Atomistry » Magnesium » PDB 4rri-4s1k » 4rur
Atomistry »
  Magnesium »
    PDB 4rri-4s1k »
      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 Dec 14 19:32:17 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