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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

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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

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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

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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

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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

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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

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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

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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

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