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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

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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

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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

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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

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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

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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

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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

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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

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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

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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: Tue Aug 20 03:30:12 2024

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