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Magnesium in PDB 5lf4: Human 20S Proteasome Complex with Delanzomib at 2.0 Angstrom

Enzymatic activity of Human 20S Proteasome Complex with Delanzomib at 2.0 Angstrom

All present enzymatic activity of Human 20S Proteasome Complex with Delanzomib at 2.0 Angstrom:
3.4.25.1;

Protein crystallography data

The structure of Human 20S Proteasome Complex with Delanzomib at 2.0 Angstrom, PDB code: 5lf4 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) 170.38 / 1.99
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 113.450, 202.760, 314.300, 90.00, 90.00, 90.00
R / Rfree (%) 18.1 / 21.6

Other elements in 5lf4:

The structure of Human 20S Proteasome Complex with Delanzomib at 2.0 Angstrom also contains other interesting chemical elements:

Potassium (K) 8 atoms
Chlorine (Cl) 52 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Human 20S Proteasome Complex with Delanzomib at 2.0 Angstrom (pdb code 5lf4). 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 Delanzomib at 2.0 Angstrom, PDB code: 5lf4:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 10 in 5lf4

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Magnesium binding site 1 out of 10 in the Human 20S Proteasome Complex with Delanzomib at 2.0 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 Delanzomib at 2.0 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg301

b:71.7
occ:1.00
 O H:HOH543 1.9 58.6 1.0
OE1 H:GLN91 2.2 54.6 1.0
O N:HOH412 2.3 36.6 1.0
O N:HOH475 2.7 35.4 1.0
O H:HOH540 2.9 78.0 1.0
O N:HOH416 2.9 46.2 1.0
CD H:GLN91 3.3 42.1 1.0
O N:ASP94 3.7 34.6 1.0
NE2 H:GLN91 3.7 38.0 1.0
OD2 N:ASP52 3.8 25.0 1.0
O H:HOH489 3.9 56.5 1.0
O H:HOH416 4.1 31.8 1.0
OD1 N:ASP52 4.4 25.0 1.0
CG N:ASP52 4.5 23.8 1.0
CG H:GLN91 4.6 37.4 1.0
C N:ASP94 4.7 30.2 1.0
ND1 H:HIS116 4.8 25.7 1.0
CB H:GLN91 5.0 33.0 1.0

Magnesium binding site 2 out of 10 in 5lf4

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Magnesium binding site 2 out of 10 in the Human 20S Proteasome Complex with Delanzomib at 2.0 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 Delanzomib at 2.0 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg302

b:32.6
occ:1.00
 O H:ILE163 2.2 38.4 1.0
O H:ASP166 2.2 35.6 1.0
O Z:ASP213 2.2 48.0 1.0
O H:SER169 2.2 39.5 1.0
O H:HOH486 2.7 42.3 1.0
C Z:ASP213 3.2 45.8 1.0
C H:SER169 3.3 35.2 1.0
C H:ILE163 3.3 35.2 1.0
C H:ASP166 3.3 32.1 1.0
CA Z:ASP213 3.7 44.8 1.0
NH1 H:ARG19 3.9 30.7 1.0
N H:SER169 4.0 32.9 1.0
CB Z:ASP213 4.0 45.6 1.0
CA H:LEU167 4.0 31.9 1.0
CA H:SER169 4.1 34.0 1.0
N H:LEU167 4.1 31.6 1.0
CA H:ILE163 4.1 33.6 1.0
O H:GLY162 4.2 31.4 1.0
OXT Z:ASP213 4.2 46.5 1.0
N H:GLY170 4.2 35.2 1.0
N H:ASP166 4.2 31.5 1.0
C H:LEU167 4.3 31.4 1.0
CA H:GLY170 4.3 35.6 1.0
N H:PHE164 4.3 36.0 1.0
CZ H:ARG19 4.4 31.1 1.0
CA H:ASP166 4.4 31.4 1.0
O H:LEU167 4.4 31.3 1.0
CB H:SER169 4.5 33.9 1.0
CA H:PHE164 4.6 36.9 1.0
C H:PHE164 4.6 35.5 1.0
NH2 H:ARG19 4.6 30.7 1.0
O Z:HOH473 4.7 44.2 1.0
O H:PHE164 4.8 35.8 1.0
N H:GLY168 4.9 31.3 1.0
N H:ASN165 4.9 34.3 1.0
CG2 H:ILE163 5.0 34.6 1.0

Magnesium binding site 3 out of 10 in 5lf4

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Magnesium binding site 3 out of 10 in the Human 20S Proteasome Complex with Delanzomib at 2.0 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 Delanzomib at 2.0 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:33.1
occ:1.00
 O I:VAL174 2.2 33.4 1.0
O I:ASP177 2.2 34.7 1.0
O I:SER180 2.2 36.7 1.0
O I:HOH453 2.2 35.6 1.0
O I:HOH415 2.6 32.8 1.0
C I:VAL174 3.3 30.9 1.0
C I:ASP177 3.3 30.5 1.0
C I:SER180 3.4 34.2 1.0
O I:HOH505 3.8 57.4 1.0
O I:HOH422 4.0 41.2 1.0
N I:ASP177 4.1 30.5 1.0
O I:HOH448 4.1 39.1 1.0
N I:SER180 4.2 32.4 1.0
CA I:ASP177 4.2 30.7 1.0
N I:ASP175 4.2 32.2 1.0
O I:ALA178 4.2 29.0 1.0
CA I:ASP175 4.2 32.0 1.0
C I:ALA178 4.3 29.4 1.0
CD1 Y:ILE27 4.3 31.3 1.0
N I:ALA178 4.3 29.5 1.0
CA I:SER180 4.3 33.8 1.0
N I:GLY181 4.3 33.3 1.0
CA I:VAL174 4.3 30.3 1.0
CB I:VAL174 4.4 30.4 1.0
CA I:ALA178 4.4 29.3 1.0
CA I:GLY181 4.4 33.7 1.0
OXT I:ASP204 4.5 34.3 1.0
CB I:ASP177 4.5 31.9 1.0
C I:ASP175 4.6 31.5 1.0
CB I:SER180 4.7 34.2 1.0
OD2 I:ASP175 4.7 36.1 1.0
CG2 I:VAL174 4.7 31.2 1.0
N I:VAL179 4.8 29.6 1.0
O I:ASP175 5.0 31.7 1.0

Magnesium binding site 4 out of 10 in 5lf4

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Magnesium binding site 4 out of 10 in the Human 20S Proteasome Complex with Delanzomib at 2.0 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 Delanzomib at 2.0 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg304

b:29.5
occ:1.00
 O I:ASP204 2.1 35.0 1.0
O Y:THR165 2.2 36.0 1.0
O Y:ASP168 2.2 31.7 1.0
O Y:SER171 2.2 33.1 1.0
O Y:HOH482 2.7 35.7 1.0
C I:ASP204 3.1 34.5 1.0
C Y:THR165 3.2 32.5 1.0
C Y:ASP168 3.3 28.6 1.0
C Y:SER171 3.4 31.0 1.0
CA I:ASP204 3.6 33.9 1.0
CA Y:THR165 3.7 31.3 1.0
CA Y:ALA169 3.8 27.4 1.0
CB I:ASP204 3.9 34.0 1.0
N Y:SER171 3.9 29.0 1.0
C Y:ALA169 3.9 27.4 1.0
NH1 Y:ARG20 3.9 28.4 1.0
N Y:ALA169 3.9 27.5 1.0
O Y:ALA169 4.0 27.1 1.0
CA Y:SER171 4.2 29.7 1.0
OXT I:ASP204 4.2 34.3 1.0
CB Y:THR165 4.3 31.3 1.0
N Y:TYR166 4.3 32.7 1.0
CA Y:ASP168 4.4 28.8 1.0
N Y:ASP168 4.4 29.8 1.0
N Y:GLY172 4.5 29.4 1.0
N Y:TYR170 4.5 27.0 1.0
CZ Y:ARG20 4.6 29.1 1.0
O Y:ALA164 4.6 29.4 1.0
O Y:TYR166 4.6 32.1 1.0
CA Y:GLY172 4.7 29.9 1.0
CB Y:SER171 4.7 29.7 1.0
C Y:TYR166 4.7 32.6 1.0
CA Y:TYR166 4.8 34.1 1.0
O I:HOH498 4.8 46.8 1.0
CB Y:ASP168 4.9 27.7 1.0
C Y:TYR170 5.0 28.4 1.0
N I:ASP204 5.0 33.3 1.0

Magnesium binding site 5 out of 10 in 5lf4

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Magnesium binding site 5 out of 10 in the Human 20S Proteasome Complex with Delanzomib at 2.0 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 Delanzomib at 2.0 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mg301

b:59.2
occ:1.00
 O J:HOH517 2.0 52.3 1.0
O K:HOH491 2.0 48.3 1.0
O J:HOH408 2.1 46.0 1.0
O J:HOH467 2.1 43.9 1.0
O J:HOH530 2.2 51.9 1.0
O J:HOH434 2.2 44.1 1.0
O K:HOH447 4.0 42.0 1.0
O J:PRO97 4.0 36.1 1.0
OD1 J:ASP52 4.2 34.6 1.0
O K:HOH441 4.2 40.8 1.0
OD2 J:ASP52 4.3 34.2 1.0
OE2 J:GLU49 4.4 43.5 1.0
O K:HOH403 4.4 50.8 1.0
O J:HOH427 4.4 61.6 1.0
CE1 J:HIS99 4.5 31.2 0.5
O J:HOH534 4.6 67.3 1.0
CG J:ASP52 4.7 34.6 1.0
ND1 J:HIS99 4.7 31.4 0.5
CE K:LYS92 4.7 43.6 1.0
CD J:PRO97 4.8 35.0 1.0
CG J:PRO97 4.9 33.9 1.0

Magnesium binding site 6 out of 10 in 5lf4

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Magnesium binding site 6 out of 10 in the Human 20S Proteasome Complex with Delanzomib at 2.0 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 Delanzomib at 2.0 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg301

b:37.5
occ:1.00
 O W:ASP204 2.2 52.5 1.0
O K:THR165 2.2 47.5 1.0
O K:ASP168 2.2 43.2 1.0
O K:SER171 2.2 46.6 1.0
O W:HOH487 2.8 49.1 1.0
C W:ASP204 3.1 53.9 1.0
C K:THR165 3.2 43.4 1.0
C K:ASP168 3.3 38.4 1.0
C K:SER171 3.4 42.9 1.0
CA W:ASP204 3.6 53.5 1.0
CA K:THR165 3.7 42.7 1.0
CA K:ALA169 3.9 37.9 1.0
NH1 K:ARG20 3.9 40.5 1.0
C K:ALA169 3.9 38.2 1.0
CB W:ASP204 3.9 53.6 1.0
N K:SER171 3.9 39.9 1.0
N K:ALA169 3.9 36.9 1.0
O K:ALA169 4.0 39.5 1.0
CA K:SER171 4.2 40.8 1.0
OXT W:ASP204 4.2 54.0 1.0
CB K:THR165 4.3 42.6 1.0
CA K:ASP168 4.3 37.8 1.0
N K:ASP168 4.3 38.5 1.0
N K:TYR166 4.4 44.1 1.0
N K:GLY172 4.5 43.0 1.0
N K:TYR170 4.6 38.1 1.0
CZ K:ARG20 4.6 41.5 1.0
O K:ALA164 4.6 40.6 1.0
CA K:GLY172 4.6 45.0 1.0
CB K:SER171 4.7 40.4 1.0
O K:TYR166 4.7 40.7 1.0
C K:TYR166 4.7 42.8 1.0
CA K:TYR166 4.8 44.7 1.0
CB K:ASP168 4.9 37.7 1.0
O W:HOH491 5.0 62.8 1.0
NH2 K:ARG20 5.0 43.9 1.0

Magnesium binding site 7 out of 10 in 5lf4

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Magnesium binding site 7 out of 10 in the Human 20S Proteasome Complex with Delanzomib at 2.0 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 Delanzomib at 2.0 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg304

b:39.5
occ:1.00
 O L:ASP213 2.2 63.4 1.0
O V:ILE163 2.2 48.7 1.0
O V:SER169 2.2 49.0 1.0
O V:ASP166 2.2 44.6 1.0
O V:HOH482 2.7 56.0 1.0
C L:ASP213 3.2 58.3 1.0
C V:SER169 3.3 46.3 1.0
C V:ILE163 3.3 44.9 1.0
C V:ASP166 3.4 40.7 1.0
CA L:ASP213 3.8 57.4 1.0
NH1 V:ARG19 3.9 41.9 1.0
N V:SER169 4.0 43.0 1.0
CA V:LEU167 4.0 40.8 1.0
CB L:ASP213 4.0 57.1 1.0
N V:LEU167 4.1 40.1 1.0
CA V:SER169 4.1 44.7 1.0
CA V:ILE163 4.1 43.8 1.0
OXT L:ASP213 4.2 57.3 1.0
O V:GLY162 4.2 40.3 1.0
N V:ASP166 4.2 40.8 1.0
N V:GLY170 4.3 46.4 1.0
C V:LEU167 4.3 40.3 1.0
N V:PHE164 4.3 45.5 1.0
CZ V:ARG19 4.4 43.4 1.0
CA V:GLY170 4.4 48.0 1.0
CA V:ASP166 4.4 40.3 1.0
O V:LEU167 4.4 40.1 1.0
O V:HOH441 4.5 50.9 1.0
CB V:SER169 4.5 44.6 1.0
CA V:PHE164 4.6 47.0 1.0
NH2 V:ARG19 4.6 43.9 1.0
C V:PHE164 4.6 45.9 1.0
N V:ASN165 4.9 44.2 1.0
O V:PHE164 4.9 47.2 1.0
N V:GLY168 4.9 40.5 1.0
CG2 V:ILE163 5.0 45.9 1.0

Magnesium binding site 8 out of 10 in 5lf4

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Magnesium binding site 8 out of 10 in the Human 20S Proteasome Complex with Delanzomib at 2.0 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 Delanzomib at 2.0 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Mg301

b:85.6
occ:1.00
 O V:HOH496 1.7 67.9 1.0
OE1 V:GLN91 2.2 72.1 1.0
O b:HOH506 2.2 78.2 1.0
O b:HOH409 2.3 44.5 1.0
O b:HOH451 2.6 57.0 1.0
O b:HOH405 2.8 43.8 1.0
CD V:GLN91 3.3 57.7 1.0
O b:ASP94 3.6 42.0 1.0
O V:HOH476 3.6 59.0 1.0
OD2 b:ASP52 3.9 31.7 1.0
NE2 V:GLN91 3.9 54.6 1.0
O V:HOH434 4.2 42.0 1.0
OD1 b:ASP52 4.4 33.1 1.0
C b:ASP94 4.6 39.6 1.0
CG b:ASP52 4.6 32.0 1.0
CG V:GLN91 4.7 52.3 1.0
ND1 V:HIS116 5.0 37.1 1.0

Magnesium binding site 9 out of 10 in 5lf4

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Magnesium binding site 9 out of 10 in the Human 20S Proteasome Complex with Delanzomib at 2.0 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 Delanzomib at 2.0 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
W:Mg301

b:38.0
occ:1.00
 O W:HOH465 2.1 38.6 1.0
O W:VAL174 2.2 48.9 1.0
O W:SER180 2.2 49.3 1.0
O W:ASP177 2.2 46.1 1.0
O W:HOH462 2.3 40.7 1.0
C W:VAL174 3.3 47.2 1.0
C W:ASP177 3.3 42.7 1.0
C W:SER180 3.4 48.5 1.0
N W:ASP177 4.1 44.8 1.0
O W:HOH443 4.1 44.6 1.0
N W:SER180 4.1 46.6 1.0
O W:HOH416 4.1 45.6 1.0
CA W:ASP177 4.2 43.8 1.0
N W:ASP175 4.2 47.4 1.0
O W:ALA178 4.2 43.7 1.0
CA W:ASP175 4.2 46.6 1.0
CD1 K:ILE27 4.3 41.5 1.0
C W:ALA178 4.3 42.9 1.0
CA W:SER180 4.3 48.6 1.0
CA W:VAL174 4.3 46.6 1.0
N W:GLY181 4.3 46.4 1.0
N W:ALA178 4.3 41.6 1.0
CB W:VAL174 4.3 45.8 1.0
CA W:GLY181 4.4 47.0 1.0
CA W:ALA178 4.4 41.6 1.0
OXT W:ASP204 4.5 54.0 1.0
CB W:ASP177 4.6 45.4 1.0
C W:ASP175 4.6 45.3 1.0
CB W:SER180 4.7 51.0 1.0
CG2 W:VAL174 4.7 47.4 1.0
OD2 W:ASP175 4.8 50.4 1.0
N W:VAL179 4.9 42.4 1.0
O W:ASP175 5.0 45.0 1.0

Magnesium binding site 10 out of 10 in 5lf4

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Magnesium binding site 10 out of 10 in the Human 20S Proteasome Complex with Delanzomib at 2.0 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 Delanzomib at 2.0 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Mg301

b:58.3
occ:1.00
 O X:HOH430 2.1 40.6 1.0
O X:HOH424 2.1 48.5 1.0
O X:HOH515 2.1 52.3 1.0
O X:HOH405 2.2 50.7 1.0
O Y:HOH522 2.2 52.8 1.0
O X:HOH522 2.2 52.8 1.0
O Y:HOH504 4.1 42.8 1.0
O X:PRO97 4.1 37.0 1.0
OD1 X:ASP52 4.2 33.4 1.0
O X:HOH433 4.2 60.0 1.0
CE1 X:HIS99 4.2 30.0 0.5
O Y:HOH448 4.3 46.8 1.0
OE2 X:GLU49 4.3 44.5 1.0
OD2 X:ASP52 4.3 32.1 1.0
ND1 X:HIS99 4.5 29.9 0.5
CE Y:LYS92 4.7 41.6 1.0
CG X:ASP52 4.7 32.3 1.0
CD X:PRO97 5.0 36.4 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 20:08:04 2024

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