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Magnesium in PDB 5dkj: Yeast 20S Proteasome in Complex with Octreotide-Pi

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

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

Protein crystallography data

The structure of Yeast 20S Proteasome in Complex with Octreotide-Pi, PDB code: 5dkj 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 (°) 136.670, 299.710, 145.430, 90.00, 113.16, 90.00
R / Rfree (%) 19 / 21

Other elements in 5dkj:

The structure of Yeast 20S Proteasome in Complex with Octreotide-Pi 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 Octreotide-Pi (pdb code 5dkj). 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 Octreotide-Pi, PDB code: 5dkj:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 5dkj

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Magnesium binding site 1 out of 8 in the Yeast 20S Proteasome in Complex with Octreotide-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 Octreotide-Pi within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:53.8
occ:1.00
 O G:MET125 2.3 51.4 1.0
O G:ARG122 2.5 46.8 1.0
OG1 G:THR8 2.5 45.6 1.0
O G:TYR119 2.8 43.7 1.0
CG2 G:THR8 3.2 49.3 1.0
O G:ALA123 3.3 57.2 1.0
C G:MET125 3.4 51.4 1.0
CB G:THR8 3.4 48.2 1.0
C G:ARG122 3.6 49.0 1.0
C G:ALA123 3.6 53.1 1.0
CA G:ALA123 3.7 51.0 1.0
C G:TYR119 4.0 42.5 1.0
N G:THR8 4.1 51.0 1.0
N G:ALA123 4.1 48.4 1.0
N G:MET125 4.2 52.7 1.0
CA G:ARG126 4.2 46.8 1.0
N G:ARG126 4.3 48.5 1.0
CA G:THR8 4.4 49.4 1.0
CA G:MET125 4.4 55.0 1.0
CD G:PRO127 4.6 43.5 1.0
N G:TYR124 4.6 54.3 1.0
CA G:TYR119 4.7 42.4 1.0
CA G:ARG122 4.9 51.7 1.0
C G:ARG126 4.9 45.5 1.0
N G:ARG122 5.0 49.9 1.0
N G:THR120 5.0 42.0 1.0
C G:TYR124 5.0 52.5 1.0
CB G:ALA123 5.0 50.6 1.0

Magnesium binding site 2 out of 8 in 5dkj

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Magnesium binding site 2 out of 8 in the Yeast 20S Proteasome in Complex with Octreotide-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 Octreotide-Pi within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:65.6
occ:1.00
 O I:ASP177 2.4 51.4 1.0
O I:SER180 2.7 54.7 1.0
O I:ALA174 2.9 52.0 1.0
C I:ASP177 3.5 50.0 1.0
OXT I:ASP204 3.7 69.0 1.0
C I:SER180 3.9 52.4 1.0
C I:ALA174 4.0 52.1 1.0
CA I:ALA178 4.2 49.3 1.0
NH1 Y:ARG19 4.2 74.7 1.0
CA I:ASP175 4.3 54.8 1.0
N I:ALA178 4.3 48.5 1.0
O I:ALA178 4.3 53.7 1.0
C I:ALA178 4.3 50.1 1.0
N I:ASP177 4.4 50.7 1.0
NH2 Y:ARG19 4.5 80.8 1.0
C I:ASP175 4.5 54.0 1.0
O I:ASP204 4.5 73.5 1.0
N I:SER180 4.5 49.4 1.0
C I:ASP204 4.5 67.5 1.0
O I:ASP175 4.6 57.3 1.0
CA I:ASP177 4.6 50.2 1.0
N I:ASP175 4.6 53.6 1.0
CZ Y:ARG19 4.8 72.8 1.0
CA I:SER180 4.8 50.4 1.0
N I:GLY181 4.8 51.4 1.0
CA I:GLY181 4.8 52.2 1.0

Magnesium binding site 3 out of 8 in 5dkj

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Magnesium binding site 3 out of 8 in the Yeast 20S Proteasome in Complex with Octreotide-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 Octreotide-Pi within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mg201

b:49.6
occ:1.00
 OE1 J:GLN118 3.4 47.8 1.0
O J:THR124 3.7 45.7 1.0
CB J:ASP120 4.0 44.3 1.0
CG J:ASP120 4.1 47.3 1.0
CD J:GLN118 4.1 43.6 1.0
N J:ASP120 4.2 41.5 1.0
OD2 J:ASP120 4.2 52.6 1.0
CG J:GLN118 4.3 42.3 1.0
CB J:THR124 4.3 45.9 1.0
O J:GLN118 4.4 40.3 1.0
CG2 J:THR124 4.4 45.6 1.0
CE1 J:HIS133 4.4 41.7 1.0
C J:THR124 4.6 45.0 1.0
CG1 I:VAL35 4.7 53.4 1.0
CA J:ASP120 4.7 42.5 1.0
OD1 J:ASP120 4.7 51.9 1.0
C J:ILE119 4.8 41.0 1.0
C J:GLN118 4.8 40.4 1.0
CD2 I:LEU28 4.8 51.9 1.0
CA J:ILE119 4.9 39.7 1.0
CB J:GLN118 5.0 41.0 1.0
OG I:SER30 5.0 61.9 1.0

Magnesium binding site 4 out of 8 in 5dkj

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Magnesium binding site 4 out of 8 in the Yeast 20S Proteasome in Complex with Octreotide-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 Octreotide-Pi within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg302

b:60.9
occ:1.00
 O K:ASP168 2.1 52.1 1.0
O W:ASP204 2.2 70.4 1.0
O K:ALA165 2.6 49.8 1.0
O K:SER171 2.6 50.7 1.0
C W:ASP204 3.2 65.8 1.0
C K:ASP168 3.2 53.5 1.0
CA K:ALA169 3.5 56.5 1.0
NH1 K:ARG19 3.6 68.1 1.0
CA W:ASP204 3.7 63.0 1.0
C K:ALA165 3.7 51.8 1.0
C K:ALA169 3.7 56.5 1.0
O K:ALA169 3.7 54.6 1.0
C K:SER171 3.8 50.5 1.0
N K:ALA169 3.8 55.6 1.0
CB W:ASP204 4.0 62.4 1.0
O K:HIS166 4.0 55.4 1.0
OXT W:ASP204 4.2 69.2 1.0
N K:SER171 4.2 51.0 1.0
CZ K:ARG19 4.3 68.4 1.0
CA K:ASP168 4.4 52.4 1.0
CA K:ALA165 4.5 53.6 1.0
C K:HIS166 4.5 53.8 1.0
N K:ASP168 4.5 52.6 1.0
CA K:SER171 4.5 50.0 1.0
N K:TYR170 4.5 56.1 1.0
NH2 K:ARG19 4.7 74.4 1.0
N K:HIS166 4.7 51.7 1.0
N K:GLY172 4.7 51.9 1.0
O K:ALA164 4.8 54.6 1.0
CA K:HIS166 4.9 53.5 1.0
CA K:GLY172 4.9 53.6 1.0
CB K:ALA169 4.9 56.9 1.0
CB K:SER171 4.9 48.9 1.0
C K:ARG167 4.9 53.3 1.0
CG W:ASP204 4.9 62.2 1.0

Magnesium binding site 5 out of 8 in 5dkj

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Magnesium binding site 5 out of 8 in the Yeast 20S Proteasome in Complex with Octreotide-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 Octreotide-Pi within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg202

b:53.0
occ:1.00
 O N:SER169 2.5 42.2 1.0
O N:ILE163 2.6 44.2 1.0
O N:ASP166 2.8 44.6 1.0
NH1 N:ARG19 3.5 46.2 1.0
CD1 a:LEU34 3.6 50.6 1.0
C N:SER169 3.7 41.2 1.0
C N:ILE163 3.8 44.4 1.0
C N:ASP166 3.8 44.2 1.0
CG2 N:ILE163 4.1 42.2 1.0
CA N:GLY167 4.1 44.5 1.0
CZ N:ARG19 4.2 46.1 1.0
O N:GLY167 4.4 45.7 1.0
N N:GLY167 4.4 44.2 1.0
CA N:ILE163 4.4 43.2 1.0
CA N:GLY170 4.4 42.2 1.0
C N:GLY167 4.4 44.2 1.0
NH2 N:ARG19 4.5 47.2 1.0
N N:GLY170 4.5 41.4 1.0
N N:SER169 4.7 41.6 1.0
CA N:SER169 4.7 40.1 1.0
N N:LYS164 4.8 45.3 1.0
CG a:LEU34 4.9 50.5 1.0
CB N:ILE163 4.9 42.4 1.0
N N:ASP166 5.0 43.8 1.0
O N:LYS164 5.0 46.1 1.0
C N:LYS164 5.0 46.3 1.0
CA N:ASP166 5.0 43.6 1.0

Magnesium binding site 6 out of 8 in 5dkj

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Magnesium binding site 6 out of 8 in the Yeast 20S Proteasome in Complex with Octreotide-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 Octreotide-Pi within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Mg302

b:67.9
occ:1.00
 O V:ASP166 2.1 49.5 1.0
OXT L:ASP222 2.1 76.0 1.0
O V:ILE163 2.2 52.5 1.0
O V:SER169 2.8 47.5 1.0
C L:ASP222 3.0 76.4 1.0
C V:ASP166 3.0 50.0 1.0
C V:ILE163 3.3 51.9 1.0
CA L:ASP222 3.7 74.3 1.0
N V:LEU167 3.8 49.7 1.0
CA V:LEU167 3.8 49.6 1.0
O V:TRP164 3.8 55.8 1.0
N V:ASP166 3.9 49.2 1.0
O L:ASP222 3.9 82.4 1.0
O V:GLY162 3.9 48.3 1.0
C V:SER169 3.9 47.7 1.0
C V:TRP164 4.0 54.3 1.0
CA V:ASP166 4.1 49.5 1.0
N V:TRP164 4.2 52.2 1.0
CA V:ILE163 4.2 50.8 1.0
NH1 V:ARG19 4.3 60.1 1.0
CA V:TRP164 4.3 54.0 1.0
C V:LEU167 4.4 50.0 1.0
CB L:ASP222 4.4 72.0 1.0
N V:ASN165 4.5 52.3 1.0
C V:ASN165 4.6 50.7 1.0
N V:SER169 4.7 47.2 1.0
CD2 V:LEU167 4.7 50.5 1.0
O V:LEU167 4.7 53.0 1.0
O L:ARG221 4.7 71.1 1.0
CA V:GLY170 4.8 51.3 1.0
CZ V:ARG19 4.8 59.2 1.0
CA V:SER169 4.8 46.7 1.0
N V:GLY170 4.8 48.0 1.0
NH2 V:ARG19 4.9 62.2 1.0
C V:GLY162 4.9 48.7 1.0
CB V:ASP166 4.9 49.6 1.0
N L:ASP222 5.0 71.6 1.0

Magnesium binding site 7 out of 8 in 5dkj

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Magnesium binding site 7 out of 8 in the Yeast 20S Proteasome in Complex with Octreotide-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 Octreotide-Pi within 5.0Å range:
probe atom residue distance (Å) B Occ
Y:Mg302

b:55.6
occ:1.00
 O Y:ASP168 2.2 52.0 1.0
O I:ASP204 2.2 73.5 1.0
O Y:ALA165 2.5 48.8 1.0
O Y:SER171 2.8 52.0 1.0
C I:ASP204 3.1 67.5 1.0
C Y:ASP168 3.2 52.0 1.0
CA Y:ALA169 3.5 53.8 1.0
C Y:ALA165 3.6 49.9 1.0
CA I:ASP204 3.6 65.1 1.0
N Y:ALA169 3.7 53.1 1.0
O Y:HIS166 3.7 51.5 1.0
NH1 Y:ARG19 3.8 74.7 1.0
C Y:ALA169 3.8 52.3 1.0
O Y:ALA169 3.9 51.4 1.0
C Y:SER171 4.0 49.6 1.0
CB I:ASP204 4.0 66.0 1.0
OXT I:ASP204 4.1 69.0 1.0
C Y:HIS166 4.3 51.1 1.0
CA Y:ASP168 4.3 51.4 1.0
N Y:ASP168 4.4 52.4 1.0
N Y:SER171 4.4 50.0 1.0
CA Y:ALA165 4.4 50.0 1.0
CZ Y:ARG19 4.5 72.8 1.0
N Y:HIS166 4.6 51.6 1.0
N Y:TYR170 4.6 52.1 1.0
CA Y:HIS166 4.7 51.4 1.0
CA Y:SER171 4.7 47.6 1.0
O Y:ALA164 4.7 50.7 1.0
C Y:ARG167 4.7 53.4 1.0
NH2 Y:ARG19 4.8 80.8 1.0
CB Y:ALA169 4.9 55.0 1.0
N Y:GLY172 5.0 50.8 1.0
N Y:ARG167 5.0 50.8 1.0
CG I:ASP204 5.0 67.1 1.0
O Y:ARG167 5.0 54.1 1.0

Magnesium binding site 8 out of 8 in 5dkj

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Magnesium binding site 8 out of 8 in the Yeast 20S Proteasome in Complex with Octreotide-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 Octreotide-Pi within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg301

b:67.1
occ:1.00
 O Z:VAL198 2.5 48.4 1.0
O Z:THR192 3.0 56.1 1.0
O Z:ASP222 3.3 71.9 1.0
O Z:HIS195 3.3 48.9 1.0
NH2 Z:ARG28 3.5 61.7 1.0
CG2 Z:THR192 3.5 58.1 1.0
C Z:VAL198 3.7 51.4 1.0
OD1 Z:ASP222 3.9 60.0 1.0
C Z:THR192 4.0 57.6 1.0
O Z:ILE196 4.1 49.4 1.0
CA Z:THR192 4.2 57.9 1.0
CA Z:ILE196 4.3 49.8 1.0
C Z:ASP222 4.3 71.5 1.0
CZ Z:ARG28 4.4 59.5 1.0
NH2 H:ARG19 4.4 64.0 1.0
C Z:HIS195 4.4 49.5 1.0
C Z:ILE196 4.4 48.9 1.0
CA Z:GLY199 4.4 54.5 1.0
N Z:GLY199 4.5 52.4 1.0
NH1 Z:ARG28 4.5 60.3 1.0
O Z:LYS220 4.5 62.2 1.0
CB Z:THR192 4.5 57.4 1.0
N Z:VAL198 4.6 49.8 1.0
CA Z:VAL198 4.7 51.4 1.0
N Z:ILE196 4.8 48.6 1.0
OXT Z:ASP222 4.9 72.9 1.0
CG Z:ASP222 5.0 60.2 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: Mon Dec 14 20:11:59 2020

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