Atomistry » Magnesium » PDB 4y2q-4y8m » 4y6v
Atomistry »
  Magnesium »
    PDB 4y2q-4y8m »
      4y6v »

Magnesium in PDB 4y6v: Yeast 20S Proteasome in Complex with Ac-Pae-Ep

Enzymatic activity of Yeast 20S Proteasome in Complex with Ac-Pae-Ep

All present enzymatic activity of Yeast 20S Proteasome in Complex with Ac-Pae-Ep:
3.4.25.1;

Protein crystallography data

The structure of Yeast 20S Proteasome in Complex with Ac-Pae-Ep, PDB code: 4y6v 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 (°) 135.850, 301.220, 145.770, 90.00, 113.15, 90.00
R / Rfree (%) 19.1 / 20.9

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Yeast 20S Proteasome in Complex with Ac-Pae-Ep (pdb code 4y6v). 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 in Complex with Ac-Pae-Ep, PDB code: 4y6v:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 4y6v

Go back to Magnesium Binding Sites List in 4y6v
Magnesium binding site 1 out of 7 in the Yeast 20S Proteasome in Complex with Ac-Pae-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 in Complex with Ac-Pae-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:50.6
occ:1.00
 O G:MET125 2.0 50.2 1.0
O G:TYR119 2.4 39.9 1.0
O G:ARG122 2.6 43.0 1.0
OG1 G:THR8 2.6 46.9 1.0
CG2 G:THR8 3.2 45.5 1.0
C G:MET125 3.3 49.4 1.0
CB G:THR8 3.5 46.0 1.0
C G:TYR119 3.6 40.1 1.0
C G:ARG122 3.7 45.0 1.0
O G:ALA123 3.7 48.2 1.0
O G:HOH410 4.0 63.8 1.0
C G:ALA123 4.0 47.5 1.0
CA G:ALA123 4.0 46.0 1.0
CA G:ARG126 4.1 43.5 1.0
N G:ARG126 4.1 45.3 1.0
N G:MET125 4.2 51.4 1.0
CA G:MET125 4.3 53.0 1.0
CD G:PRO127 4.3 40.7 1.0
N G:ALA123 4.3 44.8 1.0
CA G:TYR119 4.3 40.6 1.0
N G:THR8 4.4 47.2 1.0
N G:THR120 4.6 39.4 1.0
CA G:THR8 4.6 46.3 1.0
C G:ARG126 4.6 41.4 1.0
CA G:THR120 4.7 40.5 1.0
CB G:MET125 4.7 57.7 1.0
N G:PRO127 4.8 40.8 1.0
N G:ARG122 4.8 44.1 1.0
CB G:TYR119 4.8 41.1 1.0
C G:THR120 4.9 40.9 1.0
CA G:ARG122 4.9 46.8 1.0
N G:TYR124 4.9 48.5 1.0

Magnesium binding site 2 out of 7 in 4y6v

Go back to Magnesium Binding Sites List in 4y6v
Magnesium binding site 2 out of 7 in the Yeast 20S Proteasome in Complex with Ac-Pae-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 in Complex with Ac-Pae-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:70.8
occ:1.00
 O I:ASP177 2.5 46.4 1.0
O I:SER180 2.8 52.1 1.0
O I:ALA174 3.0 46.6 1.0
C I:ASP177 3.6 45.8 1.0
OXT I:ASP204 3.9 57.5 1.0
C I:ALA174 4.0 46.2 1.0
C I:SER180 4.0 49.3 1.0
O I:ALA178 4.2 47.2 1.0
CA I:ASP175 4.2 48.6 1.0
CA I:ALA178 4.3 45.1 1.0
NH1 Y:ARG19 4.3 50.0 1.0
C I:ALA178 4.4 45.8 1.0
N I:ALA178 4.4 44.4 1.0
O I:ASP204 4.5 54.7 1.0
C I:ASP175 4.5 47.8 1.0
NH2 Y:ARG19 4.5 52.6 1.0
N I:ASP177 4.5 46.8 1.0
N I:ASP175 4.6 47.4 1.0
O I:ASP175 4.6 49.8 1.0
C I:ASP204 4.6 53.4 1.0
CA I:ASP177 4.7 45.4 1.0
N I:SER180 4.7 46.2 1.0
CZ Y:ARG19 4.8 51.1 1.0
OD1 I:ASP175 4.9 50.2 1.0
CA I:SER180 4.9 48.0 1.0
CA I:GLY181 4.9 46.0 1.0
N I:GLY181 4.9 46.9 1.0

Magnesium binding site 3 out of 7 in 4y6v

Go back to Magnesium Binding Sites List in 4y6v
Magnesium binding site 3 out of 7 in the Yeast 20S Proteasome in Complex with Ac-Pae-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 in Complex with Ac-Pae-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg302

b:51.8
occ:1.00
 O Y:SER171 2.2 44.5 1.0
O Y:ASP168 2.3 42.2 1.0
O I:ASP204 2.3 54.7 1.0
O Y:HOH406 2.5 34.6 1.0
O Y:ALA165 2.6 41.0 1.0
C I:ASP204 3.3 53.4 1.0
C Y:SER171 3.4 44.6 1.0
NH1 Y:ARG19 3.4 50.0 1.0
C Y:ASP168 3.4 43.5 1.0
O Y:ALA169 3.5 42.2 1.0
C Y:ALA169 3.6 43.0 1.0
C Y:ALA165 3.7 42.5 1.0
CA Y:ALA169 3.7 43.3 1.0
CA I:ASP204 3.9 51.2 1.0
N Y:SER171 3.9 44.0 1.0
CB I:ASP204 4.0 51.8 1.0
N Y:ALA169 4.0 43.9 1.0
CZ Y:ARG19 4.2 51.1 1.0
OXT I:ASP204 4.2 57.5 1.0
CA Y:SER171 4.2 44.5 1.0
CA Y:ALA165 4.3 43.2 1.0
N Y:TYR170 4.4 43.4 1.0
N Y:GLY172 4.4 44.3 1.0
NH2 Y:ARG19 4.6 52.6 1.0
CA Y:GLY172 4.6 44.8 1.0
CA Y:ASP168 4.6 43.5 1.0
O Y:HIS166 4.7 41.9 1.0
CB Y:SER171 4.7 44.3 1.0
N Y:ASP168 4.7 43.4 1.0
N Y:HIS166 4.8 42.8 1.0
CG I:ASP204 4.8 51.3 1.0
O Y:ALA164 4.8 43.1 1.0
C Y:HIS166 4.9 41.6 1.0
C Y:TYR170 4.9 44.7 1.0
NE Y:ARG19 5.0 49.1 1.0

Magnesium binding site 4 out of 7 in 4y6v

Go back to Magnesium Binding Sites List in 4y6v
Magnesium binding site 4 out of 7 in the Yeast 20S Proteasome in Complex with Ac-Pae-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 in Complex with Ac-Pae-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg301

b:49.8
occ:1.00
 O K:ASP168 2.3 44.0 1.0
O W:ASP204 2.3 54.8 1.0
O K:ALA165 2.4 45.0 1.0
O K:SER171 2.5 49.1 1.0
C W:ASP204 3.1 52.5 1.0
C K:ASP168 3.3 43.7 1.0
C K:ALA165 3.5 45.0 1.0
CA W:ASP204 3.6 50.7 1.0
NH1 K:ARG19 3.7 52.9 1.0
CA K:ALA169 3.7 44.0 1.0
O K:ALA169 3.7 44.9 1.0
C K:SER171 3.7 47.1 1.0
C K:ALA169 3.8 45.2 1.0
CB W:ASP204 3.9 50.5 1.0
N K:ALA169 3.9 43.4 1.0
OXT W:ASP204 4.0 52.7 1.0
N K:SER171 4.2 47.0 1.0
CA K:ALA165 4.2 45.5 1.0
O K:HIS166 4.3 44.7 1.0
CZ K:ARG19 4.5 52.3 1.0
CA K:SER171 4.5 46.4 1.0
N K:ASP168 4.5 42.0 1.0
C K:HIS166 4.5 43.5 1.0
CA K:ASP168 4.5 42.7 1.0
N K:TYR170 4.6 45.8 1.0
N K:HIS166 4.6 44.2 1.0
O K:ALA164 4.7 45.6 1.0
N K:GLY172 4.7 47.2 1.0
CA K:HIS166 4.8 43.5 1.0
NH2 K:ARG19 4.8 54.1 1.0
CG W:ASP204 4.9 50.3 1.0
CA K:GLY172 4.9 49.0 1.0
CB K:SER171 4.9 45.4 1.0
C K:ARG167 4.9 42.2 1.0

Magnesium binding site 5 out of 7 in 4y6v

Go back to Magnesium Binding Sites List in 4y6v
Magnesium binding site 5 out of 7 in the Yeast 20S Proteasome in Complex with Ac-Pae-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 in Complex with Ac-Pae-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg301

b:58.9
occ:1.00
 O V:ASP166 2.1 43.8 1.0
OXT L:ASP222 2.2 59.2 1.0
O V:ILE163 2.2 44.5 1.0
O V:SER169 2.3 45.2 1.0
C L:ASP222 3.1 61.6 1.0
C V:ASP166 3.2 44.8 1.0
C V:ILE163 3.3 46.1 1.0
C V:SER169 3.4 46.9 1.0
CA L:ASP222 3.7 62.1 1.0
O V:GLY162 3.8 44.8 1.0
CA V:LEU167 3.9 46.4 1.0
N V:LEU167 3.9 45.9 1.0
O L:ASP222 3.9 65.3 1.0
NH1 V:ARG19 3.9 54.6 1.0
N V:ASP166 4.1 45.1 1.0
CA V:ILE163 4.1 45.9 1.0
N V:SER169 4.2 45.2 1.0
CA V:ASP166 4.2 44.8 1.0
CB L:ASP222 4.2 63.8 1.0
C V:LEU167 4.2 46.3 1.0
N V:TRP164 4.3 47.2 1.0
CA V:SER169 4.3 46.1 1.0
C V:TRP164 4.3 49.3 1.0
N V:GLY170 4.3 47.6 1.0
CA V:GLY170 4.4 51.9 1.0
O V:LEU167 4.4 44.4 1.0
O V:TRP164 4.5 50.4 1.0
CA V:TRP164 4.5 48.1 1.0
CZ V:ARG19 4.6 53.5 1.0
N V:ASN165 4.6 48.5 1.0
CB V:SER169 4.7 45.6 1.0
C V:ASN165 4.8 46.1 1.0
C V:GLY162 4.8 45.5 1.0
NH2 V:ARG19 4.8 56.3 1.0
N V:GLY168 4.9 46.9 1.0
N V:ILE163 4.9 46.1 1.0
CB V:ASP166 5.0 44.4 1.0

Magnesium binding site 6 out of 7 in 4y6v

Go back to Magnesium Binding Sites List in 4y6v
Magnesium binding site 6 out of 7 in the Yeast 20S Proteasome in Complex with Ac-Pae-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 in Complex with Ac-Pae-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg201

b:45.8
occ:1.00
 O N:ILE163 2.7 44.0 1.0
O N:SER169 2.7 45.9 1.0
O N:ASP166 3.2 43.3 1.0
CD1 a:LEU34 3.5 45.2 1.0
NH1 N:ARG19 3.6 43.8 1.0
C N:ILE163 3.8 42.6 1.0
C N:SER169 3.9 42.9 1.0
CG2 N:ILE163 4.0 39.8 1.0
C N:ASP166 4.1 41.2 1.0
CZ N:ARG19 4.2 43.2 1.0
CA N:GLY167 4.3 40.4 1.0
NH2 N:ARG19 4.4 44.6 1.0
O N:GLY167 4.4 42.1 1.0
CA N:GLY170 4.5 43.7 1.0
CA N:ILE163 4.5 41.2 1.0
C N:GLY167 4.6 40.5 1.0
N N:GLY167 4.6 40.3 1.0
N N:GLY170 4.7 42.5 1.0
CG a:LEU34 4.8 45.3 1.0
CB N:ILE163 4.9 40.0 1.0
N N:LYS164 4.9 43.3 1.0
N N:SER169 4.9 40.4 1.0
CA N:SER169 5.0 41.0 1.0

Magnesium binding site 7 out of 7 in 4y6v

Go back to Magnesium Binding Sites List in 4y6v
Magnesium binding site 7 out of 7 in the Yeast 20S Proteasome in Complex with Ac-Pae-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 in Complex with Ac-Pae-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg301

b:57.9
occ:1.00
 O Z:VAL198 2.5 48.9 1.0
O Z:THR192 2.8 55.1 1.0
O Z:HIS195 2.8 45.9 1.0
C Z:VAL198 3.7 49.8 1.0
O Z:ILE196 3.8 51.6 1.0
NH2 Z:ARG28 3.8 52.5 1.0
C Z:HIS195 3.8 47.5 1.0
C Z:THR192 3.9 55.0 1.0
O Z:ASP222 3.9 68.5 1.0
CA Z:ILE196 3.9 46.7 1.0
C Z:ILE196 3.9 47.4 1.0
CG2 Z:THR192 4.0 56.0 1.0
CA Z:THR192 4.2 54.1 1.0
NH2 H:ARG19 4.2 58.5 1.0
N Z:VAL198 4.3 47.6 1.0
N Z:ILE196 4.3 46.4 1.0
CA Z:VAL198 4.5 49.2 1.0
N Z:GLY199 4.7 50.0 1.0
OD1 Z:ASP222 4.7 66.3 1.0
CB Z:THR192 4.7 54.9 1.0
CZ Z:ARG28 4.7 52.9 1.0
C Z:ASP222 4.7 65.1 1.0
CA Z:GLY199 4.7 51.0 1.0
N Z:GLN197 4.8 46.7 1.0
NH1 H:ARG19 4.8 56.0 1.0
CZ H:ARG19 4.9 55.7 1.0
NH1 Z:ARG28 5.0 54.5 1.0
CB Z:VAL198 5.0 48.3 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 22:47:47 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy