Atomistry » Magnesium » PDB 4y2r-4y8n » 4y7y
Atomistry »
  Magnesium »
    PDB 4y2r-4y8n »
      4y7y »

Magnesium in PDB 4y7y: Yeast 20S Proteasome in Complex with Ac-Laa-Ep

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

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

Protein crystallography data

The structure of Yeast 20S Proteasome in Complex with Ac-Laa-Ep, PDB code: 4y7y 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 / 2.40
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 136.680, 299.820, 144.750, 90.00, 113.07, 90.00
R / Rfree (%) 21.2 / 23.5

Other elements in 4y7y:

The structure of Yeast 20S Proteasome in Complex with Ac-Laa-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-Laa-Ep (pdb code 4y7y). 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-Laa-Ep, PDB code: 4y7y:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 4y7y

Go back to Magnesium Binding Sites List in 4y7y
Magnesium binding site 1 out of 7 in the Yeast 20S Proteasome in Complex with Ac-Laa-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-Laa-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:43.8
occ:1.00
 O G:ARG122 2.3 41.8 1.0
O G:MET125 2.3 43.6 1.0
O G:HOH426 2.3 51.6 1.0
OG1 G:THR8 2.6 40.4 1.0
O G:TYR119 2.6 35.8 1.0
O G:ALA123 3.4 43.2 1.0
CG2 G:THR8 3.4 43.2 1.0
C G:ARG122 3.4 43.0 1.0
C G:MET125 3.4 43.4 1.0
CB G:THR8 3.6 42.5 1.0
CA G:ALA123 3.6 43.6 1.0
C G:ALA123 3.6 44.7 1.0
C G:TYR119 3.8 37.6 1.0
N G:ALA123 3.9 43.5 1.0
N G:MET125 4.1 44.4 1.0
N G:THR8 4.3 43.9 1.0
N G:ARG126 4.3 40.1 1.0
CA G:MET125 4.3 45.8 1.0
CA G:ARG126 4.4 38.6 1.0
CA G:TYR119 4.5 36.5 1.0
N G:TYR124 4.6 45.9 1.0
CA G:THR8 4.6 44.1 1.0
CA G:ARG122 4.6 45.4 1.0
CD G:PRO127 4.7 37.3 1.0
N G:ARG122 4.7 43.5 1.0
N G:THR120 4.8 38.1 1.0
CB G:MET125 4.9 50.4 1.0
C G:ARG126 5.0 38.0 1.0
CB G:ALA123 5.0 43.3 1.0
C G:TYR124 5.0 44.8 1.0
CA G:THR120 5.0 37.2 1.0

Magnesium binding site 2 out of 7 in 4y7y

Go back to Magnesium Binding Sites List in 4y7y
Magnesium binding site 2 out of 7 in the Yeast 20S Proteasome in Complex with Ac-Laa-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-Laa-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:48.4
occ:1.00
 O I:HOH436 2.4 40.2 1.0
O I:SER180 2.5 46.4 1.0
O I:ALA174 2.5 46.5 1.0
O I:ASP177 2.6 39.0 1.0
C I:ALA174 3.5 47.3 1.0
O I:HOH413 3.6 49.9 1.0
C I:SER180 3.6 43.4 1.0
C I:ASP177 3.8 42.4 1.0
CA I:ASP175 3.9 48.0 1.0
OXT I:ASP204 4.0 51.6 1.0
N I:ASP175 4.1 48.0 1.0
C I:ASP175 4.4 45.4 1.0
CA I:GLY181 4.4 43.9 1.0
N I:GLY181 4.5 43.0 1.0
OD1 I:ASP175 4.5 53.7 1.0
N I:ASP177 4.5 43.2 1.0
O I:ALA178 4.5 44.6 1.0
N I:SER180 4.6 43.3 1.0
O I:ASP175 4.6 43.2 1.0
CA I:SER180 4.6 43.4 1.0
CA I:ALA174 4.6 47.1 1.0
C I:ALA178 4.7 44.5 1.0
N I:ALA178 4.7 42.4 1.0
CA I:ALA178 4.7 43.3 1.0
CA I:ASP177 4.7 43.7 1.0
CB I:ALA174 4.9 47.3 1.0
C I:ASP204 4.9 55.9 1.0
O I:ASP204 5.0 60.3 1.0

Magnesium binding site 3 out of 7 in 4y7y

Go back to Magnesium Binding Sites List in 4y7y
Magnesium binding site 3 out of 7 in the Yeast 20S Proteasome in Complex with Ac-Laa-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-Laa-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg302

b:53.0
occ:1.00
 O Y:ASP168 2.2 44.8 1.0
O Y:ALA165 2.2 44.6 1.0
O I:ASP204 2.3 60.3 1.0
O Y:SER171 2.5 45.0 1.0
O Y:HOH415 2.6 42.1 1.0
C I:ASP204 3.1 55.9 1.0
C Y:ASP168 3.3 42.8 1.0
C Y:ALA165 3.4 43.8 1.0
C Y:SER171 3.6 44.9 1.0
CA I:ASP204 3.6 54.9 1.0
CA Y:ALA169 3.7 43.5 1.0
O Y:ALA169 3.7 42.1 1.0
C Y:ALA169 3.8 42.6 1.0
N Y:ALA169 3.9 43.6 1.0
CB I:ASP204 3.9 55.7 1.0
NH1 Y:ARG19 4.0 50.6 1.0
OXT I:ASP204 4.0 51.6 1.0
N Y:SER171 4.1 41.5 1.0
CA Y:ALA165 4.2 44.5 1.0
O Y:HIS166 4.3 44.8 1.0
CA Y:SER171 4.4 42.6 1.0
C Y:HIS166 4.4 44.8 1.0
N Y:HIS166 4.4 42.4 1.0
CA Y:ASP168 4.5 41.0 1.0
N Y:ASP168 4.5 42.1 1.0
CZ Y:ARG19 4.5 49.6 1.0
N Y:TYR170 4.6 43.0 1.0
O Y:ALA164 4.6 39.3 1.0
CA Y:HIS166 4.6 44.3 1.0
N Y:GLY172 4.6 46.8 1.0
NH2 Y:ARG19 4.7 51.0 1.0
CA Y:GLY172 4.7 47.7 1.0
CB Y:SER171 4.8 41.7 1.0
C Y:ARG167 4.9 43.8 1.0
N Y:ARG167 4.9 44.9 1.0
CG I:ASP204 5.0 56.5 1.0

Magnesium binding site 4 out of 7 in 4y7y

Go back to Magnesium Binding Sites List in 4y7y
Magnesium binding site 4 out of 7 in the Yeast 20S Proteasome in Complex with Ac-Laa-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-Laa-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg301

b:51.6
occ:1.00
 O K:ALA165 2.1 49.3 1.0
O K:ASP168 2.2 44.5 1.0
O W:ASP204 2.3 54.9 1.0
O K:SER171 2.5 43.5 1.0
C W:ASP204 3.1 52.1 1.0
C K:ASP168 3.3 44.1 1.0
C K:ALA165 3.3 49.0 1.0
CA W:ASP204 3.6 50.2 1.0
C K:SER171 3.7 44.4 1.0
CA K:ALA169 3.7 43.9 1.0
O K:ALA169 3.8 46.6 1.0
CB W:ASP204 3.9 49.4 1.0
C K:ALA169 3.9 44.3 1.0
N K:ALA169 3.9 44.6 1.0
OXT W:ASP204 4.0 52.6 1.0
NH1 K:ARG19 4.1 47.5 1.0
CA K:ALA165 4.1 47.6 1.0
N K:SER171 4.2 42.3 1.0
O K:HIS166 4.2 51.0 1.0
C K:HIS166 4.3 49.5 1.0
N K:HIS166 4.3 47.7 1.0
N K:ASP168 4.4 44.7 1.0
CA K:SER171 4.4 43.5 1.0
CA K:ASP168 4.4 43.8 1.0
CA K:HIS166 4.5 48.9 1.0
O K:ALA164 4.5 49.1 1.0
CZ K:ARG19 4.6 47.8 1.0
N K:GLY172 4.6 46.5 1.0
N K:TYR170 4.7 43.5 1.0
CA K:GLY172 4.8 46.8 1.0
NH2 K:ARG19 4.8 51.8 1.0
CB K:SER171 4.8 43.3 1.0
N K:ARG167 4.8 48.7 1.0
C K:ARG167 4.8 45.4 1.0
CG W:ASP204 4.9 49.5 1.0
N W:ASP204 5.0 51.0 1.0

Magnesium binding site 5 out of 7 in 4y7y

Go back to Magnesium Binding Sites List in 4y7y
Magnesium binding site 5 out of 7 in the Yeast 20S Proteasome in Complex with Ac-Laa-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-Laa-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg301

b:45.4
occ:1.00
 O V:ASP166 2.1 45.6 1.0
O V:SER169 2.2 45.3 1.0
OXT L:ASP222 2.3 52.8 1.0
O V:ILE163 2.3 45.2 1.0
C V:ASP166 3.1 45.5 1.0
C L:ASP222 3.2 54.9 1.0
C V:ILE163 3.4 49.6 1.0
C V:SER169 3.4 45.5 1.0
O V:GLY162 3.7 46.3 1.0
CA L:ASP222 3.8 54.7 1.0
CA V:LEU167 3.8 44.4 1.0
N V:LEU167 3.9 45.4 1.0
NH1 V:ARG19 3.9 48.9 1.0
O L:ASP222 4.0 58.2 1.0
N V:ASP166 4.0 46.2 1.0
CA V:ILE163 4.1 50.2 1.0
CA V:ASP166 4.2 45.5 1.0
N V:SER169 4.2 43.0 1.0
C V:LEU167 4.3 44.2 1.0
CA V:SER169 4.3 44.3 1.0
C V:TRP164 4.3 50.6 1.0
N V:TRP164 4.3 50.1 1.0
N V:GLY170 4.3 46.5 1.0
CB L:ASP222 4.4 56.0 1.0
O V:TRP164 4.4 52.0 1.0
CA V:GLY170 4.4 47.9 1.0
CZ V:ARG19 4.4 48.1 1.0
O V:LEU167 4.5 44.1 1.0
CA V:TRP164 4.5 50.8 1.0
NH2 V:ARG19 4.6 51.0 1.0
N V:ASN165 4.6 49.6 1.0
CB V:SER169 4.7 44.1 1.0
C V:GLY162 4.7 48.5 1.0
C V:ASN165 4.8 46.8 1.0
N V:GLY168 4.9 43.2 1.0
CB V:ASP166 4.9 44.9 1.0
N V:ILE163 4.9 49.8 1.0

Magnesium binding site 6 out of 7 in 4y7y

Go back to Magnesium Binding Sites List in 4y7y
Magnesium binding site 6 out of 7 in the Yeast 20S Proteasome in Complex with Ac-Laa-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-Laa-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg201

b:43.8
occ:1.00
 O N:SER169 2.5 44.3 1.0
O N:ILE163 2.6 41.2 1.0
O N:ASP166 2.9 39.9 1.0
NH1 N:ARG19 3.6 46.4 1.0
C N:SER169 3.7 40.4 1.0
CD1 a:LEU34 3.7 41.8 1.0
C N:ILE163 3.8 44.0 1.0
CG2 N:ILE163 3.9 43.6 1.0
C N:ASP166 4.0 41.2 1.0
CZ N:ARG19 4.2 45.0 1.0
CA N:GLY167 4.3 40.8 1.0
O N:GLY167 4.3 39.1 1.0
CA N:GLY170 4.4 42.7 1.0
CA N:ILE163 4.4 43.3 1.0
N N:GLY170 4.5 40.8 1.0
NH2 N:ARG19 4.5 44.5 1.0
C N:GLY167 4.5 39.3 1.0
N N:GLY167 4.5 41.7 1.0
N N:SER169 4.7 38.2 1.0
CA N:SER169 4.7 37.9 1.0
O a:HOH316 4.8 40.0 1.0
N N:LYS164 4.8 45.0 1.0
CB N:ILE163 4.8 42.9 1.0
O N:LYS164 4.9 47.0 1.0
C N:LYS164 5.0 47.0 1.0

Magnesium binding site 7 out of 7 in 4y7y

Go back to Magnesium Binding Sites List in 4y7y
Magnesium binding site 7 out of 7 in the Yeast 20S Proteasome in Complex with Ac-Laa-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-Laa-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg301

b:65.0
occ:1.00
 O Z:VAL198 2.3 43.8 1.0
O Z:THR192 2.7 51.1 1.0
O Z:HIS195 3.0 42.8 1.0
CG2 Z:THR192 3.5 51.5 1.0
NH2 Z:ARG28 3.5 52.5 1.0
C Z:VAL198 3.5 46.6 1.0
C Z:THR192 3.6 51.2 1.0
O Z:ASP222 3.8 58.6 1.0
CA Z:THR192 3.9 50.2 1.0
O Z:ILE196 4.1 42.7 1.0
C Z:HIS195 4.1 41.6 1.0
CB Z:THR192 4.3 50.9 1.0
CA Z:ILE196 4.3 41.5 1.0
C Z:ILE196 4.3 41.6 1.0
N Z:VAL198 4.3 44.0 1.0
N Z:GLY199 4.4 47.7 1.0
CA Z:GLY199 4.4 48.7 1.0
CA Z:VAL198 4.4 45.4 1.0
OD1 Z:ASP222 4.4 55.0 1.0
CZ Z:ARG28 4.5 51.8 1.0
NH2 H:ARG19 4.7 54.9 1.0
N Z:ILE196 4.7 40.9 1.0
C Z:ASP222 4.7 56.3 1.0
NH1 Z:ARG28 4.7 55.1 1.0
O Z:LYS220 4.8 52.6 1.0
N Z:GLU193 4.9 51.7 1.0
CB Z:VAL198 4.9 45.7 1.0
OG1 Z:THR192 5.0 51.3 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 22:52:14 2024

Last articles

Cl in 3KZP
Cl in 3KXP
Cl in 3KXA
Cl in 3KYZ
Cl in 3KYN
Cl in 3KYA
Cl in 3KW0
Cl in 3KXR
Cl in 3KWE
Cl in 3KWK
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy