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

Magnesium in PDB 4qvn: Ycp BETA5-M45V Mutant in Complex with Bortezomib

Enzymatic activity of Ycp BETA5-M45V Mutant in Complex with Bortezomib

All present enzymatic activity of Ycp BETA5-M45V Mutant in Complex with Bortezomib:
3.4.25.1;

Protein crystallography data

The structure of Ycp BETA5-M45V Mutant in Complex with Bortezomib, PDB code: 4qvn 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 / 2.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 134.900, 300.780, 145.160, 90.00, 113.09, 90.00
R / Rfree (%) 17.5 / 21.3

Other elements in 4qvn:

The structure of Ycp BETA5-M45V Mutant 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 BETA5-M45V Mutant in Complex with Bortezomib (pdb code 4qvn). 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-M45V Mutant in Complex with Bortezomib, PDB code: 4qvn:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 4qvn

Go back to Magnesium Binding Sites List in 4qvn
Magnesium binding site 1 out of 7 in the Ycp BETA5-M45V Mutant 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 BETA5-M45V Mutant in Complex with Bortezomib within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:64.2
occ:1.00
 O G:MET125 2.2 63.4 1.0
OG1 G:THR8 2.7 55.8 1.0
O G:ARG122 2.7 60.3 1.0
O G:ALA123 3.0 69.1 1.0
O G:TYR119 3.1 61.4 1.0
CG2 G:THR8 3.3 60.9 1.0
C G:MET125 3.3 62.6 1.0
C G:ALA123 3.5 63.2 1.0
CB G:THR8 3.5 58.5 1.0
CA G:ALA123 3.6 62.5 1.0
C G:ARG122 3.7 62.9 1.0
N G:THR8 4.0 60.6 1.0
N G:ARG126 4.1 58.8 1.0
CA G:ARG126 4.1 58.3 1.0
N G:ALA123 4.1 63.1 1.0
N G:MET125 4.1 63.7 1.0
C G:TYR119 4.3 56.3 1.0
CA G:MET125 4.3 66.8 1.0
CA G:THR8 4.4 60.3 1.0
N G:TYR124 4.4 64.0 1.0
CD G:PRO127 4.6 56.9 1.0
C G:TYR124 4.8 64.1 1.0
C G:ARG126 4.9 58.0 1.0
CB G:ALA123 4.9 62.6 1.0
CA G:TYR119 5.0 53.5 1.0

Magnesium binding site 2 out of 7 in 4qvn

Go back to Magnesium Binding Sites List in 4qvn
Magnesium binding site 2 out of 7 in the Ycp BETA5-M45V Mutant 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 BETA5-M45V Mutant in Complex with Bortezomib within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:68.7
occ:1.00
 O I:ASP177 2.3 65.4 1.0
O I:SER180 2.5 61.0 1.0
O I:ALA174 3.0 63.0 1.0
OXT I:ASP204 3.5 94.9 1.0
C I:ASP177 3.5 62.0 1.0
C I:SER180 3.7 63.2 1.0
O I:ALA178 4.0 66.6 1.0
C I:ALA174 4.1 65.5 1.0
CA I:ALA178 4.1 60.0 1.0
C I:ALA178 4.1 60.0 1.0
N I:ALA178 4.2 58.4 1.0
O I:ASP204 4.3 83.6 1.0
C I:ASP204 4.3 83.9 1.0
N I:SER180 4.4 60.8 1.0
NH1 Y:ARG19 4.4 84.1 1.0
CA I:ASP175 4.4 68.0 1.0
N I:ASP177 4.5 63.1 1.0
CA I:ASP177 4.6 62.3 1.0
NH2 Y:ARG19 4.6 86.4 1.0
CA I:SER180 4.6 62.3 1.0
N I:GLY181 4.7 63.6 1.0
C I:ASP175 4.7 66.0 1.0
N I:ASP175 4.7 67.2 1.0
O I:ASP175 4.7 71.0 1.0
CA I:GLY181 4.7 66.9 1.0
CZ Y:ARG19 4.9 81.4 1.0
N I:LEU179 4.9 56.6 1.0

Magnesium binding site 3 out of 7 in 4qvn

Go back to Magnesium Binding Sites List in 4qvn
Magnesium binding site 3 out of 7 in the Ycp BETA5-M45V Mutant 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 BETA5-M45V Mutant in Complex with Bortezomib within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mg201

b:45.9
occ:1.00
 OE1 J:GLN118 3.2 60.2 1.0
O J:THR124 3.8 62.4 1.0
CB J:ASP120 3.9 54.0 1.0
CD J:GLN118 4.1 52.9 1.0
CG J:ASP120 4.1 55.4 1.0
OD2 J:ASP120 4.1 55.9 1.0
N J:ASP120 4.2 53.3 1.0
CG J:GLN118 4.3 52.1 1.0
CE1 J:HIS133 4.3 56.1 1.0
CB J:THR124 4.4 56.9 1.0
O J:GLN118 4.5 54.2 1.0
CG2 J:THR124 4.5 55.2 1.0
CG1 I:VAL35 4.6 68.1 1.0
CA J:ASP120 4.7 52.5 1.0
OD1 J:ASP120 4.8 61.2 1.0
OG I:SER30 4.8 72.5 1.0
C J:THR124 4.8 55.8 1.0
C J:ILE119 4.9 52.9 1.0
CD2 I:LEU28 4.9 63.4 1.0
C J:GLN118 4.9 51.0 1.0
ND1 J:HIS133 5.0 55.5 1.0

Magnesium binding site 4 out of 7 in 4qvn

Go back to Magnesium Binding Sites List in 4qvn
Magnesium binding site 4 out of 7 in the Ycp BETA5-M45V Mutant 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 BETA5-M45V Mutant in Complex with Bortezomib within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg302

b:66.8
occ:1.00
 O W:ASP204 2.3 75.6 1.0
O K:ASP168 2.4 59.7 1.0
O K:ALA165 2.4 63.5 1.0
O K:SER171 2.9 56.9 1.0
C W:ASP204 3.1 73.1 1.0
C K:ASP168 3.3 58.9 1.0
CA W:ASP204 3.5 72.1 1.0
C K:ALA165 3.6 64.8 1.0
O K:HIS166 3.6 65.2 1.0
CA K:ALA169 3.7 60.3 1.0
CB W:ASP204 3.8 70.8 1.0
NH1 K:ARG19 3.9 84.9 1.0
N K:ALA169 3.9 59.8 1.0
O K:ALA169 4.0 62.7 1.0
C K:ALA169 4.0 62.4 1.0
C K:HIS166 4.0 63.6 1.0
OXT W:ASP204 4.1 82.5 1.0
C K:SER171 4.1 57.3 1.0
N K:ASP168 4.4 60.1 1.0
N K:HIS166 4.4 63.8 1.0
CA K:ASP168 4.4 58.7 1.0
CA K:ALA165 4.5 66.2 1.0
CA K:HIS166 4.5 63.1 1.0
CZ K:ARG19 4.5 84.7 1.0
C K:ARG167 4.6 61.2 1.0
N K:SER171 4.7 54.6 1.0
O K:ALA164 4.7 72.0 1.0
O K:ARG167 4.7 60.2 1.0
N K:ARG167 4.8 57.4 1.0
NH2 K:ARG19 4.8 88.4 1.0
N K:TYR170 4.8 63.4 1.0
N W:ASP204 4.9 71.2 1.0
CG W:ASP204 4.9 73.0 1.0
CA K:SER171 5.0 56.6 1.0
CB K:ALA169 5.0 59.0 1.0

Magnesium binding site 5 out of 7 in 4qvn

Go back to Magnesium Binding Sites List in 4qvn
Magnesium binding site 5 out of 7 in the Ycp BETA5-M45V Mutant 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 BETA5-M45V Mutant in Complex with Bortezomib within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg303

b:61.8
occ:1.00
 O K:ILE82 2.9 55.9 1.0
C K:ILE82 3.7 55.3 1.0
CB K:ASN85 3.7 50.7 1.0
CA K:ILE82 3.8 55.2 1.0
N K:LEU86 3.8 54.8 1.0
CG2 K:ILE82 3.9 56.2 1.0
CB K:LEU86 4.2 53.3 1.0
CA K:LEU86 4.3 52.8 1.0
C K:ASN85 4.3 51.8 1.0
CB K:ILE82 4.3 55.6 1.0
CH2 K:TRP58 4.4 55.3 1.0
CA K:ASN85 4.5 48.7 1.0
CG1 K:ILE82 4.7 55.0 1.0
O K:LYS81 4.7 50.9 1.0
CG K:ASN85 4.9 52.7 1.0
OD1 K:ASN85 4.9 56.3 1.0
O K:ASN85 5.0 51.0 1.0
N K:LEU83 5.0 55.0 1.0

Magnesium binding site 6 out of 7 in 4qvn

Go back to Magnesium Binding Sites List in 4qvn
Magnesium binding site 6 out of 7 in the Ycp BETA5-M45V Mutant 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 BETA5-M45V Mutant in Complex with Bortezomib within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg202

b:58.1
occ:1.00
 O N:SER169 2.6 50.5 1.0
O N:ILE163 2.7 55.8 1.0
O N:ASP166 2.9 57.3 1.0
NH1 N:ARG19 3.6 63.7 1.0
CD1 a:LEU34 3.6 64.7 1.0
C N:ILE163 3.8 57.1 1.0
C N:SER169 3.8 53.2 1.0
C N:ASP166 3.9 53.9 1.0
CG2 N:ILE163 4.0 57.7 1.0
CA N:GLY167 4.2 54.5 1.0
CZ N:ARG19 4.2 60.5 1.0
O N:GLY167 4.4 52.0 1.0
CA N:GLY170 4.4 57.1 1.0
CA N:ILE163 4.4 57.1 1.0
N N:GLY167 4.5 53.5 1.0
NH2 N:ARG19 4.5 60.3 1.0
C N:GLY167 4.5 53.4 1.0
N N:GLY170 4.6 54.2 1.0
N N:LYS164 4.8 59.0 1.0
CG a:LEU34 4.8 64.5 1.0
N N:SER169 4.8 54.5 1.0
CB N:ILE163 4.8 57.2 1.0
CA N:SER169 4.9 52.7 1.0
O N:LYS164 4.9 66.5 1.0
C N:LYS164 4.9 60.7 1.0
N N:ASP166 5.0 55.2 1.0

Magnesium binding site 7 out of 7 in 4qvn

Go back to Magnesium Binding Sites List in 4qvn
Magnesium binding site 7 out of 7 in the Ycp BETA5-M45V Mutant 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 BETA5-M45V Mutant in Complex with Bortezomib within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg301

b:65.0
occ:1.00
 O Z:VAL198 2.5 57.2 1.0
O Z:THR192 2.6 73.0 1.0
O Z:HIS195 2.7 57.0 1.0
C Z:THR192 3.6 69.5 1.0
CG2 Z:THR192 3.7 74.1 1.0
C Z:VAL198 3.7 63.7 1.0
C Z:HIS195 3.7 63.2 1.0
NH2 Z:ARG28 3.8 74.9 1.0
CA Z:ILE196 3.9 63.8 1.0
O Z:ILE196 3.9 67.2 1.0
CA Z:THR192 3.9 71.0 1.0
C Z:ILE196 4.0 63.3 1.0
O Z:ASP222 4.0 88.0 1.0
N Z:ILE196 4.2 63.0 1.0
N Z:VAL198 4.4 61.0 1.0
NH2 H:ARG19 4.4 77.0 1.0
CB Z:THR192 4.4 71.3 1.0
OD1 Z:ASP222 4.4 84.2 1.0
CA Z:VAL198 4.5 62.5 1.0
N Z:GLY199 4.7 64.6 1.0
CA Z:GLY199 4.7 67.9 1.0
CZ Z:ARG28 4.7 73.1 1.0
N Z:GLU193 4.8 62.8 1.0
C Z:ASP222 4.9 83.9 1.0
N Z:HIS195 4.9 65.4 1.0
N Z:GLN197 4.9 62.2 1.0
CA Z:HIS195 4.9 62.9 1.0
CB Z:VAL198 4.9 64.4 1.0
NH1 Z:ARG28 5.0 77.4 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 02:19:58 2024

Last articles

Cl in 5F4W
Cl in 5F62
Cl in 5F63
Cl in 5F4Q
Cl in 5F60
Cl in 5F5P
Cl in 5F53
Cl in 5F4U
Cl in 5F4S
Cl in 5F4R
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy