Magnesium in PDB 6g8m: Yeast 20S Proteasome in Complex with Cystargolide B Derivative 1

Enzymatic activity of Yeast 20S Proteasome in Complex with Cystargolide B Derivative 1

All present enzymatic activity of Yeast 20S Proteasome in Complex with Cystargolide B Derivative 1:
3.4.25.1;

Protein crystallography data

The structure of Yeast 20S Proteasome in Complex with Cystargolide B Derivative 1, PDB code: 6g8m was solved by M.Groll, R.Tello-Aburto, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.00 / 2.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 136.750, 301.020, 145.460, 90.00, 113.64, 90.00
R / Rfree (%) 17.9 / 21.4

Other elements in 6g8m:

The structure of Yeast 20S Proteasome in Complex with Cystargolide B Derivative 1 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 Cystargolide B Derivative 1 (pdb code 6g8m). 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 Cystargolide B Derivative 1, PDB code: 6g8m:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 6g8m

Go back to Magnesium Binding Sites List in 6g8m
Magnesium binding site 1 out of 8 in the Yeast 20S Proteasome in Complex with Cystargolide B Derivative 1


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 Cystargolide B Derivative 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:61.5
occ:1.00
 O G:MET125 2.1 60.1 1.0
O G:ARG122 2.6 50.8 1.0
O G:TYR119 2.6 52.4 1.0
OG1 G:THR8 2.6 50.9 1.0
CG2 G:THR8 3.2 53.6 1.0
C G:MET125 3.3 58.6 1.0
CB G:THR8 3.5 53.5 1.0
O G:ALA123 3.5 63.7 1.0
C G:ARG122 3.7 53.8 1.0
C G:TYR119 3.8 49.4 1.0
C G:ALA123 3.8 58.6 1.0
CA G:ALA123 3.8 55.7 1.0
CA G:ARG126 4.1 52.9 1.0
N G:ARG126 4.1 53.4 1.0
N G:ALA123 4.2 54.7 1.0
N G:THR8 4.2 54.8 1.0
N G:MET125 4.3 60.4 1.0
CD G:PRO127 4.4 51.3 1.0
CA G:MET125 4.4 63.2 1.0
CA G:THR8 4.5 53.5 1.0
CA G:TYR119 4.6 47.9 1.0
C G:ARG126 4.7 51.7 1.0
N G:TYR124 4.7 58.7 1.0
N G:THR120 4.8 48.4 1.0
N G:PRO127 4.8 50.7 1.0
CB G:MET125 4.9 69.0 1.0
CA G:ARG122 4.9 58.2 1.0
CA G:THR120 4.9 48.8 1.0
N G:ARG122 5.0 53.8 1.0

Magnesium binding site 2 out of 8 in 6g8m

Go back to Magnesium Binding Sites List in 6g8m
Magnesium binding site 2 out of 8 in the Yeast 20S Proteasome in Complex with Cystargolide B Derivative 1


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 Cystargolide B Derivative 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:65.7
occ:1.00
 O I:SER180 2.5 61.0 1.0
O I:ASP177 2.5 57.1 1.0
O I:ALA174 2.9 59.1 1.0
OXT I:ASP204 3.6 75.2 1.0
C I:ASP177 3.7 56.5 1.0
C I:SER180 3.7 58.9 1.0
C I:ALA174 4.0 59.5 1.0
O I:ALA178 4.2 65.5 1.0
CA I:ASP175 4.3 60.5 1.0
O I:ASP204 4.4 71.6 1.0
CA I:ALA178 4.4 58.2 1.0
C I:ALA178 4.4 60.1 1.0
C I:ASP204 4.5 70.0 1.0
N I:ALA178 4.5 55.8 1.0
N I:SER180 4.5 54.1 1.0
NH1 Y:ARG19 4.5 68.8 1.0
N I:ASP175 4.5 60.5 1.0
N I:ASP177 4.5 57.4 1.0
C I:ASP175 4.6 60.3 1.0
N I:GLY181 4.6 58.2 1.0
CA I:GLY181 4.6 58.8 1.0
O I:ASP175 4.6 65.7 1.0
CA I:SER180 4.6 57.4 1.0
CA I:ASP177 4.7 57.4 1.0
NH2 Y:ARG19 4.8 74.2 1.0
OD1 I:ASP175 5.0 67.1 1.0

Magnesium binding site 3 out of 8 in 6g8m

Go back to Magnesium Binding Sites List in 6g8m
Magnesium binding site 3 out of 8 in the Yeast 20S Proteasome in Complex with Cystargolide B Derivative 1


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 Cystargolide B Derivative 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg302

b:66.8
occ:1.00
 O K:ALA165 2.3 52.1 1.0
O K:ASP168 2.3 52.2 1.0
O W:ASP204 2.5 77.6 1.0
O K:SER171 2.8 60.5 1.0
C W:ASP204 3.2 72.7 1.0
C K:ASP168 3.3 53.2 1.0
C K:ALA165 3.5 55.7 1.0
CA W:ASP204 3.6 67.2 1.0
CA K:ALA169 3.7 54.5 1.0
O K:HIS166 3.8 57.4 1.0
NH1 K:ARG19 3.8 65.8 1.0
N K:ALA169 3.9 53.3 1.0
O K:ALA169 3.9 57.6 1.0
CB W:ASP204 3.9 66.5 1.0
C K:ALA169 3.9 56.2 1.0
C K:SER171 4.0 56.7 1.0
OXT W:ASP204 4.1 76.2 1.0
C K:HIS166 4.2 56.0 1.0
CA K:ALA165 4.3 55.3 1.0
N K:ASP168 4.4 51.8 1.0
CA K:ASP168 4.4 53.1 1.0
N K:SER171 4.4 58.0 1.0
N K:HIS166 4.5 56.3 1.0
CZ K:ARG19 4.6 63.7 1.0
CA K:HIS166 4.6 55.6 1.0
O K:ALA164 4.7 56.9 1.0
C K:ARG167 4.7 54.9 1.0
N K:TYR170 4.7 56.2 1.0
CA K:SER171 4.8 54.5 1.0
N K:ARG167 4.9 54.3 1.0
N W:ASP204 5.0 66.3 1.0
CG W:ASP204 5.0 65.7 1.0
NH2 K:ARG19 5.0 68.0 1.0
N K:GLY172 5.0 56.9 1.0

Magnesium binding site 4 out of 8 in 6g8m

Go back to Magnesium Binding Sites List in 6g8m
Magnesium binding site 4 out of 8 in the Yeast 20S Proteasome in Complex with Cystargolide B Derivative 1


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 Cystargolide B Derivative 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg202

b:59.5
occ:1.00
 O N:ILE163 2.8 57.5 1.0
O N:SER169 2.8 55.9 1.0
O N:ASP166 3.4 55.1 1.0
NH1 N:ARG19 3.5 57.4 1.0
CD1 a:LEU34 3.7 61.4 1.0
C N:ILE163 3.9 55.8 1.0
CG2 N:ILE163 3.9 52.8 1.0
C N:SER169 3.9 53.0 1.0
CZ N:ARG19 4.1 56.8 1.0
NH2 N:ARG19 4.2 59.7 1.0
C N:ASP166 4.3 52.7 1.0
CA N:GLY170 4.3 53.8 1.0
CA N:GLY167 4.4 54.6 1.0
O N:GLY167 4.5 52.6 1.0
CA N:ILE163 4.5 54.0 1.0
N N:GLY170 4.6 52.0 1.0
C N:GLY167 4.7 53.2 1.0
N N:GLY167 4.7 53.0 1.0
CB N:ILE163 4.8 53.2 1.0
N N:LYS164 4.9 56.6 1.0
NE N:ARG19 5.0 56.9 1.0
CG a:LEU34 5.0 62.2 1.0

Magnesium binding site 5 out of 8 in 6g8m

Go back to Magnesium Binding Sites List in 6g8m
Magnesium binding site 5 out of 8 in the Yeast 20S Proteasome in Complex with Cystargolide B Derivative 1


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 Cystargolide B Derivative 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Mg302

b:85.9
occ:1.00
 O V:ILE163 2.2 50.9 1.0
O V:ASP166 2.2 49.8 1.0
OXT L:ASP222 2.3 72.9 1.0
O V:SER169 2.9 61.1 1.0
C V:ASP166 3.1 55.7 1.0
C L:ASP222 3.1 72.7 1.0
C V:ILE163 3.3 56.7 1.0
CA L:ASP222 3.8 73.0 1.0
N V:LEU167 3.8 54.5 1.0
O V:TRP164 3.8 62.6 1.0
CA V:LEU167 3.8 55.3 1.0
C V:TRP164 3.9 59.5 1.0
N V:ASP166 3.9 56.6 1.0
O V:GLY162 3.9 56.1 1.0
O L:ASP222 3.9 80.0 1.0
C V:SER169 4.0 58.8 1.0
CA V:ASP166 4.1 56.4 1.0
N V:TRP164 4.1 59.8 1.0
NH1 V:ARG19 4.2 65.6 1.0
CA V:TRP164 4.2 60.1 1.0
CA V:ILE163 4.3 56.8 1.0
N V:ASN165 4.3 59.8 1.0
C V:ASN165 4.4 55.8 1.0
CB L:ASP222 4.4 73.7 1.0
C V:LEU167 4.5 54.0 1.0
O L:ARG221 4.7 66.4 1.0
O V:LEU167 4.7 53.2 1.0
N V:SER169 4.7 55.6 1.0
CD2 V:LEU167 4.8 54.7 1.0
CZ V:ARG19 4.8 62.9 1.0
CA V:ASN165 4.9 58.0 1.0
CA V:SER169 4.9 55.8 1.0
CA V:GLY170 4.9 61.0 1.0
C V:GLY162 4.9 56.4 1.0
N V:GLY170 4.9 58.0 1.0
NH2 V:ARG19 5.0 66.9 1.0
N L:ASP222 5.0 70.3 1.0

Magnesium binding site 6 out of 8 in 6g8m

Go back to Magnesium Binding Sites List in 6g8m
Magnesium binding site 6 out of 8 in the Yeast 20S Proteasome in Complex with Cystargolide B Derivative 1


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 Cystargolide B Derivative 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
W:Mg301

b:71.7
occ:1.00
 O W:ASP177 2.4 55.6 1.0
O W:SER180 2.6 62.4 1.0
O W:ALA174 3.1 56.8 1.0
C W:ASP177 3.5 57.3 1.0
OXT W:ASP204 3.6 76.2 1.0
C W:SER180 3.8 60.2 1.0
O W:ALA178 4.0 62.5 1.0
CA W:ALA178 4.1 59.5 1.0
C W:ALA178 4.2 57.9 1.0
C W:ALA174 4.2 59.0 1.0
O W:ASP204 4.2 77.6 1.0
NH1 K:ARG19 4.2 65.8 1.0
N W:ALA178 4.2 59.1 1.0
C W:ASP204 4.4 72.7 1.0
N W:SER180 4.4 60.5 1.0
CA W:ASP175 4.4 63.0 1.0
N W:ASP177 4.5 59.9 1.0
CA W:ASP177 4.6 59.0 1.0
NH2 K:ARG19 4.7 68.0 1.0
C W:ASP175 4.7 66.0 1.0
CA W:SER180 4.7 59.8 1.0
N W:GLY181 4.7 57.9 1.0
O W:ASP175 4.7 75.5 1.0
N W:ASP175 4.7 62.0 1.0
CA W:GLY181 4.8 58.6 1.0
CZ K:ARG19 4.8 63.7 1.0
N W:LEU179 5.0 58.5 1.0

Magnesium binding site 7 out of 8 in 6g8m

Go back to Magnesium Binding Sites List in 6g8m
Magnesium binding site 7 out of 8 in the Yeast 20S Proteasome in Complex with Cystargolide B Derivative 1


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 Cystargolide B Derivative 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
Y:Mg302

b:71.9
occ:1.00
 O Y:ASP168 2.3 53.8 1.0
O I:ASP204 2.4 71.6 1.0
O Y:ALA165 2.5 55.2 1.0
O Y:SER171 2.8 58.5 1.0
C I:ASP204 3.2 70.0 1.0
C Y:ASP168 3.3 53.5 1.0
CA Y:ALA169 3.6 54.4 1.0
C Y:ALA165 3.7 55.3 1.0
O Y:ALA169 3.7 53.4 1.0
CA I:ASP204 3.7 64.3 1.0
NH1 Y:ARG19 3.7 68.8 1.0
C Y:ALA169 3.8 55.0 1.0
N Y:ALA169 3.8 53.9 1.0
O Y:HIS166 3.9 57.1 1.0
CB I:ASP204 4.0 65.5 1.0
C Y:SER171 4.0 55.5 1.0
OXT I:ASP204 4.1 75.2 1.0
C Y:HIS166 4.4 54.7 1.0
N Y:SER171 4.4 51.7 1.0
CA Y:ALA165 4.4 55.5 1.0
N Y:ASP168 4.5 54.6 1.0
CA Y:ASP168 4.5 54.7 1.0
CZ Y:ARG19 4.5 69.0 1.0
N Y:HIS166 4.6 55.4 1.0
N Y:TYR170 4.7 54.6 1.0
C Y:ARG167 4.8 56.1 1.0
CA Y:HIS166 4.8 55.0 1.0
O Y:ALA164 4.8 54.2 1.0
CA Y:SER171 4.8 52.2 1.0
CB Y:ALA169 4.9 53.2 1.0
NH2 Y:ARG19 4.9 74.2 1.0
N Y:ARG167 5.0 54.1 1.0

Magnesium binding site 8 out of 8 in 6g8m

Go back to Magnesium Binding Sites List in 6g8m
Magnesium binding site 8 out of 8 in the Yeast 20S Proteasome in Complex with Cystargolide B Derivative 1


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 Cystargolide B Derivative 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg301

b:70.2
occ:1.00
 O Z:VAL198 2.5 60.1 1.0
O Z:HIS195 2.7 53.4 1.0
O Z:THR192 2.7 64.8 1.0
O Z:ILE196 3.5 68.2 1.0
C Z:HIS195 3.7 54.9 1.0
NH2 Z:ARG28 3.7 64.4 1.0
C Z:VAL198 3.7 61.5 1.0
CA Z:ILE196 3.7 56.5 1.0
C Z:THR192 3.8 64.7 1.0
C Z:ILE196 3.8 57.1 1.0
O Z:ASP222 3.8 75.7 1.0
CG2 Z:THR192 4.0 67.2 1.0
CA Z:THR192 4.2 65.5 1.0
N Z:ILE196 4.2 53.6 1.0
NH2 H:ARG19 4.2 68.8 1.0
N Z:VAL198 4.3 59.4 1.0
CA Z:VAL198 4.5 59.0 1.0
N Z:GLY199 4.7 62.3 1.0
OD1 Z:ASP222 4.7 79.7 1.0
N Z:GLN197 4.7 54.4 1.0
CZ Z:ARG28 4.7 65.0 1.0
C Z:ASP222 4.7 74.2 1.0
CB Z:THR192 4.7 65.5 1.0
CA Z:GLY199 4.8 63.7 1.0
N Z:HIS195 4.9 56.2 1.0
CA Z:HIS195 4.9 55.2 1.0
CB Z:VAL198 5.0 59.1 1.0
CZ H:ARG19 5.0 64.0 1.0
NH1 Z:ARG28 5.0 66.5 1.0
NH1 H:ARG19 5.0 64.0 1.0
N Z:GLU193 5.0 65.9 1.0

Reference:

D.Niroula, L.P.Hallada, C.Le Chapelain, S.K.Ganegamage, D.Dotson, S.Rogelj, M.Groll, R.Tello-Aburto. Design, Synthesis, and Evaluation of Cystargolide-Based Beta-Lactones As Potent Proteasome Inhibitors. Eur J Med Chem V. 157 962 2018.
ISSN: ISSN 1768-3254
PubMed: 30165344
DOI: 10.1016/J.EJMECH.2018.08.052
Page generated: Mon Dec 14 22:44:13 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy