Magnesium in PDB 5m2b: Yeast 20S Proteasome with Human BETA5I (1-138) and Human BETA6 (97- 111; 118-133) in Complex with Thiazole Based Inhibitor RO19

Enzymatic activity of Yeast 20S Proteasome with Human BETA5I (1-138) and Human BETA6 (97- 111; 118-133) in Complex with Thiazole Based Inhibitor RO19

All present enzymatic activity of Yeast 20S Proteasome with Human BETA5I (1-138) and Human BETA6 (97- 111; 118-133) in Complex with Thiazole Based Inhibitor RO19:
3.4.25.1;

Protein crystallography data

The structure of Yeast 20S Proteasome with Human BETA5I (1-138) and Human BETA6 (97- 111; 118-133) in Complex with Thiazole Based Inhibitor RO19, PDB code: 5m2b was solved by M.Groll, 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 (°) 135.160, 301.150, 145.980, 90.00, 112.81, 90.00
R / Rfree (%) 20 / 21.8

Other elements in 5m2b:

The structure of Yeast 20S Proteasome with Human BETA5I (1-138) and Human BETA6 (97- 111; 118-133) in Complex with Thiazole Based Inhibitor RO19 also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Yeast 20S Proteasome with Human BETA5I (1-138) and Human BETA6 (97- 111; 118-133) in Complex with Thiazole Based Inhibitor RO19 (pdb code 5m2b). 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 with Human BETA5I (1-138) and Human BETA6 (97- 111; 118-133) in Complex with Thiazole Based Inhibitor RO19, PDB code: 5m2b:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 5m2b

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Magnesium binding site 1 out of 7 in the Yeast 20S Proteasome with Human BETA5I (1-138) and Human BETA6 (97- 111; 118-133) in Complex with Thiazole Based Inhibitor RO19


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 with Human BETA5I (1-138) and Human BETA6 (97- 111; 118-133) in Complex with Thiazole Based Inhibitor RO19 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:48.4
occ:1.00
 O G:MET125 2.2 40.9 1.0
O G:ARG122 2.4 38.8 1.0
O G:TYR119 2.5 35.6 1.0
OG1 G:THR8 2.6 39.1 1.0
CG2 G:THR8 3.2 40.7 1.0
C G:MET125 3.4 42.8 1.0
O G:ALA123 3.4 44.3 1.0
C G:ARG122 3.5 41.0 1.0
CB G:THR8 3.5 40.0 1.0
C G:TYR119 3.7 34.7 1.0
C G:ALA123 3.7 43.0 1.0
CA G:ALA123 3.7 41.5 1.0
N G:ALA123 4.1 41.3 1.0
N G:MET125 4.2 45.4 1.0
N G:ARG126 4.3 39.9 1.0
CA G:ARG126 4.3 38.5 1.0
N G:THR8 4.3 41.2 1.0
CA G:MET125 4.3 46.6 1.0
CA G:TYR119 4.5 34.0 1.0
CA G:THR8 4.5 40.1 1.0
CD G:PRO127 4.6 35.1 1.0
N G:TYR124 4.7 43.8 1.0
N G:THR120 4.7 34.6 1.0
CA G:ARG122 4.7 42.5 1.0
N G:ARG122 4.7 39.6 1.0
CA G:THR120 4.8 34.4 1.0
CB G:MET125 4.8 51.3 1.0
C G:ARG126 4.9 37.0 1.0
C G:THR120 4.9 34.6 1.0
CB G:TYR119 5.0 34.0 1.0

Magnesium binding site 2 out of 7 in 5m2b

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Magnesium binding site 2 out of 7 in the Yeast 20S Proteasome with Human BETA5I (1-138) and Human BETA6 (97- 111; 118-133) in Complex with Thiazole Based Inhibitor RO19


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 with Human BETA5I (1-138) and Human BETA6 (97- 111; 118-133) in Complex with Thiazole Based Inhibitor RO19 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:59.8
occ:1.00
 O Y:ASP167 2.1 46.5 1.0
O I:ASP204 2.1 52.6 1.0
O Y:SER170 2.2 47.1 1.0
O Y:ALA164 2.3 43.9 1.0
C I:ASP204 3.2 53.7 1.0
C Y:ASP167 3.3 44.7 1.0
NH1 Y:ARG19 3.4 58.2 1.0
C Y:SER170 3.4 45.2 1.0
C Y:ALA164 3.4 41.2 1.0
CA Y:ALA168 3.7 47.7 1.0
O Y:ALA168 3.8 49.1 1.0
C Y:ALA168 3.8 48.1 1.0
CA I:ASP204 3.8 54.0 1.0
N Y:ALA168 3.9 46.4 1.0
CB I:ASP204 4.0 54.8 1.0
N Y:SER170 4.0 43.8 1.0
CA Y:ALA164 4.0 41.3 1.0
OXT I:ASP204 4.2 53.8 1.0
CZ Y:ARG19 4.2 56.6 1.0
CA Y:SER170 4.3 43.7 1.0
O Y:HIS165 4.3 44.1 1.0
N Y:GLY171 4.4 45.3 1.0
CA Y:ASP167 4.5 42.9 1.0
CA Y:GLY171 4.5 46.5 1.0
N Y:HIS165 4.5 40.6 1.0
N Y:ASP167 4.5 44.3 1.0
N Y:TYR169 4.6 47.6 1.0
C Y:HIS165 4.6 42.9 1.0
NH2 Y:ARG19 4.6 56.7 1.0
O Y:ALA163 4.6 40.9 1.0
CB Y:SER170 4.7 42.2 1.0
CA Y:HIS165 4.8 41.5 1.0
CB Y:ALA164 4.8 41.6 1.0
CG I:ASP204 4.9 54.1 1.0
C Y:ARG166 5.0 44.5 1.0

Magnesium binding site 3 out of 7 in 5m2b

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Magnesium binding site 3 out of 7 in the Yeast 20S Proteasome with Human BETA5I (1-138) and Human BETA6 (97- 111; 118-133) in Complex with Thiazole Based Inhibitor RO19


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 with Human BETA5I (1-138) and Human BETA6 (97- 111; 118-133) in Complex with Thiazole Based Inhibitor RO19 within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mg201

b:47.2
occ:1.00
 OE1 J:GLN118 3.1 37.8 1.0
O J:THR124 3.4 37.8 1.0
CB J:ASP120 3.7 35.1 1.0
N J:ASP120 3.7 32.1 1.0
CG J:ASP120 3.9 37.4 1.0
CD J:GLN118 3.9 35.7 1.0
OD2 J:ASP120 3.9 41.3 1.0
CG J:GLN118 3.9 33.8 1.0
CE1 J:HIS133 4.0 35.0 1.0
O J:GLN118 4.2 33.4 1.0
CB J:THR124 4.2 36.3 1.0
CA J:ASP120 4.3 33.4 1.0
C J:ILE119 4.4 32.1 1.0
C J:THR124 4.4 36.0 1.0
C J:GLN118 4.5 32.2 1.0
CG2 J:THR124 4.5 35.8 1.0
CA J:ILE119 4.5 31.0 1.0
OD1 J:ASP120 4.6 39.8 1.0
N J:ILE119 4.6 31.3 1.0
CB J:GLN118 4.8 32.8 1.0
ND1 J:HIS133 4.8 35.4 1.0
CA J:THR124 4.9 36.0 1.0
NE2 J:HIS133 5.0 34.2 1.0
CG1 I:VAL35 5.0 47.4 1.0

Magnesium binding site 4 out of 7 in 5m2b

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Magnesium binding site 4 out of 7 in the Yeast 20S Proteasome with Human BETA5I (1-138) and Human BETA6 (97- 111; 118-133) in Complex with Thiazole Based Inhibitor RO19


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 with Human BETA5I (1-138) and Human BETA6 (97- 111; 118-133) in Complex with Thiazole Based Inhibitor RO19 within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg302

b:52.3
occ:1.00
 O W:ASP204 2.1 50.4 1.0
O K:ASP167 2.1 48.1 1.0
O K:ALA164 2.2 44.4 1.0
O K:SER170 2.4 43.9 1.0
C W:ASP204 3.1 49.4 1.0
C K:ASP167 3.3 45.0 1.0
C K:ALA164 3.3 43.9 1.0
NH1 K:ARG19 3.6 55.8 1.0
C K:SER170 3.6 44.7 1.0
CA W:ASP204 3.7 49.5 1.0
CA K:ALA168 3.7 47.3 1.0
N K:ALA168 3.9 46.3 1.0
C K:ALA168 4.0 46.9 1.0
CB W:ASP204 4.0 50.0 1.0
O K:ALA168 4.0 44.6 1.0
O K:HIS165 4.0 43.6 1.0
CA K:ALA164 4.0 42.9 1.0
OXT W:ASP204 4.1 51.1 1.0
N K:SER170 4.3 44.2 1.0
C K:HIS165 4.3 43.4 1.0
N K:HIS165 4.4 43.5 1.0
N K:ASP167 4.4 44.3 1.0
CZ K:ARG19 4.4 54.0 1.0
CA K:ASP167 4.4 43.6 1.0
CA K:SER170 4.5 43.8 1.0
O K:ALA163 4.6 42.7 1.0
N K:GLY171 4.6 46.5 1.0
CA K:HIS165 4.6 43.9 1.0
CA K:GLY171 4.7 48.1 1.0
N K:TYR169 4.7 47.2 1.0
NH2 K:ARG19 4.8 54.8 1.0
C K:ARG166 4.8 44.4 1.0
CB K:ALA164 4.9 43.5 1.0
CB K:SER170 4.9 42.5 1.0
CG W:ASP204 4.9 50.5 1.0
N K:ARG166 4.9 43.4 1.0

Magnesium binding site 5 out of 7 in 5m2b

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Magnesium binding site 5 out of 7 in the Yeast 20S Proteasome with Human BETA5I (1-138) and Human BETA6 (97- 111; 118-133) in Complex with Thiazole Based Inhibitor RO19


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 with Human BETA5I (1-138) and Human BETA6 (97- 111; 118-133) in Complex with Thiazole Based Inhibitor RO19 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg301

b:52.8
occ:1.00
 OXT L:ASP222 1.9 69.1 1.0
O V:ASP166 2.1 42.8 1.0
O V:SER169 2.3 45.5 1.0
O V:ILE163 2.3 44.9 1.0
C L:ASP222 3.0 67.5 1.0
C V:ASP166 3.1 42.1 1.0
C V:SER169 3.4 44.7 1.0
C V:ILE163 3.4 46.0 1.0
CA V:LEU167 3.7 42.3 1.0
CA L:ASP222 3.8 65.4 1.0
N V:LEU167 3.8 42.1 1.0
NH1 V:ARG19 3.8 51.9 1.0
O L:ASP222 3.9 70.7 1.0
O V:GLY162 4.0 46.2 1.0
C V:LEU167 4.1 42.3 1.0
N V:ASP166 4.1 42.2 1.0
N V:SER169 4.2 42.6 1.0
CA V:ILE163 4.2 45.7 1.0
CA V:ASP166 4.2 41.9 1.0
O V:LEU167 4.3 41.5 1.0
CB L:ASP222 4.3 64.0 1.0
CA V:SER169 4.3 43.2 1.0
N V:GLY170 4.4 45.6 1.0
O V:TRP164 4.4 48.9 1.0
CA V:GLY170 4.4 47.2 1.0
C V:TRP164 4.4 47.4 1.0
N V:TRP164 4.4 46.6 1.0
CZ V:ARG19 4.4 49.9 1.0
NH2 V:ARG19 4.6 49.8 1.0
CA V:TRP164 4.7 47.9 1.0
CB V:SER169 4.7 43.3 1.0
N V:GLY168 4.8 43.2 1.0
N V:ASN165 4.8 45.9 1.0
C V:ASN165 4.9 43.2 1.0
C V:GLY162 4.9 44.9 1.0
CD2 V:LEU167 4.9 42.2 1.0
CB V:ASP166 5.0 41.6 1.0

Magnesium binding site 6 out of 7 in 5m2b

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Magnesium binding site 6 out of 7 in the Yeast 20S Proteasome with Human BETA5I (1-138) and Human BETA6 (97- 111; 118-133) in Complex with Thiazole Based Inhibitor RO19


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 with Human BETA5I (1-138) and Human BETA6 (97- 111; 118-133) in Complex with Thiazole Based Inhibitor RO19 within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg201

b:42.6
occ:1.00
 O N:ILE163 2.5 39.2 1.0
O N:SER169 2.5 37.2 1.0
O N:ASP166 2.7 37.0 1.0
C N:ILE163 3.6 39.3 1.0
C N:SER169 3.7 36.0 1.0
CD1 a:LEU34 3.7 47.5 1.0
C N:ASP166 3.8 36.8 1.0
NH1 N:ARG19 3.8 40.8 1.0
CG2 N:ILE163 3.9 38.0 1.0
CA N:GLY167 4.1 37.5 1.0
CZ N:ARG19 4.3 39.9 1.0
CA N:ILE163 4.3 38.4 1.0
N N:GLY167 4.3 37.4 1.0
CA N:GLY170 4.4 38.2 1.0
O N:GLY167 4.5 37.8 1.0
NH2 N:ARG19 4.5 39.9 1.0
C N:GLY167 4.5 37.5 1.0
N N:GLY170 4.5 36.9 1.0
N N:SER169 4.7 36.0 1.0
CA N:SER169 4.7 35.1 1.0
N N:LYS164 4.7 41.1 1.0
CB N:ILE163 4.7 37.8 1.0
N N:ASP166 4.9 36.5 1.0
CG a:LEU34 4.9 47.1 1.0
CA N:ASP166 4.9 36.7 1.0
C N:LYS164 4.9 42.3 1.0
O N:LYS164 5.0 43.6 1.0

Magnesium binding site 7 out of 7 in 5m2b

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Magnesium binding site 7 out of 7 in the Yeast 20S Proteasome with Human BETA5I (1-138) and Human BETA6 (97- 111; 118-133) in Complex with Thiazole Based Inhibitor RO19


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 with Human BETA5I (1-138) and Human BETA6 (97- 111; 118-133) in Complex with Thiazole Based Inhibitor RO19 within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg301

b:50.0
occ:1.00
 O Z:THR192 2.5 56.5 1.0
O Z:VAL198 2.6 50.6 1.0
O Z:HIS195 2.7 47.5 1.0
C Z:THR192 3.5 57.0 1.0
C Z:HIS195 3.7 48.2 1.0
C Z:VAL198 3.8 52.0 1.0
CG2 Z:THR192 3.8 58.7 1.0
CA Z:ILE196 3.9 50.3 1.0
CA Z:THR192 3.9 57.6 1.0
NH2 Z:ARG28 3.9 56.5 1.0
O Z:ILE196 4.0 56.1 1.0
O Z:ASP222 4.0 64.8 1.0
C Z:ILE196 4.1 51.4 1.0
N Z:ILE196 4.2 48.5 1.0
NH2 H:ARG19 4.4 59.4 1.0
N Z:VAL198 4.4 49.8 1.0
OD1 Z:ASP222 4.5 62.0 1.0
CB Z:THR192 4.5 57.4 1.0
CA Z:VAL198 4.6 51.5 1.0
N Z:GLU193 4.7 58.0 1.0
N Z:HIS195 4.8 49.2 1.0
N Z:GLY199 4.8 52.5 1.0
CA Z:HIS195 4.8 49.2 1.0
CA Z:GLY199 4.9 54.4 1.0
N Z:GLN197 4.9 50.8 1.0
O Z:ALA191 5.0 54.5 1.0
CB Z:VAL198 5.0 51.5 1.0
C Z:ASP222 5.0 65.2 1.0

Reference:

H.Cui, R.Baur, C.Le Chapelain, C.Dubiella, W.Heinemeyer, E.M.Huber, M.Groll. Structural Elucidation of A Nonpeptidic Inhibitor Specific For the Human Immunoproteasome. Chembiochem V. 18 523 2017.
ISSN: ESSN 1439-7633
PubMed: 28098422
DOI: 10.1002/CBIC.201700021
Page generated: Mon Dec 14 20:50:16 2020

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