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Magnesium in PDB 6zp6: Yeast 20S Proteasome in Complex with Glidobactin-Like Natural Product HB334

Enzymatic activity of Yeast 20S Proteasome in Complex with Glidobactin-Like Natural Product HB334

All present enzymatic activity of Yeast 20S Proteasome in Complex with Glidobactin-Like Natural Product HB334:
3.4.25.1;

Protein crystallography data

The structure of Yeast 20S Proteasome in Complex with Glidobactin-Like Natural Product HB334, PDB code: 6zp6 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 / 2.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 135.72, 301.64, 144.36, 90, 113.08, 90
R / Rfree (%) 17.4 / 20.2

Other elements in 6zp6:

The structure of Yeast 20S Proteasome in Complex with Glidobactin-Like Natural Product HB334 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 HB334 (pdb code 6zp6). 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 HB334, PDB code: 6zp6:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 6zp6

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Magnesium binding site 1 out of 8 in the Yeast 20S Proteasome in Complex with Glidobactin-Like Natural Product HB334


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 HB334 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:56.9
occ:1.00
 O G:MET125 2.1 69.0 1.0
O G:ARG122 2.6 62.6 1.0
O G:TYR119 2.6 59.8 1.0
OG1 G:THR8 2.7 63.5 1.0
CG2 G:THR8 3.3 65.4 1.0
O G:ALA123 3.3 70.8 1.0
C G:MET125 3.3 66.5 1.0
CB G:THR8 3.5 65.0 1.0
C G:ALA123 3.7 68.0 1.0
C G:ARG122 3.7 64.0 1.0
CA G:ALA123 3.7 66.3 1.0
C G:TYR119 3.8 58.2 1.0
CA G:ARG126 4.1 61.2 1.0
N G:ARG126 4.1 61.7 1.0
N G:MET125 4.2 67.6 1.0
N G:ALA123 4.2 64.4 1.0
N G:THR8 4.3 67.4 1.0
CA G:MET125 4.3 70.4 1.0
CD G:PRO127 4.5 59.0 1.0
CA G:THR8 4.6 66.6 1.0
N G:TYR124 4.6 68.2 1.0
CA G:TYR119 4.6 57.5 1.0
C G:ARG126 4.7 59.7 1.0
N G:PRO127 4.9 58.8 1.0
N G:THR120 4.9 57.4 1.0
CB G:MET125 4.9 75.2 1.0
CA G:ARG122 4.9 66.1 1.0
C G:TYR124 4.9 66.6 1.0
N G:ARG122 5.0 62.5 1.0

Magnesium binding site 2 out of 8 in 6zp6

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Magnesium binding site 2 out of 8 in the Yeast 20S Proteasome in Complex with Glidobactin-Like Natural Product HB334


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 HB334 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:78.5
occ:1.00
 O I:ASP177 2.7 63.6 1.0
O I:SER180 2.8 67.3 1.0
O I:ALA174 2.9 70.5 1.0
OXT I:ASP204 3.5 94.2 1.0
C I:ASP177 3.8 64.2 1.0
C I:ALA174 4.0 69.0 1.0
C I:SER180 4.0 65.6 1.0
CA I:ASP175 4.0 71.6 1.0
O I:ASP204 4.2 83.4 1.0
O I:ASP175 4.2 80.3 1.0
NH1 Y:ARG19 4.2 81.7 1.0
O I:ALA178 4.2 70.6 1.0
C I:ASP204 4.3 82.6 1.0
C I:ASP175 4.3 72.2 1.0
NH2 Y:ARG19 4.4 79.5 1.0
N I:ASP175 4.5 69.7 1.0
CA I:ALA178 4.5 64.8 1.0
C I:ALA178 4.5 66.2 1.0
N I:ALA178 4.6 62.3 1.0
N I:ASP177 4.6 64.7 1.0
CZ Y:ARG19 4.7 77.9 1.0
OD1 I:ASP175 4.8 74.0 1.0
CA I:GLY181 4.8 65.8 1.0
N I:SER180 4.8 64.2 1.0
CA I:ASP177 4.8 65.4 1.0
N I:GLY181 4.9 64.5 1.0
CA I:SER180 5.0 65.0 1.0

Magnesium binding site 3 out of 8 in 6zp6

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Magnesium binding site 3 out of 8 in the Yeast 20S Proteasome in Complex with Glidobactin-Like Natural Product HB334


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 HB334 within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg902

b:66.6
occ:1.00
 O K:ASP168 2.3 60.7 1.0
O K:ALA165 2.4 66.5 1.0
O W:ASP204 2.4 94.1 1.0
O K:SER171 2.5 68.0 1.0
C K:ASP168 3.3 62.3 1.0
C W:ASP204 3.3 86.3 1.0
C K:ALA165 3.5 64.3 1.0
CA K:ALA169 3.6 66.4 1.0
CA W:ASP204 3.6 79.5 1.0
O K:ALA169 3.6 64.1 1.0
C K:ALA169 3.7 66.4 1.0
NH1 K:ARG19 3.7 80.3 1.0
C K:SER171 3.7 65.1 1.0
CB W:ASP204 3.8 77.7 1.0
N K:ALA169 3.8 65.9 1.0
O K:HIS166 3.9 66.4 1.0
N K:SER171 4.2 63.3 1.0
CA K:ALA165 4.3 64.6 1.0
OXT W:ASP204 4.3 93.9 1.0
C K:HIS166 4.4 64.5 1.0
CA K:ASP168 4.5 62.0 1.0
CA K:SER171 4.5 62.6 1.0
CZ K:ARG19 4.5 77.2 1.0
N K:ASP168 4.5 63.0 1.0
N K:TYR170 4.5 66.3 1.0
N K:HIS166 4.6 63.4 1.0
O K:ALA164 4.6 66.5 1.0
N K:GLY172 4.7 64.9 1.0
CA K:HIS166 4.8 64.6 1.0
C K:ARG167 4.9 65.6 1.0
CA K:GLY172 4.9 66.6 1.0
CG W:ASP204 4.9 77.0 1.0
CB K:ALA169 5.0 67.0 1.0
NH2 K:ARG19 5.0 79.8 1.0
CB K:SER171 5.0 61.4 1.0

Magnesium binding site 4 out of 8 in 6zp6

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Magnesium binding site 4 out of 8 in the Yeast 20S Proteasome in Complex with Glidobactin-Like Natural Product HB334


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 HB334 within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg201

b:47.7
occ:1.00
 O N:SER169 2.6 57.9 1.0
O N:ILE163 2.8 54.2 1.0
O N:ASP166 3.1 58.0 1.0
NH1 N:ARG19 3.4 62.9 1.0
CD1 a:LEU34 3.6 67.3 1.0
C N:SER169 3.8 56.9 1.0
C N:ILE163 3.9 57.2 1.0
CZ N:ARG19 4.0 62.5 1.0
CG2 N:ILE163 4.0 57.9 1.0
C N:ASP166 4.1 55.5 1.0
CA N:GLY167 4.2 55.8 1.0
NH2 N:ARG19 4.2 65.8 1.0
O N:GLY167 4.3 56.2 1.0
CA N:GLY170 4.4 59.8 1.0
C N:GLY167 4.5 56.1 1.0
CA N:ILE163 4.5 57.1 1.0
N N:GLY167 4.5 55.0 1.0
N N:GLY170 4.5 57.7 1.0
CG a:LEU34 4.9 67.2 1.0
CB N:ILE163 4.9 57.0 1.0
CA N:SER169 4.9 55.0 1.0
N N:SER169 4.9 55.3 1.0
N N:LYS164 4.9 59.9 1.0
NE N:ARG19 4.9 61.8 1.0

Magnesium binding site 5 out of 8 in 6zp6

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Magnesium binding site 5 out of 8 in the Yeast 20S Proteasome in Complex with Glidobactin-Like Natural Product HB334


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 HB334 within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Mg902

b:97.0
occ:1.00
 OXT L:ASP222 2.4 85.9 1.0
O V:ASP166 2.4 56.8 1.0
O V:ILE163 2.4 59.1 1.0
C L:ASP222 3.1 85.9 1.0
C V:ASP166 3.1 59.1 1.0
O V:TRP164 3.3 67.8 1.0
O V:SER169 3.5 59.1 1.0
C V:ILE163 3.5 61.1 1.0
C V:TRP164 3.5 64.7 1.0
N V:LEU167 3.7 59.7 1.0
CA L:ASP222 3.7 85.6 1.0
CA V:LEU167 3.7 59.0 1.0
N V:ASP166 3.8 59.2 1.0
O L:ASP222 3.8 89.2 1.0
CA V:ASP166 4.0 59.1 1.0
CA V:TRP164 4.1 63.1 1.0
N V:ASN165 4.1 64.0 1.0
C V:ASN165 4.2 61.6 1.0
N V:TRP164 4.2 61.7 1.0
O V:GLY162 4.2 58.2 1.0
O L:ARG221 4.3 78.3 1.0
CD2 V:LEU167 4.3 58.0 1.0
C V:LEU167 4.5 60.2 1.0
NH1 V:ARG19 4.6 75.0 1.0
CA V:ASN165 4.6 61.3 1.0
CB L:ASP222 4.6 84.4 1.0
CD1 L:ILE35 4.6 72.8 1.0
C V:SER169 4.6 61.2 1.0
CA V:ILE163 4.7 60.5 1.0
O V:ASN165 4.8 64.9 1.0
O V:LEU167 4.8 58.9 1.0
N L:ASP222 4.8 83.5 1.0
CB V:LEU167 4.9 58.6 1.0

Magnesium binding site 6 out of 8 in 6zp6

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Magnesium binding site 6 out of 8 in the Yeast 20S Proteasome in Complex with Glidobactin-Like Natural Product HB334


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 HB334 within 5.0Å range:
probe atom residue distance (Å) B Occ
W:Mg301

b:88.8
occ:1.00
 O W:ASP177 2.4 66.7 1.0
O W:SER180 2.7 70.8 1.0
O W:ALA174 3.1 61.0 1.0
C W:ASP177 3.5 65.6 1.0
OXT W:ASP204 3.6 93.9 1.0
O W:ALA178 3.9 69.5 1.0
C W:SER180 4.0 68.5 1.0
NH1 K:ARG19 4.0 80.3 1.0
CA W:ALA178 4.1 65.1 1.0
C W:ALA178 4.1 65.5 1.0
O W:ASP204 4.2 94.1 1.0
C W:ALA174 4.2 65.2 1.0
N W:ALA178 4.2 64.6 1.0
CA W:ASP175 4.3 71.9 1.0
C W:ASP204 4.3 86.3 1.0
NH2 K:ARG19 4.4 79.8 1.0
O W:ASP175 4.4 75.1 1.0
C W:ASP175 4.5 71.7 1.0
N W:ASP177 4.5 68.1 1.0
CZ K:ARG19 4.5 77.2 1.0
N W:SER180 4.5 66.6 1.0
CA W:ASP177 4.6 66.6 1.0
N W:ASP175 4.7 69.1 1.0
CA W:SER180 4.8 67.1 1.0
N W:GLY181 4.9 66.4 1.0
CA W:GLY181 4.9 67.1 1.0
N W:LEU179 4.9 64.1 1.0

Magnesium binding site 7 out of 8 in 6zp6

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Magnesium binding site 7 out of 8 in the Yeast 20S Proteasome in Complex with Glidobactin-Like Natural Product HB334


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 HB334 within 5.0Å range:
probe atom residue distance (Å) B Occ
Y:Mg902

b:82.1
occ:1.00
 O Y:ASP168 2.4 60.9 1.0
O I:ASP204 2.4 83.4 1.0
O Y:ALA165 2.5 60.0 1.0
O Y:SER171 3.0 67.0 1.0
C I:ASP204 3.2 82.6 1.0
C Y:ASP168 3.2 60.9 1.0
CA Y:ALA169 3.4 61.6 1.0
CA I:ASP204 3.6 79.3 1.0
O Y:HIS166 3.7 64.3 1.0
N Y:ALA169 3.7 62.4 1.0
O Y:ALA169 3.7 62.8 1.0
C Y:ALA165 3.7 59.9 1.0
C Y:ALA169 3.7 62.3 1.0
NH1 Y:ARG19 3.9 81.7 1.0
CB I:ASP204 3.9 79.6 1.0
OXT I:ASP204 4.1 94.2 1.0
C Y:HIS166 4.2 60.8 1.0
C Y:SER171 4.2 63.2 1.0
N Y:ASP168 4.4 61.4 1.0
CA Y:ASP168 4.4 61.1 1.0
CA Y:ALA165 4.6 59.1 1.0
N Y:SER171 4.6 59.7 1.0
N Y:HIS166 4.6 60.7 1.0
C Y:ARG167 4.6 61.6 1.0
N Y:TYR170 4.7 61.8 1.0
CA Y:HIS166 4.7 60.1 1.0
CB Y:ALA169 4.8 61.7 1.0
CZ Y:ARG19 4.8 77.9 1.0
O Y:ALA164 4.8 61.9 1.0
O Y:ARG167 4.8 63.8 1.0
N Y:ARG167 4.9 58.3 1.0
CA Y:SER171 5.0 60.1 1.0
N I:ASP204 5.0 77.2 1.0

Magnesium binding site 8 out of 8 in 6zp6

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Magnesium binding site 8 out of 8 in the Yeast 20S Proteasome in Complex with Glidobactin-Like Natural Product HB334


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 HB334 within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg301

b:63.0
occ:1.00
 O Z:VAL198 2.7 70.0 1.0
O Z:HIS195 2.8 57.8 1.0
O Z:THR192 2.9 72.9 1.0
O Z:ILE196 3.4 66.3 1.0
O Z:ASP222 3.6 91.1 1.0
NH2 Z:ARG28 3.6 73.8 1.0
CA Z:ILE196 3.6 62.0 1.0
C Z:ILE196 3.7 62.3 1.0
C Z:HIS195 3.8 61.4 1.0
C Z:VAL198 3.8 68.7 1.0
C Z:THR192 4.0 74.3 1.0
NH2 H:ARG19 4.1 77.0 1.0
CG2 Z:THR192 4.1 76.2 1.0
N Z:ILE196 4.1 60.4 1.0
N Z:VAL198 4.3 64.4 1.0
CA Z:THR192 4.3 73.0 1.0
OD1 Z:ASP222 4.5 84.0 1.0
C Z:ASP222 4.6 88.9 1.0
NH1 H:ARG19 4.6 75.3 1.0
CA Z:VAL198 4.6 65.7 1.0
N Z:GLN197 4.6 61.7 1.0
CZ Z:ARG28 4.7 71.7 1.0
CZ H:ARG19 4.7 73.7 1.0
N Z:GLY199 4.8 68.5 1.0
CB Z:THR192 4.9 74.3 1.0
CB Z:ILE196 4.9 61.9 1.0
CA Z:GLY199 4.9 69.9 1.0
NH1 Z:ARG28 4.9 74.9 1.0
OXT Z:ASP222 4.9 87.3 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 02:29:31 2024

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