Atomistry » Magnesium » PDB 4qq8-4qwi » 4qvl
Atomistry »
  Magnesium »
    PDB 4qq8-4qwi »
      4qvl »

Magnesium in PDB 4qvl: Ycp in Complex with Bortezomib

Enzymatic activity of Ycp in Complex with Bortezomib

All present enzymatic activity of Ycp in Complex with Bortezomib:
3.4.25.1;

Protein crystallography data

The structure of Ycp in Complex with Bortezomib, PDB code: 4qvl 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 (°) 134.910, 300.210, 144.760, 90.00, 112.85, 90.00
R / Rfree (%) 18.7 / 21.5

Other elements in 4qvl:

The structure of Ycp in Complex with Bortezomib also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Ycp in Complex with Bortezomib (pdb code 4qvl). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Ycp in Complex with Bortezomib, PDB code: 4qvl:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 4qvl

Go back to Magnesium Binding Sites List in 4qvl
Magnesium binding site 1 out of 8 in the Ycp in Complex with Bortezomib


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Ycp in Complex with Bortezomib within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:58.0
occ:1.00
 O G:MET125 2.2 52.2 1.0
O G:ARG122 2.6 50.1 1.0
OG1 G:THR8 2.6 47.6 1.0
O G:TYR119 2.8 48.3 1.0
CG2 G:THR8 3.2 51.1 1.0
O G:ALA123 3.3 53.9 1.0
C G:MET125 3.3 52.3 1.0
CB G:THR8 3.5 49.7 1.0
C G:ALA123 3.6 53.4 1.0
C G:ARG122 3.6 52.0 1.0
CA G:ALA123 3.7 53.0 1.0
C G:TYR119 4.0 45.6 1.0
N G:THR8 4.1 52.3 1.0
N G:ALA123 4.1 52.2 1.0
CA G:ARG126 4.2 47.7 1.0
N G:ARG126 4.2 47.5 1.0
N G:MET125 4.2 54.3 1.0
CA G:MET125 4.3 57.0 1.0
CA G:THR8 4.4 51.2 1.0
CD G:PRO127 4.6 45.7 1.0
N G:TYR124 4.6 55.1 1.0
CA G:TYR119 4.8 44.1 1.0
C G:ARG126 4.8 47.4 1.0
CA G:ARG122 4.9 53.7 1.0
C G:TYR124 4.9 54.5 1.0
CB G:MET125 5.0 62.2 1.0
CB G:ALA123 5.0 52.0 1.0

Magnesium binding site 2 out of 8 in 4qvl

Go back to Magnesium Binding Sites List in 4qvl
Magnesium binding site 2 out of 8 in the Ycp in Complex with Bortezomib


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Ycp in Complex with Bortezomib within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:72.7
occ:1.00
 O I:ASP177 2.3 50.4 1.0
O I:ALA174 2.7 53.6 1.0
O I:SER180 2.8 48.0 1.0
C I:ASP177 3.5 50.9 1.0
C I:ALA174 3.8 54.5 1.0
OXT I:ASP204 3.8 66.4 1.0
C I:SER180 3.9 52.0 1.0
CA I:ASP175 4.1 56.0 1.0
N I:ASP177 4.3 51.1 1.0
CA I:ALA178 4.3 50.6 1.0
N I:ALA178 4.3 49.0 1.0
NH1 Y:ARG19 4.3 69.7 1.0
C I:ASP175 4.4 56.5 1.0
O I:ALA178 4.4 49.4 1.0
N I:ASP175 4.4 55.3 1.0
C I:ALA178 4.4 51.4 1.0
CA I:ASP177 4.5 51.9 1.0
O I:ASP175 4.6 59.7 1.0
NH2 Y:ARG19 4.6 73.3 1.0
N I:SER180 4.6 50.0 1.0
O I:ASP204 4.6 62.0 1.0
C I:ASP204 4.7 62.7 1.0
CZ Y:ARG19 4.8 67.7 1.0
CA I:SER180 4.8 51.2 1.0
N I:GLY181 4.8 52.8 1.0
CA I:GLY181 4.9 54.9 1.0
CG2 Y:VAL26 4.9 53.9 1.0
OD1 I:ASP175 4.9 56.9 1.0
CA I:ALA174 5.0 50.8 1.0
N I:ARG176 5.0 52.4 1.0

Magnesium binding site 3 out of 8 in 4qvl

Go back to Magnesium Binding Sites List in 4qvl
Magnesium binding site 3 out of 8 in the Ycp in Complex with Bortezomib


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Ycp in Complex with Bortezomib within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mg201

b:39.5
occ:1.00
 OE1 J:GLN118 3.3 50.1 1.0
CB J:ASP120 3.7 43.7 1.0
OD2 J:ASP120 3.8 48.5 1.0
O J:THR124 3.8 51.6 1.0
CG J:ASP120 3.8 45.4 1.0
N J:ASP120 4.1 41.9 1.0
CD J:GLN118 4.1 45.9 1.0
CE1 J:HIS133 4.3 43.3 1.0
CG J:GLN118 4.3 44.1 1.0
CB J:THR124 4.3 47.4 1.0
CG2 J:THR124 4.5 48.1 1.0
CA J:ASP120 4.5 42.2 1.0
O J:GLN118 4.6 39.8 1.0
OD1 J:ASP120 4.6 49.9 1.0
CG1 I:VAL35 4.7 52.4 1.0
OG I:SER30 4.7 57.5 1.0
C J:ILE119 4.7 41.5 1.0
C J:THR124 4.8 47.8 1.0
C J:GLN118 4.9 40.8 1.0
ND1 J:HIS133 4.9 42.2 1.0

Magnesium binding site 4 out of 8 in 4qvl

Go back to Magnesium Binding Sites List in 4qvl
Magnesium binding site 4 out of 8 in the Ycp in Complex with Bortezomib


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Ycp in Complex with Bortezomib within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg302

b:57.5
occ:1.00
 O K:ASP168 2.2 48.7 1.0
O W:ASP204 2.4 54.0 1.0
O K:ALA165 2.4 53.6 1.0
O K:SER171 2.8 54.0 1.0
C W:ASP204 3.2 54.3 1.0
C K:ASP168 3.2 49.1 1.0
C K:ALA165 3.5 52.4 1.0
CA K:ALA169 3.6 52.4 1.0
CA W:ASP204 3.6 57.5 1.0
N K:ALA169 3.8 51.6 1.0
O K:HIS166 3.8 51.5 1.0
NH1 K:ARG19 3.8 66.2 1.0
O K:ALA169 3.8 52.6 1.0
C K:ALA169 3.8 53.0 1.0
CB W:ASP204 3.9 57.9 1.0
C K:SER171 3.9 51.9 1.0
OXT W:ASP204 4.1 51.5 1.0
C K:HIS166 4.2 50.4 1.0
CA K:ASP168 4.3 48.6 1.0
N K:ASP168 4.3 50.0 1.0
CA K:ALA165 4.3 53.0 1.0
N K:SER171 4.4 49.0 1.0
CZ K:ARG19 4.5 64.9 1.0
N K:HIS166 4.5 52.2 1.0
O K:ALA164 4.6 57.4 1.0
C K:ARG167 4.7 51.6 1.0
CA K:HIS166 4.7 51.5 1.0
CA K:SER171 4.7 48.7 1.0
N K:TYR170 4.7 52.6 1.0
NH2 K:ARG19 4.8 67.3 1.0
N K:ARG167 4.9 49.4 1.0
N K:GLY172 4.9 53.0 1.0
O K:ARG167 4.9 52.6 1.0
CB K:ALA169 4.9 51.1 1.0
CG W:ASP204 5.0 57.4 1.0
N W:ASP204 5.0 56.5 1.0
CA K:GLY172 5.0 53.7 1.0

Magnesium binding site 5 out of 8 in 4qvl

Go back to Magnesium Binding Sites List in 4qvl
Magnesium binding site 5 out of 8 in the Ycp in Complex with Bortezomib


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Ycp in Complex with Bortezomib within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg202

b:55.1
occ:1.00
 O N:SER169 2.5 41.1 1.0
O N:ILE163 2.6 45.5 1.0
O N:ASP166 2.8 49.2 1.0
NH1 N:ARG19 3.5 48.4 1.0
CD1 a:LEU34 3.6 50.6 1.0
C N:SER169 3.7 42.1 1.0
C N:ILE163 3.7 45.6 1.0
C N:ASP166 3.9 44.7 1.0
CG2 N:ILE163 4.0 43.7 1.0
CA N:GLY167 4.2 44.8 1.0
CZ N:ARG19 4.2 46.3 1.0
CA N:ILE163 4.4 45.1 1.0
CA N:GLY170 4.4 44.5 1.0
O N:GLY167 4.4 44.0 1.0
N N:GLY167 4.4 43.9 1.0
NH2 N:ARG19 4.5 49.1 1.0
C N:GLY167 4.5 43.2 1.0
N N:GLY170 4.5 42.7 1.0
N N:SER169 4.7 43.1 1.0
CA N:SER169 4.7 41.6 1.0
CB N:ILE163 4.8 43.9 1.0
N N:LYS164 4.8 47.6 1.0
CG a:LEU34 4.9 50.6 1.0
N N:ASP166 5.0 42.3 1.0
C N:LYS164 5.0 48.5 1.0
O N:LYS164 5.0 51.6 1.0

Magnesium binding site 6 out of 8 in 4qvl

Go back to Magnesium Binding Sites List in 4qvl
Magnesium binding site 6 out of 8 in the Ycp in Complex with Bortezomib


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Ycp in Complex with Bortezomib within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Mg302

b:70.3
occ:1.00
 O V:ILE163 2.2 47.2 1.0
OXT L:ASP222 2.2 66.5 1.0
O V:ASP166 2.3 46.0 1.0
O V:SER169 2.8 50.9 1.0
C L:ASP222 3.0 68.9 1.0
C V:ASP166 3.2 49.2 1.0
C V:ILE163 3.3 52.3 1.0
CA L:ASP222 3.7 67.8 1.0
O V:TRP164 3.7 58.7 1.0
O L:ASP222 3.8 70.7 1.0
N V:LEU167 3.8 50.2 1.0
CA V:LEU167 3.8 49.1 1.0
C V:SER169 3.9 50.0 1.0
C V:TRP164 3.9 55.7 1.0
O V:GLY162 3.9 49.8 1.0
N V:ASP166 3.9 50.4 1.0
N V:TRP164 4.1 54.2 1.0
NH1 V:ARG19 4.1 59.1 1.0
CA V:ASP166 4.2 49.4 1.0
CA V:TRP164 4.2 54.5 1.0
CA V:ILE163 4.2 52.2 1.0
CB L:ASP222 4.4 69.0 1.0
N V:ASN165 4.4 52.5 1.0
C V:LEU167 4.4 47.3 1.0
C V:ASN165 4.6 51.2 1.0
N V:SER169 4.6 47.2 1.0
O V:LEU167 4.7 46.1 1.0
CA V:GLY170 4.7 54.4 1.0
N V:GLY170 4.7 51.7 1.0
CA V:SER169 4.8 47.0 1.0
CZ V:ARG19 4.8 58.0 1.0
CD2 V:LEU167 4.8 48.8 1.0
O L:ARG221 4.8 61.6 1.0
C V:GLY162 4.9 50.3 1.0
NH2 V:ARG19 4.9 60.2 1.0
N L:ASP222 5.0 66.7 1.0
CA V:ASN165 5.0 51.7 1.0

Magnesium binding site 7 out of 8 in 4qvl

Go back to Magnesium Binding Sites List in 4qvl
Magnesium binding site 7 out of 8 in the Ycp in Complex with Bortezomib


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Ycp in Complex with Bortezomib within 5.0Å range:
probe atom residue distance (Å) B Occ
Y:Mg302

b:47.0
occ:1.00
 O I:ASP204 2.3 62.0 1.0
O Y:ASP168 2.3 53.7 1.0
O Y:ALA165 2.4 50.2 1.0
O Y:SER171 2.9 49.5 1.0
C I:ASP204 3.1 62.7 1.0
C Y:ASP168 3.3 51.3 1.0
CA I:ASP204 3.5 62.8 1.0
CA Y:ALA169 3.6 52.1 1.0
C Y:ALA165 3.6 49.6 1.0
O Y:HIS166 3.7 51.9 1.0
NH1 Y:ARG19 3.8 69.7 1.0
N Y:ALA169 3.8 53.7 1.0
CB I:ASP204 3.8 63.7 1.0
O Y:ALA169 3.9 53.4 1.0
C Y:ALA169 3.9 51.9 1.0
OXT I:ASP204 4.0 66.4 1.0
C Y:SER171 4.0 49.0 1.0
C Y:HIS166 4.2 52.0 1.0
N Y:ASP168 4.4 52.2 1.0
CA Y:ASP168 4.4 51.1 1.0
CA Y:ALA165 4.5 50.5 1.0
CZ Y:ARG19 4.5 67.7 1.0
N Y:SER171 4.5 48.6 1.0
N Y:HIS166 4.6 52.6 1.0
CA Y:HIS166 4.7 52.2 1.0
C Y:ARG167 4.7 54.2 1.0
O Y:ALA164 4.7 54.9 1.0
NH2 Y:ARG19 4.8 73.3 1.0
N Y:TYR170 4.8 49.8 1.0
CA Y:SER171 4.8 47.5 1.0
N I:ASP204 4.9 59.4 1.0
N Y:ARG167 4.9 52.1 1.0
CB Y:ALA169 4.9 51.7 1.0
CG I:ASP204 4.9 64.0 1.0
O Y:ARG167 4.9 54.7 1.0
N Y:GLY172 5.0 51.4 1.0

Magnesium binding site 8 out of 8 in 4qvl

Go back to Magnesium Binding Sites List in 4qvl
Magnesium binding site 8 out of 8 in the Ycp in Complex with Bortezomib


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Ycp in Complex with Bortezomib within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg301

b:74.8
occ:1.00
 O Z:VAL198 2.4 60.1 1.0
O Z:THR192 3.0 57.9 1.0
O Z:HIS195 3.3 51.1 1.0
NH2 Z:ARG28 3.4 62.3 1.0
O Z:ASP222 3.5 72.8 1.0
CG2 Z:THR192 3.6 64.2 1.0
C Z:VAL198 3.6 59.0 1.0
O Z:ILE196 3.9 56.7 1.0
C Z:THR192 3.9 61.7 1.0
OD1 Z:ASP222 4.1 63.5 1.0
CA Z:ILE196 4.2 53.2 1.0
CA Z:THR192 4.2 62.6 1.0
C Z:ILE196 4.2 53.1 1.0
NH2 H:ARG19 4.3 66.2 1.0
C Z:HIS195 4.3 52.9 1.0
CZ Z:ARG28 4.3 61.4 1.0
C Z:ASP222 4.4 71.0 1.0
CA Z:GLY199 4.4 58.7 1.0
NH1 Z:ARG28 4.5 62.5 1.0
N Z:GLY199 4.5 58.0 1.0
N Z:VAL198 4.5 53.5 1.0
CB Z:THR192 4.5 62.6 1.0
CA Z:VAL198 4.6 55.1 1.0
O Z:LYS220 4.7 64.6 1.0
N Z:ILE196 4.7 52.5 1.0
OXT Z:ASP222 4.9 73.0 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 02:19:50 2024

Last articles

Zn in 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy