Atomistry » Magnesium » PDB 4y8n-4yes » 4ya9
Atomistry »
  Magnesium »
    PDB 4y8n-4yes »
      4ya9 »

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

Go back to Magnesium Binding Sites List in 4ya9
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

Go back to Magnesium Binding Sites List in 4ya9
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

Go back to Magnesium Binding Sites List in 4ya9
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

Go back to Magnesium Binding Sites List in 4ya9
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

Go back to Magnesium Binding Sites List in 4ya9
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

Go back to Magnesium Binding Sites List in 4ya9
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

Go back to Magnesium Binding Sites List in 4ya9
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

Go back to Magnesium Binding Sites List in 4ya9
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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy