Atomistry » Magnesium » PDB 6gog-6gtp » 6gop
Atomistry »
  Magnesium »
    PDB 6gog-6gtp »
      6gop »

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

Go back to Magnesium Binding Sites List in 6gop
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

Go back to Magnesium Binding Sites List in 6gop
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

Go back to Magnesium Binding Sites List in 6gop
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

Go back to Magnesium Binding Sites List in 6gop
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

Go back to Magnesium Binding Sites List in 6gop
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

Go back to Magnesium Binding Sites List in 6gop
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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy