Atomistry » Magnesium » PDB 4qwi-4r02 » 4qz5
Atomistry »
  Magnesium »
    PDB 4qwi-4r02 »
      4qz5 »

Magnesium in PDB 4qz5: Ycp BETA5-A49T-Mutant in Complex with Onx 0914

Enzymatic activity of Ycp BETA5-A49T-Mutant in Complex with Onx 0914

All present enzymatic activity of Ycp BETA5-A49T-Mutant in Complex with Onx 0914:
3.4.25.1;

Protein crystallography data

The structure of Ycp BETA5-A49T-Mutant in Complex with Onx 0914, PDB code: 4qz5 was solved by E.M.Huber, W.Heinemeyer, M.Groll, 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 (°) 135.560, 299.580, 144.910, 90.00, 112.81, 90.00
R / Rfree (%) 19.5 / 22.4

Other elements in 4qz5:

The structure of Ycp BETA5-A49T-Mutant 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 Ycp BETA5-A49T-Mutant in Complex with Onx 0914 (pdb code 4qz5). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the Ycp BETA5-A49T-Mutant in Complex with Onx 0914, PDB code: 4qz5:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 4qz5

Go back to Magnesium Binding Sites List in 4qz5
Magnesium binding site 1 out of 7 in the Ycp BETA5-A49T-Mutant 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 Ycp BETA5-A49T-Mutant 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 58.0 1.0
OG1 G:THR8 2.9 48.4 1.0
O G:TYR119 3.0 44.0 1.0
O G:ARG122 3.0 46.7 1.0
O G:ALA123 3.2 52.2 1.0
C G:MET125 3.3 55.4 1.0
CG2 G:THR8 3.3 53.4 1.0
CB G:THR8 3.7 52.6 1.0
C G:ALA123 3.8 53.4 1.0
CA G:ARG126 3.9 50.0 1.0
N G:ARG126 3.9 51.1 1.0
CA G:ALA123 3.9 53.6 1.0
C G:ARG122 4.1 50.8 1.0
N G:THR8 4.1 54.8 1.0
C G:TYR119 4.2 47.0 1.0
CD G:PRO127 4.2 47.6 1.0
N G:MET125 4.3 55.6 1.0
CA G:MET125 4.4 57.7 1.0
N G:ALA123 4.5 52.4 1.0
CA G:THR8 4.6 54.7 1.0
C G:ARG126 4.6 50.9 1.0
N G:PRO127 4.7 48.8 1.0
N G:TYR124 4.8 57.8 1.0
CA G:TYR119 4.9 46.5 1.0
C G:TYR124 4.9 55.2 1.0
CB G:ARG126 5.0 49.0 1.0

Magnesium binding site 2 out of 7 in 4qz5

Go back to Magnesium Binding Sites List in 4qz5
Magnesium binding site 2 out of 7 in the Ycp BETA5-A49T-Mutant 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 Ycp BETA5-A49T-Mutant in Complex with Onx 0914 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:48.8
occ:1.00
 O I:ASP177 2.2 47.1 1.0
O I:SER180 2.6 48.1 1.0
O I:ALA174 2.8 52.1 1.0
C I:ASP177 3.3 46.3 1.0
C I:SER180 3.8 46.8 1.0
OXT I:ASP204 3.9 51.4 1.0
O I:ALA178 3.9 48.4 1.0
C I:ALA174 3.9 51.5 1.0
CA I:ALA178 4.0 46.3 1.0
C I:ALA178 4.0 47.0 1.0
N I:ALA178 4.1 45.9 1.0
CA I:ASP175 4.3 50.9 1.0
N I:ASP177 4.3 44.9 1.0
N I:SER180 4.4 44.5 1.0
CA I:ASP177 4.4 46.4 1.0
NH1 Y:ARG19 4.5 58.5 1.0
C I:ASP175 4.5 49.5 1.0
N I:ASP175 4.6 50.8 1.0
O I:ASP175 4.6 51.1 1.0
CA I:SER180 4.7 46.1 1.0
O I:ASP204 4.7 62.6 1.0
C I:ASP204 4.8 59.1 1.0
N I:GLY181 4.8 45.3 1.0
N I:LEU179 4.8 45.9 1.0
CA I:GLY181 4.8 45.2 1.0
CG2 Y:VAL26 4.9 54.6 1.0
NH2 Y:ARG19 4.9 58.3 1.0

Magnesium binding site 3 out of 7 in 4qz5

Go back to Magnesium Binding Sites List in 4qz5
Magnesium binding site 3 out of 7 in the Ycp BETA5-A49T-Mutant 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 Ycp BETA5-A49T-Mutant in Complex with Onx 0914 within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg302

b:58.3
occ:1.00
 O K:ASP168 2.1 48.9 1.0
O W:ASP204 2.2 61.6 1.0
O K:ALA165 2.3 45.7 1.0
O K:SER171 2.5 46.2 1.0
C W:ASP204 3.1 58.5 1.0
C K:ASP168 3.2 46.7 1.0
C K:ALA165 3.5 46.1 1.0
CA K:ALA169 3.6 46.9 1.0
C K:SER171 3.6 46.2 1.0
CA W:ASP204 3.7 54.4 1.0
C K:ALA169 3.7 47.6 1.0
O K:ALA169 3.7 53.6 1.0
N K:ALA169 3.8 47.5 1.0
NH1 K:ARG19 4.0 54.6 1.0
OXT W:ASP204 4.0 67.1 1.0
CB W:ASP204 4.0 53.2 1.0
N K:SER171 4.0 45.0 1.0
O K:HIS166 4.0 52.2 1.0
CA K:ALA165 4.3 47.2 1.0
CA K:SER171 4.3 44.5 1.0
C K:HIS166 4.3 47.6 1.0
CA K:ASP168 4.4 45.2 1.0
N K:ASP168 4.4 45.8 1.0
N K:TYR170 4.5 45.0 1.0
N K:HIS166 4.5 45.9 1.0
CZ K:ARG19 4.5 54.2 1.0
O K:ALA164 4.5 45.5 1.0
N K:GLY172 4.6 46.0 1.0
CA K:HIS166 4.7 47.0 1.0
CA K:GLY172 4.7 47.2 1.0
NH2 K:ARG19 4.8 58.1 1.0
CB K:SER171 4.8 44.2 1.0
C K:ARG167 4.8 45.3 1.0
CB K:ALA169 5.0 46.1 1.0
N K:ARG167 5.0 44.3 1.0
CG W:ASP204 5.0 54.1 1.0

Magnesium binding site 4 out of 7 in 4qz5

Go back to Magnesium Binding Sites List in 4qz5
Magnesium binding site 4 out of 7 in the Ycp BETA5-A49T-Mutant 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 Ycp BETA5-A49T-Mutant in Complex with Onx 0914 within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg202

b:48.0
occ:1.00
 O N:SER169 2.5 54.9 1.0
O N:ILE163 2.6 54.8 1.0
O N:ASP166 3.0 56.3 1.0
CD1 a:LEU34 3.6 54.2 1.0
NH1 N:ARG19 3.6 57.8 1.0
C N:SER169 3.7 53.7 1.0
C N:ILE163 3.7 54.7 1.0
CG2 N:ILE163 3.9 54.7 1.0
C N:ASP166 4.1 54.6 1.0
CZ N:ARG19 4.2 56.7 1.0
CA N:GLY170 4.3 56.1 1.0
CA N:GLY167 4.4 55.4 1.0
NH2 N:ARG19 4.4 55.7 1.0
CA N:ILE163 4.5 54.9 1.0
N N:GLY170 4.5 54.0 1.0
O N:GLY167 4.6 52.9 1.0
N N:GLY167 4.7 53.2 1.0
C N:GLY167 4.7 54.0 1.0
N N:LYS164 4.8 53.5 1.0
N N:SER169 4.8 49.7 1.0
CA N:SER169 4.8 51.0 1.0
CB N:ILE163 4.8 53.3 1.0
O N:LYS164 4.9 58.6 1.0
CG a:LEU34 4.9 55.2 1.0
CA N:LYS164 4.9 57.2 1.0
C N:LYS164 4.9 58.0 1.0

Magnesium binding site 5 out of 7 in 4qz5

Go back to Magnesium Binding Sites List in 4qz5
Magnesium binding site 5 out of 7 in the Ycp BETA5-A49T-Mutant 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 Ycp BETA5-A49T-Mutant in Complex with Onx 0914 within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Mg302

b:66.8
occ:1.00
 O V:ASP166 2.2 59.7 1.0
O V:ILE163 2.2 63.1 1.0
OXT L:ASP222 2.4 66.5 1.0
C V:ASP166 3.1 63.0 1.0
C L:ASP222 3.1 68.5 1.0
O V:SER169 3.2 59.8 1.0
C V:ILE163 3.3 69.1 1.0
O V:TRP164 3.3 69.1 1.0
C V:TRP164 3.4 68.4 1.0
N V:ASP166 3.6 61.8 1.0
CA L:ASP222 3.7 65.0 1.0
O V:GLY162 3.8 63.5 1.0
O L:ASP222 3.8 73.0 1.0
N V:LEU167 3.8 64.4 1.0
N V:ASN165 3.9 67.6 1.0
CA V:TRP164 3.9 67.9 1.0
CA V:LEU167 4.0 65.4 1.0
CA V:ASP166 4.0 62.9 1.0
N V:TRP164 4.0 66.4 1.0
C V:ASN165 4.1 64.0 1.0
CA V:ILE163 4.4 68.3 1.0
C V:SER169 4.4 61.8 1.0
CA V:ASN165 4.5 66.3 1.0
CB L:ASP222 4.5 64.6 1.0
O L:ARG221 4.6 54.4 1.0
CD2 V:LEU167 4.7 63.5 1.0
NH1 V:ARG19 4.7 78.0 1.0
C V:LEU167 4.7 62.2 1.0
O V:ASN165 4.8 62.4 1.0
C V:GLY162 4.8 65.6 1.0
CD1 L:ILE35 4.8 56.1 1.0
N L:ASP222 4.9 64.3 1.0
CB V:ASP166 4.9 60.6 1.0

Magnesium binding site 6 out of 7 in 4qz5

Go back to Magnesium Binding Sites List in 4qz5
Magnesium binding site 6 out of 7 in the Ycp BETA5-A49T-Mutant 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 Ycp BETA5-A49T-Mutant in Complex with Onx 0914 within 5.0Å range:
probe atom residue distance (Å) B Occ
Y:Mg302

b:54.3
occ:1.00
 O Y:ASP168 2.2 43.1 1.0
O I:ASP204 2.3 62.6 1.0
O Y:ALA165 2.3 44.0 1.0
O Y:SER171 2.7 52.6 1.0
C I:ASP204 3.1 59.1 1.0
C Y:ASP168 3.2 44.6 1.0
C Y:ALA165 3.5 47.6 1.0
CA I:ASP204 3.6 57.5 1.0
CA Y:ALA169 3.6 46.5 1.0
C Y:SER171 3.8 48.2 1.0
N Y:ALA169 3.8 45.5 1.0
C Y:ALA169 3.8 45.6 1.0
O Y:ALA169 3.8 49.5 1.0
O Y:HIS166 3.9 40.9 1.0
OXT I:ASP204 3.9 51.4 1.0
CB I:ASP204 4.0 59.2 1.0
NH1 Y:ARG19 4.0 58.5 1.0
C Y:HIS166 4.2 44.7 1.0
N Y:SER171 4.2 42.8 1.0
CA Y:ALA165 4.4 47.3 1.0
CA Y:ASP168 4.4 44.1 1.0
N Y:ASP168 4.4 43.8 1.0
N Y:HIS166 4.4 48.3 1.0
CA Y:HIS166 4.5 44.7 1.0
CA Y:SER171 4.5 44.5 1.0
CZ Y:ARG19 4.6 56.1 1.0
O Y:ALA164 4.6 45.4 1.0
N Y:TYR170 4.6 44.0 1.0
N Y:GLY172 4.7 49.3 1.0
C Y:ARG167 4.8 43.0 1.0
NH2 Y:ARG19 4.8 58.3 1.0
CA Y:GLY172 4.9 49.7 1.0
N Y:ARG167 4.9 43.9 1.0
N I:ASP204 4.9 55.2 1.0
CB Y:SER171 5.0 42.4 1.0
CB Y:ALA169 5.0 46.6 1.0

Magnesium binding site 7 out of 7 in 4qz5

Go back to Magnesium Binding Sites List in 4qz5
Magnesium binding site 7 out of 7 in the Ycp BETA5-A49T-Mutant 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 Ycp BETA5-A49T-Mutant in Complex with Onx 0914 within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg301

b:71.2
occ:1.00
 O Z:VAL198 2.6 58.6 1.0
O Z:THR192 2.8 58.5 1.0
O Z:HIS195 3.2 44.6 1.0
NH2 Z:ARG28 3.4 68.1 1.0
O Z:ASP222 3.5 71.8 1.0
CG2 Z:THR192 3.6 59.4 1.0
C Z:VAL198 3.8 55.9 1.0
C Z:THR192 3.8 58.3 1.0
O Z:ILE196 3.9 53.4 1.0
OD1 Z:ASP222 4.1 67.4 1.0
CA Z:THR192 4.1 57.7 1.0
C Z:HIS195 4.2 48.0 1.0
CA Z:ILE196 4.2 48.3 1.0
C Z:ILE196 4.3 48.8 1.0
NH2 H:ARG19 4.3 71.1 1.0
CZ Z:ARG28 4.4 62.6 1.0
C Z:ASP222 4.4 69.9 1.0
CB Z:THR192 4.5 57.6 1.0
CA Z:GLY199 4.6 57.5 1.0
NH1 Z:ARG28 4.6 63.0 1.0
N Z:VAL198 4.6 52.0 1.0
N Z:GLY199 4.6 55.6 1.0
N Z:ILE196 4.7 47.6 1.0
CA Z:VAL198 4.8 52.8 1.0
O Z:LYS220 4.8 65.9 1.0
OXT Z:ASP222 4.9 73.5 1.0
NH1 H:ARG19 4.9 72.1 1.0

Reference:

E.M.Huber, W.Heinemeyer, M.Groll. Bortezomib-Resistant Mutant Proteasomes: Structural and Biochemical Evaluation with Carfilzomib and Onx 0914. Structure 2015.
ISSN: ISSN 0969-2126
PubMed: 25599643
DOI: 10.1016/J.STR.2014.11.019
Page generated: Tue Aug 20 02:38:09 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