Atomistry » Magnesium » PDB 4rrk-4s1l » 4rur
Atomistry »
  Magnesium »
    PDB 4rrk-4s1l »
      4rur »

Magnesium in PDB 4rur: Yeast 20S Proteasome in Complex with the Alkaloid Indolo-Phakellin (4)

Enzymatic activity of Yeast 20S Proteasome in Complex with the Alkaloid Indolo-Phakellin (4)

All present enzymatic activity of Yeast 20S Proteasome in Complex with the Alkaloid Indolo-Phakellin (4):
3.4.25.1;

Protein crystallography data

The structure of Yeast 20S Proteasome in Complex with the Alkaloid Indolo-Phakellin (4), PDB code: 4rur was solved by P.Beck, T.A.Lansdell, N.M.Hewlett, J.J.Tepe, M.Groll, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.00 / 2.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 136.080, 300.880, 145.990, 90.00, 113.11, 90.00
R / Rfree (%) 19 / 21.3

Other elements in 4rur:

The structure of Yeast 20S Proteasome in Complex with the Alkaloid Indolo-Phakellin (4) also contains other interesting chemical elements:

Bromine (Br) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Yeast 20S Proteasome in Complex with the Alkaloid Indolo-Phakellin (4) (pdb code 4rur). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 9 binding sites of Magnesium where determined in the Yeast 20S Proteasome in Complex with the Alkaloid Indolo-Phakellin (4), PDB code: 4rur:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Magnesium binding site 1 out of 9 in 4rur

Go back to Magnesium Binding Sites List in 4rur
Magnesium binding site 1 out of 9 in the Yeast 20S Proteasome in Complex with the Alkaloid Indolo-Phakellin (4)


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 the Alkaloid Indolo-Phakellin (4) within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:66.2
occ:1.00
 O G:TYR119 2.0 43.5 1.0
O G:MET125 2.0 48.8 1.0
O G:ARG122 2.5 43.9 1.0
OG1 G:THR8 2.8 43.2 1.0
C G:TYR119 3.2 41.5 1.0
CG2 G:THR8 3.3 44.5 1.0
C G:MET125 3.3 48.2 1.0
CB G:THR8 3.6 44.8 1.0
C G:ARG122 3.7 45.1 1.0
CA G:TYR119 4.0 40.9 1.0
CA G:ARG126 4.1 43.8 1.0
N G:ARG126 4.1 44.1 1.0
O G:ALA123 4.1 45.2 1.0
N G:THR120 4.2 40.3 1.0
CD G:PRO127 4.3 41.3 1.0
CA G:ALA123 4.3 45.9 1.0
CA G:MET125 4.3 52.3 1.0
C G:ALA123 4.3 46.8 1.0
N G:MET125 4.3 50.2 1.0
N G:ALA123 4.4 45.6 1.0
CA G:THR120 4.5 40.6 1.0
CB G:TYR119 4.5 41.4 1.0
C G:ARG126 4.5 42.3 1.0
CB G:MET125 4.6 57.8 1.0
N G:PRO127 4.6 40.4 1.0
N G:ARG122 4.7 44.8 1.0
C G:THR120 4.7 40.2 1.0
N G:THR8 4.7 45.7 1.0
CA G:THR8 4.8 45.6 1.0
CA G:ARG122 4.8 47.5 1.0
O G:HOH442 4.9 56.1 1.0
CG G:PRO127 4.9 41.1 1.0
N G:GLN121 4.9 39.4 1.0

Magnesium binding site 2 out of 9 in 4rur

Go back to Magnesium Binding Sites List in 4rur
Magnesium binding site 2 out of 9 in the Yeast 20S Proteasome in Complex with the Alkaloid Indolo-Phakellin (4)


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 the Alkaloid Indolo-Phakellin (4) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:70.2
occ:1.00
 O I:HOH428 2.0 73.3 1.0
O I:SER180 2.3 51.0 1.0
O I:ALA174 2.5 43.9 1.0
O I:ASP177 2.8 43.6 1.0
C I:ALA174 3.4 45.4 1.0
C I:SER180 3.5 48.9 1.0
O I:HOH406 3.6 45.4 1.0
CA I:ASP175 3.8 48.6 1.0
C I:ASP177 4.0 44.5 1.0
N I:ASP175 4.0 46.7 1.0
OXT I:ASP204 4.2 54.0 1.0
CA I:GLY181 4.2 46.6 1.0
N I:GLY181 4.2 47.9 1.0
OD1 I:ASP175 4.3 56.7 1.0
C I:ASP175 4.4 49.0 1.0
CA I:ALA174 4.5 43.6 1.0
CA I:SER180 4.5 47.7 1.0
N I:SER180 4.6 46.0 1.0
N I:ASP177 4.6 45.7 1.0
CB I:ALA174 4.6 42.4 1.0
O I:ASP175 4.7 52.2 1.0
O I:ALA178 4.7 49.7 1.0
CA I:ASP177 4.8 45.0 1.0
C I:ALA178 4.9 46.7 1.0
N I:ALA178 4.9 44.0 1.0
CB I:SER180 4.9 49.3 1.0
CA I:ALA178 5.0 44.8 1.0

Magnesium binding site 3 out of 9 in 4rur

Go back to Magnesium Binding Sites List in 4rur
Magnesium binding site 3 out of 9 in the Yeast 20S Proteasome in Complex with the Alkaloid Indolo-Phakellin (4)


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 the Alkaloid Indolo-Phakellin (4) within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg301

b:53.6
occ:1.00
 O K:ASP168 2.2 44.0 1.0
O K:ALA165 2.4 43.8 1.0
O K:SER171 2.4 43.5 1.0
O W:ASP204 2.5 49.2 1.0
C W:ASP204 3.2 53.3 1.0
C K:ASP168 3.2 42.1 1.0
C K:ALA165 3.5 43.6 1.0
C K:SER171 3.6 44.1 1.0
CA W:ASP204 3.7 51.4 1.0
CA K:ALA169 3.7 42.6 1.0
NH1 K:ARG19 3.7 52.3 1.0
O K:ALA169 3.7 46.5 1.0
C K:ALA169 3.8 44.8 1.0
N K:ALA169 3.9 41.5 1.0
CB W:ASP204 3.9 51.1 1.0
OXT W:ASP204 4.0 56.0 1.0
N K:SER171 4.1 47.0 1.0
CA K:ALA165 4.2 44.3 1.0
O K:HIS166 4.2 45.5 1.0
CA K:SER171 4.4 44.4 1.0
CA K:ASP168 4.4 41.6 1.0
N K:ASP168 4.4 42.1 1.0
CZ K:ARG19 4.5 51.2 1.0
C K:HIS166 4.5 42.5 1.0
N K:TYR170 4.5 44.6 1.0
N K:HIS166 4.5 43.4 1.0
O K:ALA164 4.6 43.6 1.0
N K:GLY172 4.6 44.5 1.0
CA K:GLY172 4.7 46.9 1.0
CB K:SER171 4.8 43.9 1.0
CA K:HIS166 4.8 43.6 1.0
NH2 K:ARG19 4.8 54.5 1.0
CG W:ASP204 4.9 50.7 1.0
C K:ARG167 4.9 42.8 1.0

Magnesium binding site 4 out of 9 in 4rur

Go back to Magnesium Binding Sites List in 4rur
Magnesium binding site 4 out of 9 in the Yeast 20S Proteasome in Complex with the Alkaloid Indolo-Phakellin (4)


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 the Alkaloid Indolo-Phakellin (4) within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg201

b:65.0
occ:1.00
 O N:SER169 2.1 47.1 1.0
O N:ASP166 2.7 48.6 1.0
O N:ILE163 2.7 44.6 1.0
C N:SER169 3.3 45.6 1.0
NH1 N:ARG19 3.5 49.0 1.0
O N:HOH329 3.5 44.6 1.0
C N:ASP166 3.7 44.6 1.0
C N:ILE163 3.8 45.4 1.0
CD1 a:LEU34 3.9 47.3 1.0
CG2 N:ILE163 3.9 44.8 1.0
CA N:GLY167 4.0 44.5 1.0
CZ N:ARG19 4.1 48.6 1.0
O N:GLY167 4.1 43.5 1.0
CA N:GLY170 4.2 46.9 1.0
N N:GLY170 4.2 46.0 1.0
C N:GLY167 4.2 44.3 1.0
CA N:ILE163 4.3 44.6 1.0
N N:GLY167 4.3 44.2 1.0
N N:SER169 4.3 43.4 1.0
CA N:SER169 4.3 43.5 1.0
NH2 N:ARG19 4.4 49.4 1.0
CB N:ILE163 4.7 44.1 1.0
CB N:SER169 4.8 43.4 1.0
NE N:ARG19 4.8 48.7 1.0
CA N:ASP166 4.9 44.5 1.0
N N:LYS164 4.9 47.3 1.0
N N:ASP166 4.9 43.9 1.0

Magnesium binding site 5 out of 9 in 4rur

Go back to Magnesium Binding Sites List in 4rur
Magnesium binding site 5 out of 9 in the Yeast 20S Proteasome in Complex with the Alkaloid Indolo-Phakellin (4)


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 the Alkaloid Indolo-Phakellin (4) within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg202

b:73.3
occ:1.00
 O N:HOH304 2.6 51.6 1.0
OD1 N:ASP51 3.0 45.8 1.0
OE1 H:GLN91 3.0 73.1 1.0
OD2 N:ASP51 3.4 49.2 1.0
CG N:ASP51 3.6 45.4 1.0
O H:HOH303 3.6 45.6 1.0
O N:ASN92 3.9 55.0 1.0
CD H:GLN91 4.1 67.0 1.0
NE2 H:GLN91 4.4 69.4 1.0
OG N:SER48 4.6 39.4 1.0
ND1 H:HIS116 4.7 45.8 1.0

Magnesium binding site 6 out of 9 in 4rur

Go back to Magnesium Binding Sites List in 4rur
Magnesium binding site 6 out of 9 in the Yeast 20S Proteasome in Complex with the Alkaloid Indolo-Phakellin (4)


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 the Alkaloid Indolo-Phakellin (4) within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Mg301

b:55.9
occ:1.00
 O V:ASP166 2.1 47.4 1.0
O V:ILE163 2.2 48.5 1.0
O V:SER169 2.3 49.4 1.0
OXT L:ASP222 2.3 63.0 1.0
O V:HOH416 2.5 48.8 1.0
C L:ASP222 3.2 62.9 1.0
C V:ASP166 3.2 47.0 1.0
C V:ILE163 3.2 49.9 1.0
C V:SER169 3.4 49.6 1.0
O V:GLY162 3.7 47.1 1.0
CA L:ASP222 3.8 62.3 1.0
CA V:LEU167 3.9 49.0 1.0
N V:LEU167 3.9 48.0 1.0
CA V:ILE163 4.0 48.9 1.0
NH1 V:ARG19 4.0 56.0 1.0
O L:ASP222 4.0 68.1 1.0
N V:ASP166 4.1 47.8 1.0
N V:TRP164 4.2 49.4 1.0
CA V:ASP166 4.2 47.4 1.0
N V:SER169 4.2 48.2 1.0
N V:GLY170 4.3 51.0 1.0
C V:LEU167 4.3 49.0 1.0
CA V:SER169 4.3 48.9 1.0
C V:TRP164 4.3 50.1 1.0
CA V:GLY170 4.3 54.0 1.0
CB L:ASP222 4.3 63.6 1.0
O V:LEU167 4.4 48.2 1.0
CA V:TRP164 4.5 50.4 1.0
O V:TRP164 4.5 50.3 1.0
N V:ASN165 4.6 49.2 1.0
CZ V:ARG19 4.6 55.1 1.0
CB V:SER169 4.6 49.5 1.0
C V:GLY162 4.7 48.5 1.0
C V:ASN165 4.8 48.1 1.0
NH2 V:ARG19 4.8 56.8 1.0
N V:ILE163 4.8 48.6 1.0
CB V:ASP166 4.9 46.6 1.0
N V:GLY168 5.0 48.1 1.0

Magnesium binding site 7 out of 9 in 4rur

Go back to Magnesium Binding Sites List in 4rur
Magnesium binding site 7 out of 9 in the Yeast 20S Proteasome in Complex with the Alkaloid Indolo-Phakellin (4)


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 the Alkaloid Indolo-Phakellin (4) within 5.0Å range:
probe atom residue distance (Å) B Occ
W:Mg301

b:64.9
occ:1.00
 O W:HOH401 1.8 64.4 1.0
O W:ALA174 2.2 47.5 1.0
O W:ASP177 2.2 48.8 1.0
O W:HOH416 2.3 41.0 1.0
O W:SER180 2.5 50.1 1.0
C W:ALA174 3.3 47.1 1.0
C W:ASP177 3.4 46.2 1.0
C W:SER180 3.6 49.1 1.0
CA W:ASP175 3.8 49.9 1.0
N W:ASP175 3.9 49.4 1.0
N W:ASP177 4.0 47.0 1.0
C W:ASP175 4.1 50.1 1.0
CA W:ASP177 4.2 46.8 1.0
N W:ALA178 4.3 45.6 1.0
N W:SER180 4.4 48.6 1.0
CA W:ALA174 4.4 44.7 1.0
O W:ASP175 4.4 51.0 1.0
CA W:SER180 4.5 49.3 1.0
O W:HOH410 4.5 45.3 1.0
O W:ALA178 4.5 49.4 1.0
CA W:ALA178 4.5 46.1 1.0
N W:GLY181 4.5 48.7 1.0
C W:ALA178 4.5 47.2 1.0
OXT W:ASP204 4.6 56.0 1.0
CA W:GLY181 4.6 48.5 1.0
OD1 W:ASP175 4.6 52.0 1.0
N W:ARG176 4.6 48.1 1.0
CB W:ASP177 4.7 47.1 1.0
CB W:ALA174 4.7 44.0 1.0
CB W:SER180 4.8 50.7 1.0

Magnesium binding site 8 out of 9 in 4rur

Go back to Magnesium Binding Sites List in 4rur
Magnesium binding site 8 out of 9 in the Yeast 20S Proteasome in Complex with the Alkaloid Indolo-Phakellin (4)


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 the Alkaloid Indolo-Phakellin (4) within 5.0Å range:
probe atom residue distance (Å) B Occ
Y:Mg301

b:49.7
occ:1.00
 O Y:ASP168 2.2 42.8 1.0
O Y:SER171 2.3 43.1 1.0
O Y:ALA165 2.3 43.6 1.0
O Y:HOH411 2.4 46.6 1.0
O I:ASP204 2.4 47.5 1.0
C I:ASP204 3.2 50.6 1.0
C Y:ASP168 3.3 41.5 1.0
C Y:ALA165 3.5 43.1 1.0
C Y:SER171 3.5 42.9 1.0
NH1 Y:ARG19 3.7 48.9 1.0
CA I:ASP204 3.7 50.4 1.0
O Y:ALA169 3.7 45.2 1.0
CA Y:ALA169 3.8 41.4 1.0
C Y:ALA169 3.8 43.2 1.0
CB I:ASP204 3.9 51.1 1.0
N Y:ALA169 3.9 40.9 1.0
N Y:SER171 4.1 43.1 1.0
OXT I:ASP204 4.1 54.0 1.0
CA Y:ALA165 4.1 43.0 1.0
O Y:HIS166 4.3 44.8 1.0
CA Y:SER171 4.3 42.9 1.0
CZ Y:ARG19 4.4 49.0 1.0
CA Y:ASP168 4.5 41.9 1.0
N Y:ASP168 4.5 42.4 1.0
N Y:GLY172 4.5 42.9 1.0
C Y:HIS166 4.5 42.2 1.0
N Y:HIS166 4.5 43.1 1.0
N Y:TYR170 4.6 43.6 1.0
O Y:ALA164 4.6 41.8 1.0
CA Y:GLY172 4.7 43.6 1.0
NH2 Y:ARG19 4.8 50.0 1.0
CB Y:SER171 4.8 42.5 1.0
CG I:ASP204 4.8 49.9 1.0
CA Y:HIS166 4.8 41.7 1.0
CB Y:ALA165 5.0 43.6 1.0
C Y:ARG167 5.0 42.5 1.0

Magnesium binding site 9 out of 9 in 4rur

Go back to Magnesium Binding Sites List in 4rur
Magnesium binding site 9 out of 9 in the Yeast 20S Proteasome in Complex with the Alkaloid Indolo-Phakellin (4)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Yeast 20S Proteasome in Complex with the Alkaloid Indolo-Phakellin (4) within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg302

b:0.7
occ:1.00
 O Z:THR192 2.2 56.9 1.0
NH2 H:ARG19 3.3 60.0 1.0
O Z:HIS195 3.3 42.6 1.0
C Z:THR192 3.4 55.5 1.0
O Z:VAL198 3.8 48.5 1.0
C Z:HIS195 4.1 44.7 1.0
CZ H:ARG19 4.1 59.4 1.0
OD1 Z:ASP222 4.1 60.3 1.0
CG2 Z:THR192 4.2 55.9 1.0
CA Z:ILE196 4.3 45.2 1.0
O Z:GLU193 4.3 59.1 1.0
CA Z:THR192 4.3 54.6 1.0
O Z:ASP222 4.3 60.4 1.0
NH1 H:ARG19 4.4 59.4 1.0
C Z:GLU193 4.4 56.0 1.0
N Z:GLU193 4.4 55.9 1.0
N Z:ILE196 4.5 44.3 1.0
CA Z:GLU193 4.5 55.5 1.0
O Z:ILE196 4.7 50.5 1.0
N Z:HIS195 4.7 46.9 1.0
C Z:ILE196 4.8 46.1 1.0
CG Z:ASP222 4.8 59.9 1.0
C Z:ASP222 4.8 61.8 1.0
CB Z:THR192 4.9 55.2 1.0
N Z:ARG194 5.0 54.3 1.0
OXT Z:ASP222 5.0 62.5 1.0

Reference:

P.Beck, T.A.Lansdell, N.M.Hewlett, J.J.Tepe, M.Groll. Indolo-Phakellins As BETA5-Specific Noncovalent Proteasome Inhibitors To Be Published.
Page generated: Mon Aug 11 23:36:46 2025

Last articles

Zn in 9WV4
Zn in 9YC2
Zn in 9YT5
Zn in 9Z4D
Zn in 9YT3
Zn in 9YT2
Zn in 9YS1
Zn in 9VH0
Zn in 9YRZ
Zn in 9YRX
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy