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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

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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

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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

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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

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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

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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

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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

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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

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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: Mon Dec 14 19:25:31 2020

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