 1.0
O Y:HIS166 4.4 39.6 1.0
CA Y:ASP168 4.5 37.5 1.0
N Y:ASP168 4.5 38.1 1.0
O I:HOH426 4.5 54.0 1.0
N Y:GLY172 4.5 42.7 1.0
NH2 Y:ARG19 4.6 48.5 1.0
C Y:HIS166 4.6 39.8 1.0
N Y:HIS166 4.6 40.1 1.0
O Y:ALA164 4.7 38.4 1.0
CA Y:GLY172 4.7 44.8 1.0
CB Y:SER171 4.8 39.6 1.0
CA Y:HIS166 4.8 39.3 1.0
CB Y:ALA169 4.9 38.9 1.0
C Y:TYR170 5.0 40.0 1.0

Magnesium binding site 5 out of 7 in 4ya7

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Magnesium binding site 5 out of 7 in the Yeast 20S Proteasome BETA2-H114D 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-H114D Mutant in Complex with Ac-Lae-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg301

b:51.4
occ:1.00
 O K:ALA165 2.1 40.1 1.0
O K:ASP168 2.2 39.9 1.0
O W:ASP204 2.3 44.2 1.0
O K:SER171 2.6 40.3 1.0
C W:ASP204 3.0 42.6 1.0
C K:ASP168 3.2 37.1 1.0
C K:ALA165 3.3 40.2 1.0
CA W:ASP204 3.6 41.9 1.0
C K:SER171 3.7 39.9 1.0
CA K:ALA169 3.7 36.5 1.0
N K:ALA169 3.9 36.3 1.0
O K:ALA169 3.9 40.6 1.0
C K:ALA169 3.9 37.4 1.0
OXT W:ASP204 3.9 42.5 1.0
CB W:ASP204 3.9 41.7 1.0
O K:HIS166 4.0 42.2 1.0
CA K:ALA165 4.1 40.3 1.0
C K:HIS166 4.2 40.6 1.0
NH1 K:ARG19 4.2 44.0 1.0
N K:HIS166 4.2 39.4 1.0
N K:SER171 4.3 37.6 1.0
N K:ASP168 4.3 37.7 1.0
CA K:ASP168 4.4 36.7 1.0
CA K:HIS166 4.4 40.0 1.0
O K:ALA164 4.4 39.6 1.0
CA K:SER171 4.5 37.9 1.0
CZ K:ARG19 4.7 43.1 1.0
N K:TYR170 4.7 36.9 1.0
N K:GLY172 4.7 41.5 1.0
N K:ARG167 4.7 39.9 1.0
C K:ARG167 4.8 38.6 1.0
CA K:GLY172 4.8 41.9 1.0
CB K:SER171 4.8 37.6 1.0
NH2 K:ARG19 4.8 44.0 1.0
N W:ASP204 4.9 42.2 1.0
CG W:ASP204 5.0 42.9 1.0

Magnesium binding site 6 out of 7 in 4ya7

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Magnesium binding site 6 out of 7 in the Yeast 20S Proteasome BETA2-H114D 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-H114D Mutant in Complex with Ac-Lae-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg301

b:42.8
occ:1.00
 O V:ASP166 2.0 39.3 1.0
O V:ILE163 2.2 43.7 1.0
OXT L:ASP222 2.3 49.4 1.0
O V:SER169 2.3 41.2 1.0
C V:ASP166 3.0 38.7 1.0
C L:ASP222 3.1 50.5 1.0
C V:ILE163 3.3 44.0 1.0
C V:SER169 3.5 39.7 1.0
O V:GLY162 3.6 40.7 1.0
CA L:ASP222 3.8 49.5 1.0
N V:LEU167 3.8 38.0 1.0
O L:ASP222 3.9 53.9 1.0
CA V:LEU167 3.9 37.0 1.0
N V:ASP166 3.9 39.5 1.0
CA V:ASP166 4.0 38.8 1.0
CA V:ILE163 4.1 43.8 1.0
NH1 V:ARG19 4.1 41.2 1.0
C V:TRP164 4.1 43.3 1.0
N V:TRP164 4.2 44.0 1.0
O V:TRP164 4.3 44.4 1.0
N V:SER169 4.3 38.1 1.0
CB L:ASP222 4.3 49.4 1.0
C V:LEU167 4.3 37.0 1.0
CA V:SER169 4.4 38.3 1.0
CA V:TRP164 4.4 44.3 1.0
N V:ASN165 4.4 42.1 1.0
N V:GLY170 4.4 40.2 1.0
CA V:GLY170 4.5 41.9 1.0
C V:ASN165 4.6 40.2 1.0
CZ V:ARG19 4.6 40.1 1.0
C V:GLY162 4.6 42.6 1.0
O V:LEU167 4.6 36.8 1.0
CB V:SER169 4.7 38.1 1.0
NH2 V:ARG19 4.8 42.6 1.0
CB V:ASP166 4.8 39.0 1.0
N V:ILE163 4.9 43.3 1.0
N V:GLY168 5.0 37.0 1.0
CD2 V:LEU167 5.0 36.9 1.0

Magnesium binding site 7 out of 7 in 4ya7

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Magnesium binding site 7 out of 7 in the Yeast 20S Proteasome BETA2-H114D 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-H114D Mutant in Complex with Ac-Lae-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg201

b:42.7
occ:1.00
 O N:SER169 2.5 33.9 1.0
O N:ILE163 2.5 36.3 1.0
O N:ASP166 2.8 36.2 1.0
CD1 a:LEU34 3.6 33.9 1.0
C N:ILE163 3.7 36.9 1.0
C N:SER169 3.7 32.8 1.0
NH1 N:ARG19 3.7 35.9 1.0
C N:ASP166 3.8 34.6 1.0
CG2 N:ILE163 3.9 34.9 1.0
CA N:GLY167 4.2 32.5 1.0
O N:GLY167 4.3 31.9 1.0
CA N:ILE163 4.3 35.4 1.0
CZ N:ARG19 4.4 34.9 1.0
N N:GLY167 4.4 33.4 1.0
C N:GLY167 4.4 31.9 1.0
CA N:GLY170 4.4 34.7 1.0
N N:GLY170 4.5 33.1 1.0
N N:SER169 4.6 31.4 1.0
CA N:SER169 4.6 31.1 1.0
NH2 N:ARG19 4.6 34.8 1.0
N N:LYS164 4.7 38.2 1.0
CB N:ILE163 4.8 34.8 1.0
CG a:LEU34 4.8 34.3 1.0
O N:LYS164 4.9 41.2 1.0
C N:LYS164 4.9 40.3 1.0
CA N:LYS164 4.9 39.8 1.0
N N:ASP166 4.9 35.2 1.0
CA N:ASP166 5.0 34.8 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 23:10:06 2024

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