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Magnesium in PDB 6gop: Yeast 20S Proteasome in Complex with Homosalinosporamide A

Enzymatic activity of Yeast 20S Proteasome in Complex with Homosalinosporamide A

All present enzymatic activity of Yeast 20S Proteasome in Complex with Homosalinosporamide A:
3.4.25.1;

Protein crystallography data

The structure of Yeast 20S Proteasome in Complex with Homosalinosporamide A, PDB code: 6gop was solved by M.Groll, D.Romo, 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 (°) 135.040, 299.810, 144.410, 90.00, 112.56, 90.00
R / Rfree (%) 19.7 / 23.3

Other elements in 6gop:

The structure of Yeast 20S Proteasome in Complex with Homosalinosporamide A also contains other interesting chemical elements:

Chlorine (Cl) 10 atoms

Magnesium Binding Sites:

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

Magnesium binding site 1 out of 7 in 6gop

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Magnesium binding site 1 out of 7 in the Yeast 20S Proteasome in Complex with Homosalinosporamide A


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

b:46.4
occ:1.00
 O G:MET125 2.1 47.5 1.0
O G:TYR119 2.6 36.7 1.0
OG1 G:THR8 2.6 39.2 1.0
O G:ARG122 2.7 41.2 1.0
CG2 G:THR8 3.2 39.5 1.0
O G:ALA123 3.3 54.8 1.0
C G:MET125 3.3 45.6 1.0
CB G:THR8 3.5 39.6 1.0
C G:ALA123 3.7 47.5 1.0
CA G:ALA123 3.8 45.0 1.0
C G:TYR119 3.8 35.3 1.0
C G:ARG122 3.8 42.9 1.0
CA G:ARG126 4.0 40.0 1.0
N G:ARG126 4.1 41.8 1.0
N G:THR8 4.2 42.9 1.0
N G:MET125 4.2 46.2 1.0
N G:ALA123 4.3 43.3 1.0
CA G:MET125 4.3 48.7 1.0
CD G:PRO127 4.4 37.3 1.0
CA G:THR8 4.5 41.3 1.0
CA G:TYR119 4.6 33.3 1.0
C G:ARG126 4.6 38.9 1.0
N G:TYR124 4.7 48.9 1.0
N G:PRO127 4.8 36.6 1.0
N G:THR120 4.8 34.8 1.0
C G:TYR124 4.9 44.7 1.0
CB G:MET125 4.9 54.6 1.0

Magnesium binding site 2 out of 7 in 6gop

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Magnesium binding site 2 out of 7 in the Yeast 20S Proteasome in Complex with Homosalinosporamide A


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

b:39.4
occ:1.00
 O I:ASP204 2.2 52.7 1.0
O Y:ASP168 2.4 38.0 1.0
O Y:ALA165 2.5 36.3 1.0
C I:ASP204 3.0 53.4 1.0
O Y:SER171 3.2 37.5 1.0
C Y:ASP168 3.2 38.4 1.0
CA Y:ALA169 3.4 38.7 1.0
CA I:ASP204 3.5 52.1 1.0
O I:HOH414 3.6 47.0 1.0
O Y:HIS166 3.6 35.1 1.0
NH1 Y:ARG19 3.6 55.0 1.0
N Y:ALA169 3.7 39.3 1.0
C Y:ALA165 3.7 36.8 1.0
O Y:ALA169 3.8 36.0 1.0
C Y:ALA169 3.8 37.7 1.0
CB I:ASP204 3.9 53.2 1.0
OXT I:ASP204 4.0 52.3 1.0
C Y:HIS166 4.1 37.2 1.0
C Y:SER171 4.4 38.0 1.0
N Y:ASP168 4.4 37.4 1.0
CA Y:ASP168 4.4 37.5 1.0
O I:HOH410 4.5 59.3 1.0
N Y:HIS166 4.5 37.5 1.0
CA Y:HIS166 4.6 36.0 1.0
C Y:ARG167 4.6 38.3 1.0
CA Y:ALA165 4.6 37.1 1.0
N Y:SER171 4.7 36.3 1.0
CB Y:ALA169 4.7 38.0 1.0
N Y:ARG167 4.7 37.6 1.0
N Y:TYR170 4.8 38.7 1.0
CZ Y:ARG19 4.8 53.7 1.0
O Y:ALA164 4.8 38.8 1.0
O Y:ARG167 4.8 36.7 1.0
N I:ASP204 4.9 51.2 1.0

Magnesium binding site 3 out of 7 in 6gop

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Magnesium binding site 3 out of 7 in the Yeast 20S Proteasome in Complex with Homosalinosporamide A


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

b:34.7
occ:1.00
 OE1 J:GLN118 3.3 34.8 1.0
O J:THR124 3.6 34.5 1.0
CB J:ASP120 3.7 33.0 1.0
OD2 J:ASP120 3.8 33.9 1.0
CG J:ASP120 3.8 33.5 1.0
N J:ASP120 4.0 31.5 1.0
CD J:GLN118 4.2 32.5 1.0
CB J:THR124 4.2 34.8 1.0
CE1 J:HIS133 4.2 33.1 1.0
CG2 J:THR124 4.3 34.3 1.0
CG J:GLN118 4.4 32.6 1.0
CA J:ASP120 4.5 31.6 1.0
OD1 J:ASP120 4.5 33.9 1.0
C J:THR124 4.6 34.3 1.0
O J:GLN118 4.6 30.1 1.0
CG1 I:VAL35 4.6 42.9 1.0
C J:ILE119 4.8 30.8 1.0
ND1 J:HIS133 4.8 32.5 1.0
OG I:SER30 5.0 46.8 1.0
C J:GLN118 5.0 30.0 1.0
CA J:ILE119 5.0 28.7 1.0
O J:HOH307 5.0 36.3 1.0

Magnesium binding site 4 out of 7 in 6gop

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Magnesium binding site 4 out of 7 in the Yeast 20S Proteasome in Complex with Homosalinosporamide A


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

b:37.6
occ:1.00
 O K:ALA165 2.4 40.5 1.0
O K:ASP168 2.4 35.6 1.0
O W:ASP204 2.5 53.5 1.0
C K:ASP168 3.1 36.6 1.0
O K:HIS166 3.2 42.9 1.0
C W:ASP204 3.2 52.5 1.0
O K:SER171 3.4 40.0 1.0
C K:ALA165 3.5 39.0 1.0
CA W:ASP204 3.5 51.4 1.0
CA K:ALA169 3.6 38.3 1.0
N K:ALA169 3.6 37.5 1.0
C K:HIS166 3.7 40.0 1.0
CB W:ASP204 4.0 49.8 1.0
NH1 K:ARG19 4.0 51.6 1.0
C K:ALA169 4.1 38.9 1.0
OXT W:ASP204 4.1 58.6 1.0
N K:ASP168 4.1 36.7 1.0
O K:ALA169 4.2 38.9 1.0
CA K:HIS166 4.2 39.6 1.0
C K:ARG167 4.2 39.0 1.0
CA K:ASP168 4.2 36.5 1.0
N K:HIS166 4.3 38.8 1.0
N K:ARG167 4.3 39.2 1.0
O K:ARG167 4.5 41.0 1.0
CA K:ALA165 4.5 38.4 1.0
O K:ALA164 4.6 39.8 1.0
C K:SER171 4.6 38.4 1.0
CA K:ARG167 4.8 38.8 1.0
CB K:ALA169 4.8 37.6 1.0
N W:ASP204 4.9 49.6 1.0
N K:SER171 4.9 35.0 1.0
NE1 W:TRP182 4.9 44.2 1.0
N K:TYR170 5.0 38.9 1.0

Magnesium binding site 5 out of 7 in 6gop

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Magnesium binding site 5 out of 7 in the Yeast 20S Proteasome in Complex with Homosalinosporamide A


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 Homosalinosporamide A within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg301

b:56.7
occ:1.00
 O V:ASP166 2.0 36.1 1.0
OXT L:ASP222 2.1 66.0 1.0
O V:ILE163 2.3 40.3 1.0
O V:SER169 2.7 35.7 1.0
C V:ASP166 3.0 36.9 1.0
C L:ASP222 3.1 59.6 1.0
C V:ILE163 3.4 42.6 1.0
O V:TRP164 3.6 50.4 1.0
N V:LEU167 3.6 36.5 1.0
CA V:LEU167 3.7 36.4 1.0
CA L:ASP222 3.7 57.5 1.0
N V:ASP166 3.9 36.8 1.0
C V:TRP164 3.9 44.6 1.0
C V:SER169 3.9 36.2 1.0
O V:GLY162 3.9 41.3 1.0
O L:ASP222 4.0 61.2 1.0
CA V:ASP166 4.0 36.8 1.0
N V:TRP164 4.2 43.0 1.0
C V:LEU167 4.2 36.2 1.0
CA V:TRP164 4.2 42.9 1.0
NH1 V:ARG19 4.3 51.2 1.0
CB L:ASP222 4.3 56.7 1.0
CA V:ILE163 4.3 42.5 1.0
N V:ASN165 4.4 42.4 1.0
C V:ASN165 4.4 39.6 1.0
O V:LEU167 4.5 38.0 1.0
N V:SER169 4.5 34.9 1.0
CA V:SER169 4.7 34.9 1.0
CD2 V:LEU167 4.7 31.2 1.0
O L:ARG221 4.7 54.4 1.0
CB V:ASP166 4.9 35.7 1.0
N V:GLY170 4.9 37.1 1.0
CB V:SER169 4.9 35.2 1.0
C V:GLY162 4.9 41.5 1.0
N L:ASP222 4.9 54.7 1.0
CB V:LEU167 4.9 34.6 1.0
CA V:GLY170 4.9 39.4 1.0
CA V:ASN165 5.0 40.9 1.0

Magnesium binding site 6 out of 7 in 6gop

Go back to Magnesium Binding Sites List in 6gop
Magnesium binding site 6 out of 7 in the Yeast 20S Proteasome in Complex with Homosalinosporamide A


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 Homosalinosporamide A within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg202

b:30.8
occ:1.00
 O N:SER169 2.5 32.3 1.0
O N:ILE163 2.7 34.4 1.0
O N:ASP166 3.1 34.8 1.0
NH1 N:ARG19 3.6 37.1 1.0
C N:SER169 3.7 33.0 1.0
CD1 a:LEU34 3.7 42.6 1.0
C N:ILE163 3.8 35.6 1.0
CG2 N:ILE163 3.9 35.6 1.0
CA N:GLY170 4.2 35.7 1.0
C N:ASP166 4.2 35.4 1.0
CZ N:ARG19 4.3 36.8 1.0
NH2 N:ARG19 4.4 36.5 1.0
N N:GLY170 4.4 33.5 1.0
CA N:ILE163 4.4 35.8 1.0
O N:GLY167 4.5 34.4 1.0
CA N:GLY167 4.5 35.8 1.0
C N:GLY167 4.7 34.4 1.0
O a:HOH322 4.8 22.8 1.0
N N:GLY167 4.8 34.8 1.0
CB N:ILE163 4.8 35.3 1.0
N N:LYS164 4.8 37.6 1.0
CA N:SER169 4.9 31.9 1.0
N N:SER169 4.9 33.5 1.0
O N:LYS164 5.0 38.5 1.0

Magnesium binding site 7 out of 7 in 6gop

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Magnesium binding site 7 out of 7 in the Yeast 20S Proteasome in Complex with Homosalinosporamide A


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

b:35.9
occ:1.00
 O Z:VAL198 2.2 46.6 1.0
O Z:HOH406 2.5 27.8 1.0
O Z:THR192 2.9 51.1 1.0
O Z:HIS195 3.2 38.3 1.0
O Z:ASP222 3.3 60.0 1.0
NH2 Z:ARG28 3.4 50.4 1.0
C Z:VAL198 3.5 45.5 1.0
CG2 Z:THR192 3.5 50.3 1.0
C Z:THR192 3.8 52.0 1.0
O Z:ILE196 3.9 36.8 1.0
CA Z:THR192 4.1 51.3 1.0
OD1 Z:ASP222 4.2 59.9 1.0
CA Z:GLY199 4.3 46.4 1.0
C Z:HIS195 4.3 39.6 1.0
C Z:ILE196 4.3 37.2 1.0
N Z:GLY199 4.3 45.7 1.0
CA Z:ILE196 4.3 39.5 1.0
CZ Z:ARG28 4.3 47.9 1.0
C Z:ASP222 4.4 62.0 1.0
CB Z:THR192 4.4 50.5 1.0
N Z:VAL198 4.4 40.0 1.0
CA Z:VAL198 4.5 41.7 1.0
NH1 Z:ARG28 4.5 48.2 1.0
O Z:LYS220 4.6 53.1 1.0
NH2 H:ARG19 4.6 60.5 1.0
N Z:ILE196 4.8 39.0 1.0
OXT Z:ASP222 5.0 57.3 1.0

Reference:

M.Groll, H.Nguyen, S.Vellalath, D.Romo. (-)-Homosalinosporamide A and Its Mode of Proteasome Inhibition: An X-Ray Crystallographic Study. Mar Drugs V. 16 2018.
ISSN: ISSN 1660-3397
PubMed: 30029468
DOI: 10.3390/MD16070240
Page generated: Tue Oct 1 01:19:03 2024

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