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Magnesium in PDB 4ya9: Yeast 20S Proteasome BETA2-H114D Mutant in Complex with Ac-Lad-Ep

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

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

Protein crystallography data

The structure of Yeast 20S Proteasome BETA2-H114D Mutant in Complex with Ac-Lad-Ep, PDB code: 4ya9 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 (°) 135.380, 299.690, 145.310, 90.00, 112.83, 90.00
R / Rfree (%) 22 / 24.1

Other elements in 4ya9:

The structure of Yeast 20S Proteasome BETA2-H114D Mutant in Complex with Ac-Lad-Ep also contains other interesting chemical elements:

Potassium (K) 2 atoms
Chlorine (Cl) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Yeast 20S Proteasome BETA2-H114D Mutant in Complex with Ac-Lad-Ep (pdb code 4ya9). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Yeast 20S Proteasome BETA2-H114D Mutant in Complex with Ac-Lad-Ep, PDB code: 4ya9:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 4ya9

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Magnesium binding site 1 out of 8 in the Yeast 20S Proteasome BETA2-H114D Mutant in Complex with Ac-Lad-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-Lad-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:50.8
occ:1.00
 O G:MET125 2.4 38.6 1.0
OG1 G:THR8 2.6 35.0 1.0
O G:ARG122 2.6 37.2 1.0
O G:TYR119 3.0 33.9 1.0
O G:ALA123 3.1 41.2 1.0
CG2 G:THR8 3.4 38.9 1.0
C G:MET125 3.5 39.9 1.0
C G:ALA123 3.5 41.9 1.0
CB G:THR8 3.5 37.2 1.0
CA G:ALA123 3.6 39.9 1.0
C G:ARG122 3.7 38.7 1.0
N G:THR8 4.0 39.2 1.0
N G:ALA123 4.1 38.1 1.0
C G:TYR119 4.2 33.1 1.0
N G:MET125 4.2 42.6 1.0
N G:ARG126 4.3 36.9 1.0
CA G:ARG126 4.3 34.9 1.0
CA G:MET125 4.4 43.5 1.0
CA G:THR8 4.4 38.1 1.0
N G:TYR124 4.5 44.0 1.0
CD G:PRO127 4.7 32.7 1.0
CA G:TYR119 4.9 32.2 1.0
CB G:ALA123 4.9 39.6 1.0
C G:TYR124 4.9 42.6 1.0
C G:ARG126 5.0 34.1 1.0
CA G:ARG122 5.0 40.7 1.0

Magnesium binding site 2 out of 8 in 4ya9

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Magnesium binding site 2 out of 8 in the Yeast 20S Proteasome BETA2-H114D Mutant in Complex with Ac-Lad-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-Lad-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:47.9
occ:1.00
 O I:ASP177 2.4 39.6 1.0
O I:SER180 2.8 36.3 1.0
O I:ALA174 2.8 41.7 1.0
C I:ASP177 3.5 38.2 1.0
OXT I:ASP204 3.8 47.9 1.0
C I:ALA174 3.9 43.8 1.0
O I:HOH428 4.0 35.8 1.0
C I:SER180 4.0 37.8 1.0
CA I:ASP175 4.1 42.4 1.0
O I:ALA178 4.2 39.8 1.0
CA I:ALA178 4.2 37.7 1.0
N I:ALA178 4.3 37.1 1.0
C I:ALA178 4.3 39.1 1.0
C I:ASP175 4.4 39.8 1.0
N I:ASP177 4.4 35.9 1.0
N I:ASP175 4.4 42.9 1.0
O I:ASP175 4.5 41.1 1.0
NH1 Y:ARG19 4.5 48.0 1.0
CA I:ASP177 4.5 37.9 1.0
O I:ASP204 4.6 51.1 1.0
N I:SER180 4.6 37.1 1.0
C I:ASP204 4.6 52.2 1.0
NH2 Y:ARG19 4.8 46.4 1.0
OD1 I:ASP175 4.9 46.0 1.0
CA I:SER180 4.9 37.8 1.0
N I:GLY181 4.9 37.7 1.0
CA I:GLY181 4.9 39.1 1.0

Magnesium binding site 3 out of 8 in 4ya9

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Magnesium binding site 3 out of 8 in the Yeast 20S Proteasome BETA2-H114D Mutant in Complex with Ac-Lad-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-Lad-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg302

b:41.1
occ:1.00
 O Y:ASP168 2.1 37.6 1.0
O Y:SER171 2.3 37.9 1.0
O Y:ALA165 2.4 35.3 1.0
O I:ASP204 2.5 51.1 1.0
O Y:HOH401 2.6 33.1 1.0
C Y:ASP168 3.2 36.4 1.0
C I:ASP204 3.3 52.2 1.0
C Y:ALA165 3.5 35.1 1.0
C Y:SER171 3.5 37.9 1.0
CA Y:ALA169 3.6 36.3 1.0
O Y:ALA169 3.7 39.1 1.0
C Y:ALA169 3.7 37.3 1.0
CA I:ASP204 3.8 52.4 1.0
N Y:ALA169 3.8 37.0 1.0
NH1 Y:ARG19 4.0 48.0 1.0
N Y:SER171 4.0 37.1 1.0
CB I:ASP204 4.1 52.6 1.0
OXT I:ASP204 4.2 47.9 1.0
O Y:HIS166 4.2 36.2 1.0
CA Y:ALA165 4.2 35.1 1.0
CA Y:SER171 4.3 35.8 1.0
CA Y:ASP168 4.4 35.9 1.0
C Y:HIS166 4.4 35.3 1.0
CZ Y:ARG19 4.4 45.9 1.0
N Y:ASP168 4.4 37.2 1.0
N Y:TYR170 4.5 37.5 1.0
N Y:HIS166 4.5 35.9 1.0
N Y:GLY172 4.5 40.1 1.0
O Y:ALA164 4.6 35.3 1.0
NH2 Y:ARG19 4.7 46.4 1.0
CA Y:GLY172 4.7 41.8 1.0
CA Y:HIS166 4.7 35.7 1.0
CB Y:SER171 4.7 34.6 1.0
C Y:ARG167 4.9 37.0 1.0
N Y:ARG167 5.0 34.7 1.0

Magnesium binding site 4 out of 8 in 4ya9

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Magnesium binding site 4 out of 8 in the Yeast 20S Proteasome BETA2-H114D Mutant in Complex with Ac-Lad-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-Lad-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mg201

b:30.0
occ:1.00
 O J:THR124 3.8 32.0 1.0
CB J:ASP120 3.9 30.4 1.0
OE1 J:GLN118 3.9 38.4 1.0
OD2 J:ASP120 4.0 38.0 1.0
CG J:ASP120 4.0 34.5 1.0
CB J:THR124 4.1 31.9 1.0
CG2 J:THR124 4.2 31.1 1.0
N J:ASP120 4.3 27.2 1.0
CD J:GLN118 4.6 35.1 1.0
CG J:GLN118 4.6 33.0 1.0
CE1 J:HIS133 4.6 27.9 1.0
OD1 J:ASP120 4.7 38.0 1.0
C J:THR124 4.7 31.9 1.0
CA J:ASP120 4.7 28.4 1.0
CD2 I:LEU28 4.7 40.4 1.0
O J:GLN118 4.8 29.2 1.0
CG1 I:VAL35 4.8 40.4 1.0
C J:ILE119 5.0 27.2 1.0
OG1 J:THR124 5.0 32.3 1.0

Magnesium binding site 5 out of 8 in 4ya9

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Magnesium binding site 5 out of 8 in the Yeast 20S Proteasome BETA2-H114D Mutant in Complex with Ac-Lad-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-Lad-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg301

b:55.4
occ:1.00
 O K:ASP168 2.3 38.0 1.0
O K:ALA165 2.3 37.0 1.0
O W:ASP204 2.5 46.5 1.0
C W:ASP204 3.1 46.4 1.0
O K:SER171 3.1 37.4 1.0
C K:ASP168 3.2 36.0 1.0
O K:HIS166 3.5 41.8 1.0
C K:ALA165 3.5 38.2 1.0
CA K:ALA169 3.6 36.4 1.0
CA W:ASP204 3.6 44.6 1.0
N K:ALA169 3.7 35.6 1.0
C K:HIS166 3.8 38.7 1.0
OXT W:ASP204 3.9 47.5 1.0
C K:ALA169 4.0 39.4 1.0
O K:ALA169 4.1 42.7 1.0
N K:ASP168 4.2 36.3 1.0
CB W:ASP204 4.2 44.3 1.0
CA K:HIS166 4.2 39.1 1.0
N K:HIS166 4.3 38.3 1.0
CA K:ASP168 4.3 34.9 1.0
C K:SER171 4.3 39.3 1.0
C K:ARG167 4.4 37.0 1.0
N K:ARG167 4.5 36.5 1.0
CA K:ALA165 4.5 38.1 1.0
NH1 K:ARG19 4.5 44.4 1.0
O K:ALA164 4.6 34.6 1.0
N K:SER171 4.7 38.1 1.0
O K:ARG167 4.7 39.6 1.0
N K:TYR170 4.9 38.5 1.0
N W:ASP204 4.9 44.6 1.0
CB K:ALA169 4.9 35.3 1.0
CA K:ARG167 4.9 36.2 1.0

Magnesium binding site 6 out of 8 in 4ya9

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Magnesium binding site 6 out of 8 in the Yeast 20S Proteasome BETA2-H114D Mutant in Complex with Ac-Lad-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-Lad-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg301

b:46.3
occ:1.00
 O V:ASP166 2.0 36.9 1.0
OXT L:ASP222 2.2 54.1 1.0
O V:ILE163 2.2 41.9 1.0
O V:SER169 2.7 39.9 1.0
C V:ASP166 3.0 37.3 1.0
C L:ASP222 3.0 55.9 1.0
C V:ILE163 3.3 43.5 1.0
CA L:ASP222 3.7 52.7 1.0
N V:LEU167 3.7 37.0 1.0
O V:GLY162 3.7 37.1 1.0
N V:ASP166 3.7 37.7 1.0
O L:ASP222 3.8 59.9 1.0
C V:SER169 3.8 38.2 1.0
CA V:LEU167 3.8 36.7 1.0
C V:TRP164 3.9 43.5 1.0
O V:TRP164 3.9 45.7 1.0
CA V:ASP166 4.0 36.9 1.0
N V:TRP164 4.1 42.1 1.0
CA V:ILE163 4.2 44.1 1.0
CA V:TRP164 4.2 42.8 1.0
NH1 V:ARG19 4.3 42.5 1.0
N V:ASN165 4.3 40.8 1.0
CB L:ASP222 4.3 50.2 1.0
C V:LEU167 4.4 36.2 1.0
C V:ASN165 4.5 37.5 1.0
N V:SER169 4.5 35.5 1.0
CA V:SER169 4.6 36.3 1.0
O V:LEU167 4.7 37.5 1.0
N V:GLY170 4.7 38.9 1.0
C V:GLY162 4.7 39.6 1.0
CA V:GLY170 4.8 40.3 1.0
CB V:ASP166 4.8 36.0 1.0
CZ V:ARG19 4.8 42.1 1.0
CD2 V:LEU167 4.8 36.6 1.0
CA V:ASN165 4.9 39.4 1.0
O L:ARG221 4.9 52.1 1.0
NH2 V:ARG19 4.9 45.1 1.0
N V:ILE163 5.0 41.4 1.0
CB V:SER169 5.0 36.5 1.0

Magnesium binding site 7 out of 8 in 4ya9

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Magnesium binding site 7 out of 8 in the Yeast 20S Proteasome BETA2-H114D Mutant in Complex with Ac-Lad-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-Lad-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg201

b:40.8
occ:1.00
 O N:SER169 2.4 32.3 1.0
O N:ILE163 2.8 34.3 1.0
O N:ASP166 2.9 34.8 1.0
C N:SER169 3.6 31.7 1.0
NH1 N:ARG19 3.6 34.5 1.0
CD1 a:LEU34 3.7 34.6 1.0
C N:ILE163 3.9 33.7 1.0
C N:ASP166 3.9 34.0 1.0
CG2 N:ILE163 4.1 34.6 1.0
CA N:GLY167 4.1 32.4 1.0
O N:GLY167 4.2 30.6 1.0
CZ N:ARG19 4.2 34.6 1.0
CA N:GLY170 4.3 35.8 1.0
C N:GLY167 4.4 31.5 1.0
NH2 N:ARG19 4.4 36.0 1.0
N N:GLY170 4.4 33.9 1.0
N N:GLY167 4.5 32.6 1.0
CA N:ILE163 4.5 33.2 1.0
N N:SER169 4.6 30.3 1.0
O N:HOH319 4.6 27.4 1.0
CA N:SER169 4.6 29.6 1.0
O a:HOH320 4.9 27.3 1.0
CB N:ILE163 4.9 34.0 1.0
N N:LYS164 4.9 34.7 1.0
CG a:LEU34 4.9 35.2 1.0

Magnesium binding site 8 out of 8 in 4ya9

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Magnesium binding site 8 out of 8 in the Yeast 20S Proteasome BETA2-H114D Mutant in Complex with Ac-Lad-Ep


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Yeast 20S Proteasome BETA2-H114D Mutant in Complex with Ac-Lad-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
W:Mg301

b:30.0
occ:1.00
 O W:LEU125 2.8 37.3 1.0
O W:LEU94 2.9 35.0 1.0
N W:TYR102 3.0 36.1 1.0
CB W:PRO101 3.2 34.6 1.0
CA W:PRO101 3.2 35.5 1.0
C W:PRO101 3.6 36.2 1.0
O W:ARG97 3.7 38.6 1.0
C W:LEU94 3.7 34.1 1.0
CA W:LEU94 3.7 34.0 1.0
CB W:ARG97 3.7 44.3 1.0
CD2 W:LEU94 3.9 32.3 1.0
CB W:LEU94 4.0 33.4 1.0
C W:LEU125 4.0 34.7 1.0
CD2 W:TYR102 4.0 37.7 1.0
O W:TYR102 4.0 36.1 1.0
CA W:TYR102 4.0 35.5 1.0
CB W:TYR102 4.1 35.5 1.0
C W:ARG97 4.3 38.3 1.0
CA W:ILE126 4.3 36.6 1.0
CG W:TYR102 4.4 37.4 1.0
CA W:ARG97 4.5 40.1 1.0
C W:TYR102 4.5 34.5 1.0
N W:PRO101 4.5 36.0 1.0
CG W:LEU94 4.6 32.3 1.0
N W:ILE126 4.6 35.4 1.0
CG W:PRO101 4.7 34.2 1.0
CG2 W:ILE126 4.7 36.8 1.0
N W:ARG97 4.8 38.2 1.0
O W:PRO101 4.8 38.8 1.0
CG W:ARG97 4.8 51.7 1.0
N W:TYR95 4.9 33.0 1.0
CE2 W:TYR102 5.0 38.9 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 23:10:13 2024

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