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Magnesium in PDB 6zp8: Yeast 20S Proteasome in Complex with Glidobactin-Like Natural Product HB335

Enzymatic activity of Yeast 20S Proteasome in Complex with Glidobactin-Like Natural Product HB335

All present enzymatic activity of Yeast 20S Proteasome in Complex with Glidobactin-Like Natural Product HB335:
3.4.25.1;

Protein crystallography data

The structure of Yeast 20S Proteasome in Complex with Glidobactin-Like Natural Product HB335, PDB code: 6zp8 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 / 3.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 136.16, 300.12, 144.83, 90, 113.11, 90
R / Rfree (%) 16.7 / 20

Other elements in 6zp8:

The structure of Yeast 20S Proteasome in Complex with Glidobactin-Like Natural Product HB335 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 HB335 (pdb code 6zp8). 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 HB335, PDB code: 6zp8:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 6zp8

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Magnesium binding site 1 out of 8 in the Yeast 20S Proteasome in Complex with Glidobactin-Like Natural Product HB335


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 HB335 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:48.1
occ:1.00
 O G:MET125 2.1 58.0 1.0
OG1 G:THR8 2.7 48.5 1.0
O G:ARG122 2.8 49.8 1.0
O G:TYR119 2.8 46.1 1.0
CG2 G:THR8 3.2 49.3 1.0
O G:ALA123 3.3 59.4 1.0
C G:MET125 3.3 54.6 1.0
CB G:THR8 3.5 48.6 1.0
C G:ALA123 3.7 55.3 1.0
CA G:ALA123 3.9 52.4 1.0
C G:ARG122 3.9 50.5 1.0
CA G:ARG126 4.0 48.3 1.0
C G:TYR119 4.0 45.2 1.0
N G:ARG126 4.0 50.2 1.0
N G:THR8 4.2 52.5 1.0
N G:MET125 4.3 56.3 1.0
CD G:PRO127 4.3 46.3 1.0
N G:ALA123 4.3 50.9 1.0
CA G:MET125 4.3 58.0 1.0
CA G:THR8 4.5 50.6 1.0
C G:ARG126 4.6 45.6 1.0
N G:TYR124 4.7 56.5 1.0
CA G:TYR119 4.8 44.2 1.0
N G:PRO127 4.8 45.0 1.0
C G:TYR124 4.9 55.7 1.0
CB G:MET125 5.0 64.2 1.0

Magnesium binding site 2 out of 8 in 6zp8

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Magnesium binding site 2 out of 8 in the Yeast 20S Proteasome in Complex with Glidobactin-Like Natural Product HB335


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 HB335 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:77.7
occ:1.00
 O I:ASP177 2.9 51.8 1.0
O I:SER180 2.9 51.1 1.0
O I:ALA174 3.2 53.8 1.0
OXT I:ASP204 3.3 75.8 1.0
O I:ASP204 3.9 72.4 1.0
C I:ASP177 4.0 53.5 1.0
C I:ASP204 4.0 69.3 1.0
NH1 Y:ARG19 4.1 62.8 1.0
C I:SER180 4.1 54.5 1.0
C I:ALA174 4.2 56.2 1.0
O I:ALA178 4.2 61.0 1.0
CA I:ASP175 4.3 58.6 1.0
NH2 Y:ARG19 4.3 63.7 1.0
O I:ASP175 4.5 64.1 1.0
CA I:ALA178 4.5 53.7 1.0
C I:ALA178 4.6 55.9 1.0
C I:ASP175 4.6 59.3 1.0
CZ Y:ARG19 4.6 61.3 1.0
N I:ALA178 4.7 50.7 1.0
N I:ASP175 4.7 57.6 1.0
CA I:GLY181 4.8 56.3 1.0
N I:ASP177 4.8 55.0 1.0
OD1 I:ASP175 4.9 63.5 1.0
N I:GLY181 4.9 54.7 1.0
N I:SER180 4.9 52.0 1.0

Magnesium binding site 3 out of 8 in 6zp8

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Magnesium binding site 3 out of 8 in the Yeast 20S Proteasome in Complex with Glidobactin-Like Natural Product HB335


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 HB335 within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg902

b:68.5
occ:1.00
 O K:ASP168 2.3 48.2 1.0
O K:ALA165 2.3 50.2 1.0
O W:ASP204 2.7 72.1 1.0
O K:SER171 3.0 52.9 1.0
C W:ASP204 3.2 68.7 1.0
C K:ASP168 3.2 50.3 1.0
CA W:ASP204 3.5 64.1 1.0
C K:ALA165 3.5 51.0 1.0
O K:HIS166 3.6 57.0 1.0
CA K:ALA169 3.6 52.5 1.0
N K:ALA169 3.7 53.1 1.0
CB W:ASP204 3.8 62.9 1.0
C K:ALA169 3.9 53.5 1.0
O K:ALA169 3.9 57.9 1.0
OXT W:ASP204 4.0 79.2 1.0
C K:HIS166 4.0 51.8 1.0
NH1 K:ARG19 4.2 64.9 1.0
C K:SER171 4.2 52.8 1.0
N K:ASP168 4.3 49.4 1.0
CA K:ASP168 4.3 49.6 1.0
CA K:ALA165 4.4 51.7 1.0
N K:HIS166 4.4 50.2 1.0
CA K:HIS166 4.5 51.0 1.0
C K:ARG167 4.5 51.3 1.0
N K:SER171 4.6 51.9 1.0
O K:ALA164 4.6 52.6 1.0
N K:ARG167 4.7 50.2 1.0
N K:TYR170 4.7 52.6 1.0
O K:ARG167 4.8 54.2 1.0
N W:ASP204 4.9 64.3 1.0
CA K:SER171 4.9 51.1 1.0
CB K:ALA169 4.9 51.5 1.0
CZ K:ARG19 5.0 61.0 1.0

Magnesium binding site 4 out of 8 in 6zp8

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Magnesium binding site 4 out of 8 in the Yeast 20S Proteasome in Complex with Glidobactin-Like Natural Product HB335


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 HB335 within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg201

b:36.6
occ:1.00
 O N:SER169 2.5 50.0 1.0
O N:ILE163 2.7 47.8 1.0
O N:ASP166 2.8 48.2 1.0
NH1 N:ARG19 3.4 51.2 1.0
CD1 a:LEU34 3.6 53.5 1.0
C N:SER169 3.7 47.4 1.0
C N:ASP166 3.8 46.4 1.0
C N:ILE163 3.9 47.3 1.0
CA N:GLY167 4.0 45.4 1.0
CZ N:ARG19 4.1 50.2 1.0
CG2 N:ILE163 4.1 47.0 1.0
O N:GLY167 4.2 44.2 1.0
N N:GLY167 4.3 45.5 1.0
C N:GLY167 4.3 45.1 1.0
CA N:GLY170 4.4 49.1 1.0
NH2 N:ARG19 4.5 52.0 1.0
CA N:ILE163 4.5 46.1 1.0
N N:GLY170 4.5 47.3 1.0
N N:SER169 4.7 46.1 1.0
CA N:SER169 4.7 45.3 1.0
CG a:LEU34 4.8 53.5 1.0
N N:LYS164 4.9 47.8 1.0
CB N:ILE163 5.0 45.5 1.0
NE N:ARG19 5.0 50.0 1.0
CA N:ASP166 5.0 46.1 1.0
N N:ASP166 5.0 46.2 1.0

Magnesium binding site 5 out of 8 in 6zp8

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Magnesium binding site 5 out of 8 in the Yeast 20S Proteasome in Complex with Glidobactin-Like Natural Product HB335


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 HB335 within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Mg902

b:78.9
occ:1.00
 OXT L:ASP222 2.3 73.6 1.0
O V:ILE163 2.3 44.7 1.0
O V:ASP166 2.3 44.3 1.0
C L:ASP222 3.0 71.3 1.0
C V:ASP166 3.1 48.8 1.0
O V:SER169 3.2 55.4 1.0
O V:TRP164 3.4 55.1 1.0
C V:ILE163 3.4 50.0 1.0
C V:TRP164 3.6 52.5 1.0
CA L:ASP222 3.7 68.5 1.0
N V:LEU167 3.7 50.7 1.0
O L:ASP222 3.8 76.4 1.0
CA V:LEU167 3.8 49.5 1.0
N V:ASP166 3.9 47.1 1.0
O V:GLY162 4.1 49.3 1.0
CA V:TRP164 4.1 52.1 1.0
CA V:ASP166 4.1 48.3 1.0
N V:ASN165 4.1 52.1 1.0
N V:TRP164 4.2 51.5 1.0
C V:ASN165 4.2 49.1 1.0
C V:SER169 4.4 51.6 1.0
NH1 V:ARG19 4.5 60.1 1.0
CA V:ILE163 4.5 50.1 1.0
O L:ARG221 4.5 68.2 1.0
CB L:ASP222 4.5 69.1 1.0
C V:LEU167 4.5 49.2 1.0
CD2 V:LEU167 4.6 47.9 1.0
CA V:ASN165 4.7 50.7 1.0
O V:LEU167 4.7 48.5 1.0
O V:ASN165 4.8 47.7 1.0
N L:ASP222 4.9 67.1 1.0
CD1 L:ILE35 4.9 56.6 1.0
CB V:LEU167 5.0 48.9 1.0

Magnesium binding site 6 out of 8 in 6zp8

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Magnesium binding site 6 out of 8 in the Yeast 20S Proteasome in Complex with Glidobactin-Like Natural Product HB335


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 HB335 within 5.0Å range:
probe atom residue distance (Å) B Occ
W:Mg301

b:70.5
occ:1.00
 O W:ASP177 2.6 50.2 1.0
O W:SER180 2.8 56.4 1.0
O W:ALA174 3.1 53.2 1.0
O W:HOH405 3.2 41.6 1.0
OXT W:ASP204 3.6 79.2 1.0
C W:ASP177 3.7 52.2 1.0
C W:SER180 4.0 54.9 1.0
O W:ALA178 4.0 53.1 1.0
O W:ASP204 4.1 72.1 1.0
NH1 K:ARG19 4.1 64.9 1.0
C W:ALA174 4.2 54.6 1.0
CA W:ALA178 4.2 53.0 1.0
C W:ASP204 4.3 68.7 1.0
C W:ALA178 4.3 53.4 1.0
CA W:ASP175 4.3 57.7 1.0
N W:ALA178 4.4 51.3 1.0
NH2 K:ARG19 4.4 63.1 1.0
O W:ASP175 4.5 64.2 1.0
C W:ASP175 4.5 58.0 1.0
N W:ASP177 4.6 55.3 1.0
CZ K:ARG19 4.6 61.0 1.0
N W:SER180 4.7 53.8 1.0
N W:ASP175 4.7 56.3 1.0
CA W:ASP177 4.7 54.1 1.0
CA W:GLY181 4.9 55.4 1.0
N W:GLY181 4.9 54.6 1.0
CA W:SER180 4.9 55.4 1.0

Magnesium binding site 7 out of 8 in 6zp8

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Magnesium binding site 7 out of 8 in the Yeast 20S Proteasome in Complex with Glidobactin-Like Natural Product HB335


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 HB335 within 5.0Å range:
probe atom residue distance (Å) B Occ
Y:Mg902

b:68.7
occ:1.00
 O Y:ASP168 2.3 49.0 1.0
O I:ASP204 2.5 72.4 1.0
O Y:ALA165 2.6 51.2 1.0
O Y:SER171 2.9 56.4 1.0
C I:ASP204 3.1 69.3 1.0
C Y:ASP168 3.2 49.6 1.0
CA Y:ALA169 3.4 49.8 1.0
O Y:ALA169 3.5 52.5 1.0
CA I:ASP204 3.6 65.3 1.0
C Y:ALA169 3.6 49.7 1.0
N Y:ALA169 3.7 51.2 1.0
C Y:ALA165 3.8 49.7 1.0
NH1 Y:ARG19 3.8 62.8 1.0
CB I:ASP204 3.9 65.8 1.0
O Y:HIS166 4.0 51.2 1.0
OXT I:ASP204 4.0 75.8 1.0
C Y:SER171 4.1 53.3 1.0
N Y:SER171 4.4 49.3 1.0
C Y:HIS166 4.4 49.6 1.0
CA Y:ASP168 4.5 50.2 1.0
N Y:TYR170 4.5 48.5 1.0
N Y:ASP168 4.5 50.9 1.0
CA Y:ALA165 4.6 49.3 1.0
CZ Y:ARG19 4.6 61.3 1.0
N Y:HIS166 4.7 50.1 1.0
CB Y:ALA169 4.8 48.6 1.0
CA Y:SER171 4.8 49.6 1.0
C Y:ARG167 4.8 51.7 1.0
O Y:ALA164 4.8 51.1 1.0
CA Y:HIS166 4.9 49.2 1.0
CG I:ASP204 5.0 69.2 1.0

Magnesium binding site 8 out of 8 in 6zp8

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Magnesium binding site 8 out of 8 in the Yeast 20S Proteasome in Complex with Glidobactin-Like Natural Product HB335


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 HB335 within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg301

b:56.1
occ:1.00
 O Z:VAL198 2.7 56.4 1.0
O Z:THR192 3.0 54.3 1.0
O Z:HIS195 3.2 45.8 1.0
O Z:ASP222 3.3 74.0 1.0
NH2 Z:ARG28 3.5 60.1 1.0
O Z:ILE196 3.8 57.1 1.0
C Z:VAL198 3.9 55.1 1.0
CG2 Z:THR192 3.9 62.5 1.0
NH2 H:ARG19 4.0 65.6 1.0
OD1 Z:ASP222 4.0 74.1 1.0
C Z:THR192 4.0 58.9 1.0
CA Z:ILE196 4.1 49.6 1.0
C Z:ILE196 4.1 50.0 1.0
C Z:HIS195 4.2 49.4 1.0
C Z:ASP222 4.3 72.5 1.0
CA Z:THR192 4.4 59.2 1.0
CZ Z:ARG28 4.5 58.1 1.0
N Z:VAL198 4.6 51.4 1.0
NH1 Z:ARG28 4.6 61.6 1.0
O Z:LYS220 4.6 62.9 1.0
N Z:ILE196 4.6 48.7 1.0
CA Z:GLY199 4.7 56.9 1.0
OXT Z:ASP222 4.7 74.3 1.0
N Z:GLY199 4.7 54.8 1.0
CB Z:THR192 4.8 60.3 1.0
CA Z:VAL198 4.8 52.4 1.0
CZ H:ARG19 4.8 62.1 1.0
NH1 H:ARG19 4.8 63.8 1.0
CG Z:ASP222 5.0 68.9 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 02:29:58 2024

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