Atomistry » Magnesium » PDB 4y8o-4yf4 » 4y9z
Atomistry »
  Magnesium »
    PDB 4y8o-4yf4 »
      4y9z »

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

Go back to Magnesium Binding Sites List in 4y9z
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

Go back to Magnesium Binding Sites List in 4y9z
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

Go back to Magnesium Binding Sites List in 4y9z
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

Go back to Magnesium Binding Sites List in 4y9z
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

Go back to Magnesium Binding Sites List in 4y9z
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

Go back to Magnesium Binding Sites List in 4y9z
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

Go back to Magnesium Binding Sites List in 4y9z
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: Tue Aug 12 04:02:54 2025

Last articles

Mg in 5JVH
Mg in 5K0N
Mg in 5K0L
Mg in 5JZQ
Mg in 5K0K
Mg in 5JYG
Mg in 5JZJ
Mg in 5JZD
Mg in 5JYS
Mg in 5JYD
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy