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Magnesium in PDB 4qvv: Ycp BETA5-A49V Mutant in Complex with Bortezomib

Enzymatic activity of Ycp BETA5-A49V Mutant in Complex with Bortezomib

All present enzymatic activity of Ycp BETA5-A49V Mutant in Complex with Bortezomib:
3.4.25.1;

Protein crystallography data

The structure of Ycp BETA5-A49V Mutant in Complex with Bortezomib, PDB code: 4qvv 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 (°) 136.520, 300.750, 145.350, 90.00, 113.24, 90.00
R / Rfree (%) 19.9 / 23.5

Other elements in 4qvv:

The structure of Ycp BETA5-A49V 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-A49V Mutant in Complex with Bortezomib (pdb code 4qvv). 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 BETA5-A49V Mutant in Complex with Bortezomib, PDB code: 4qvv:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 4qvv

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Magnesium binding site 1 out of 8 in the Ycp BETA5-A49V 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-A49V Mutant in Complex with Bortezomib within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:51.5
occ:1.00
O G:MET125 2.2 53.2 1.0
OG1 G:THR8 2.7 41.3 1.0
O G:ARG122 2.8 41.7 1.0
O G:TYR119 2.9 43.1 1.0
CG2 G:THR8 3.2 46.3 1.0
O G:ALA123 3.2 55.2 1.0
C G:MET125 3.3 50.8 1.0
CB G:THR8 3.5 45.2 1.0
C G:ALA123 3.7 50.5 1.0
CA G:ALA123 3.8 47.9 1.0
C G:ARG122 3.8 44.6 1.0
CA G:ARG126 4.0 45.1 1.0
N G:ARG126 4.1 46.3 1.0
C G:TYR119 4.1 41.8 1.0
N G:THR8 4.1 48.5 1.0
N G:MET125 4.3 52.9 1.0
N G:ALA123 4.3 45.4 1.0
CD G:PRO127 4.3 41.3 1.0
CA G:MET125 4.4 54.9 1.0
CA G:THR8 4.5 46.9 1.0
C G:ARG126 4.7 44.1 1.0
N G:TYR124 4.7 53.4 1.0
N G:PRO127 4.8 41.4 1.0
CA G:TYR119 4.9 40.5 1.0
C G:TYR124 5.0 50.8 1.0

Magnesium binding site 2 out of 8 in 4qvv

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Magnesium binding site 2 out of 8 in the Ycp BETA5-A49V 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-A49V Mutant in Complex with Bortezomib within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:63.8
occ:1.00
O I:SER180 2.7 50.0 1.0
O I:ASP177 2.8 44.8 1.0
O I:ALA174 2.9 47.5 1.0
OXT I:ASP204 3.6 59.1 1.0
C I:ALA174 3.8 52.9 1.0
C I:SER180 3.9 51.0 1.0
CA I:ASP175 3.9 54.6 1.0
C I:ASP177 4.0 47.6 1.0
N I:ASP175 4.3 56.3 1.0
C I:ASP175 4.3 53.5 1.0
O I:ASP175 4.4 54.0 1.0
CA I:GLY181 4.5 53.8 1.0
C I:ASP204 4.5 63.1 1.0
NH1 Y:ARG19 4.6 63.2 1.0
OD1 I:ASP175 4.6 62.3 1.0
N I:GLY181 4.6 51.4 1.0
N I:ASP177 4.6 49.4 1.0
O I:ASP204 4.6 64.6 1.0
NH2 Y:ARG19 4.7 69.5 1.0
O I:ALA178 4.8 53.6 1.0
CA I:ALA178 4.8 47.9 1.0
N I:SER180 4.8 50.6 1.0
N I:ALA178 4.8 45.8 1.0
CA I:ASP177 4.9 47.7 1.0
CA I:SER180 4.9 49.4 1.0
C I:ALA178 4.9 49.3 1.0
CA I:ALA174 4.9 50.6 1.0

Magnesium binding site 3 out of 8 in 4qvv

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Magnesium binding site 3 out of 8 in the Ycp BETA5-A49V 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-A49V Mutant in Complex with Bortezomib within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mg201

b:42.1
occ:1.00
OE1 J:GLN118 3.2 44.4 1.0
O J:THR124 3.7 44.2 1.0
CB J:ASP120 3.7 39.5 1.0
N J:ASP120 3.9 38.1 1.0
CG J:ASP120 3.9 41.1 1.0
OD2 J:ASP120 4.0 45.7 1.0
CD J:GLN118 4.0 40.1 1.0
CG J:GLN118 4.1 39.6 1.0
CE1 J:HIS133 4.1 41.5 1.0
CB J:THR124 4.3 44.3 1.0
O J:GLN118 4.4 39.2 1.0
CA J:ASP120 4.4 37.8 1.0
C J:ILE119 4.6 37.0 1.0
CG2 J:THR124 4.6 44.2 1.0
OD1 J:ASP120 4.6 42.5 1.0
C J:THR124 4.7 42.0 1.0
C J:GLN118 4.7 38.0 1.0
CG1 I:VAL35 4.7 49.8 1.0
CA J:ILE119 4.8 36.7 1.0
ND1 J:HIS133 4.8 39.4 1.0
N J:ILE119 4.9 35.8 1.0
CB J:GLN118 4.9 39.1 1.0
OG I:SER30 5.0 52.3 1.0

Magnesium binding site 4 out of 8 in 4qvv

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Magnesium binding site 4 out of 8 in the Ycp BETA5-A49V 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-A49V Mutant in Complex with Bortezomib within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg302

b:55.6
occ:1.00
O K:ASP168 2.2 44.5 1.0
O K:ALA165 2.4 48.7 1.0
O W:ASP204 2.5 57.1 1.0
C K:ASP168 3.1 46.3 1.0
O K:SER171 3.3 47.8 1.0
C W:ASP204 3.3 59.1 1.0
O K:HIS166 3.4 50.2 1.0
CA K:ALA169 3.6 49.1 1.0
C K:ALA165 3.6 47.0 1.0
CA W:ASP204 3.7 57.4 1.0
N K:ALA169 3.7 48.4 1.0
C K:HIS166 3.9 46.7 1.0
C K:ALA169 4.1 49.2 1.0
N K:ASP168 4.1 47.4 1.0
CB W:ASP204 4.2 56.2 1.0
NH1 K:ARG19 4.2 62.3 1.0
OXT W:ASP204 4.2 63.5 1.0
O K:ALA169 4.2 45.3 1.0
CA K:ASP168 4.2 45.4 1.0
C K:ARG167 4.3 48.3 1.0
CA K:HIS166 4.4 46.8 1.0
N K:HIS166 4.4 45.8 1.0
C K:SER171 4.4 48.1 1.0
N K:ARG167 4.5 46.3 1.0
CA K:ALA165 4.5 47.8 1.0
O K:ARG167 4.5 50.5 1.0
O K:ALA164 4.6 48.5 1.0
N K:SER171 4.8 47.7 1.0
CB K:ALA169 4.8 48.0 1.0
N K:TYR170 4.9 48.4 1.0
CA K:ARG167 4.9 46.3 1.0
CZ K:ARG19 4.9 62.2 1.0
NE1 W:TRP182 4.9 52.5 1.0

Magnesium binding site 5 out of 8 in 4qvv

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Magnesium binding site 5 out of 8 in the Ycp BETA5-A49V 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-A49V Mutant in Complex with Bortezomib within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg303

b:45.1
occ:1.00
O K:ILE82 2.9 43.7 1.0
C K:ILE82 3.7 39.5 1.0
CA K:ILE82 3.8 39.0 1.0
CB K:ASN85 3.8 36.0 1.0
N K:LEU86 3.8 36.0 1.0
CG2 K:ILE82 3.9 40.6 1.0
CB K:LEU86 4.2 35.4 1.0
CA K:LEU86 4.2 36.1 1.0
C K:ASN85 4.3 34.9 1.0
CB K:ILE82 4.4 40.2 1.0
CH2 K:TRP58 4.5 36.8 1.0
CA K:ASN85 4.6 34.4 1.0
O K:LYS81 4.7 38.7 1.0
CG1 K:ILE82 4.7 42.0 1.0
CG K:ASN85 4.9 37.1 1.0
OD1 K:ASN85 4.9 41.1 1.0
O K:ASN85 5.0 33.9 1.0

Magnesium binding site 6 out of 8 in 4qvv

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Magnesium binding site 6 out of 8 in the Ycp BETA5-A49V 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-A49V Mutant in Complex with Bortezomib within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg202

b:39.2
occ:1.00
O N:SER169 2.5 36.8 1.0
O N:ILE163 2.6 40.6 1.0
O N:ASP166 2.7 43.8 1.0
NH1 N:ARG19 3.6 42.9 1.0
C N:SER169 3.7 36.3 1.0
CD1 a:LEU34 3.7 47.3 1.0
C N:ILE163 3.7 40.4 1.0
C N:ASP166 3.8 39.4 1.0
CG2 N:ILE163 4.0 38.1 1.0
CA N:GLY167 4.1 39.0 1.0
O N:GLY167 4.3 36.7 1.0
CZ N:ARG19 4.3 41.0 1.0
N N:GLY167 4.3 38.3 1.0
C N:GLY167 4.4 37.0 1.0
CA N:ILE163 4.4 39.2 1.0
CA N:GLY170 4.4 38.7 1.0
N N:GLY170 4.5 36.4 1.0
N N:SER169 4.6 35.8 1.0
CA N:SER169 4.6 34.2 1.0
NH2 N:ARG19 4.7 43.1 1.0
N N:LYS164 4.8 41.8 1.0
CB N:ILE163 4.8 37.9 1.0
N N:ASP166 4.9 38.7 1.0
CG a:LEU34 4.9 47.1 1.0
CA N:ASP166 4.9 38.2 1.0
O N:LYS164 4.9 43.7 1.0
C N:LYS164 5.0 41.2 1.0
O a:HOH310 5.0 34.2 1.0

Magnesium binding site 7 out of 8 in 4qvv

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Magnesium binding site 7 out of 8 in the Ycp BETA5-A49V 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-A49V Mutant in Complex with Bortezomib within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Mg302

b:62.2
occ:1.00
O V:ILE163 2.2 47.5 1.0
O V:ASP166 2.3 48.2 1.0
OXT L:ASP222 2.4 59.4 1.0
C V:ASP166 3.1 46.0 1.0
C L:ASP222 3.2 62.8 1.0
O V:SER169 3.2 46.0 1.0
C V:ILE163 3.3 46.6 1.0
O V:TRP164 3.3 46.8 1.0
C V:TRP164 3.5 47.7 1.0
N V:ASP166 3.6 42.7 1.0
N V:LEU167 3.8 45.8 1.0
CA L:ASP222 3.8 65.4 1.0
O L:ASP222 3.9 69.6 1.0
CA V:LEU167 3.9 45.0 1.0
O V:GLY162 3.9 47.6 1.0
CA V:ASP166 3.9 43.0 1.0
CA V:TRP164 4.0 48.1 1.0
N V:ASN165 4.0 45.3 1.0
N V:TRP164 4.0 47.7 1.0
C V:ASN165 4.2 43.1 1.0
C V:SER169 4.3 43.8 1.0
CA V:ILE163 4.4 46.5 1.0
NH1 V:ARG19 4.5 52.1 1.0
CD2 V:LEU167 4.5 41.2 1.0
CA V:ASN165 4.6 43.6 1.0
CB L:ASP222 4.6 67.8 1.0
O L:ARG221 4.6 63.4 1.0
C V:LEU167 4.7 46.5 1.0
O V:ASN165 4.9 41.9 1.0
C V:GLY162 4.9 46.6 1.0
CB V:ASP166 4.9 40.8 1.0
N V:SER169 5.0 40.4 1.0

Magnesium binding site 8 out of 8 in 4qvv

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Magnesium binding site 8 out of 8 in the Ycp BETA5-A49V 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 8 of Ycp BETA5-A49V Mutant in Complex with Bortezomib within 5.0Å range:
probe atom residue distance (Å) B Occ
Y:Mg302

b:52.4
occ:1.00
O I:ASP204 2.3 64.6 1.0
O Y:ASP168 2.3 47.1 1.0
O Y:ALA165 2.4 45.8 1.0
O Y:SER171 3.0 43.7 1.0
C I:ASP204 3.1 63.1 1.0
C Y:ASP168 3.3 47.1 1.0
C Y:ALA165 3.6 47.9 1.0
CA I:ASP204 3.6 60.8 1.0
O Y:HIS166 3.6 54.8 1.0
CA Y:ALA169 3.7 47.2 1.0
N Y:ALA169 3.8 48.8 1.0
NH1 Y:ARG19 3.9 63.2 1.0
CB I:ASP204 4.0 63.1 1.0
C Y:ALA169 4.0 46.4 1.0
C Y:HIS166 4.1 50.5 1.0
OXT I:ASP204 4.1 59.1 1.0
O Y:ALA169 4.1 51.9 1.0
C Y:SER171 4.2 43.9 1.0
N Y:ASP168 4.3 47.6 1.0
CA Y:ASP168 4.4 46.1 1.0
CA Y:ALA165 4.5 47.8 1.0
N Y:HIS166 4.5 50.7 1.0
CA Y:HIS166 4.5 48.5 1.0
C Y:ARG167 4.6 48.1 1.0
N Y:SER171 4.6 41.6 1.0
CZ Y:ARG19 4.6 61.7 1.0
O Y:ALA164 4.7 47.2 1.0
N Y:ARG167 4.7 47.3 1.0
N Y:TYR170 4.9 43.2 1.0
O Y:ARG167 4.9 49.5 1.0
CA Y:SER171 4.9 39.6 1.0
NH2 Y:ARG19 4.9 69.5 1.0
CB Y:ALA169 5.0 45.6 1.0
N I:ASP204 5.0 57.5 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: Mon Dec 14 19:25:56 2020

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