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Magnesium in PDB 6zou: Yeast 20S Proteasome in Complex with Glidobactin-Like Natural Product HB333

Enzymatic activity of Yeast 20S Proteasome in Complex with Glidobactin-Like Natural Product HB333

All present enzymatic activity of Yeast 20S Proteasome in Complex with Glidobactin-Like Natural Product HB333:
3.4.25.1;

Protein crystallography data

The structure of Yeast 20S Proteasome in Complex with Glidobactin-Like Natural Product HB333, PDB code: 6zou was solved by L.Zhao, C.Le Chapelain, A.O.Brachmann, M.Kaiser, M.Groll, H.B.Bode, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.00 / 2.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 136.78, 300.24, 145.74, 90, 113.32, 90
R / Rfree (%) 17.2 / 21.2

Other elements in 6zou:

The structure of Yeast 20S Proteasome in Complex with Glidobactin-Like Natural Product HB333 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 Glidobactin-Like Natural Product HB333 (pdb code 6zou). 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 Glidobactin-Like Natural Product HB333, PDB code: 6zou:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 6zou

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Magnesium binding site 1 out of 8 in the Yeast 20S Proteasome in Complex with Glidobactin-Like Natural Product HB333


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 Glidobactin-Like Natural Product HB333 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:63.4
occ:1.00
 O G:MET125 2.1 65.7 1.0
O G:TYR119 2.4 54.2 1.0
O G:ARG122 2.5 56.9 1.0
OG1 G:THR8 2.7 58.9 1.0
CG2 G:THR8 3.2 57.4 1.0
C G:MET125 3.3 62.3 1.0
CB G:THR8 3.5 56.8 1.0
O G:ALA123 3.6 65.4 1.0
C G:TYR119 3.6 53.5 1.0
C G:ARG122 3.6 58.4 1.0
C G:ALA123 3.9 63.0 1.0
CA G:ALA123 3.9 60.8 1.0
CA G:ARG126 4.1 56.4 1.0
N G:ARG126 4.1 57.0 1.0
N G:ALA123 4.2 59.0 1.0
N G:MET125 4.3 63.3 1.0
CA G:TYR119 4.3 51.5 1.0
CA G:MET125 4.3 65.4 1.0
CD G:PRO127 4.4 54.2 1.0
N G:THR8 4.4 58.9 1.0
C G:ARG126 4.6 54.6 1.0
N G:THR120 4.6 52.3 1.0
CA G:THR8 4.6 58.0 1.0
CB G:MET125 4.8 70.4 1.0
N G:PRO127 4.8 54.0 1.0
N G:TYR124 4.8 63.9 1.0
CA G:THR120 4.8 51.9 1.0
CB G:TYR119 4.8 52.1 1.0
N G:ARG122 4.8 57.4 1.0
CA G:ARG122 4.8 59.7 1.0
C G:THR120 4.9 52.1 1.0

Magnesium binding site 2 out of 8 in 6zou

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Magnesium binding site 2 out of 8 in the Yeast 20S Proteasome in Complex with Glidobactin-Like Natural Product HB333


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 Glidobactin-Like Natural Product HB333 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:78.7
occ:1.00
 O I:SER180 2.8 61.2 1.0
O I:ALA174 2.9 60.9 1.0
O I:ASP177 3.2 59.7 1.0
OXT I:ASP204 3.4 82.8 1.0
C I:ALA174 3.7 63.4 1.0
CA I:ASP175 3.8 65.3 1.0
C I:SER180 4.0 62.5 1.0
OD1 I:ASP175 4.1 70.7 1.0
N I:ASP175 4.1 64.3 1.0
C I:ASP175 4.3 66.0 1.0
O I:ASP175 4.3 74.1 1.0
C I:ASP204 4.4 74.6 1.0
C I:ASP177 4.4 60.0 1.0
CA I:GLY181 4.5 63.3 1.0
O I:ASP204 4.5 74.3 1.0
NH2 Y:ARG19 4.6 75.0 1.0
N I:GLY181 4.7 61.7 1.0
NH1 Y:ARG19 4.7 72.0 1.0
CB I:ASP175 4.9 65.6 1.0
N I:ASP177 4.9 61.3 1.0
CA I:ALA174 4.9 60.4 1.0
CG I:ASP175 4.9 67.0 1.0
O I:ALA178 5.0 65.2 1.0

Magnesium binding site 3 out of 8 in 6zou

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Magnesium binding site 3 out of 8 in the Yeast 20S Proteasome in Complex with Glidobactin-Like Natural Product HB333


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 Glidobactin-Like Natural Product HB333 within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg302

b:92.1
occ:1.00
 O K:ASP168 2.3 52.9 1.0
O K:ALA165 2.3 60.2 1.0
O W:ASP204 2.6 79.2 1.0
C K:ASP168 3.2 57.9 1.0
O K:HIS166 3.2 66.8 1.0
C W:ASP204 3.2 78.1 1.0
O K:SER171 3.3 67.4 1.0
C K:ALA165 3.5 60.7 1.0
CA W:ASP204 3.5 70.5 1.0
CA K:ALA169 3.6 60.0 1.0
N K:ALA169 3.7 60.8 1.0
C K:HIS166 3.8 61.4 1.0
CB W:ASP204 4.0 69.2 1.0
C K:ALA169 4.0 60.5 1.0
O K:ALA169 4.1 56.8 1.0
OXT W:ASP204 4.1 86.6 1.0
N K:ASP168 4.2 58.9 1.0
CA K:ASP168 4.3 57.8 1.0
CA K:HIS166 4.3 60.4 1.0
NH1 K:ARG19 4.3 71.3 1.0
N K:HIS166 4.3 61.1 1.0
C K:ARG167 4.3 60.0 1.0
N K:ARG167 4.5 58.6 1.0
CA K:ALA165 4.5 60.3 1.0
C K:SER171 4.5 63.7 1.0
O K:ARG167 4.5 64.4 1.0
O K:ALA164 4.6 61.1 1.0
NE1 W:TRP182 4.8 64.1 1.0
N W:ASP204 4.8 68.8 1.0
N K:SER171 4.9 60.9 1.0
CB K:ALA169 4.9 59.6 1.0
CA K:ARG167 4.9 59.1 1.0
N K:TYR170 4.9 59.8 1.0

Magnesium binding site 4 out of 8 in 6zou

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Magnesium binding site 4 out of 8 in the Yeast 20S Proteasome in Complex with Glidobactin-Like Natural Product HB333


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 Glidobactin-Like Natural Product HB333 within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg201

b:46.6
occ:1.00
 O N:SER169 2.6 60.5 1.0
O N:ILE163 2.7 52.2 1.0
O N:ASP166 3.0 51.5 1.0
NH1 N:ARG19 3.5 59.7 1.0
CD1 a:LEU34 3.6 60.9 1.0
C N:SER169 3.8 56.3 1.0
C N:ILE163 3.8 54.5 1.0
C N:ASP166 3.9 50.9 1.0
CG2 N:ILE163 4.1 53.7 1.0
CA N:GLY167 4.2 52.7 1.0
CZ N:ARG19 4.2 56.7 1.0
O N:GLY167 4.3 50.6 1.0
CA N:GLY170 4.4 55.7 1.0
N N:GLY167 4.5 51.1 1.0
NH2 N:ARG19 4.5 58.5 1.0
C N:GLY167 4.5 52.2 1.0
CA N:ILE163 4.5 53.5 1.0
N N:GLY170 4.5 56.1 1.0
CG a:LEU34 4.8 60.6 1.0
N N:LYS164 4.8 56.4 1.0
CA N:SER169 4.8 53.5 1.0
N N:SER169 4.9 53.8 1.0
O N:LYS164 4.9 66.1 1.0
CB N:ILE163 4.9 52.5 1.0
C N:LYS164 5.0 59.2 1.0

Magnesium binding site 5 out of 8 in 6zou

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Magnesium binding site 5 out of 8 in the Yeast 20S Proteasome in Complex with Glidobactin-Like Natural Product HB333


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 Glidobactin-Like Natural Product HB333 within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Mg302

b:99.2
occ:1.00
 O V:ASP166 2.1 52.5 1.0
O V:ILE163 2.2 58.5 1.0
OXT L:ASP222 2.2 72.2 1.0
O V:SER169 2.4 72.3 1.0
C V:ASP166 3.1 58.0 1.0
C L:ASP222 3.1 73.7 1.0
C V:ILE163 3.3 60.1 1.0
C V:SER169 3.5 63.1 1.0
CA V:LEU167 3.8 58.6 1.0
N V:LEU167 3.8 59.8 1.0
CA L:ASP222 3.8 73.5 1.0
NH1 V:ARG19 3.9 69.4 1.0
O V:GLY162 3.9 51.9 1.0
O L:ASP222 4.0 82.2 1.0
N V:ASP166 4.1 59.3 1.0
CA V:ILE163 4.1 58.7 1.0
O V:TRP164 4.2 61.9 1.0
CA V:ASP166 4.2 58.1 1.0
C V:LEU167 4.2 58.2 1.0
C V:TRP164 4.2 61.3 1.0
N V:SER169 4.3 57.1 1.0
N V:TRP164 4.3 62.0 1.0
CA V:SER169 4.3 58.7 1.0
CB L:ASP222 4.3 75.7 1.0
N V:GLY170 4.4 62.9 1.0
O V:LEU167 4.4 59.4 1.0
CA V:GLY170 4.4 63.9 1.0
CA V:TRP164 4.5 60.9 1.0
CZ V:ARG19 4.5 66.6 1.0
CB V:SER169 4.7 58.6 1.0
N V:ASN165 4.7 60.8 1.0
NH2 V:ARG19 4.8 72.8 1.0
C V:ASN165 4.8 58.6 1.0
C V:GLY162 4.9 55.4 1.0
CB V:ASP166 5.0 58.0 1.0
N V:GLY168 5.0 57.6 1.0

Magnesium binding site 6 out of 8 in 6zou

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Magnesium binding site 6 out of 8 in the Yeast 20S Proteasome in Complex with Glidobactin-Like Natural Product HB333


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 Glidobactin-Like Natural Product HB333 within 5.0Å range:
probe atom residue distance (Å) B Occ
W:Mg301

b:87.5
occ:1.00
 O W:ASP177 2.3 64.7 1.0
O W:SER180 2.6 62.6 1.0
O W:ALA174 2.9 57.7 1.0
C W:ASP177 3.5 61.7 1.0
OXT W:ASP204 3.7 86.6 1.0
C W:SER180 3.8 62.9 1.0
C W:ALA174 4.0 62.5 1.0
O W:ALA178 4.1 68.1 1.0
CA W:ALA178 4.2 60.6 1.0
NH1 K:ARG19 4.2 71.3 1.0
CA W:ASP175 4.2 66.3 1.0
C W:ALA178 4.2 62.2 1.0
N W:ALA178 4.3 59.2 1.0
N W:ASP177 4.4 62.9 1.0
C W:ASP175 4.4 67.5 1.0
O W:ASP175 4.5 75.2 1.0
O W:ASP204 4.5 79.2 1.0
N W:SER180 4.5 63.7 1.0
CA W:ASP177 4.5 61.6 1.0
C W:ASP204 4.6 78.1 1.0
N W:ASP175 4.6 65.2 1.0
NH2 K:ARG19 4.6 72.9 1.0
CA W:SER180 4.7 63.7 1.0
N W:GLY181 4.7 62.2 1.0
CZ K:ARG19 4.7 68.8 1.0
CA W:GLY181 4.8 64.0 1.0
OD1 W:ASP175 5.0 71.1 1.0

Magnesium binding site 7 out of 8 in 6zou

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Magnesium binding site 7 out of 8 in the Yeast 20S Proteasome in Complex with Glidobactin-Like Natural Product HB333


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 Glidobactin-Like Natural Product HB333 within 5.0Å range:
probe atom residue distance (Å) B Occ
Y:Mg302

b:83.1
occ:1.00
 O I:ASP204 2.3 74.3 1.0
O Y:ASP168 2.3 58.0 1.0
O Y:ALA165 2.5 57.8 1.0
O Y:SER171 2.9 67.6 1.0
C I:ASP204 3.1 74.6 1.0
C Y:ASP168 3.3 57.8 1.0
CA Y:ALA169 3.5 57.9 1.0
O Y:ALA169 3.6 63.0 1.0
CA I:ASP204 3.6 70.9 1.0
C Y:ALA169 3.7 59.4 1.0
C Y:ALA165 3.7 58.0 1.0
N Y:ALA169 3.7 59.4 1.0
NH1 Y:ARG19 3.8 72.0 1.0
O Y:HIS166 3.8 61.1 1.0
CB I:ASP204 4.0 71.4 1.0
OXT I:ASP204 4.0 82.8 1.0
C Y:SER171 4.1 60.5 1.0
C Y:HIS166 4.3 58.4 1.0
CA Y:ASP168 4.5 58.5 1.0
N Y:SER171 4.5 56.1 1.0
N Y:ASP168 4.5 60.1 1.0
CA Y:ALA165 4.6 57.9 1.0
CZ Y:ARG19 4.6 71.1 1.0
N Y:TYR170 4.6 57.2 1.0
N Y:HIS166 4.7 58.6 1.0
CA Y:HIS166 4.8 57.6 1.0
C Y:ARG167 4.8 60.0 1.0
CB Y:ALA169 4.8 57.6 1.0
O Y:ALA164 4.9 59.4 1.0
CA Y:SER171 4.9 57.6 1.0
O Y:ARG167 4.9 61.7 1.0

Magnesium binding site 8 out of 8 in 6zou

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Magnesium binding site 8 out of 8 in the Yeast 20S Proteasome in Complex with Glidobactin-Like Natural Product HB333


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 Glidobactin-Like Natural Product HB333 within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg301

b:62.3
occ:1.00
 O Z:VAL198 2.6 65.4 1.0
O Z:THR192 3.1 57.7 1.0
O Z:HIS195 3.1 53.8 1.0
O Z:ASP222 3.4 77.1 1.0
NH2 Z:ARG28 3.5 66.1 1.0
O Z:ILE196 3.5 59.1 1.0
C Z:ILE196 3.8 55.3 1.0
C Z:VAL198 3.8 62.0 1.0
CA Z:ILE196 3.8 55.1 1.0
C Z:HIS195 4.0 55.0 1.0
NH2 H:ARG19 4.1 72.7 1.0
C Z:THR192 4.1 64.3 1.0
CG2 Z:THR192 4.1 67.2 1.0
OD1 Z:ASP222 4.3 76.1 1.0
C Z:ASP222 4.4 76.0 1.0
N Z:VAL198 4.4 57.1 1.0
N Z:ILE196 4.4 54.0 1.0
CZ Z:ARG28 4.5 64.8 1.0
CA Z:THR192 4.5 65.3 1.0
NH1 H:ARG19 4.6 72.3 1.0
CA Z:VAL198 4.7 58.9 1.0
NH1 Z:ARG28 4.7 67.5 1.0
OXT Z:ASP222 4.7 71.5 1.0
CZ H:ARG19 4.7 68.9 1.0
N Z:GLY199 4.7 61.3 1.0
N Z:GLN197 4.8 53.6 1.0
CA Z:GLY199 4.8 62.5 1.0
O Z:LYS220 4.9 68.6 1.0
CB Z:THR192 5.0 65.4 1.0

Reference:

L.Zhao, C.Le Chapelain, A.O.Brachmann, M.Kaiser, M.Groll, H.B.Bode. Activation, Structure, Biosynthesis and Bioactivity of Glidobactin-Like Proteasome Inhibitors From Photorhabdus Laumondii. Chembiochem V. 22 1582 2021.
ISSN: ESSN 1439-7633
PubMed: 33452852
DOI: 10.1002/CBIC.202100014
Page generated: Wed Oct 2 02:29:17 2024

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