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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

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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

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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

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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

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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

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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

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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

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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

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