Atomistry » Magnesium » PDB 5kty-5l5u » 5l5f
Atomistry »
  Magnesium »
    PDB 5kty-5l5u »
      5l5f »

Magnesium in PDB 5l5f: Yeast 20S Proteasome with Human BETA5I (1-138) and Human BETA6 (97- 111; 118-133) in Complex with Bortezomib

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

All present enzymatic activity of Yeast 20S Proteasome with Human BETA5I (1-138) and Human BETA6 (97- 111; 118-133) in Complex with Bortezomib:
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 Bortezomib, PDB code: 5l5f was solved by M.Groll, E.M.Huber, 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 (°) 135.510, 300.910, 144.920, 90.00, 112.59, 90.00
R / Rfree (%) 20.5 / 22.8

Other elements in 5l5f:

The structure of Yeast 20S Proteasome with Human BETA5I (1-138) and Human BETA6 (97- 111; 118-133) in Complex with Bortezomib 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 Bortezomib (pdb code 5l5f). 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 with Human BETA5I (1-138) and Human BETA6 (97- 111; 118-133) in Complex with Bortezomib, PDB code: 5l5f:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 5l5f

Go back to Magnesium Binding Sites List in 5l5f
Magnesium binding site 1 out of 8 in the Yeast 20S Proteasome with Human BETA5I (1-138) and Human BETA6 (97- 111; 118-133) in Complex with Bortezomib


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 Bortezomib within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:46.7
occ:1.00
 O G:MET125 2.2 41.6 1.0
O G:ARG122 2.4 40.1 1.0
O G:TYR119 2.5 34.2 1.0
OG1 G:THR8 2.7 39.1 1.0
CG2 G:THR8 3.2 40.3 1.0
C G:MET125 3.4 42.8 1.0
O G:ALA123 3.4 45.2 1.0
C G:ARG122 3.5 40.5 1.0
CB G:THR8 3.5 39.4 1.0
C G:ALA123 3.7 43.5 1.0
CA G:ALA123 3.7 41.2 1.0
C G:TYR119 3.7 34.7 1.0
N G:ALA123 4.1 40.0 1.0
N G:MET125 4.2 44.5 1.0
N G:ARG126 4.2 40.1 1.0
CA G:ARG126 4.3 38.4 1.0
N G:THR8 4.3 40.4 1.0
CA G:MET125 4.3 45.2 1.0
CA G:TYR119 4.5 34.0 1.0
CA G:THR8 4.5 40.1 1.0
CD G:PRO127 4.5 35.7 1.0
N G:TYR124 4.6 44.0 1.0
CA G:ARG122 4.7 43.5 1.0
N G:THR120 4.7 34.4 1.0
N G:ARG122 4.8 40.5 1.0
CB G:MET125 4.9 50.7 1.0
C G:ARG126 4.9 37.2 1.0
CA G:THR120 4.9 34.2 1.0
C G:THR120 4.9 34.6 1.0

Magnesium binding site 2 out of 8 in 5l5f

Go back to Magnesium Binding Sites List in 5l5f
Magnesium binding site 2 out of 8 in the Yeast 20S Proteasome with Human BETA5I (1-138) and Human BETA6 (97- 111; 118-133) in Complex with Bortezomib


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 Bortezomib within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:46.8
occ:1.00
 O Y:ASP167 2.1 44.9 1.0
O Y:ALA164 2.3 39.4 1.0
O I:ASP204 2.4 49.2 1.0
O Y:SER170 2.4 47.0 1.0
C Y:ASP167 3.2 41.9 1.0
C I:ASP204 3.3 52.7 1.0
C Y:ALA164 3.4 38.6 1.0
NH1 Y:ARG19 3.5 54.7 1.0
C Y:SER170 3.6 42.7 1.0
CA I:ASP204 3.7 53.5 1.0
CA Y:ALA168 3.8 44.1 1.0
CB I:ASP204 3.9 54.5 1.0
C Y:ALA168 3.9 44.7 1.0
O Y:ALA168 3.9 45.8 1.0
N Y:ALA168 3.9 42.6 1.0
N Y:SER170 4.1 41.5 1.0
CA Y:ALA164 4.1 38.8 1.0
O Y:HIS165 4.2 40.4 1.0
OXT I:ASP204 4.2 53.7 1.0
CZ Y:ARG19 4.3 52.0 1.0
CA Y:SER170 4.3 40.5 1.0
CA Y:ASP167 4.4 40.0 1.0
N Y:ASP167 4.4 41.6 1.0
C Y:HIS165 4.4 40.0 1.0
N Y:HIS165 4.5 39.4 1.0
N Y:GLY171 4.6 43.5 1.0
O Y:ALA163 4.6 37.9 1.0
N Y:TYR169 4.6 43.8 1.0
NH2 Y:ARG19 4.7 52.7 1.0
CA Y:GLY171 4.7 44.2 1.0
CA Y:HIS165 4.7 38.9 1.0
CB Y:SER170 4.8 39.0 1.0
CG I:ASP204 4.9 55.1 1.0
C Y:ARG166 4.9 42.1 1.0
CB Y:ALA164 4.9 39.2 1.0

Magnesium binding site 3 out of 8 in 5l5f

Go back to Magnesium Binding Sites List in 5l5f
Magnesium binding site 3 out of 8 in the Yeast 20S Proteasome with Human BETA5I (1-138) and Human BETA6 (97- 111; 118-133) in Complex with Bortezomib


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 Bortezomib within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mg201

b:62.5
occ:1.00
 OE1 J:GLN118 3.1 38.9 1.0
O J:THR124 3.5 38.4 1.0
CB J:ASP120 3.8 35.5 1.0
N J:ASP120 3.8 32.0 1.0
OD2 J:ASP120 3.8 40.6 1.0
CG J:ASP120 3.9 38.1 1.0
CD J:GLN118 3.9 36.2 1.0
CG J:GLN118 4.0 34.4 1.0
CE1 J:HIS133 4.1 35.1 1.0
CB J:THR124 4.2 36.5 1.0
O J:GLN118 4.3 33.3 1.0
CA J:ASP120 4.4 33.4 1.0
CG2 J:THR124 4.4 36.9 1.0
C J:THR124 4.5 36.8 1.0
C J:ILE119 4.5 32.4 1.0
C J:GLN118 4.6 32.9 1.0
OD1 J:ASP120 4.6 40.5 1.0
CA J:ILE119 4.7 31.1 1.0
CG1 I:VAL35 4.8 46.8 1.0
N J:ILE119 4.8 31.5 1.0
ND1 J:HIS133 4.8 34.9 1.0
CB J:GLN118 4.8 33.8 1.0
CA J:THR124 5.0 36.2 1.0

Magnesium binding site 4 out of 8 in 5l5f

Go back to Magnesium Binding Sites List in 5l5f
Magnesium binding site 4 out of 8 in the Yeast 20S Proteasome with Human BETA5I (1-138) and Human BETA6 (97- 111; 118-133) in Complex with Bortezomib


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 Bortezomib within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg302

b:46.5
occ:1.00
 O K:ASP167 2.2 42.6 1.0
O W:ASP204 2.2 49.4 1.0
O K:ALA164 2.3 40.0 1.0
O K:SER170 2.4 43.1 1.0
C W:ASP204 3.1 49.8 1.0
C K:ASP167 3.3 42.5 1.0
C K:ALA164 3.5 40.3 1.0
NH1 K:ARG19 3.5 55.6 1.0
CA W:ASP204 3.6 49.2 1.0
C K:SER170 3.6 43.1 1.0
CA K:ALA168 3.8 45.4 1.0
CB W:ASP204 3.8 49.7 1.0
O K:ALA168 3.9 46.3 1.0
C K:ALA168 3.9 44.7 1.0
N K:ALA168 3.9 43.6 1.0
OXT W:ASP204 4.1 50.4 1.0
N K:SER170 4.1 42.0 1.0
CA K:ALA164 4.2 40.5 1.0
O K:HIS165 4.2 42.7 1.0
CZ K:ARG19 4.3 53.7 1.0
CA K:SER170 4.4 41.1 1.0
CA K:ASP167 4.5 41.3 1.0
C K:HIS165 4.5 41.4 1.0
N K:ASP167 4.5 42.5 1.0
N K:HIS165 4.5 40.8 1.0
N K:GLY171 4.6 44.7 1.0
N K:TYR169 4.6 43.8 1.0
NH2 K:ARG19 4.7 56.3 1.0
O K:ALA163 4.7 40.4 1.0
CA K:GLY171 4.7 45.9 1.0
CG W:ASP204 4.8 51.0 1.0
CA K:HIS165 4.8 41.3 1.0
CB K:SER170 4.8 39.3 1.0
C K:ARG166 4.9 42.4 1.0
CB K:ALA164 5.0 41.6 1.0

Magnesium binding site 5 out of 8 in 5l5f

Go back to Magnesium Binding Sites List in 5l5f
Magnesium binding site 5 out of 8 in the Yeast 20S Proteasome with Human BETA5I (1-138) and Human BETA6 (97- 111; 118-133) in Complex with Bortezomib


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 Bortezomib within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg301

b:49.7
occ:1.00
 OXT L:ASP222 2.1 63.9 1.0
O V:ASP166 2.2 37.6 1.0
O V:ILE163 2.2 42.5 1.0
O V:SER169 2.3 40.6 1.0
C L:ASP222 3.1 63.6 1.0
C V:ASP166 3.1 36.3 1.0
C V:ILE163 3.3 40.8 1.0
C V:SER169 3.4 39.0 1.0
CA L:ASP222 3.8 61.5 1.0
NH1 V:ARG19 3.8 44.6 1.0
CA V:LEU167 3.8 36.5 1.0
O V:GLY162 3.8 39.9 1.0
N V:LEU167 3.8 35.9 1.0
O L:ASP222 3.9 68.1 1.0
N V:ASP166 4.0 36.9 1.0
CA V:ILE163 4.1 40.1 1.0
CA V:ASP166 4.2 36.2 1.0
N V:SER169 4.2 36.3 1.0
C V:LEU167 4.3 37.5 1.0
N V:TRP164 4.3 41.8 1.0
CA V:SER169 4.3 37.3 1.0
C V:TRP164 4.3 41.3 1.0
CB L:ASP222 4.3 60.7 1.0
N V:GLY170 4.3 40.3 1.0
CA V:GLY170 4.4 41.9 1.0
O V:TRP164 4.4 42.5 1.0
O V:LEU167 4.5 38.9 1.0
CZ V:ARG19 4.5 42.9 1.0
CA V:TRP164 4.5 42.2 1.0
N V:ASN165 4.6 39.1 1.0
CB V:SER169 4.7 37.5 1.0
C V:GLY162 4.8 39.3 1.0
C V:ASN165 4.8 37.5 1.0
NH2 V:ARG19 4.8 44.3 1.0
N V:GLY168 4.9 37.2 1.0
N V:ILE163 5.0 39.8 1.0
CB V:ASP166 5.0 35.4 1.0
CD2 V:LEU167 5.0 35.8 1.0

Magnesium binding site 6 out of 8 in 5l5f

Go back to Magnesium Binding Sites List in 5l5f
Magnesium binding site 6 out of 8 in the Yeast 20S Proteasome with Human BETA5I (1-138) and Human BETA6 (97- 111; 118-133) in Complex with Bortezomib


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 Bortezomib within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg202

b:31.4
occ:1.00
 O N:ILE163 2.5 35.7 1.0
O N:SER169 2.5 33.1 1.0
O N:ASP166 2.6 34.3 1.0
CD1 a:LEU34 3.5 44.6 1.0
C N:ILE163 3.6 37.4 1.0
C N:ASP166 3.7 34.1 1.0
C N:SER169 3.7 33.4 1.0
NH1 N:ARG19 3.8 38.8 1.0
CG2 N:ILE163 4.0 36.7 1.0
CA N:GLY167 4.1 34.6 1.0
CA N:ILE163 4.3 36.1 1.0
N N:GLY167 4.3 33.6 1.0
O N:GLY167 4.4 35.7 1.0
C N:GLY167 4.4 34.8 1.0
CZ N:ARG19 4.5 37.5 1.0
CA N:GLY170 4.5 35.8 1.0
N N:GLY170 4.6 34.4 1.0
N N:SER169 4.6 33.8 1.0
N N:LYS164 4.7 39.1 1.0
CA N:SER169 4.7 32.8 1.0
N N:ASP166 4.7 33.6 1.0
O N:LYS164 4.8 40.2 1.0
CA N:ASP166 4.8 33.8 1.0
CG a:LEU34 4.8 43.7 1.0
CB N:ILE163 4.8 35.8 1.0
C N:LYS164 4.8 39.5 1.0
NH2 N:ARG19 4.8 37.9 1.0
CA N:LYS164 4.9 40.0 1.0

Magnesium binding site 7 out of 8 in 5l5f

Go back to Magnesium Binding Sites List in 5l5f
Magnesium binding site 7 out of 8 in the Yeast 20S Proteasome with Human BETA5I (1-138) and Human BETA6 (97- 111; 118-133) in Complex with Bortezomib


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 Bortezomib within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg301

b:51.5
occ:1.00
 O Z:HOH406 2.4 36.9 1.0
O Z:VAL198 2.5 51.2 1.0
O Z:HIS195 2.6 41.5 1.0
O Z:THR192 2.6 43.1 1.0
C Z:HIS195 3.6 45.2 1.0
C Z:THR192 3.6 52.6 1.0
C Z:VAL198 3.7 49.8 1.0
CA Z:ILE196 3.7 47.5 1.0
O Z:ILE196 3.8 48.8 1.0
NH2 Z:ARG28 3.8 54.4 1.0
CG2 Z:THR192 3.8 56.4 1.0
C Z:ILE196 3.9 47.3 1.0
CA Z:THR192 3.9 54.8 1.0
N Z:ILE196 4.1 44.7 1.0
O Z:ASP222 4.1 63.5 1.0
N Z:VAL198 4.2 47.6 1.0
NH2 H:ARG19 4.3 52.2 1.0
CA Z:VAL198 4.5 49.1 1.0
CB Z:THR192 4.5 55.4 1.0
OD1 Z:ASP222 4.6 56.5 1.0
N Z:GLY199 4.6 50.6 1.0
N Z:GLN197 4.7 46.4 1.0
CA Z:HIS195 4.8 47.7 1.0
N Z:HIS195 4.8 48.3 1.0
CA Z:GLY199 4.8 52.3 1.0
CZ Z:ARG28 4.8 54.1 1.0
CB Z:VAL198 4.8 49.2 1.0
N Z:GLU193 4.9 55.1 1.0
O Z:ALA191 5.0 51.8 1.0

Magnesium binding site 8 out of 8 in 5l5f

Go back to Magnesium Binding Sites List in 5l5f
Magnesium binding site 8 out of 8 in the Yeast 20S Proteasome with Human BETA5I (1-138) and Human BETA6 (97- 111; 118-133) in Complex with Bortezomib


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 with Human BETA5I (1-138) and Human BETA6 (97- 111; 118-133) in Complex with Bortezomib within 5.0Å range:
probe atom residue distance (Å) B Occ
b:Mg203

b:30.9
occ:1.00
 O b:SER169 2.5 35.4 1.0
O b:ILE163 2.6 36.8 1.0
O b:ASP166 2.6 35.4 1.0
O b:HOH309 3.1 39.4 1.0
CD1 M:LEU34 3.6 42.5 1.0
NH1 b:ARG19 3.7 41.5 1.0
C b:ASP166 3.7 33.8 1.0
C b:SER169 3.7 34.9 1.0
C b:ILE163 3.7 37.0 1.0
CA b:GLY167 4.1 34.9 1.0
CG2 b:ILE163 4.1 37.4 1.0
N b:GLY167 4.3 33.3 1.0
O b:GLY167 4.3 36.7 1.0
CZ b:ARG19 4.3 40.6 1.0
CA b:ILE163 4.4 36.1 1.0
C b:GLY167 4.4 35.9 1.0
CA b:GLY170 4.5 37.6 1.0
N b:GLY170 4.5 36.4 1.0
N b:SER169 4.6 34.6 1.0
CA b:SER169 4.6 33.8 1.0
NH2 b:ARG19 4.7 41.4 1.0
N b:ASP166 4.8 33.4 1.0
N b:LYS164 4.8 38.4 1.0
CG M:LEU34 4.8 42.4 1.0
CA b:ASP166 4.8 33.2 1.0
CB b:ILE163 4.8 36.6 1.0
O b:LYS164 4.8 40.1 1.0
C b:LYS164 4.9 39.5 1.0

Reference:

E.M.Huber, W.Heinemeyer, G.De Bruin, H.S.Overkleeft, M.Groll. A Humanized Yeast Proteasome Identifies Unique Binding Modes of Inhibitors For the Immunosubunit Beta 5I. Embo J. V. 35 2602 2016.
ISSN: ESSN 1460-2075
PubMed: 27789522
DOI: 10.15252/EMBJ.201695222
Page generated: Sun Sep 29 19:23:19 2024

Last articles

Cl in 5XNP
Cl in 5XPF
Cl in 5XS2
Cl in 5XRB
Cl in 5XR5
Cl in 5XQE
Cl in 5XQD
Cl in 5XPE
Cl in 5XNL
Cl in 5XP7
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy