Atomistry » Magnesium » PDB 5lcf-5lmm » 5lf0
Atomistry »
  Magnesium »
    PDB 5lcf-5lmm »
      5lf0 »

Magnesium in PDB 5lf0: Human 20S Proteasome Complex with Epoxomicin at 2.4 Angstrom

Enzymatic activity of Human 20S Proteasome Complex with Epoxomicin at 2.4 Angstrom

All present enzymatic activity of Human 20S Proteasome Complex with Epoxomicin at 2.4 Angstrom:
3.4.25.1;

Protein crystallography data

The structure of Human 20S Proteasome Complex with Epoxomicin at 2.4 Angstrom, PDB code: 5lf0 was solved by J.Schrader, F.Henneberg, R.Mata, K.Tittmann, T.R.Schneider, H.Stark, G.Bourenkov, A.Chari, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 170.23 / 2.41
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 113.070, 202.370, 314.790, 90.00, 90.00, 90.00
R / Rfree (%) 17.9 / 22.9

Other elements in 5lf0:

The structure of Human 20S Proteasome Complex with Epoxomicin at 2.4 Angstrom also contains other interesting chemical elements:

Potassium (K) 6 atoms
Chlorine (Cl) 58 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Human 20S Proteasome Complex with Epoxomicin at 2.4 Angstrom (pdb code 5lf0). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 10 binding sites of Magnesium where determined in the Human 20S Proteasome Complex with Epoxomicin at 2.4 Angstrom, PDB code: 5lf0:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 10 in 5lf0

Go back to Magnesium Binding Sites List in 5lf0
Magnesium binding site 1 out of 10 in the Human 20S Proteasome Complex with Epoxomicin at 2.4 Angstrom


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Human 20S Proteasome Complex with Epoxomicin at 2.4 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg301

b:64.7
occ:1.00
 O H:HOH515 1.9 68.8 1.0
O N:HOH492 2.3 52.6 1.0
O N:HOH410 2.4 42.5 1.0
O N:HOH411 2.5 44.0 1.0
OE1 H:GLN91 2.5 71.0 1.0
O N:HOH470 2.5 48.9 1.0
CD H:GLN91 3.6 65.2 1.0
O N:ASP93 3.7 48.8 1.0
OD2 N:ASP51 3.8 43.5 1.0
NE2 H:GLN91 3.9 63.3 1.0
OD1 N:ASP51 4.1 45.6 1.0
O H:HOH486 4.2 63.2 1.0
O H:HOH412 4.3 38.1 1.0
CG N:ASP51 4.4 43.5 1.0
O N:HOH418 4.6 39.5 1.0
ND1 H:HIS116 4.8 40.0 1.0
C N:ASP93 4.8 45.7 1.0
CG H:GLN91 4.9 59.3 1.0

Magnesium binding site 2 out of 10 in 5lf0

Go back to Magnesium Binding Sites List in 5lf0
Magnesium binding site 2 out of 10 in the Human 20S Proteasome Complex with Epoxomicin at 2.4 Angstrom


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Human 20S Proteasome Complex with Epoxomicin at 2.4 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg302

b:63.5
occ:1.00
 O H:ILE163 2.3 51.0 1.0
O H:ASP166 2.3 47.0 1.0
O Z:ASP213 2.3 61.5 1.0
O H:SER169 2.3 52.0 1.0
O H:HOH478 2.6 62.4 1.0
C Z:ASP213 3.2 60.7 1.0
C H:ASP166 3.3 46.7 1.0
C H:ILE163 3.4 51.1 1.0
C H:SER169 3.5 48.2 1.0
CA Z:ASP213 3.7 59.6 1.0
CA H:LEU167 3.9 47.0 1.0
CB Z:ASP213 4.0 58.9 1.0
N H:LEU167 4.0 46.5 1.0
NH1 H:ARG19 4.0 51.3 1.0
OXT Z:ASP213 4.1 60.4 1.0
N H:SER169 4.1 47.2 1.0
C H:LEU167 4.2 46.6 1.0
CA H:ILE163 4.2 50.3 1.0
N H:ASP166 4.3 46.4 1.0
CA H:SER169 4.3 47.4 1.0
N H:PHE164 4.3 51.8 1.0
O H:LEU167 4.4 47.0 1.0
O H:GLY162 4.4 47.5 1.0
N H:GLY170 4.4 48.8 1.0
CA H:ASP166 4.4 46.6 1.0
CZ H:ARG19 4.4 51.3 1.0
CA H:GLY170 4.5 49.7 1.0
CA H:PHE164 4.5 52.5 1.0
O Z:HOH464 4.5 60.2 1.0
NH2 H:ARG19 4.5 53.0 1.0
C H:PHE164 4.6 51.4 1.0
CB H:SER169 4.7 47.8 1.0
O H:PHE164 4.7 54.1 1.0
N H:GLY168 4.9 46.9 1.0
CG Z:ASP213 5.0 58.1 1.0
N H:ASN165 5.0 49.3 1.0

Magnesium binding site 3 out of 10 in 5lf0

Go back to Magnesium Binding Sites List in 5lf0
Magnesium binding site 3 out of 10 in the Human 20S Proteasome Complex with Epoxomicin at 2.4 Angstrom


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Human 20S Proteasome Complex with Epoxomicin at 2.4 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:60.3
occ:1.00
 O I:SER180 2.3 49.5 1.0
O I:HOH477 2.3 59.0 1.0
O I:ASP177 2.3 47.9 1.0
O I:VAL174 2.3 46.5 1.0
O I:HOH414 2.5 44.4 1.0
C I:ASP177 3.4 48.4 1.0
C I:VAL174 3.4 47.7 1.0
C I:SER180 3.5 47.9 1.0
O I:HOH465 3.5 62.3 1.0
O I:HOH422 3.7 45.5 1.0
O I:HOH438 3.9 44.6 1.0
N I:ASP177 4.1 50.4 1.0
CA I:ASP175 4.2 52.8 1.0
N I:ASP175 4.2 49.9 1.0
N I:SER180 4.2 47.3 1.0
CD1 Y:ILE26 4.3 50.2 1.0
O I:ALA178 4.3 47.8 1.0
CA I:ASP177 4.3 49.7 1.0
N I:ALA178 4.3 47.9 1.0
C I:ALA178 4.3 48.2 1.0
OXT I:ASP204 4.4 56.6 1.0
N I:GLY181 4.4 48.2 1.0
CA I:SER180 4.4 47.8 1.0
CA I:GLY181 4.4 48.7 1.0
CA I:VAL174 4.4 46.4 1.0
CA I:ALA178 4.4 49.0 1.0
CB I:VAL174 4.5 45.5 1.0
C I:ASP175 4.5 51.5 1.0
CB I:ASP177 4.7 51.1 1.0
OD2 I:ASP175 4.8 53.6 1.0
O I:ASP175 4.8 52.7 1.0
CG2 I:VAL174 4.9 45.6 1.0
CB I:SER180 4.9 48.3 1.0
N I:VAL179 4.9 47.1 1.0

Magnesium binding site 4 out of 10 in 5lf0

Go back to Magnesium Binding Sites List in 5lf0
Magnesium binding site 4 out of 10 in the Human 20S Proteasome Complex with Epoxomicin at 2.4 Angstrom


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Human 20S Proteasome Complex with Epoxomicin at 2.4 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg304

b:47.9
occ:1.00
 O I:ASP204 2.2 57.0 1.0
O Y:THR164 2.3 45.0 1.0
O Y:ASP167 2.3 42.4 1.0
O Y:SER170 2.3 46.9 1.0
O Y:HOH442 2.8 47.8 1.0
C I:ASP204 3.1 55.9 1.0
C Y:ASP167 3.3 43.2 1.0
C Y:THR164 3.4 45.4 1.0
C Y:SER170 3.5 45.0 1.0
CA I:ASP204 3.6 54.2 1.0
NH1 Y:ARG19 3.7 45.4 1.0
CA Y:ALA168 3.7 44.0 1.0
C Y:ALA168 3.8 43.9 1.0
O Y:ALA168 3.8 44.0 1.0
N Y:ALA168 3.9 43.0 1.0
CA Y:THR164 3.9 45.4 1.0
N Y:SER170 3.9 41.4 1.0
CB I:ASP204 4.0 54.9 1.0
OXT I:ASP204 4.1 56.6 1.0
CA Y:SER170 4.2 43.4 1.0
CA Y:ASP167 4.4 43.6 1.0
N Y:ASP167 4.4 44.6 1.0
N Y:TYR169 4.5 42.7 1.0
O I:HOH495 4.5 52.0 1.0
CB Y:THR164 4.5 46.1 1.0
N Y:TYR165 4.5 45.2 1.0
CZ Y:ARG19 4.5 45.2 1.0
N Y:GLY171 4.6 45.0 1.0
O Y:TYR165 4.7 45.0 1.0
CA Y:GLY171 4.7 45.6 1.0
O Y:ALA163 4.8 48.9 1.0
CB Y:SER170 4.8 43.3 1.0
C Y:TYR165 4.8 45.7 1.0
CA Y:TYR165 4.9 47.2 1.0
NH2 Y:ARG19 4.9 46.3 1.0

Magnesium binding site 5 out of 10 in 5lf0

Go back to Magnesium Binding Sites List in 5lf0
Magnesium binding site 5 out of 10 in the Human 20S Proteasome Complex with Epoxomicin at 2.4 Angstrom


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Human 20S Proteasome Complex with Epoxomicin at 2.4 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mg301

b:66.0
occ:1.00
 O J:HOH495 1.9 56.0 1.0
O K:HOH483 2.0 49.9 1.0
O J:HOH406 2.2 54.0 1.0
O J:HOH453 2.2 48.8 1.0
O J:HOH516 2.3 67.8 1.0
O J:HOH445 2.4 56.0 1.0
O J:PRO97 4.1 51.0 1.0
O K:HOH454 4.1 50.4 1.0
O K:HOH438 4.1 41.6 1.0
O J:HOH436 4.2 62.6 1.0
OD1 J:ASP52 4.4 49.8 1.0
OD2 J:ASP52 4.4 47.4 1.0
O J:HOH513 4.5 64.2 1.0
OE2 J:GLU49 4.6 61.1 1.0
CE1 J:HIS99 4.6 43.0 0.5
O K:HOH411 4.7 62.0 1.0
ND1 J:HIS99 4.8 42.6 0.5
CD J:PRO97 4.8 49.2 1.0
CE K:LYS91 4.9 59.3 1.0
CG J:ASP52 4.9 47.8 1.0

Magnesium binding site 6 out of 10 in 5lf0

Go back to Magnesium Binding Sites List in 5lf0
Magnesium binding site 6 out of 10 in the Human 20S Proteasome Complex with Epoxomicin at 2.4 Angstrom


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Human 20S Proteasome Complex with Epoxomicin at 2.4 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg301

b:52.2
occ:1.00
 O K:ASP167 2.1 55.2 1.0
O W:ASP204 2.2 65.0 1.0
O K:THR164 2.3 55.2 1.0
O K:SER170 2.4 57.0 1.0
O K:HOH466 2.8 50.5 1.0
C K:ASP167 3.1 54.0 1.0
C W:ASP204 3.2 66.5 1.0
C K:THR164 3.3 55.3 1.0
C K:SER170 3.6 56.8 1.0
CA K:ALA168 3.6 53.5 1.0
CA W:ASP204 3.7 66.8 1.0
C K:ALA168 3.7 53.1 1.0
N K:ALA168 3.7 53.1 1.0
O K:ALA168 3.8 52.8 1.0
NH1 K:ARG19 3.9 60.3 1.0
CA K:THR164 3.9 55.0 1.0
N K:SER170 3.9 53.7 1.0
CB W:ASP204 4.1 66.7 1.0
OXT W:ASP204 4.1 67.3 1.0
CA K:ASP167 4.2 53.9 1.0
N K:ASP167 4.2 54.8 1.0
CA K:SER170 4.3 54.4 1.0
N K:TYR169 4.4 52.9 1.0
N K:TYR165 4.5 56.4 1.0
O K:TYR165 4.5 57.4 1.0
CB K:THR164 4.6 56.6 1.0
C K:TYR165 4.6 57.4 1.0
N K:GLY171 4.7 57.5 1.0
O K:ALA163 4.7 53.4 1.0
CZ K:ARG19 4.7 59.5 1.0
CB K:SER170 4.8 53.8 1.0
CA K:TYR165 4.8 58.6 1.0
CB K:ASP167 4.9 54.5 1.0
CA K:GLY171 4.9 59.2 1.0
C K:ARG166 4.9 55.0 1.0
O W:HOH423 4.9 52.1 1.0

Magnesium binding site 7 out of 10 in 5lf0

Go back to Magnesium Binding Sites List in 5lf0
Magnesium binding site 7 out of 10 in the Human 20S Proteasome Complex with Epoxomicin at 2.4 Angstrom


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Human 20S Proteasome Complex with Epoxomicin at 2.4 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg303

b:55.0
occ:1.00
 O L:ASP213 2.2 71.5 1.0
O V:SER169 2.3 60.0 1.0
O V:ASP166 2.3 54.2 1.0
O V:ILE163 2.4 58.9 1.0
O V:HOH466 2.7 58.3 1.0
C L:ASP213 3.1 69.6 1.0
C V:ASP166 3.4 53.8 1.0
C V:SER169 3.5 58.1 1.0
C V:ILE163 3.6 58.4 1.0
CA L:ASP213 3.7 69.2 1.0
CA V:LEU167 3.8 52.4 1.0
NH1 V:ARG19 3.8 60.5 1.0
N V:LEU167 4.0 52.1 1.0
OXT L:ASP213 4.0 69.1 1.0
CB L:ASP213 4.0 68.8 1.0
C V:LEU167 4.1 51.9 1.0
O L:HOH433 4.1 49.5 1.0
N V:SER169 4.1 56.4 1.0
O V:LEU167 4.2 50.4 1.0
CZ V:ARG19 4.3 61.4 1.0
CA V:SER169 4.3 56.8 1.0
N V:ASP166 4.4 56.2 1.0
N V:GLY170 4.4 59.8 1.0
NH2 V:ARG19 4.4 63.5 1.0
CA V:ILE163 4.4 58.5 1.0
CA V:GLY170 4.5 62.0 1.0
CA V:ASP166 4.5 54.9 1.0
N V:PHE164 4.5 58.5 1.0
O V:GLY162 4.5 56.5 1.0
CA V:PHE164 4.7 60.4 1.0
C V:PHE164 4.7 59.3 1.0
CB V:SER169 4.7 56.8 1.0
O V:PHE164 4.8 59.3 1.0
N V:GLY168 4.8 52.4 1.0
CG L:ASP213 4.9 68.4 1.0

Magnesium binding site 8 out of 10 in 5lf0

Go back to Magnesium Binding Sites List in 5lf0
Magnesium binding site 8 out of 10 in the Human 20S Proteasome Complex with Epoxomicin at 2.4 Angstrom


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Human 20S Proteasome Complex with Epoxomicin at 2.4 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Mg301

b:72.1
occ:1.00
 O V:HOH446 2.0 68.1 1.0
O V:HOH458 2.3 72.7 1.0
O b:HOH405 2.4 49.8 1.0
O b:HOH478 2.5 68.6 1.0
O b:HOH445 2.5 59.4 1.0
OE1 V:GLN91 2.6 68.0 1.0
O b:ASP93 3.7 58.3 1.0
CD V:GLN91 3.7 64.7 1.0
OD2 b:ASP51 4.0 47.3 1.0
O V:HOH486 4.0 71.7 1.0
OD1 b:ASP51 4.1 48.6 1.0
NE2 V:GLN91 4.1 65.5 1.0
CG b:ASP51 4.5 47.4 1.0
O V:HOH427 4.6 51.0 1.0
O b:HOH461 4.6 44.7 1.0
C b:ASP93 4.6 57.6 1.0
ND1 V:HIS116 4.9 52.2 1.0

Magnesium binding site 9 out of 10 in 5lf0

Go back to Magnesium Binding Sites List in 5lf0
Magnesium binding site 9 out of 10 in the Human 20S Proteasome Complex with Epoxomicin at 2.4 Angstrom


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Human 20S Proteasome Complex with Epoxomicin at 2.4 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
W:Mg301

b:56.2
occ:1.00
 O W:HOH440 2.0 42.5 1.0
O W:ASP177 2.2 56.9 1.0
O W:SER180 2.2 60.8 1.0
O W:VAL174 2.3 54.4 1.0
O W:HOH459 2.4 45.7 1.0
C W:ASP177 3.3 55.4 1.0
C W:VAL174 3.4 55.8 1.0
C W:SER180 3.5 57.8 1.0
O W:HOH404 3.7 59.4 1.0
N W:ASP177 4.0 56.3 1.0
CA W:ASP175 4.1 56.8 1.0
N W:ASP175 4.2 56.6 1.0
N W:SER180 4.2 55.7 1.0
CA W:ASP177 4.2 56.4 1.0
O W:HOH427 4.2 55.2 1.0
CD1 K:ILE26 4.2 58.1 1.0
N W:ALA178 4.3 55.0 1.0
O W:ALA178 4.3 57.2 1.0
C W:ALA178 4.3 55.9 1.0
N W:GLY181 4.4 57.9 1.0
CA W:SER180 4.4 55.9 1.0
CA W:VAL174 4.4 56.2 1.0
CA W:ALA178 4.4 55.5 1.0
CA W:GLY181 4.4 58.8 1.0
CB W:VAL174 4.5 56.0 1.0
C W:ASP175 4.5 55.0 1.0
OXT W:ASP204 4.5 67.3 1.0
CB W:ASP177 4.6 58.4 1.0
O W:ASP175 4.8 55.4 1.0
CB W:SER180 4.8 56.1 1.0
CG2 W:VAL174 4.8 57.4 1.0
OD2 W:ASP175 4.8 61.4 1.0
N W:VAL179 4.9 55.4 1.0
N W:ARG176 4.9 53.8 1.0

Magnesium binding site 10 out of 10 in 5lf0

Go back to Magnesium Binding Sites List in 5lf0
Magnesium binding site 10 out of 10 in the Human 20S Proteasome Complex with Epoxomicin at 2.4 Angstrom


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Human 20S Proteasome Complex with Epoxomicin at 2.4 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Mg301

b:54.6
occ:1.00
 O X:HOH441 2.0 58.6 1.0
O X:HOH432 2.0 53.1 1.0
O Y:HOH508 2.2 69.7 1.0
O X:HOH480 2.3 52.8 1.0
O X:HOH402 2.3 56.9 1.0
O X:HOH505 2.3 68.5 1.0
O X:HOH464 4.1 64.6 1.0
O Y:HOH493 4.1 63.2 1.0
O X:PRO97 4.2 52.3 1.0
O Y:HOH465 4.2 48.1 1.0
OD1 X:ASP52 4.3 47.2 1.0
CE1 X:HIS99 4.3 40.6 0.5
OD2 X:ASP52 4.3 46.0 1.0
OE2 X:GLU49 4.4 58.9 1.0
CE Y:LYS91 4.6 60.2 1.0
ND1 X:HIS99 4.7 40.6 0.5
CG X:ASP52 4.8 46.3 1.0
CB Y:LYS91 4.9 58.9 1.0

Reference:

J.Schrader, F.Henneberg, R.A.Mata, K.Tittmann, T.R.Schneider, H.Stark, G.Bourenkov, A.Chari. The Inhibition Mechanism of Human 20S Proteasomes Enables Next-Generation Inhibitor Design. Science V. 353 594 2016.
ISSN: ESSN 1095-9203
PubMed: 27493187
DOI: 10.1126/SCIENCE.AAF8993
Page generated: Sun Sep 29 20:05:27 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy