Atomistry » Magnesium » PDB 5ktj-5l5t » 5l5d
Atomistry »
  Magnesium »
    PDB 5ktj-5l5t »
      5l5d »

Magnesium in PDB 5l5d: Yeast 20S Proteasome with Human BETA5I (1-138) and Human BETA6 (97- 111; 118-133) in Complex with Onx 0914

Enzymatic activity of Yeast 20S Proteasome with Human BETA5I (1-138) and Human BETA6 (97- 111; 118-133) in Complex with Onx 0914

All present enzymatic activity of Yeast 20S Proteasome with Human BETA5I (1-138) and Human BETA6 (97- 111; 118-133) in Complex with Onx 0914:
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 Onx 0914, PDB code: 5l5d 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 / 2.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 134.740, 300.720, 145.720, 90.00, 112.78, 90.00
R / Rfree (%) 19.2 / 22.1

Other elements in 5l5d:

The structure of Yeast 20S Proteasome with Human BETA5I (1-138) and Human BETA6 (97- 111; 118-133) in Complex with Onx 0914 also contains other interesting chemical elements:

Chlorine (Cl) 2 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 Onx 0914 (pdb code 5l5d). 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 Onx 0914, PDB code: 5l5d:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 5l5d

Go back to Magnesium Binding Sites List in 5l5d
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 Onx 0914


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 Onx 0914 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:54.0
occ:1.00
 O G:MET125 2.2 52.3 1.0
OG1 G:THR8 2.5 43.2 1.0
O G:ARG122 2.6 45.4 1.0
O G:TYR119 2.8 48.0 1.0
CG2 G:THR8 3.2 47.6 1.0
O G:ALA123 3.2 55.4 1.0
C G:MET125 3.4 49.9 1.0
CB G:THR8 3.4 46.2 1.0
C G:ALA123 3.6 51.3 1.0
C G:ARG122 3.7 47.1 1.0
CA G:ALA123 3.7 48.6 1.0
C G:TYR119 4.0 43.5 1.0
N G:THR8 4.1 47.9 1.0
N G:ALA123 4.2 47.4 1.0
N G:MET125 4.2 50.9 1.0
N G:ARG126 4.2 45.7 1.0
CA G:ARG126 4.2 44.9 1.0
CA G:MET125 4.3 52.6 1.0
CA G:THR8 4.3 46.7 1.0
CD G:PRO127 4.6 41.8 1.0
N G:TYR124 4.6 51.8 1.0
CA G:TYR119 4.7 41.2 1.0
C G:ARG126 4.9 44.2 1.0
CB G:MET125 4.9 58.9 1.0
N G:THR120 5.0 42.3 1.0
C G:TYR124 5.0 49.9 1.0
CA G:ARG122 5.0 50.0 1.0

Magnesium binding site 2 out of 8 in 5l5d

Go back to Magnesium Binding Sites List in 5l5d
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 Onx 0914


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 Onx 0914 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:56.4
occ:1.00
 O I:ASP177 2.6 49.9 1.0
O I:SER180 2.6 51.1 1.0
O I:ALA174 3.2 51.3 1.0
OXT I:ASP204 3.3 64.6 1.0
C I:ASP177 3.7 49.5 1.0
C I:SER180 3.9 53.3 1.0
O I:ALA178 4.1 53.7 1.0
CD1 Y:ILE26 4.2 56.0 1.0
CA I:ALA178 4.2 49.5 1.0
C I:ASP204 4.2 64.5 1.0
C I:ALA178 4.3 50.4 1.0
O I:ASP204 4.3 64.8 1.0
C I:ALA174 4.3 54.5 1.0
NH1 Y:ARG19 4.3 74.2 1.0
N I:ALA178 4.4 49.6 1.0
N I:SER180 4.5 47.9 1.0
NH2 Y:ARG19 4.6 67.6 1.0
CA I:ASP175 4.7 55.2 1.0
CA I:GLY181 4.7 54.1 1.0
N I:GLY181 4.8 52.9 1.0
N I:ASP177 4.8 48.9 1.0
CA I:SER180 4.8 50.4 1.0
CZ Y:ARG19 4.8 69.3 1.0
CA I:ASP177 4.8 49.6 1.0
N I:ASP175 4.9 53.8 1.0

Magnesium binding site 3 out of 8 in 5l5d

Go back to Magnesium Binding Sites List in 5l5d
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 Onx 0914


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 Onx 0914 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg302

b:55.0
occ:1.00
 O I:ASP204 2.2 64.8 1.0
O Y:ASP167 2.2 54.7 1.0
O Y:ALA164 2.3 49.6 1.0
O Y:SER170 2.3 62.0 1.0
C I:ASP204 3.1 64.5 1.0
C Y:ASP167 3.4 53.5 1.0
NH1 Y:ARG19 3.4 74.2 1.0
C Y:ALA164 3.4 50.1 1.0
C Y:SER170 3.5 55.9 1.0
CA I:ASP204 3.6 64.0 1.0
CB I:ASP204 3.7 65.2 1.0
O Y:ALA168 3.7 57.0 1.0
CA Y:ALA168 3.8 56.9 1.0
C Y:ALA168 3.8 57.3 1.0
N Y:ALA168 4.0 55.4 1.0
N Y:SER170 4.1 51.5 1.0
CA Y:ALA164 4.1 50.5 1.0
O Y:HIS165 4.1 47.5 1.0
OXT I:ASP204 4.2 64.6 1.0
CZ Y:ARG19 4.2 69.3 1.0
CA Y:SER170 4.4 52.5 1.0
N Y:GLY171 4.5 56.1 1.0
C Y:HIS165 4.5 47.7 1.0
N Y:HIS165 4.5 52.5 1.0
CA Y:ASP167 4.5 51.7 1.0
NH2 Y:ARG19 4.6 67.6 1.0
CA Y:GLY171 4.6 57.6 1.0
N Y:TYR169 4.6 55.9 1.0
N Y:ASP167 4.6 50.5 1.0
CG I:ASP204 4.7 66.1 1.0
O Y:ALA163 4.7 49.4 1.0
CA Y:HIS165 4.8 49.6 1.0
CB Y:SER170 4.9 49.3 1.0
CB Y:ALA164 4.9 50.6 1.0

Magnesium binding site 4 out of 8 in 5l5d

Go back to Magnesium Binding Sites List in 5l5d
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 Onx 0914


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 Onx 0914 within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mg201

b:46.3
occ:1.00
 OE1 J:GLN118 3.1 47.0 1.0
O J:THR124 3.5 45.0 1.0
CB J:ASP120 3.7 41.7 1.0
OD2 J:ASP120 3.7 52.2 1.0
CG J:ASP120 3.8 45.5 1.0
N J:ASP120 3.9 39.8 1.0
CD J:GLN118 4.0 43.8 1.0
CE1 J:HIS133 4.2 41.3 1.0
CG J:GLN118 4.2 42.0 1.0
CB J:THR124 4.2 44.0 1.0
CG2 J:THR124 4.4 43.3 1.0
O J:GLN118 4.4 39.3 1.0
CA J:ASP120 4.4 39.8 1.0
C J:THR124 4.5 42.0 1.0
OD1 J:ASP120 4.6 50.2 1.0
C J:ILE119 4.6 38.8 1.0
C J:GLN118 4.8 38.8 1.0
CG1 I:VAL35 4.8 53.8 1.0
CA J:ILE119 4.8 37.7 1.0
ND1 J:HIS133 4.8 40.3 1.0
N J:ILE119 5.0 38.2 1.0

Magnesium binding site 5 out of 8 in 5l5d

Go back to Magnesium Binding Sites List in 5l5d
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 Onx 0914


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 Onx 0914 within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg302

b:52.7
occ:1.00
 O K:ASP167 2.0 56.1 1.0
O W:ASP204 2.3 63.6 1.0
O K:ALA164 2.3 48.7 1.0
O K:SER170 2.4 52.0 1.0
C K:ASP167 3.2 53.2 1.0
C W:ASP204 3.2 61.2 1.0
NH1 K:ARG19 3.5 71.5 1.0
C K:ALA164 3.5 48.1 1.0
C K:SER170 3.6 51.3 1.0
O K:ALA168 3.6 50.9 1.0
CA K:ALA168 3.6 57.4 1.0
CA W:ASP204 3.7 60.6 1.0
C K:ALA168 3.7 57.1 1.0
CB W:ASP204 3.8 59.9 1.0
N K:ALA168 3.8 54.2 1.0
N K:SER170 4.0 52.2 1.0
O K:HIS165 4.1 47.8 1.0
CA K:ALA164 4.2 49.6 1.0
OXT W:ASP204 4.2 65.5 1.0
CZ K:ARG19 4.3 68.3 1.0
CA K:SER170 4.4 50.4 1.0
CA K:ASP167 4.4 51.4 1.0
C K:HIS165 4.5 48.8 1.0
N K:ASP167 4.5 50.5 1.0
N K:TYR169 4.5 58.1 1.0
N K:HIS165 4.5 49.7 1.0
N K:GLY171 4.6 51.1 1.0
O K:ALA163 4.7 50.0 1.0
CA K:GLY171 4.8 55.5 1.0
NH2 K:ARG19 4.8 69.8 1.0
CA K:HIS165 4.8 51.2 1.0
C K:ARG166 4.9 51.9 1.0
CB K:SER170 4.9 48.1 1.0
CG W:ASP204 4.9 58.2 1.0
CB K:ASP167 5.0 51.0 1.0

Magnesium binding site 6 out of 8 in 5l5d

Go back to Magnesium Binding Sites List in 5l5d
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 Onx 0914


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 Onx 0914 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg301

b:69.0
occ:1.00
 OXT L:ASP222 2.1 74.0 1.0
O V:ASP166 2.3 44.5 1.0
O V:ILE163 2.3 53.1 1.0
C L:ASP222 2.9 74.3 1.0
C V:ASP166 3.1 45.4 1.0
O V:SER169 3.1 51.4 1.0
C V:ILE163 3.4 50.8 1.0
O V:TRP164 3.6 54.9 1.0
CA L:ASP222 3.6 72.4 1.0
O L:ASP222 3.6 79.5 1.0
N V:LEU167 3.7 45.9 1.0
C V:TRP164 3.7 50.5 1.0
N V:ASP166 3.7 43.2 1.0
CA V:LEU167 3.8 46.2 1.0
CA V:ASP166 4.0 43.9 1.0
O V:GLY162 4.1 51.3 1.0
CA V:TRP164 4.2 51.5 1.0
N V:TRP164 4.2 52.5 1.0
N V:ASN165 4.2 47.6 1.0
C V:SER169 4.3 48.9 1.0
C V:ASN165 4.4 43.3 1.0
CB L:ASP222 4.4 69.8 1.0
NH1 V:ARG19 4.4 59.1 1.0
CA V:ILE163 4.4 49.3 1.0
O L:ARG221 4.5 73.7 1.0
CD2 V:LEU167 4.5 44.1 1.0
C V:LEU167 4.5 47.2 1.0
CA V:ASN165 4.8 45.4 1.0
N L:ASP222 4.8 65.5 1.0
O V:LEU167 4.8 50.8 1.0
N V:SER169 4.9 44.7 1.0
CB V:LEU167 5.0 44.4 1.0
CD1 L:ILE35 5.0 58.4 1.0
CB V:ASP166 5.0 43.9 1.0

Magnesium binding site 7 out of 8 in 5l5d

Go back to Magnesium Binding Sites List in 5l5d
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 Onx 0914


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 Onx 0914 within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg202

b:52.5
occ:1.00
 O N:SER169 2.5 44.2 1.0
O N:ILE163 2.7 44.0 1.0
O N:ASP166 2.8 44.3 1.0
NH1 N:ARG19 3.5 46.2 1.0
C N:SER169 3.7 41.7 1.0
CD1 a:LEU34 3.7 57.4 1.0
C N:ILE163 3.8 44.0 1.0
C N:ASP166 3.9 43.6 1.0
CG2 N:ILE163 4.0 44.4 1.0
CA N:GLY167 4.1 45.7 1.0
CZ N:ARG19 4.1 44.7 1.0
O N:GLY167 4.3 45.6 1.0
CA N:GLY170 4.3 44.5 1.0
NH2 N:ARG19 4.4 44.6 1.0
CA N:ILE163 4.4 44.4 1.0
N N:GLY167 4.4 44.4 1.0
C N:GLY167 4.4 45.8 1.0
N N:GLY170 4.5 41.6 1.0
N N:SER169 4.7 42.2 1.0
CA N:SER169 4.8 40.8 1.0
CB N:ILE163 4.8 43.9 1.0
N N:LYS164 4.9 46.6 1.0
CG a:LEU34 4.9 56.6 1.0
NE N:ARG19 5.0 46.0 1.0

Magnesium binding site 8 out of 8 in 5l5d

Go back to Magnesium Binding Sites List in 5l5d
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 Onx 0914


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 Onx 0914 within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg301

b:72.6
occ:1.00
 O Z:VAL198 2.6 54.3 1.0
O Z:THR192 2.8 61.2 1.0
O Z:HIS195 3.0 54.9 1.0
O Z:ASP222 3.6 76.7 1.0
NH2 Z:ARG28 3.7 63.6 1.0
CG2 Z:THR192 3.8 68.7 1.0
C Z:VAL198 3.8 61.1 1.0
O Z:ILE196 3.9 65.9 1.0
C Z:THR192 3.9 64.3 1.0
CA Z:ILE196 3.9 58.0 1.0
C Z:HIS195 4.0 57.6 1.0
C Z:ILE196 4.0 58.7 1.0
NH2 H:ARG19 4.1 70.5 1.0
OD1 Z:ASP222 4.2 76.4 1.0
CA Z:THR192 4.3 65.3 1.0
N Z:ILE196 4.4 56.2 1.0
N Z:VAL198 4.5 57.2 1.0
C Z:ASP222 4.5 75.2 1.0
CB Z:THR192 4.7 66.1 1.0
CZ Z:ARG28 4.7 63.1 1.0
CA Z:VAL198 4.7 58.6 1.0
N Z:GLY199 4.8 62.2 1.0
CA Z:GLY199 4.8 61.9 1.0
NH1 H:ARG19 4.8 60.7 1.0
CZ H:ARG19 4.8 61.8 1.0
OXT Z:ASP222 4.9 65.7 1.0
N Z:GLN197 4.9 56.9 1.0
NH1 Z:ARG28 4.9 64.4 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 19:21:09 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy