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Magnesium in PDB 8ohz: Yeast 20S Proteasome in Complex with A Photoswitchable Cepafungin Derivative (TRANSCEP1)

Enzymatic activity of Yeast 20S Proteasome in Complex with A Photoswitchable Cepafungin Derivative (TRANSCEP1)

All present enzymatic activity of Yeast 20S Proteasome in Complex with A Photoswitchable Cepafungin Derivative (TRANSCEP1):
3.4.25.1;

Protein crystallography data

The structure of Yeast 20S Proteasome in Complex with A Photoswitchable Cepafungin Derivative (TRANSCEP1), PDB code: 8ohz 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 / 2.65
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 135.51, 300.79, 144.77, 90, 113.41, 90
R / Rfree (%) 18 / 22.2

Other elements in 8ohz:

The structure of Yeast 20S Proteasome in Complex with A Photoswitchable Cepafungin Derivative (TRANSCEP1) also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Yeast 20S Proteasome in Complex with A Photoswitchable Cepafungin Derivative (TRANSCEP1) (pdb code 8ohz). 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 A Photoswitchable Cepafungin Derivative (TRANSCEP1), PDB code: 8ohz:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 8ohz

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Magnesium binding site 1 out of 8 in the Yeast 20S Proteasome in Complex with A Photoswitchable Cepafungin Derivative (TRANSCEP1)


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 (TRANSCEP1) within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:81.2
occ:1.00
 O G:MET125 2.3 68.0 1.0
OG1 G:THR8 2.5 61.5 1.0
O G:ARG122 2.9 72.7 1.0
O G:TYR119 3.0 61.3 1.0
O G:ALA123 3.0 75.4 1.0
CG2 G:THR8 3.3 62.2 1.0
CB G:THR8 3.4 61.7 1.0
C G:MET125 3.4 72.5 1.0
C G:ALA123 3.5 76.1 1.0
CA G:ALA123 3.6 72.0 1.0
C G:ARG122 3.9 72.2 1.0
N G:THR8 3.9 65.7 1.0
N G:ALA123 4.2 71.5 1.0
N G:ARG126 4.2 68.7 1.0
CA G:ARG126 4.2 66.8 1.0
C G:TYR119 4.2 61.2 1.0
CA G:THR8 4.3 62.8 1.0
N G:MET125 4.4 73.8 1.0
CD G:PRO127 4.5 63.2 1.0
CA G:MET125 4.5 78.0 1.0
N G:TYR124 4.5 77.1 1.0
CB G:ALA123 4.9 70.1 1.0
C G:ILE7 4.9 71.3 1.0
C G:ARG126 4.9 66.8 1.0
C G:TYR124 5.0 71.8 1.0
CA G:TYR119 5.0 58.1 1.0

Magnesium binding site 2 out of 8 in 8ohz

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Magnesium binding site 2 out of 8 in the Yeast 20S Proteasome in Complex with A Photoswitchable Cepafungin Derivative (TRANSCEP1)


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 (TRANSCEP1) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:86.6
occ:1.00
 O I:ASP177 2.7 66.6 1.0
O I:SER180 2.8 69.6 1.0
OXT I:ASP204 3.3 102.7 1.0
O I:ALA174 3.4 77.1 1.0
C I:ASP177 3.8 68.4 1.0
O I:ALA178 3.9 71.9 1.0
O I:ASP204 4.0 101.2 1.0
C I:SER180 4.1 69.2 1.0
C I:ASP204 4.1 96.9 1.0
CA I:ALA178 4.2 70.5 1.0
C I:ALA178 4.2 71.5 1.0
NH1 Y:ARG19 4.3 82.0 1.0
NH2 Y:ARG19 4.4 81.5 1.0
N I:ALA178 4.4 67.4 1.0
C I:ALA174 4.5 77.5 1.0
CA I:ASP175 4.6 80.2 1.0
O I:ASP175 4.7 81.4 1.0
CZ Y:ARG19 4.7 81.2 1.0
N I:SER180 4.8 68.4 1.0
C I:ASP175 4.8 77.0 1.0
CA I:GLY181 4.9 70.6 1.0
N I:GLY181 4.9 68.2 1.0
N I:ASP177 5.0 72.5 1.0
CA I:ASP177 5.0 70.8 1.0

Magnesium binding site 3 out of 8 in 8ohz

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Magnesium binding site 3 out of 8 in the Yeast 20S Proteasome in Complex with A Photoswitchable Cepafungin Derivative (TRANSCEP1)


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 (TRANSCEP1) within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mg201

b:61.5
occ:1.00
 OE1 J:GLN118 3.2 69.0 1.0
O J:THR124 3.6 63.9 1.0
CB J:ASP120 3.6 64.0 1.0
OD2 J:ASP120 3.7 78.1 1.0
CG J:ASP120 3.8 68.6 1.0
N J:ASP120 3.9 57.8 1.0
CD J:GLN118 4.2 67.2 1.0
CG2 J:THR124 4.2 59.8 1.0
CB J:THR124 4.2 59.6 1.0
CE1 J:HIS133 4.2 71.4 1.0
CA J:ASP120 4.4 60.3 1.0
O J:GLN118 4.4 57.5 1.0
CG J:GLN118 4.5 65.0 1.0
C J:THR124 4.5 59.9 1.0
C J:ILE119 4.6 57.0 1.0
OD1 J:ASP120 4.6 73.5 1.0
CG1 I:VAL35 4.7 75.0 1.0
C J:GLN118 4.8 57.3 1.0
CA J:ILE119 4.8 57.3 1.0
ND1 J:HIS133 4.9 72.5 1.0
CA J:THR124 5.0 59.5 1.0

Magnesium binding site 4 out of 8 in 8ohz

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Magnesium binding site 4 out of 8 in the Yeast 20S Proteasome in Complex with A Photoswitchable Cepafungin Derivative (TRANSCEP1)


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 (TRANSCEP1) within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg302

b:70.5
occ:1.00
 O K:ASP168 2.2 68.7 1.0
O K:ALA165 2.2 60.8 1.0
O W:ASP204 2.4 83.1 1.0
O K:SER171 2.8 66.2 1.0
C W:ASP204 3.1 86.8 1.0
C K:ASP168 3.2 69.0 1.0
C K:ALA165 3.4 65.8 1.0
CA W:ASP204 3.5 84.7 1.0
O K:HIS166 3.6 71.5 1.0
CA K:ALA169 3.7 71.8 1.0
NH1 K:ARG19 3.7 85.7 1.0
O K:ALA169 3.8 70.1 1.0
N K:ALA169 3.8 72.0 1.0
CB W:ASP204 3.9 83.8 1.0
C K:ALA169 3.9 72.0 1.0
C K:SER171 4.0 64.0 1.0
OXT W:ASP204 4.1 92.6 1.0
C K:HIS166 4.1 70.7 1.0
CA K:ALA165 4.3 67.1 1.0
N K:HIS166 4.3 65.8 1.0
N K:ASP168 4.4 72.3 1.0
CA K:ASP168 4.4 70.5 1.0
N K:SER171 4.5 66.3 1.0
CA K:HIS166 4.5 68.4 1.0
C K:ARG167 4.5 73.6 1.0
O K:ALA164 4.6 71.1 1.0
O K:ARG167 4.7 74.3 1.0
CZ K:ARG19 4.7 81.9 1.0
CA K:SER171 4.7 62.0 1.0
N K:TYR170 4.8 70.6 1.0
N K:ARG167 4.8 69.3 1.0
N W:ASP204 4.9 83.7 1.0
CG W:ASP204 4.9 80.6 1.0
N K:GLY172 4.9 63.3 1.0

Magnesium binding site 5 out of 8 in 8ohz

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Magnesium binding site 5 out of 8 in the Yeast 20S Proteasome in Complex with A Photoswitchable Cepafungin Derivative (TRANSCEP1)


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 (TRANSCEP1) within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg201

b:59.2
occ:1.00
 O N:ILE163 2.7 60.4 1.0
O N:SER169 2.9 62.4 1.0
O N:ASP166 3.3 63.6 1.0
NH1 N:ARG19 3.4 62.5 1.0
CD1 a:LEU34 3.8 63.7 1.0
C N:ILE163 3.9 61.8 1.0
C N:SER169 4.0 60.4 1.0
CZ N:ARG19 4.0 62.3 1.0
CG2 N:ILE163 4.0 60.6 1.0
NH2 N:ARG19 4.1 61.9 1.0
C N:ASP166 4.2 63.0 1.0
CA N:GLY167 4.3 61.6 1.0
CA N:GLY170 4.3 61.5 1.0
O N:GLY167 4.4 57.1 1.0
CA N:ILE163 4.6 60.7 1.0
N N:GLY170 4.6 59.1 1.0
C N:GLY167 4.6 59.6 1.0
N N:GLY167 4.6 62.4 1.0
N N:LYS164 4.9 65.4 1.0
NE N:ARG19 4.9 64.3 1.0
CB N:ILE163 4.9 60.5 1.0

Magnesium binding site 6 out of 8 in 8ohz

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Magnesium binding site 6 out of 8 in the Yeast 20S Proteasome in Complex with A Photoswitchable Cepafungin Derivative (TRANSCEP1)


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 (TRANSCEP1) within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Mg302

b:83.7
occ:1.00
 OXT L:ASP222 2.0 102.1 1.0
O V:ASP166 2.1 63.2 1.0
O V:ILE163 2.2 64.2 1.0
O V:SER169 2.3 63.1 1.0
C V:ASP166 3.1 64.8 1.0
C L:ASP222 3.1 91.8 1.0
C V:ILE163 3.3 65.9 1.0
C V:SER169 3.5 63.8 1.0
CA L:ASP222 3.7 87.6 1.0
CA V:LEU167 3.7 68.5 1.0
N V:LEU167 3.8 67.0 1.0
NH1 V:ARG19 3.8 68.1 1.0
O V:GLY162 3.9 63.4 1.0
O V:TRP164 4.0 69.6 1.0
C V:LEU167 4.0 68.6 1.0
O V:LEU167 4.1 70.2 1.0
O L:ASP222 4.1 87.9 1.0
N V:ASP166 4.1 65.6 1.0
CA V:ILE163 4.2 64.5 1.0
CA V:ASP166 4.2 64.9 1.0
C V:TRP164 4.2 68.4 1.0
CB L:ASP222 4.3 86.1 1.0
N V:TRP164 4.3 66.6 1.0
N V:SER169 4.3 63.0 1.0
CA V:SER169 4.4 61.5 1.0
N V:GLY170 4.4 63.2 1.0
CA V:GLY170 4.4 65.4 1.0
CA V:TRP164 4.5 67.6 1.0
CZ V:ARG19 4.7 65.8 1.0
CB V:SER169 4.7 62.4 1.0
N V:ASN165 4.8 66.0 1.0
N V:GLY168 4.8 68.8 1.0
C V:GLY162 4.9 64.0 1.0
C V:ASN165 4.9 66.9 1.0
NH2 V:ARG19 5.0 67.6 1.0
CD2 V:LEU167 5.0 63.9 1.0

Magnesium binding site 7 out of 8 in 8ohz

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Magnesium binding site 7 out of 8 in the Yeast 20S Proteasome in Complex with A Photoswitchable Cepafungin Derivative (TRANSCEP1)


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 (TRANSCEP1) within 5.0Å range:
probe atom residue distance (Å) B Occ
Y:Mg302

b:81.5
occ:1.00
 O Y:ASP168 2.2 69.2 1.0
O I:ASP204 2.3 101.2 1.0
O Y:ALA165 2.7 61.1 1.0
O Y:SER171 2.7 72.8 1.0
C Y:ASP168 3.2 68.2 1.0
C I:ASP204 3.2 96.9 1.0
NH1 Y:ARG19 3.3 82.0 1.0
CA Y:ALA169 3.4 68.7 1.0
O Y:ALA169 3.4 67.6 1.0
C Y:ALA169 3.5 68.9 1.0
N Y:ALA169 3.6 69.1 1.0
CA I:ASP204 3.7 91.1 1.0
C Y:ALA165 3.8 63.2 1.0
C Y:SER171 3.9 66.9 1.0
O Y:HIS166 4.0 68.8 1.0
CB I:ASP204 4.1 92.4 1.0
OXT I:ASP204 4.1 102.7 1.0
N Y:SER171 4.3 65.3 1.0
CZ Y:ARG19 4.4 81.2 1.0
N Y:TYR170 4.4 69.0 1.0
CA Y:ASP168 4.5 68.7 1.0
C Y:HIS166 4.6 66.2 1.0
N Y:ASP168 4.6 70.5 1.0
CA Y:ALA165 4.6 61.5 1.0
CA Y:SER171 4.6 63.1 1.0
CB Y:ALA169 4.7 70.0 1.0
C Y:ARG167 4.8 71.2 1.0
N Y:HIS166 4.8 65.6 1.0
N Y:GLY172 4.9 67.8 1.0
O Y:ARG167 4.9 75.7 1.0
O Y:ALA164 4.9 58.9 1.0
NH2 Y:ARG19 4.9 81.5 1.0
CG I:ASP204 5.0 92.0 1.0

Magnesium binding site 8 out of 8 in 8ohz

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Magnesium binding site 8 out of 8 in the Yeast 20S Proteasome in Complex with A Photoswitchable Cepafungin Derivative (TRANSCEP1)


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 (TRANSCEP1) within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg301

b:73.2
occ:1.00
 O Z:VAL198 2.5 71.9 1.0
O Z:THR192 2.6 71.5 1.0
O Z:HIS195 2.9 59.6 1.0
O Z:ASP222 3.5 97.8 1.0
NH2 Z:ARG28 3.6 76.2 1.0
C Z:THR192 3.7 72.2 1.0
C Z:VAL198 3.7 71.5 1.0
O Z:ILE196 3.8 73.2 1.0
CG2 Z:THR192 3.8 73.4 1.0
C Z:HIS195 3.9 62.9 1.0
CA Z:ILE196 3.9 66.4 1.0
C Z:ILE196 4.0 67.8 1.0
CA Z:THR192 4.0 72.9 1.0
N Z:ILE196 4.3 63.7 1.0
NH2 H:ARG19 4.3 78.5 1.0
OD1 Z:ASP222 4.4 87.5 1.0
N Z:VAL198 4.4 67.0 1.0
CB Z:THR192 4.5 73.6 1.0
C Z:ASP222 4.6 99.0 1.0
CA Z:VAL198 4.6 67.3 1.0
N Z:GLY199 4.6 71.9 1.0
CA Z:GLY199 4.7 73.2 1.0
CZ Z:ARG28 4.8 75.6 1.0
N Z:GLN197 4.8 66.7 1.0
N Z:GLU193 4.9 73.6 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 14:49:25 2024

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