Atomistry » Magnesium » PDB 5ac0-5avx » 5ahj
Atomistry »
  Magnesium »
    PDB 5ac0-5avx »
      5ahj »

Magnesium in PDB 5ahj: Yeast 20S Proteasome in Complex with Macyranone A

Enzymatic activity of Yeast 20S Proteasome in Complex with Macyranone A

All present enzymatic activity of Yeast 20S Proteasome in Complex with Macyranone A:
3.4.25.1;

Protein crystallography data

The structure of Yeast 20S Proteasome in Complex with Macyranone A, PDB code: 5ahj was solved by L.Etzbach, A.Plaza, C.Dubiella, M.Groll, M.Kaiser, R.Mueller, 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 (°) 133.670, 300.700, 143.990, 90.00, 112.52, 90.00
R / Rfree (%) 19.407 / 21.894

Other elements in 5ahj:

The structure of Yeast 20S Proteasome in Complex with Macyranone A also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Magnesium Binding Sites:

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

Magnesium binding site 1 out of 7 in 5ahj

Go back to Magnesium Binding Sites List in 5ahj
Magnesium binding site 1 out of 7 in the Yeast 20S Proteasome in Complex with Macyranone A


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 Macyranone A within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg1243

b:55.1
occ:1.00
 O G:MET125 2.3 58.6 1.0
OG1 G:THR8 2.6 59.0 1.0
O G:ARG122 2.8 58.7 1.0
O G:ALA123 2.9 57.6 1.0
O G:TYR119 3.1 56.5 1.0
CG2 G:THR8 3.3 59.6 1.0
C G:MET125 3.4 60.2 1.0
C G:ALA123 3.4 59.7 1.0
CB G:THR8 3.5 58.5 1.0
CA G:ALA123 3.6 59.1 1.0
C G:ARG122 3.8 61.0 1.0
N G:THR8 3.9 59.7 1.0
CA G:ARG126 4.2 55.2 1.0
N G:ALA123 4.2 59.1 1.0
N G:ARG126 4.2 56.4 1.0
N G:MET125 4.2 65.5 1.0
CA G:THR8 4.3 59.3 1.0
C G:TYR119 4.3 53.0 1.0
CA G:MET125 4.4 65.1 1.0
N G:TYR124 4.5 61.8 1.0
CD G:PRO127 4.7 52.4 1.0
CB G:ALA123 4.9 57.8 1.0
C G:TYR124 4.9 65.8 1.0
C G:ARG126 4.9 55.0 1.0
C G:ILE7 5.0 61.2 1.0

Magnesium binding site 2 out of 7 in 5ahj

Go back to Magnesium Binding Sites List in 5ahj
Magnesium binding site 2 out of 7 in the Yeast 20S Proteasome in Complex with Macyranone A


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 Macyranone A within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg1205

b:54.3
occ:1.00
 O I:ASP177 2.1 51.2 1.0
O I:SER180 2.8 48.6 1.0
C I:ASP177 3.2 52.7 1.0
O I:ALA174 3.2 59.9 1.0
CA I:ALA178 3.5 52.1 1.0
O I:ALA178 3.5 52.8 1.0
C I:ALA178 3.6 51.0 1.0
OXT I:ASP204 3.7 63.9 1.0
N I:ALA178 3.8 51.9 1.0
C I:SER180 4.0 52.7 1.0
NH1 Y:ARG19 4.2 69.6 1.0
N I:SER180 4.3 53.2 1.0
N I:LEU179 4.4 52.5 1.0
C I:ALA174 4.4 60.1 1.0
O I:ASP204 4.4 69.5 1.0
CA I:ASP177 4.4 50.8 1.0
N I:ASP177 4.5 46.2 1.0
C I:ASP204 4.5 70.7 1.0
NH2 Y:ARG19 4.7 72.4 1.0
CG2 Y:VAL26 4.7 61.8 1.0
CA I:SER180 4.8 53.9 1.0
O I:ASP175 4.8 60.3 1.0
CA I:ASP175 4.8 59.7 1.0
CZ Y:ARG19 4.9 69.7 1.0
C I:ASP175 4.9 57.4 1.0
CB I:ALA178 4.9 52.3 1.0

Magnesium binding site 3 out of 7 in 5ahj

Go back to Magnesium Binding Sites List in 5ahj
Magnesium binding site 3 out of 7 in the Yeast 20S Proteasome in Complex with Macyranone A


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 Macyranone A within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg1214

b:50.5
occ:1.00
 O K:ASP168 2.2 54.5 1.0
O K:ALA165 2.3 52.2 1.0
O W:ASP204 2.5 57.9 1.0
O K:HIS166 3.1 54.5 1.0
C W:ASP204 3.2 59.3 1.0
C K:ASP168 3.2 53.9 1.0
O K:SER171 3.2 52.6 1.0
C K:ALA165 3.4 52.3 1.0
CA W:ASP204 3.6 60.5 1.0
CA K:ALA169 3.6 55.3 1.0
C K:HIS166 3.7 52.4 1.0
N K:ALA169 3.8 55.1 1.0
OXT W:ASP204 4.0 61.0 1.0
C K:ALA169 4.0 55.7 1.0
O K:ALA169 4.1 55.1 1.0
CA K:HIS166 4.1 51.9 1.0
CB W:ASP204 4.2 59.9 1.0
N K:ASP168 4.2 52.6 1.0
N K:HIS166 4.2 50.9 1.0
CA K:ASP168 4.3 53.0 1.0
C K:SER171 4.4 52.4 1.0
C K:ARG167 4.4 53.0 1.0
NH1 K:ARG19 4.4 70.0 1.0
CA K:ALA165 4.5 53.5 1.0
O K:ALA164 4.5 56.8 1.0
N K:ARG167 4.5 52.0 1.0
O K:ARG167 4.6 50.2 1.0
N K:SER171 4.7 51.4 1.0
N W:ASP204 4.8 61.2 1.0
NE1 W:TRP182 4.9 55.4 1.0
N K:TYR170 4.9 55.8 1.0
CB K:ALA169 4.9 54.4 1.0
CA K:ARG167 4.9 53.4 1.0
CZ K:ARG19 5.0 67.8 1.0

Magnesium binding site 4 out of 7 in 5ahj

Go back to Magnesium Binding Sites List in 5ahj
Magnesium binding site 4 out of 7 in the Yeast 20S Proteasome in Complex with Macyranone A


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 Macyranone A within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg1197

b:48.3
occ:1.00
 O N:ILE163 2.8 42.4 1.0
O N:SER169 2.9 42.4 1.0
O N:ASP166 3.4 46.4 1.0
NH1 N:ARG19 3.5 47.7 1.0
CD1 a:LEU34 3.5 52.9 1.0
C N:ILE163 4.0 46.3 1.0
C N:SER169 4.1 42.8 1.0
CG2 N:ILE163 4.1 47.2 1.0
CZ N:ARG19 4.2 46.7 1.0
CA N:GLY167 4.2 45.2 1.0
C N:ASP166 4.3 44.9 1.0
NH2 N:ARG19 4.4 47.7 1.0
O N:GLY167 4.4 45.6 1.0
CA N:GLY170 4.5 47.5 1.0
C N:GLY167 4.6 44.6 1.0
N N:GLY167 4.7 44.2 1.0
CA N:ILE163 4.7 46.7 1.0
N N:GLY170 4.7 45.0 1.0
CG a:LEU34 4.8 52.9 1.0
O N:LYS164 4.9 54.8 1.0
N N:LYS164 4.9 48.4 1.0

Magnesium binding site 5 out of 7 in 5ahj

Go back to Magnesium Binding Sites List in 5ahj
Magnesium binding site 5 out of 7 in the Yeast 20S Proteasome in Complex with Macyranone A


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 Macyranone A within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Mg1223

b:70.9
occ:1.00
 OXT L:ASP222 2.1 81.5 1.0
O V:ILE163 2.2 58.2 1.0
O V:ASP166 2.3 52.5 1.0
O V:SER169 3.0 52.6 1.0
C V:ASP166 3.1 50.4 1.0
C L:ASP222 3.1 76.2 1.0
C V:ILE163 3.3 59.4 1.0
O V:TRP164 3.4 60.7 1.0
C V:TRP164 3.7 58.0 1.0
N V:LEU167 3.7 48.9 1.0
CA L:ASP222 3.8 72.3 1.0
CA V:LEU167 3.8 49.0 1.0
N V:ASP166 3.8 48.2 1.0
O V:GLY162 3.9 54.0 1.0
O L:ASP222 4.0 76.4 1.0
CA V:ASP166 4.1 49.1 1.0
CA V:TRP164 4.1 57.9 1.0
N V:TRP164 4.1 59.0 1.0
C V:SER169 4.1 50.8 1.0
N V:ASN165 4.3 54.8 1.0
NH1 V:ARG19 4.3 66.6 1.0
CA V:ILE163 4.4 58.9 1.0
C V:ASN165 4.4 49.0 1.0
C V:LEU167 4.4 49.7 1.0
CB L:ASP222 4.5 66.4 1.0
CD2 V:LEU167 4.6 46.6 1.0
O L:ARG221 4.6 69.7 1.0
N V:SER169 4.8 48.2 1.0
O V:LEU167 4.8 51.2 1.0
CA V:ASN165 4.8 51.8 1.0
C V:GLY162 4.9 55.7 1.0
N L:ASP222 5.0 72.4 1.0
CZ V:ARG19 5.0 61.3 1.0
CB V:LEU167 5.0 47.5 1.0
CB V:ASP166 5.0 48.5 1.0
CA V:SER169 5.0 49.1 1.0

Magnesium binding site 6 out of 7 in 5ahj

Go back to Magnesium Binding Sites List in 5ahj
Magnesium binding site 6 out of 7 in the Yeast 20S Proteasome in Complex with Macyranone A


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 Macyranone A within 5.0Å range:
probe atom residue distance (Å) B Occ
Y:Mg1214

b:53.3
occ:1.00
 O Y:ASP168 2.1 53.8 1.0
O I:ASP204 2.2 69.5 1.0
O Y:ALA165 2.5 50.7 1.0
O Y:SER171 2.7 53.8 1.0
C I:ASP204 3.0 70.7 1.0
C Y:ASP168 3.2 52.5 1.0
CA Y:ALA169 3.4 51.4 1.0
O Y:ALA169 3.6 54.7 1.0
CA I:ASP204 3.6 70.4 1.0
C Y:ALA169 3.6 52.0 1.0
C Y:ALA165 3.7 53.2 1.0
N Y:ALA169 3.7 52.8 1.0
NH1 Y:ARG19 3.8 69.6 1.0
O Y:HIS166 3.8 46.1 1.0
C Y:SER171 3.9 53.7 1.0
OXT I:ASP204 3.9 63.9 1.0
CB I:ASP204 4.0 69.7 1.0
N Y:SER171 4.2 49.5 1.0
C Y:HIS166 4.3 51.5 1.0
CZ Y:ARG19 4.4 69.7 1.0
CA Y:ASP168 4.4 50.2 1.0
N Y:TYR170 4.4 51.8 1.0
N Y:ASP168 4.5 50.3 1.0
CA Y:ALA165 4.5 55.3 1.0
CA Y:SER171 4.6 51.3 1.0
N Y:HIS166 4.6 54.1 1.0
NH2 Y:ARG19 4.7 72.4 1.0
O Y:ALA164 4.7 54.1 1.0
CA Y:HIS166 4.7 52.2 1.0
CB Y:ALA169 4.8 50.2 1.0
C Y:ARG167 4.8 50.3 1.0
N Y:GLY172 4.9 55.6 1.0
N I:ASP204 5.0 67.3 1.0

Magnesium binding site 7 out of 7 in 5ahj

Go back to Magnesium Binding Sites List in 5ahj
Magnesium binding site 7 out of 7 in the Yeast 20S Proteasome in Complex with Macyranone A


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 Macyranone A within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg1223

b:75.0
occ:1.00
 O Z:THR192 2.7 62.2 1.0
O Z:VAL198 2.7 52.2 1.0
O Z:HIS195 2.8 58.8 1.0
O Z:ASP222 3.5 77.1 1.0
NH1 Z:ARG28 3.5 59.7 1.0
C Z:THR192 3.7 64.5 1.0
CG2 Z:THR192 3.8 63.7 1.0
C Z:HIS195 3.8 58.3 1.0
C Z:VAL198 3.9 55.4 1.0
O Z:ILE196 3.9 67.2 1.0
CA Z:ILE196 3.9 58.2 1.0
C Z:ILE196 4.1 59.9 1.0
CA Z:THR192 4.1 62.5 1.0
N Z:ILE196 4.3 57.5 1.0
NH2 H:ARG19 4.3 70.1 1.0
OD1 Z:ASP222 4.4 77.2 1.0
N Z:VAL198 4.5 54.0 1.0
CB Z:THR192 4.6 59.8 1.0
CZ Z:ARG28 4.6 59.6 1.0
C Z:ASP222 4.6 79.5 1.0
CA Z:VAL198 4.7 56.1 1.0
N Z:GLY199 4.7 54.9 1.0
CA Z:GLY199 4.8 58.2 1.0
NH2 Z:ARG28 4.9 59.0 1.0
N Z:GLU193 4.9 65.1 1.0
NH1 H:ARG19 4.9 72.8 1.0
CZ H:ARG19 5.0 68.0 1.0
N Z:HIS195 5.0 56.4 1.0
N Z:GLN197 5.0 56.3 1.0

Reference:

L.Etzbach, A.Plaza, C.Dubiella, M.Groll, M.Kaiser, R.Mueller. Macyranones: Structure, Biosynthesis and Binding Mode of An Antiparacsitic Epoxyketone That Targets the 20S Proteasome To Be Published.
Page generated: Sun Sep 29 00:32:09 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