Atomistry » Magnesium » PDB 4y2r-4y8n » 4y75
Atomistry »
  Magnesium »
    PDB 4y2r-4y8n »
      4y75 »

Magnesium in PDB 4y75: Yeast 20S Proteasome in Complex with Ac-Paf-Ep

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

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

Protein crystallography data

The structure of Yeast 20S Proteasome in Complex with Ac-Paf-Ep, PDB code: 4y75 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 (°) 134.730, 300.060, 145.480, 90.00, 112.85, 90.00
R / Rfree (%) 18.9 / 21.5

Other elements in 4y75:

The structure of Yeast 20S Proteasome in Complex with Ac-Paf-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 in Complex with Ac-Paf-Ep (pdb code 4y75). 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-Paf-Ep, PDB code: 4y75:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 4y75

Go back to Magnesium Binding Sites List in 4y75
Magnesium binding site 1 out of 7 in the Yeast 20S Proteasome in Complex with Ac-Paf-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-Paf-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:61.0
occ:1.00
 O G:MET125 2.3 55.8 1.0
OG1 G:THR8 2.7 50.2 1.0
O G:ARG122 2.8 52.0 1.0
O G:TYR119 2.9 49.8 1.0
O G:ALA123 3.2 57.6 1.0
CG2 G:THR8 3.3 53.1 1.0
C G:MET125 3.4 53.1 1.0
CB G:THR8 3.6 52.4 1.0
C G:ALA123 3.7 55.1 1.0
CA G:ALA123 3.8 52.4 1.0
C G:ARG122 3.9 52.7 1.0
N G:THR8 4.1 53.4 1.0
CA G:ARG126 4.1 47.8 1.0
N G:ARG126 4.1 48.9 1.0
C G:TYR119 4.1 48.8 1.0
N G:MET125 4.2 55.0 1.0
N G:ALA123 4.3 52.8 1.0
CA G:MET125 4.4 55.3 1.0
CD G:PRO127 4.5 46.2 1.0
CA G:THR8 4.5 53.4 1.0
N G:TYR124 4.7 57.5 1.0
C G:ARG126 4.8 47.9 1.0
CA G:TYR119 4.9 46.5 1.0
N G:PRO127 5.0 46.0 1.0
C G:TYR124 5.0 56.2 1.0

Magnesium binding site 2 out of 7 in 4y75

Go back to Magnesium Binding Sites List in 4y75
Magnesium binding site 2 out of 7 in the Yeast 20S Proteasome in Complex with Ac-Paf-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-Paf-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:61.0
occ:1.00
 O I:ASP177 2.5 51.6 1.0
O I:ALA174 2.6 52.4 1.0
O I:SER180 2.7 44.1 1.0
C I:ALA174 3.6 54.7 1.0
C I:ASP177 3.7 50.1 1.0
C I:SER180 3.8 49.4 1.0
CA I:ASP175 3.9 53.3 1.0
OXT I:ASP204 3.9 52.8 1.0
N I:ASP175 4.1 53.8 1.0
C I:ASP175 4.3 52.2 1.0
N I:ASP177 4.4 49.5 1.0
O I:ASP175 4.5 51.6 1.0
OD1 I:ASP175 4.5 56.0 1.0
CA I:ALA178 4.5 48.0 1.0
N I:ALA178 4.6 47.9 1.0
O I:ALA178 4.6 56.1 1.0
CA I:ASP177 4.6 49.9 1.0
C I:ALA178 4.6 50.0 1.0
CA I:GLY181 4.7 48.9 1.0
N I:SER180 4.7 48.6 1.0
N I:GLY181 4.7 49.0 1.0
CA I:ALA174 4.8 54.6 1.0
NH1 Y:ARG19 4.8 59.9 1.0
CA I:SER180 4.8 49.5 1.0
C I:ASP204 4.8 57.5 1.0
NH2 Y:ARG19 4.9 61.2 1.0
O I:ASP204 4.9 57.3 1.0
N I:ARG176 5.0 50.5 1.0
CB I:ALA174 5.0 54.4 1.0

Magnesium binding site 3 out of 7 in 4y75

Go back to Magnesium Binding Sites List in 4y75
Magnesium binding site 3 out of 7 in the Yeast 20S Proteasome in Complex with Ac-Paf-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-Paf-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg302

b:49.7
occ:1.00
 O Y:ASP168 2.2 46.0 1.0
O Y:ALA165 2.3 51.0 1.0
O I:ASP204 2.3 57.3 1.0
O Y:SER171 2.8 52.1 1.0
C I:ASP204 3.1 57.5 1.0
C Y:ASP168 3.1 46.8 1.0
C Y:ALA165 3.5 50.0 1.0
CA Y:ALA169 3.6 48.3 1.0
CA I:ASP204 3.6 57.2 1.0
N Y:ALA169 3.7 47.2 1.0
O Y:HIS166 3.8 50.5 1.0
C Y:ALA169 3.8 49.9 1.0
O Y:ALA169 3.8 52.2 1.0
C Y:SER171 3.9 51.5 1.0
OXT I:ASP204 4.0 52.8 1.0
C Y:HIS166 4.1 50.2 1.0
CB I:ASP204 4.1 58.7 1.0
N Y:ASP168 4.2 48.4 1.0
NH1 Y:ARG19 4.2 59.9 1.0
CA Y:ASP168 4.3 46.7 1.0
N Y:SER171 4.3 46.4 1.0
CA Y:ALA165 4.4 50.4 1.0
N Y:HIS166 4.4 50.5 1.0
CA Y:HIS166 4.5 49.3 1.0
O Y:ALA164 4.5 52.4 1.0
C Y:ARG167 4.6 48.3 1.0
N Y:TYR170 4.6 48.9 1.0
CA Y:SER171 4.6 48.9 1.0
N Y:ARG167 4.7 49.8 1.0
CZ Y:ARG19 4.8 58.2 1.0
N Y:GLY172 4.9 53.3 1.0
CB Y:ALA169 4.9 47.8 1.0
NH2 Y:ARG19 5.0 61.2 1.0
O Y:ARG167 5.0 46.9 1.0
N I:ASP204 5.0 56.4 1.0
CB Y:SER171 5.0 49.4 1.0

Magnesium binding site 4 out of 7 in 4y75

Go back to Magnesium Binding Sites List in 4y75
Magnesium binding site 4 out of 7 in the Yeast 20S Proteasome in Complex with Ac-Paf-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-Paf-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg301

b:59.4
occ:1.00
 O K:ASP168 2.2 49.2 1.0
O K:ALA165 2.3 47.1 1.0
O W:ASP204 2.3 51.6 1.0
O K:SER171 2.9 52.4 1.0
C W:ASP204 3.1 50.4 1.0
C K:ASP168 3.1 46.2 1.0
C K:ALA165 3.4 47.6 1.0
CA K:ALA169 3.6 46.7 1.0
CA W:ASP204 3.7 49.4 1.0
N K:ALA169 3.7 46.4 1.0
O K:HIS166 3.7 51.6 1.0
C K:ALA169 3.8 48.6 1.0
O K:ALA169 3.9 52.5 1.0
OXT W:ASP204 3.9 54.8 1.0
C K:SER171 3.9 48.1 1.0
C K:HIS166 4.0 49.1 1.0
CB W:ASP204 4.2 48.8 1.0
N K:ASP168 4.2 44.4 1.0
CA K:ASP168 4.3 45.0 1.0
NH1 K:ARG19 4.3 52.1 1.0
N K:HIS166 4.3 46.9 1.0
CA K:ALA165 4.3 48.8 1.0
N K:SER171 4.4 45.7 1.0
CA K:HIS166 4.4 48.0 1.0
O K:ALA164 4.5 50.2 1.0
C K:ARG167 4.6 47.2 1.0
N K:TYR170 4.6 46.4 1.0
CA K:SER171 4.7 46.0 1.0
N K:ARG167 4.7 47.1 1.0
CZ K:ARG19 4.8 52.0 1.0
N K:GLY172 4.9 48.3 1.0
O K:ARG167 4.9 47.8 1.0
CB K:ALA169 4.9 45.3 1.0
CB K:SER171 5.0 44.3 1.0

Magnesium binding site 5 out of 7 in 4y75

Go back to Magnesium Binding Sites List in 4y75
Magnesium binding site 5 out of 7 in the Yeast 20S Proteasome in Complex with Ac-Paf-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-Paf-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg301

b:69.8
occ:1.00
 O V:ILE163 2.1 65.8 1.0
O V:ASP166 2.2 59.7 1.0
OXT L:ASP222 2.3 62.7 1.0
O V:SER169 2.9 62.0 1.0
C L:ASP222 3.0 61.5 1.0
C V:ASP166 3.1 62.3 1.0
C V:ILE163 3.1 69.1 1.0
O V:TRP164 3.6 61.1 1.0
CA L:ASP222 3.6 59.6 1.0
C V:TRP164 3.6 63.1 1.0
O V:GLY162 3.7 64.5 1.0
N V:ASP166 3.7 59.8 1.0
O L:ASP222 3.8 65.8 1.0
N V:LEU167 3.9 63.7 1.0
N V:TRP164 3.9 68.7 1.0
CA V:TRP164 4.0 66.6 1.0
CA V:ASP166 4.0 61.0 1.0
CA V:LEU167 4.0 62.6 1.0
N V:ASN165 4.1 62.3 1.0
C V:SER169 4.1 61.3 1.0
CA V:ILE163 4.1 66.9 1.0
CB L:ASP222 4.3 60.5 1.0
C V:ASN165 4.3 60.8 1.0
NH1 V:ARG19 4.4 64.6 1.0
NH2 V:ARG19 4.5 61.2 1.0
C V:LEU167 4.6 61.1 1.0
O L:ARG221 4.7 54.9 1.0
C V:GLY162 4.7 64.4 1.0
CA V:ASN165 4.7 63.2 1.0
CZ V:ARG19 4.7 62.0 1.0
N V:SER169 4.8 58.9 1.0
N L:ASP222 4.9 61.0 1.0
CD2 V:LEU167 4.9 60.5 1.0
N V:ILE163 4.9 63.5 1.0
CA V:SER169 4.9 60.9 1.0
CB V:ASP166 4.9 59.5 1.0
O V:LEU167 4.9 62.8 1.0
N V:GLY170 5.0 62.8 1.0
CA V:GLY170 5.0 64.0 1.0

Magnesium binding site 6 out of 7 in 4y75

Go back to Magnesium Binding Sites List in 4y75
Magnesium binding site 6 out of 7 in the Yeast 20S Proteasome in Complex with Ac-Paf-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-Paf-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg201

b:61.8
occ:1.00
 O N:SER169 2.4 50.9 1.0
O N:ILE163 2.5 51.5 1.0
O N:ASP166 2.8 50.8 1.0
CD1 a:LEU34 3.6 49.4 1.0
C N:SER169 3.6 47.7 1.0
C N:ILE163 3.7 50.6 1.0
C N:ASP166 3.9 47.5 1.0
NH1 N:ARG19 3.9 48.4 1.0
CG2 N:ILE163 4.0 49.3 1.0
CA N:GLY167 4.2 46.0 1.0
CA N:GLY170 4.3 49.6 1.0
CA N:ILE163 4.4 49.5 1.0
N N:GLY170 4.4 48.8 1.0
O N:GLY167 4.4 43.4 1.0
CZ N:ARG19 4.4 47.2 1.0
N N:GLY167 4.5 46.7 1.0
C N:GLY167 4.5 45.8 1.0
N N:SER169 4.6 44.7 1.0
NH2 N:ARG19 4.6 46.7 1.0
CA N:SER169 4.6 44.4 1.0
N N:LYS164 4.7 50.7 1.0
CB N:ILE163 4.8 48.6 1.0
O N:LYS164 4.9 55.9 1.0
C N:LYS164 4.9 52.0 1.0
CG a:LEU34 4.9 49.5 1.0
CA N:LYS164 5.0 51.1 1.0

Magnesium binding site 7 out of 7 in 4y75

Go back to Magnesium Binding Sites List in 4y75
Magnesium binding site 7 out of 7 in the Yeast 20S Proteasome in Complex with Ac-Paf-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-Paf-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg301

b:71.0
occ:1.00
 O Z:VAL198 2.5 57.7 1.0
O Z:THR192 2.7 65.9 1.0
O Z:HIS195 3.0 48.5 1.0
NH2 Z:ARG28 3.5 63.4 1.0
CG2 Z:THR192 3.7 62.9 1.0
O Z:ASP222 3.7 62.3 1.0
C Z:VAL198 3.7 58.4 1.0
C Z:THR192 3.7 63.3 1.0
O Z:ILE196 3.9 55.1 1.0
C Z:HIS195 4.0 53.6 1.0
CA Z:THR192 4.1 62.1 1.0
CA Z:ILE196 4.1 52.8 1.0
C Z:ILE196 4.2 54.1 1.0
OD1 Z:ASP222 4.4 61.8 1.0
NH2 H:ARG19 4.5 66.9 1.0
CB Z:THR192 4.5 61.1 1.0
N Z:VAL198 4.5 54.6 1.0
CZ Z:ARG28 4.5 60.6 1.0
N Z:ILE196 4.6 54.3 1.0
N Z:GLY199 4.6 58.1 1.0
CA Z:GLY199 4.6 59.7 1.0
C Z:ASP222 4.6 65.5 1.0
CA Z:VAL198 4.7 56.2 1.0
NH1 Z:ARG28 4.8 61.1 1.0
O Z:LYS220 4.9 63.1 1.0
N Z:GLU193 4.9 60.4 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 22:47:48 2024

Last articles

Ca in 5SZM
Ca in 5SZL
Ca in 5SY1
Ca in 5SWI
Ca in 5SVE
Ca in 5SSX
Ca in 5SV0
Ca in 5STD
Ca in 5SSZ
Ca in 5SSY
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy