Atomistry » Magnesium » PDB 5cr0-5d2h » 5d0v
Atomistry »
  Magnesium »
    PDB 5cr0-5d2h »
      5d0v »

Magnesium in PDB 5d0v: Yeast 20S Proteasome BETA5-T1C Mutant in Complex with Carfilzomib

Enzymatic activity of Yeast 20S Proteasome BETA5-T1C Mutant in Complex with Carfilzomib

All present enzymatic activity of Yeast 20S Proteasome BETA5-T1C Mutant in Complex with Carfilzomib:
3.4.25.1;

Protein crystallography data

The structure of Yeast 20S Proteasome BETA5-T1C Mutant in Complex with Carfilzomib, PDB code: 5d0v was solved by E.M.Huber, M.Groll, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.00 / 2.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 135.170, 299.940, 144.940, 90.00, 112.56, 90.00
R / Rfree (%) 19.3 / 22

Other elements in 5d0v:

The structure of Yeast 20S Proteasome BETA5-T1C Mutant in Complex with Carfilzomib also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Yeast 20S Proteasome BETA5-T1C Mutant in Complex with Carfilzomib (pdb code 5d0v). 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 BETA5-T1C Mutant in Complex with Carfilzomib, PDB code: 5d0v:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 5d0v

Go back to Magnesium Binding Sites List in 5d0v
Magnesium binding site 1 out of 8 in the Yeast 20S Proteasome BETA5-T1C Mutant in Complex with Carfilzomib


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 BETA5-T1C Mutant in Complex with Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:54.2
occ:1.00
 O G:MET125 2.1 52.8 1.0
OG1 G:THR8 2.7 48.1 1.0
O G:TYR119 2.8 44.0 1.0
O G:ARG122 2.8 47.8 1.0
C G:MET125 3.2 51.4 1.0
CG2 G:THR8 3.3 49.6 1.0
O G:ALA123 3.3 51.4 1.0
CB G:THR8 3.5 48.6 1.0
C G:ALA123 3.7 51.8 1.0
CA G:ALA123 3.9 50.5 1.0
C G:ARG122 3.9 50.1 1.0
CA G:ARG126 3.9 45.6 1.0
N G:ARG126 4.0 48.5 1.0
C G:TYR119 4.0 43.9 1.0
N G:THR8 4.2 49.9 1.0
N G:MET125 4.2 54.2 1.0
CA G:MET125 4.3 55.1 1.0
N G:ALA123 4.4 50.2 1.0
CD G:PRO127 4.4 42.6 1.0
CA G:THR8 4.5 49.4 1.0
C G:ARG126 4.6 44.2 1.0
N G:TYR124 4.7 53.4 1.0
CA G:TYR119 4.7 42.4 1.0
N G:PRO127 4.8 43.5 1.0
C G:TYR124 4.9 53.3 1.0
CB G:MET125 5.0 58.7 1.0

Magnesium binding site 2 out of 8 in 5d0v

Go back to Magnesium Binding Sites List in 5d0v
Magnesium binding site 2 out of 8 in the Yeast 20S Proteasome BETA5-T1C Mutant in Complex with Carfilzomib


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 BETA5-T1C Mutant in Complex with Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg303

b:38.1
occ:1.00
 OD1 N:ASP51 2.6 27.5 1.0
O N:ASN92 2.7 52.1 1.0
OE1 H:GLN91 2.8 56.2 1.0
OD2 N:ASP51 3.3 39.6 1.0
CG N:ASP51 3.3 23.4 1.0
NE2 H:GLN91 3.4 58.6 1.0
CD H:GLN91 3.5 52.9 1.0
C N:ASN92 4.0 50.8 1.0
CZ H:PHE88 4.4 35.0 1.0
CE1 H:PHE88 4.5 35.1 1.0
CD2 N:LEU93 4.6 48.5 1.0
CB N:ASP51 4.7 28.3 1.0
CA N:LEU93 4.8 47.3 1.0
N N:LEU93 4.8 49.0 1.0
CB N:ASN92 4.9 56.4 1.0
CA N:ASN92 4.9 52.3 1.0

Magnesium binding site 3 out of 8 in 5d0v

Go back to Magnesium Binding Sites List in 5d0v
Magnesium binding site 3 out of 8 in the Yeast 20S Proteasome BETA5-T1C Mutant in Complex with Carfilzomib


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 BETA5-T1C Mutant in Complex with Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:58.2
occ:1.00
 O I:ASP177 2.6 54.7 1.0
O I:SER180 2.7 55.0 1.0
O I:ALA174 2.8 56.4 1.0
OXT I:ASP204 3.5 77.8 1.0
C I:ASP177 3.7 52.9 1.0
C I:ALA174 3.8 56.7 1.0
C I:SER180 3.9 54.7 1.0
CA I:ASP175 4.0 58.1 1.0
O I:ALA178 4.2 59.4 1.0
NH1 Y:ARG19 4.2 71.0 1.0
C I:ASP175 4.3 56.3 1.0
N I:ASP175 4.4 56.5 1.0
O I:ASP175 4.4 59.0 1.0
CA I:ALA178 4.4 52.6 1.0
C I:ASP204 4.4 73.8 1.0
NH2 Y:ARG19 4.4 70.8 1.0
O I:ASP204 4.5 73.3 1.0
C I:ALA178 4.5 55.6 1.0
N I:ALA178 4.5 51.0 1.0
N I:ASP177 4.6 51.2 1.0
CA I:GLY181 4.7 55.8 1.0
CZ Y:ARG19 4.7 68.0 1.0
OD1 I:ASP175 4.7 61.0 1.0
CA I:ASP177 4.7 52.4 1.0
N I:GLY181 4.7 55.6 1.0
N I:SER180 4.8 51.5 1.0
CA I:SER180 4.9 53.3 1.0

Magnesium binding site 4 out of 8 in 5d0v

Go back to Magnesium Binding Sites List in 5d0v
Magnesium binding site 4 out of 8 in the Yeast 20S Proteasome BETA5-T1C Mutant in Complex with Carfilzomib


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 BETA5-T1C Mutant in Complex with Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg302

b:59.2
occ:1.00
 O I:ASP204 2.2 73.3 1.0
O Y:ASP168 2.4 54.7 1.0
O Y:ALA165 2.5 51.1 1.0
O Y:SER171 2.8 56.9 1.0
C I:ASP204 3.1 73.8 1.0
C Y:ASP168 3.3 53.8 1.0
CA Y:ALA169 3.4 55.9 1.0
CA I:ASP204 3.5 71.9 1.0
O Y:ALA169 3.6 55.2 1.0
C Y:ALA169 3.7 54.1 1.0
C Y:ALA165 3.7 50.6 1.0
N Y:ALA169 3.7 56.4 1.0
O Y:HIS166 3.8 51.4 1.0
NH1 Y:ARG19 3.8 71.0 1.0
CB I:ASP204 4.0 71.0 1.0
C Y:SER171 4.0 52.5 1.0
OXT I:ASP204 4.1 77.8 1.0
N Y:SER171 4.3 50.8 1.0
C Y:HIS166 4.3 53.2 1.0
CA Y:ASP168 4.5 52.6 1.0
CA Y:ALA165 4.5 50.2 1.0
N Y:ASP168 4.5 53.5 1.0
CZ Y:ARG19 4.5 68.0 1.0
N Y:TYR170 4.6 52.9 1.0
N Y:HIS166 4.7 51.4 1.0
CA Y:SER171 4.7 50.3 1.0
CA Y:HIS166 4.8 52.0 1.0
C Y:ARG167 4.8 55.0 1.0
CB Y:ALA169 4.8 57.8 1.0
O Y:ALA164 4.8 51.4 1.0
NH2 Y:ARG19 4.9 70.8 1.0
N I:ASP204 4.9 70.5 1.0
O Y:ARG167 5.0 58.0 1.0
N Y:GLY172 5.0 53.4 1.0

Magnesium binding site 5 out of 8 in 5d0v

Go back to Magnesium Binding Sites List in 5d0v
Magnesium binding site 5 out of 8 in the Yeast 20S Proteasome BETA5-T1C Mutant in Complex with Carfilzomib


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 BETA5-T1C Mutant in Complex with Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg301

b:59.0
occ:1.00
 O K:ASP168 2.3 54.6 1.0
O K:ALA165 2.3 60.6 1.0
O W:ASP204 2.4 72.8 1.0
C K:ASP168 3.1 55.7 1.0
C W:ASP204 3.1 72.3 1.0
O K:SER171 3.2 53.4 1.0
O K:HIS166 3.2 61.4 1.0
CA K:ALA169 3.5 58.2 1.0
C K:ALA165 3.5 56.8 1.0
CA W:ASP204 3.5 69.2 1.0
N K:ALA169 3.6 57.4 1.0
C K:HIS166 3.8 57.8 1.0
C K:ALA169 3.9 59.5 1.0
O K:ALA169 4.0 62.5 1.0
CB W:ASP204 4.1 68.4 1.0
OXT W:ASP204 4.1 75.3 1.0
N K:ASP168 4.2 55.2 1.0
CA K:ASP168 4.2 54.8 1.0
NH1 K:ARG19 4.3 70.6 1.0
C K:ARG167 4.3 56.9 1.0
N K:HIS166 4.4 55.3 1.0
C K:SER171 4.4 54.6 1.0
CA K:HIS166 4.4 56.7 1.0
CA K:ALA165 4.5 56.4 1.0
O K:ARG167 4.5 60.7 1.0
N K:ARG167 4.6 56.0 1.0
O K:ALA164 4.6 62.2 1.0
N K:SER171 4.7 55.6 1.0
N K:TYR170 4.8 58.1 1.0
CB K:ALA169 4.8 58.5 1.0
N W:ASP204 4.8 66.7 1.0
NE1 W:TRP182 4.8 61.2 1.0
CA K:ARG167 5.0 55.8 1.0

Magnesium binding site 6 out of 8 in 5d0v

Go back to Magnesium Binding Sites List in 5d0v
Magnesium binding site 6 out of 8 in the Yeast 20S Proteasome BETA5-T1C Mutant in Complex with Carfilzomib


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 BETA5-T1C Mutant in Complex with Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg301

b:69.9
occ:1.00
 OXT L:ASP222 2.1 66.2 1.0
O V:ASP166 2.3 50.1 1.0
O V:ILE163 2.4 56.9 1.0
C L:ASP222 2.9 67.8 1.0
C V:ASP166 3.1 50.2 1.0
O V:TRP164 3.1 54.4 1.0
O V:SER169 3.3 52.6 1.0
C V:ILE163 3.5 57.7 1.0
C V:TRP164 3.5 53.9 1.0
CA L:ASP222 3.6 67.3 1.0
N V:ASP166 3.7 48.4 1.0
O L:ASP222 3.8 65.7 1.0
N V:LEU167 3.8 50.8 1.0
CA V:LEU167 3.9 49.5 1.0
CA V:TRP164 4.0 55.1 1.0
CA V:ASP166 4.0 47.7 1.0
O V:GLY162 4.0 56.1 1.0
N V:TRP164 4.1 56.6 1.0
N V:ASN165 4.1 51.5 1.0
C V:ASN165 4.2 49.1 1.0
O L:ARG221 4.3 62.7 1.0
CB L:ASP222 4.4 66.2 1.0
CD2 V:LEU167 4.5 47.2 1.0
C V:SER169 4.5 50.9 1.0
CA V:ILE163 4.6 57.4 1.0
NH1 V:ARG19 4.6 62.1 1.0
CA V:ASN165 4.6 50.9 1.0
C V:LEU167 4.6 50.4 1.0
N L:ASP222 4.7 64.8 1.0
CD1 L:ILE35 4.7 56.9 1.0
O V:ASN165 4.9 45.6 1.0
C L:ARG221 5.0 63.5 1.0

Magnesium binding site 7 out of 8 in 5d0v

Go back to Magnesium Binding Sites List in 5d0v
Magnesium binding site 7 out of 8 in the Yeast 20S Proteasome BETA5-T1C Mutant in Complex with Carfilzomib


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 BETA5-T1C Mutant in Complex with Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg202

b:41.7
occ:1.00
 O N:SER169 2.6 45.0 1.0
O N:ILE163 2.8 45.5 1.0
O N:ASP166 3.0 46.6 1.0
NH1 N:ARG19 3.5 45.1 1.0
CD1 a:LEU34 3.6 50.7 1.0
C N:SER169 3.9 43.3 1.0
C N:ILE163 3.9 46.0 1.0
C N:ASP166 4.0 44.0 1.0
CG2 N:ILE163 4.1 45.6 1.0
CA N:GLY167 4.2 42.6 1.0
CZ N:ARG19 4.2 44.8 1.0
O N:GLY167 4.3 43.2 1.0
O a:HOH308 4.4 41.5 1.0
NH2 N:ARG19 4.5 46.5 1.0
CA N:GLY170 4.5 45.7 1.0
C N:GLY167 4.5 42.7 1.0
N N:GLY167 4.5 42.6 1.0
CA N:ILE163 4.6 45.4 1.0
N N:GLY170 4.7 43.9 1.0
N N:SER169 4.8 42.7 1.0
CG a:LEU34 4.8 50.7 1.0
CA N:SER169 4.9 40.8 1.0
N N:LYS164 4.9 47.0 1.0
O N:LYS164 4.9 52.3 1.0

Magnesium binding site 8 out of 8 in 5d0v

Go back to Magnesium Binding Sites List in 5d0v
Magnesium binding site 8 out of 8 in the Yeast 20S Proteasome BETA5-T1C Mutant in Complex with Carfilzomib


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 BETA5-T1C Mutant in Complex with Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg301

b:61.6
occ:1.00
 O Z:THR192 2.5 60.5 1.0
O Z:VAL198 2.7 57.3 1.0
O Z:HIS195 2.8 49.6 1.0
C Z:THR192 3.6 62.5 1.0
O Z:ASP222 3.7 60.5 1.0
C Z:HIS195 3.7 51.7 1.0
CG2 Z:THR192 3.8 61.7 1.0
NH2 Z:ARG28 3.8 65.8 1.0
CA Z:ILE196 3.9 51.6 1.0
O Z:ILE196 3.9 50.9 1.0
C Z:VAL198 3.9 57.1 1.0
CA Z:THR192 4.0 61.1 1.0
C Z:ILE196 4.1 50.4 1.0
NH2 H:ARG19 4.2 67.5 1.0
N Z:ILE196 4.2 51.6 1.0
OD1 Z:ASP222 4.4 73.3 1.0
N Z:VAL198 4.5 52.5 1.0
CB Z:THR192 4.6 59.8 1.0
C Z:ASP222 4.7 68.9 1.0
CA Z:VAL198 4.8 55.0 1.0
N Z:GLU193 4.8 62.1 1.0
NH1 H:ARG19 4.8 61.9 1.0
N Z:HIS195 4.8 53.3 1.0
N Z:GLY199 4.9 57.1 1.0
CZ H:ARG19 4.9 61.8 1.0
CZ Z:ARG28 4.9 60.6 1.0
CA Z:HIS195 4.9 51.7 1.0
CA Z:GLY199 4.9 56.3 1.0

Reference:

E.M.Huber, W.Heinemeyer, X.Li, C.S.Arendt, M.Hochstrasser, M.Groll. A Unified Mechanism For Proteolysis and Autocatalytic Activation in the 20S Proteasome. Nat Commun V. 7 10900 2016.
ISSN: ESSN 2041-1723
PubMed: 26964885
DOI: 10.1038/NCOMMS10900
Page generated: Sun Sep 29 02:25:52 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