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Magnesium in PDB 8oi1: Yeast 20S Proteasome in Complex with A Photoswitchable Cepafungin Derivative (TRANSCEP4)

Enzymatic activity of Yeast 20S Proteasome in Complex with A Photoswitchable Cepafungin Derivative (TRANSCEP4)

All present enzymatic activity of Yeast 20S Proteasome in Complex with A Photoswitchable Cepafungin Derivative (TRANSCEP4):
3.4.25.1;

Protein crystallography data

The structure of Yeast 20S Proteasome in Complex with A Photoswitchable Cepafungin Derivative (TRANSCEP4), PDB code: 8oi1 was solved by J.Morstein, A.Amatuni, A.Schuster, W.Kuttenlochner, T.Ko, M.Groll, A.Adibekian, H.Renata, D.H.Trauner, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.95
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 135.47, 300.56, 143.85, 90, 113.1, 90
R / Rfree (%) 17.4 / 22.4

Other elements in 8oi1:

The structure of Yeast 20S Proteasome in Complex with A Photoswitchable Cepafungin Derivative (TRANSCEP4) also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 11;

Binding sites:

The binding sites of Magnesium atom in the Yeast 20S Proteasome in Complex with A Photoswitchable Cepafungin Derivative (TRANSCEP4) (pdb code 8oi1). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 11 binding sites of Magnesium where determined in the Yeast 20S Proteasome in Complex with A Photoswitchable Cepafungin Derivative (TRANSCEP4), PDB code: 8oi1:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 11 in 8oi1

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Magnesium binding site 1 out of 11 in the Yeast 20S Proteasome in Complex with A Photoswitchable Cepafungin Derivative (TRANSCEP4)


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 A Photoswitchable Cepafungin Derivative (TRANSCEP4) within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:89.7
occ:1.00
 O G:MET125 2.5 85.0 1.0
OG1 G:THR8 2.6 66.6 1.0
O G:ALA123 2.8 102.1 1.0
O G:ARG122 3.1 85.8 1.0
O G:TYR119 3.3 72.1 1.0
CG2 G:THR8 3.3 69.7 1.0
C G:ALA123 3.4 98.3 1.0
CB G:THR8 3.5 70.0 1.0
CA G:ALA123 3.5 89.3 1.0
C G:MET125 3.6 91.1 1.0
N G:THR8 3.7 77.4 1.0
C G:ARG122 4.1 86.5 1.0
CA G:THR8 4.2 73.6 1.0
CA G:ARG126 4.2 82.9 1.0
N G:ALA123 4.2 86.2 1.0
N G:ARG126 4.3 87.4 1.0
N G:TYR124 4.5 98.3 1.0
N G:MET125 4.5 98.7 1.0
C G:TYR119 4.5 73.9 1.0
CD G:PRO127 4.5 79.1 1.0
C G:ILE7 4.6 84.5 1.0
CA G:MET125 4.7 100.2 1.0
CA G:ILE7 4.7 84.8 1.0
CB G:ALA123 4.8 88.4 1.0
C G:TYR124 4.9 96.8 1.0
O F:HOH302 5.0 47.9 1.0
CB G:ILE7 5.0 83.3 1.0

Magnesium binding site 2 out of 11 in 8oi1

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Magnesium binding site 2 out of 11 in the Yeast 20S Proteasome in Complex with A Photoswitchable Cepafungin Derivative (TRANSCEP4)


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 A Photoswitchable Cepafungin Derivative (TRANSCEP4) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:92.1
occ:1.00
 O I:SER180 2.7 85.5 1.0
O I:ASP177 2.9 80.8 1.0
O I:ALA174 3.2 88.8 1.0
OXT I:ASP204 3.3 108.0 1.0
C I:SER180 3.9 83.5 1.0
C I:ASP177 4.0 84.7 1.0
C I:ASP204 4.2 105.0 1.0
C I:ALA174 4.2 87.8 1.0
O I:ASP204 4.2 108.8 1.0
NH2 Y:ARG19 4.3 90.2 1.0
O I:ALA178 4.4 81.9 1.0
CA I:ASP175 4.4 89.7 1.0
CA I:GLY181 4.5 85.3 1.0
CA I:ALA178 4.5 83.0 1.0
C I:ALA178 4.6 81.9 1.0
N I:GLY181 4.6 82.0 1.0
N I:ALA178 4.7 82.9 1.0
O I:ASP175 4.7 95.0 1.0
NH1 Y:ARG19 4.8 97.7 1.0
C I:ASP175 4.8 89.0 1.0
N I:ASP175 4.8 87.6 1.0
OD1 I:ASP175 4.8 87.7 1.0
CZ Y:ARG19 4.9 93.8 1.0
MG I:MG302 4.9 117.9 1.0
N I:SER180 4.9 82.8 1.0

Magnesium binding site 3 out of 11 in 8oi1

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Magnesium binding site 3 out of 11 in the Yeast 20S Proteasome in Complex with A Photoswitchable Cepafungin Derivative (TRANSCEP4)


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 A Photoswitchable Cepafungin Derivative (TRANSCEP4) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg302

b:117.9
occ:1.00
 MG Y:MG302 3.4 84.6 1.0
NE I:ARG27 3.4 88.1 1.0
O I:ASP204 3.5 108.8 1.0
OXT I:ASP204 3.6 108.0 1.0
O I:ALA178 3.6 81.9 1.0
C I:ASP204 3.7 105.0 1.0
CA Y:ALA169 3.8 79.8 1.0
CD I:ARG27 4.1 86.6 1.0
NE1 I:TRP182 4.1 84.0 1.0
CB Y:ALA169 4.1 77.9 1.0
O Y:HIS166 4.2 74.8 1.0
CD1 I:TRP182 4.2 81.9 1.0
CZ I:ARG27 4.2 88.6 1.0
NH2 I:ARG27 4.2 89.2 1.0
N Y:ALA169 4.5 78.8 1.0
CE2 I:TRP182 4.5 80.9 1.0
O Y:ALA169 4.7 82.0 1.0
O Y:ARG167 4.7 87.5 1.0
CA I:ASP204 4.7 99.0 1.0
CG I:TRP182 4.7 81.2 1.0
C Y:ALA169 4.8 81.6 1.0
C I:ALA178 4.8 81.9 1.0
O Y:ASP168 4.9 75.1 1.0
MG I:MG301 4.9 92.1 1.0
CD2 I:TRP182 4.9 78.9 1.0
C Y:ASP168 4.9 76.6 1.0

Magnesium binding site 4 out of 11 in 8oi1

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Magnesium binding site 4 out of 11 in the Yeast 20S Proteasome in Complex with A Photoswitchable Cepafungin Derivative (TRANSCEP4)


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 A Photoswitchable Cepafungin Derivative (TRANSCEP4) within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mg201

b:61.7
occ:1.00
 OE1 J:GLN118 3.2 74.7 1.0
O J:THR124 3.5 76.9 1.0
OD2 J:ASP120 3.6 90.7 1.0
CB J:ASP120 3.8 80.1 1.0
CG J:ASP120 3.8 84.1 1.0
CG2 J:THR124 4.0 71.8 1.0
N J:ASP120 4.0 76.7 1.0
CB J:THR124 4.1 71.5 1.0
CD J:GLN118 4.3 75.8 1.0
O J:GLN118 4.5 71.0 1.0
CE1 J:HIS133 4.5 92.1 1.0
C J:THR124 4.5 72.7 1.0
OD1 J:ASP120 4.5 85.2 1.0
CA J:ASP120 4.5 76.4 1.0
CG1 I:VAL35 4.5 77.5 1.0
CG J:GLN118 4.7 76.7 1.0
C J:ILE119 4.8 74.5 1.0
CD2 I:LEU28 4.9 72.5 1.0
C J:GLN118 4.9 73.4 1.0
CA J:THR124 4.9 70.8 1.0

Magnesium binding site 5 out of 11 in 8oi1

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Magnesium binding site 5 out of 11 in the Yeast 20S Proteasome in Complex with A Photoswitchable Cepafungin Derivative (TRANSCEP4)


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 A Photoswitchable Cepafungin Derivative (TRANSCEP4) within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg302

b:88.0
occ:1.00
 O W:ASP204 2.2 101.0 1.0
O K:ALA165 2.3 79.8 1.0
O K:ASP168 2.3 71.5 1.0
O K:SER171 2.9 74.3 1.0
C W:ASP204 3.0 100.2 1.0
C K:ASP168 3.2 74.6 1.0
O K:HIS166 3.5 85.3 1.0
CA W:ASP204 3.5 95.1 1.0
CA K:ALA169 3.5 79.5 1.0
C K:ALA165 3.5 81.2 1.0
NH1 K:ARG19 3.5 103.4 1.0
N K:ALA169 3.7 76.8 1.0
O K:ALA169 3.8 80.1 1.0
C K:ALA169 3.8 80.2 1.0
CB W:ASP204 4.0 96.2 1.0
OXT W:ASP204 4.0 104.7 1.0
C K:HIS166 4.1 85.4 1.0
C K:SER171 4.1 74.2 1.0
N K:ASP168 4.4 79.8 1.0
CA K:ALA165 4.4 82.0 1.0
N K:HIS166 4.4 81.4 1.0
CA K:ASP168 4.4 78.1 1.0
N K:SER171 4.5 76.9 1.0
CA K:HIS166 4.5 84.1 1.0
C K:ARG167 4.6 84.0 1.0
CZ K:ARG19 4.6 104.0 1.0
O K:ARG167 4.6 81.4 1.0
N K:TYR170 4.7 81.9 1.0
O K:ALA164 4.7 83.5 1.0
CA K:SER171 4.8 73.2 1.0
N K:ARG167 4.8 83.6 1.0
CB K:ALA169 4.9 78.8 1.0
N W:ASP204 4.9 92.6 1.0
CG W:ASP204 4.9 94.3 1.0

Magnesium binding site 6 out of 11 in 8oi1

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Magnesium binding site 6 out of 11 in the Yeast 20S Proteasome in Complex with A Photoswitchable Cepafungin Derivative (TRANSCEP4)


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 A Photoswitchable Cepafungin Derivative (TRANSCEP4) within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg303

b:92.5
occ:1.00
 O K:ILE82 3.2 72.8 1.0
CB K:ASN85 3.8 71.1 1.0
N K:LEU86 4.0 71.7 1.0
C K:ILE82 4.1 70.5 1.0
CA K:ILE82 4.1 70.3 1.0
CG2 K:ILE82 4.3 70.1 1.0
C K:ASN85 4.3 72.3 1.0
CA K:LEU86 4.4 71.3 1.0
CB K:LEU86 4.5 71.7 1.0
CH2 K:TRP58 4.6 69.6 1.0
CA K:ASN85 4.6 71.3 1.0
CB K:ILE82 4.7 70.2 1.0
O K:ASN85 4.9 74.5 1.0

Magnesium binding site 7 out of 11 in 8oi1

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Magnesium binding site 7 out of 11 in the Yeast 20S Proteasome in Complex with A Photoswitchable Cepafungin Derivative (TRANSCEP4)


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 A Photoswitchable Cepafungin Derivative (TRANSCEP4) within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg201

b:73.0
occ:1.00
 O N:ILE163 2.6 75.7 1.0
O N:SER169 2.7 84.4 1.0
O N:ASP166 2.9 76.6 1.0
NH1 N:ARG19 3.3 82.7 1.0
CD1 a:LEU34 3.7 72.7 1.0
C N:ILE163 3.8 74.8 1.0
C N:SER169 3.8 81.2 1.0
C N:ASP166 3.9 73.2 1.0
CZ N:ARG19 3.9 80.4 1.0
CA N:GLY167 4.0 71.1 1.0
CG2 N:ILE163 4.1 71.0 1.0
NH2 N:ARG19 4.1 79.7 1.0
O N:GLY167 4.2 69.2 1.0
N N:GLY167 4.3 72.0 1.0
C N:GLY167 4.3 70.9 1.0
CA N:GLY170 4.3 82.4 1.0
CA N:ILE163 4.5 72.5 1.0
N N:GLY170 4.5 83.6 1.0
O N:LYS164 4.7 86.9 1.0
N N:LYS164 4.8 78.4 1.0
NE N:ARG19 4.9 79.9 1.0
C N:LYS164 4.9 83.0 1.0
CA N:SER169 4.9 77.4 1.0
N N:SER169 4.9 74.2 1.0
CB N:ILE163 4.9 70.9 1.0
CG a:LEU34 5.0 76.7 1.0

Magnesium binding site 8 out of 11 in 8oi1

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Magnesium binding site 8 out of 11 in the Yeast 20S Proteasome in Complex with A Photoswitchable Cepafungin Derivative (TRANSCEP4)


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 A Photoswitchable Cepafungin Derivative (TRANSCEP4) within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg202

b:76.2
occ:1.00
 OE1 H:GLN91 2.5 101.2 1.0
OD1 N:ASP51 3.2 76.0 1.0
OD2 N:ASP51 3.4 71.9 1.0
O N:ASN92 3.4 83.5 1.0
CD H:GLN91 3.6 89.1 1.0
CG N:ASP51 3.7 72.0 1.0
NE2 H:GLN91 4.1 94.4 1.0
C N:ASN92 4.4 80.5 1.0
CG H:GLN91 4.9 81.1 1.0

Magnesium binding site 9 out of 11 in 8oi1

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Magnesium binding site 9 out of 11 in the Yeast 20S Proteasome in Complex with A Photoswitchable Cepafungin Derivative (TRANSCEP4)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Yeast 20S Proteasome in Complex with A Photoswitchable Cepafungin Derivative (TRANSCEP4) within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Mg302

b:104.6
occ:1.00
 O V:ILE163 2.1 78.3 1.0
OXT L:ASP222 2.2 106.6 1.0
O V:ASP166 2.2 72.4 1.0
O V:SER169 2.7 74.2 1.0
C L:ASP222 3.1 98.8 1.0
C V:ASP166 3.1 77.0 1.0
C V:ILE163 3.3 80.1 1.0
O V:TRP164 3.5 83.5 1.0
NH1 V:ARG19 3.7 89.4 1.0
CA V:LEU167 3.7 81.7 1.0
CA L:ASP222 3.7 94.4 1.0
N V:LEU167 3.7 78.8 1.0
C V:TRP164 3.9 81.0 1.0
C V:SER169 3.9 76.4 1.0
O V:GLY162 4.0 75.8 1.0
O L:ASP222 4.0 97.8 1.0
N V:ASP166 4.1 78.1 1.0
N V:TRP164 4.1 79.7 1.0
CA V:ASP166 4.2 77.3 1.0
CA V:TRP164 4.2 79.6 1.0
CA V:ILE163 4.3 79.7 1.0
C V:LEU167 4.3 82.1 1.0
O L:ARG221 4.4 85.9 1.0
O V:LEU167 4.5 81.9 1.0
N V:ASN165 4.5 78.7 1.0
CB L:ASP222 4.5 93.8 1.0
N V:SER169 4.7 78.8 1.0
CD2 V:LEU167 4.7 80.3 1.0
C V:ASN165 4.7 80.5 1.0
CA V:GLY170 4.7 76.0 1.0
N V:GLY170 4.8 72.4 1.0
CA V:SER169 4.8 76.3 1.0
CZ V:ARG19 4.8 84.6 1.0
N L:ASP222 4.9 90.6 1.0
C V:GLY162 4.9 77.3 1.0
CB V:LEU167 5.0 80.9 1.0

Magnesium binding site 10 out of 11 in 8oi1

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Magnesium binding site 10 out of 11 in the Yeast 20S Proteasome in Complex with A Photoswitchable Cepafungin Derivative (TRANSCEP4)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Yeast 20S Proteasome in Complex with A Photoswitchable Cepafungin Derivative (TRANSCEP4) within 5.0Å range:
probe atom residue distance (Å) B Occ
Y:Mg302

b:84.6
occ:1.00
 O Y:ASP168 2.3 75.1 1.0
O I:ASP204 2.4 108.8 1.0
O Y:ALA165 2.5 78.9 1.0
O Y:SER171 2.9 85.7 1.0
C I:ASP204 3.2 105.0 1.0
C Y:ASP168 3.2 76.6 1.0
MG I:MG302 3.4 117.9 1.0
CA Y:ALA169 3.4 79.8 1.0
NH1 Y:ARG19 3.5 97.7 1.0
O Y:HIS166 3.6 74.8 1.0
CA I:ASP204 3.6 99.0 1.0
C Y:ALA165 3.6 76.7 1.0
N Y:ALA169 3.6 78.8 1.0
O Y:ALA169 3.7 82.0 1.0
C Y:ALA169 3.7 81.6 1.0
CB I:ASP204 4.1 98.2 1.0
OXT I:ASP204 4.1 108.0 1.0
C Y:SER171 4.1 79.9 1.0
C Y:HIS166 4.1 77.7 1.0
N Y:ASP168 4.4 81.2 1.0
CA Y:ASP168 4.4 78.8 1.0
CA Y:ALA165 4.5 74.3 1.0
N Y:HIS166 4.5 78.0 1.0
N Y:SER171 4.5 77.2 1.0
C Y:ARG167 4.5 83.6 1.0
O Y:ARG167 4.6 87.5 1.0
N Y:TYR170 4.6 83.8 1.0
CZ Y:ARG19 4.6 93.8 1.0
CA Y:HIS166 4.6 79.7 1.0
CB Y:ALA169 4.8 77.9 1.0
O Y:ALA164 4.8 68.8 1.0
CA Y:SER171 4.9 76.5 1.0
N Y:ARG167 4.9 79.4 1.0
N I:ASP204 5.0 97.1 1.0

Reference:

J.Morstein, A.Amatuni, A.Shuster, W.Kuttenlochner, T.Ko, D.Abegg, M.Groll, A.Adibekian, H.Renata, D.Trauner. Optical Control of Proteasomal Protein Degradation with A Photoswitchable Lipopeptide. Angew.Chem.Int.Ed.Engl. 14791 2023.
ISSN: ESSN 1521-3773
PubMed: 38109686
DOI: 10.1002/ANIE.202314791
Page generated: Fri Oct 4 14:49:26 2024

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