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Magnesium in PDB 5dki: Yeast 20S Proteasome in Complex with Alkyne-Pi

Enzymatic activity of Yeast 20S Proteasome in Complex with Alkyne-Pi

All present enzymatic activity of Yeast 20S Proteasome in Complex with Alkyne-Pi:
3.4.25.1;

Protein crystallography data

The structure of Yeast 20S Proteasome in Complex with Alkyne-Pi, PDB code: 5dki was solved by P.Beck, H.Cui, 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 (°) 137.160, 298.090, 145.960, 90.00, 113.11, 90.00
R / Rfree (%) 19.9 / 21.9

Other elements in 5dki:

The structure of Yeast 20S Proteasome in Complex with Alkyne-Pi also contains other interesting chemical elements:

Chlorine (Cl) 5 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Yeast 20S Proteasome in Complex with Alkyne-Pi (pdb code 5dki). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Yeast 20S Proteasome in Complex with Alkyne-Pi, PDB code: 5dki:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 5dki

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Magnesium binding site 1 out of 8 in the Yeast 20S Proteasome in Complex with Alkyne-Pi


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 Alkyne-Pi within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:50.7
occ:1.00
 O G:MET125 2.3 47.2 1.0
OG1 G:THR8 2.5 44.3 1.0
O G:ARG122 2.6 42.3 1.0
O G:TYR119 2.8 40.1 1.0
CG2 G:THR8 3.2 45.5 1.0
O G:ALA123 3.3 48.5 1.0
CB G:THR8 3.4 45.1 1.0
C G:MET125 3.4 47.7 1.0
C G:ALA123 3.7 48.2 1.0
C G:ARG122 3.7 45.2 1.0
CA G:ALA123 3.7 46.5 1.0
C G:TYR119 4.0 39.2 1.0
N G:THR8 4.0 46.9 1.0
N G:ALA123 4.2 45.1 1.0
O G:HOH412 4.2 60.1 1.0
CA G:ARG126 4.2 43.1 1.0
N G:ARG126 4.2 44.6 1.0
N G:MET125 4.3 49.5 1.0
CA G:THR8 4.4 45.6 1.0
CA G:MET125 4.4 51.3 1.0
CD G:PRO127 4.5 39.7 1.0
N G:TYR124 4.7 50.2 1.0
CA G:TYR119 4.7 38.7 1.0
C G:ARG126 4.9 42.9 1.0
CA G:ARG122 5.0 47.8 1.0

Magnesium binding site 2 out of 8 in 5dki

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Magnesium binding site 2 out of 8 in the Yeast 20S Proteasome in Complex with Alkyne-Pi


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 Alkyne-Pi within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:56.6
occ:1.00
 O I:ASP177 2.3 44.5 1.0
O I:ALA174 2.6 47.4 1.0
O I:SER180 2.7 46.4 1.0
C I:ASP177 3.5 44.9 1.0
C I:ALA174 3.6 47.0 1.0
C I:SER180 3.8 45.7 1.0
OXT I:ASP204 4.0 62.4 1.0
CA I:ASP175 4.0 49.9 1.0
N I:ASP177 4.2 44.9 1.0
C I:ASP175 4.2 49.5 1.0
N I:ASP175 4.2 48.6 1.0
N I:ALA178 4.3 43.9 1.0
CA I:ASP177 4.4 45.0 1.0
CA I:ALA178 4.4 44.6 1.0
O I:ASP175 4.4 51.6 1.0
N I:SER180 4.6 43.1 1.0
C I:ALA178 4.6 45.4 1.0
NH1 Y:ARG19 4.6 66.7 1.0
O I:ALA178 4.6 49.4 1.0
CA I:SER180 4.7 44.7 1.0
N I:GLY181 4.7 45.9 1.0
CA I:GLY181 4.7 47.7 1.0
CA I:ALA174 4.8 44.4 1.0
NH2 Y:ARG19 4.8 72.3 1.0
N I:ARG176 4.8 45.8 1.0
C I:ASP204 4.9 61.4 1.0
O I:ASP204 4.9 63.8 1.0
OD1 I:ASP175 4.9 53.8 1.0
CB I:ASP177 4.9 46.3 1.0

Magnesium binding site 3 out of 8 in 5dki

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Magnesium binding site 3 out of 8 in the Yeast 20S Proteasome in Complex with Alkyne-Pi


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 Alkyne-Pi within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg302

b:53.7
occ:1.00
 O I:ASP204 2.2 63.8 1.0
O Y:ASP168 2.2 43.6 1.0
O Y:SER171 2.6 46.8 1.0
O Y:ALA165 2.6 44.8 1.0
C I:ASP204 3.2 61.4 1.0
C Y:ASP168 3.3 46.5 1.0
NH1 Y:ARG19 3.5 66.7 1.0
CA Y:ALA169 3.5 49.3 1.0
CA I:ASP204 3.7 59.1 1.0
C Y:ALA169 3.7 48.5 1.0
O Y:ALA169 3.7 45.3 1.0
C Y:SER171 3.8 43.8 1.0
C Y:ALA165 3.8 44.6 1.0
N Y:ALA169 3.8 48.2 1.0
CB I:ASP204 3.9 59.8 1.0
O Y:HIS166 4.1 45.3 1.0
OXT I:ASP204 4.2 62.4 1.0
N Y:SER171 4.2 43.5 1.0
CZ Y:ARG19 4.2 64.8 1.0
CA Y:ASP168 4.5 45.8 1.0
CA Y:ALA165 4.5 44.6 1.0
CA Y:SER171 4.5 41.9 1.0
C Y:HIS166 4.6 46.2 1.0
N Y:ASP168 4.6 46.7 1.0
N Y:TYR170 4.6 47.6 1.0
NH2 Y:ARG19 4.6 72.3 1.0
N Y:GLY172 4.8 45.4 1.0
N Y:HIS166 4.8 46.4 1.0
CG I:ASP204 4.9 61.2 1.0
CA Y:GLY172 4.9 46.7 1.0
CB Y:ALA169 4.9 50.2 1.0
O Y:ALA164 4.9 46.8 1.0
C Y:ARG167 4.9 48.4 1.0
CA Y:HIS166 5.0 46.7 1.0
CB Y:SER171 5.0 40.0 1.0

Magnesium binding site 4 out of 8 in 5dki

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Magnesium binding site 4 out of 8 in the Yeast 20S Proteasome in Complex with Alkyne-Pi


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 Alkyne-Pi within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mg201

b:43.5
occ:1.00
 OE1 J:GLN118 3.3 45.4 1.0
O J:THR124 3.8 40.1 1.0
CB J:ASP120 3.9 39.5 1.0
CD J:GLN118 4.1 41.0 1.0
CG J:ASP120 4.1 42.2 1.0
OD2 J:ASP120 4.1 47.9 1.0
N J:ASP120 4.2 37.0 1.0
CG J:GLN118 4.2 38.6 1.0
CE1 J:HIS133 4.3 37.2 1.0
CB J:THR124 4.4 42.5 1.0
O J:GLN118 4.5 36.9 1.0
CG2 J:THR124 4.6 42.8 1.0
CG1 I:VAL35 4.7 47.9 1.0
CA J:ASP120 4.7 37.8 1.0
OD1 J:ASP120 4.7 46.9 1.0
C J:ILE119 4.8 36.3 1.0
C J:THR124 4.8 40.5 1.0
C J:GLN118 4.8 36.1 1.0
CD2 I:LEU28 4.9 46.0 1.0
OG I:SER30 4.9 56.2 1.0
CA J:ILE119 5.0 35.3 1.0
CB J:GLN118 5.0 37.2 1.0

Magnesium binding site 5 out of 8 in 5dki

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Magnesium binding site 5 out of 8 in the Yeast 20S Proteasome in Complex with Alkyne-Pi


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 Alkyne-Pi within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg302

b:49.6
occ:1.00
 O K:ASP168 2.2 48.1 1.0
O W:ASP204 2.3 57.0 1.0
O K:ALA165 2.4 49.3 1.0
O K:SER171 2.8 48.1 1.0
C K:ASP168 3.2 48.7 1.0
C W:ASP204 3.2 57.5 1.0
C K:ALA165 3.5 49.3 1.0
CA K:ALA169 3.6 51.9 1.0
CA W:ASP204 3.7 57.2 1.0
O K:HIS166 3.7 53.7 1.0
N K:ALA169 3.8 50.4 1.0
NH1 K:ARG19 3.9 63.6 1.0
C K:ALA169 4.0 52.2 1.0
CB W:ASP204 4.0 57.3 1.0
C K:SER171 4.0 47.5 1.0
O K:ALA169 4.0 52.1 1.0
C K:HIS166 4.2 50.8 1.0
OXT W:ASP204 4.2 61.1 1.0
N K:ASP168 4.3 49.3 1.0
CA K:ASP168 4.3 48.0 1.0
CA K:ALA165 4.4 50.8 1.0
N K:SER171 4.4 46.4 1.0
N K:HIS166 4.5 49.0 1.0
CA K:HIS166 4.6 50.3 1.0
C K:ARG167 4.6 50.5 1.0
CZ K:ARG19 4.6 62.9 1.0
O K:ALA164 4.6 50.0 1.0
CA K:SER171 4.7 46.2 1.0
N K:TYR170 4.7 50.9 1.0
N K:ARG167 4.8 49.3 1.0
O K:ARG167 4.9 51.2 1.0
CG W:ASP204 4.9 57.0 1.0
NH2 K:ARG19 4.9 68.7 1.0
N K:GLY172 5.0 48.1 1.0
CB K:ALA169 5.0 51.7 1.0

Magnesium binding site 6 out of 8 in 5dki

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Magnesium binding site 6 out of 8 in the Yeast 20S Proteasome in Complex with Alkyne-Pi


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 Alkyne-Pi within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg301

b:59.6
occ:1.00
 OXT L:ASP222 2.0 67.1 1.0
O V:ASP166 2.1 43.2 1.0
O V:ILE163 2.2 48.5 1.0
O V:SER169 2.8 45.4 1.0
C L:ASP222 3.0 68.9 1.0
C V:ASP166 3.1 44.2 1.0
C V:ILE163 3.3 47.3 1.0
CA L:ASP222 3.7 67.9 1.0
O V:TRP164 3.8 51.5 1.0
N V:LEU167 3.8 43.9 1.0
CA V:LEU167 3.8 43.8 1.0
O L:ASP222 3.8 75.8 1.0
N V:ASP166 3.9 44.3 1.0
O V:GLY162 3.9 40.8 1.0
C V:TRP164 3.9 49.4 1.0
C V:SER169 3.9 43.6 1.0
CA V:ASP166 4.1 44.0 1.0
N V:TRP164 4.2 46.8 1.0
NH1 V:ARG19 4.2 54.2 1.0
CA V:ILE163 4.3 46.4 1.0
CA V:TRP164 4.3 48.9 1.0
CB L:ASP222 4.3 66.4 1.0
N V:ASN165 4.4 47.6 1.0
C V:LEU167 4.5 44.2 1.0
C V:ASN165 4.5 44.7 1.0
N V:SER169 4.7 41.4 1.0
CD2 V:LEU167 4.7 43.9 1.0
O V:LEU167 4.8 46.0 1.0
CA V:GLY170 4.8 47.5 1.0
CA V:SER169 4.8 42.1 1.0
CZ V:ARG19 4.8 53.5 1.0
N V:GLY170 4.8 44.9 1.0
C V:GLY162 4.9 43.4 1.0
O L:ARG221 4.9 65.3 1.0
NH2 V:ARG19 4.9 55.4 1.0
CA V:ASN165 5.0 45.7 1.0
CB V:ASP166 5.0 44.3 1.0

Magnesium binding site 7 out of 8 in 5dki

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Magnesium binding site 7 out of 8 in the Yeast 20S Proteasome in Complex with Alkyne-Pi


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 Alkyne-Pi within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg202

b:45.4
occ:1.00
 O N:SER169 2.5 38.0 1.0
O N:ILE163 2.6 39.0 1.0
O N:ASP166 2.9 41.1 1.0
NH1 N:ARG19 3.6 40.2 1.0
CD1 a:LEU34 3.7 46.3 1.0
C N:SER169 3.7 36.6 1.0
C N:ILE163 3.8 40.4 1.0
C N:ASP166 3.9 39.4 1.0
CG2 N:ILE163 4.0 38.1 1.0
CZ N:ARG19 4.2 40.6 1.0
CA N:GLY167 4.3 39.1 1.0
CA N:GLY170 4.4 37.5 1.0
CA N:ILE163 4.4 39.0 1.0
O N:GLY167 4.5 41.3 1.0
NH2 N:ARG19 4.5 42.5 1.0
N N:GLY170 4.5 36.4 1.0
N N:GLY167 4.5 38.8 1.0
C N:GLY167 4.6 39.1 1.0
N N:SER169 4.7 36.9 1.0
CA N:SER169 4.7 35.6 1.0
N N:LYS164 4.8 41.6 1.0
CB N:ILE163 4.9 38.4 1.0
O a:HOH312 5.0 43.7 1.0
CG a:LEU34 5.0 46.3 1.0
C N:LYS164 5.0 42.8 1.0

Magnesium binding site 8 out of 8 in 5dki

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Magnesium binding site 8 out of 8 in the Yeast 20S Proteasome in Complex with Alkyne-Pi


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Yeast 20S Proteasome in Complex with Alkyne-Pi within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg301

b:67.4
occ:1.00
 O Z:VAL198 2.5 43.9 1.0
O Z:THR192 3.0 52.5 1.0
O Z:ASP222 3.2 68.6 1.0
NH2 Z:ARG28 3.4 57.2 1.0
CG2 Z:THR192 3.5 54.8 1.0
O Z:HIS195 3.5 46.6 1.0
C Z:VAL198 3.7 48.2 1.0
OD1 Z:ASP222 3.8 57.0 1.0
C Z:THR192 4.0 53.6 1.0
O Z:ILE196 4.2 46.2 1.0
CA Z:GLY199 4.3 50.5 1.0
CA Z:THR192 4.3 53.9 1.0
C Z:ASP222 4.3 66.5 1.0
CZ Z:ARG28 4.3 54.3 1.0
O Z:LYS220 4.4 58.0 1.0
NH2 H:ARG19 4.4 60.7 1.0
NH1 Z:ARG28 4.4 55.6 1.0
N Z:GLY199 4.4 49.0 1.0
CA Z:ILE196 4.5 45.8 1.0
CB Z:THR192 4.5 53.6 1.0
C Z:ILE196 4.5 45.1 1.0
C Z:HIS195 4.6 46.3 1.0
N Z:VAL198 4.7 47.8 1.0
CA Z:VAL198 4.8 48.1 1.0
CG Z:ASP222 4.9 56.1 1.0
OXT Z:ASP222 4.9 67.3 1.0

Reference:

P.Beck, H.Cui, J.D.Hegemann, M.A.Marahiel, A.Kruger, M.Groll. Targeted Delivery of Proteasome Inhibitors to Somatostatin-Receptor-Expressing Cancer Cells By Octreotide Conjugation. Chemmedchem V. 10 1969 2015.
ISSN: ESSN 1860-7187
PubMed: 26471124
DOI: 10.1002/CMDC.201500449
Page generated: Tue Aug 12 07:00:43 2025

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