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Magnesium in PDB 4qvp: Ycp BETA5-M45T Mutant in Complex with Bortezomib

Enzymatic activity of Ycp BETA5-M45T Mutant in Complex with Bortezomib

All present enzymatic activity of Ycp BETA5-M45T Mutant in Complex with Bortezomib:
3.4.25.1;

Protein crystallography data

The structure of Ycp BETA5-M45T Mutant in Complex with Bortezomib, PDB code: 4qvp 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 / 2.30
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 136.100, 300.820, 144.820, 90.00, 113.06, 90.00
R / Rfree (%) 20.6 / 22.5

Other elements in 4qvp:

The structure of Ycp BETA5-M45T 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-M45T Mutant in Complex with Bortezomib (pdb code 4qvp). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 9 binding sites of Magnesium where determined in the Ycp BETA5-M45T Mutant in Complex with Bortezomib, PDB code: 4qvp:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Magnesium binding site 1 out of 9 in 4qvp

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Magnesium binding site 1 out of 9 in the Ycp BETA5-M45T 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-M45T Mutant in Complex with Bortezomib within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:47.4
occ:1.00
O G:MET125 2.2 42.2 1.0
O G:ARG122 2.2 41.1 1.0
O G:HOH421 2.4 36.0 1.0
O G:TYR119 2.5 34.3 1.0
OG1 G:THR8 2.6 37.7 1.0
CG2 G:THR8 3.3 39.4 1.0
C G:ARG122 3.4 41.8 1.0
C G:MET125 3.4 43.2 1.0
CB G:THR8 3.5 39.2 1.0
O G:ALA123 3.5 45.9 1.0
C G:TYR119 3.6 34.4 1.0
CA G:ALA123 3.7 43.1 1.0
C G:ALA123 3.7 44.7 1.0
N G:ALA123 4.0 41.9 1.0
N G:MET125 4.2 45.2 1.0
N G:ARG126 4.3 39.9 1.0
CA G:ARG126 4.3 38.8 1.0
CA G:MET125 4.3 46.6 1.0
N G:THR8 4.3 41.6 1.0
CA G:TYR119 4.4 33.5 1.0
CA G:THR8 4.5 41.1 1.0
CA G:ARG122 4.6 43.8 1.0
N G:ARG122 4.6 41.0 1.0
CD G:PRO127 4.6 35.4 1.0
N G:TYR124 4.6 45.8 1.0
N G:THR120 4.7 34.5 1.0
CB G:MET125 4.8 52.2 1.0
CA G:THR120 4.8 34.1 1.0
C G:ARG126 4.9 36.9 1.0
C G:THR120 4.9 34.8 1.0
CB G:TYR119 4.9 33.3 1.0

Magnesium binding site 2 out of 9 in 4qvp

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Magnesium binding site 2 out of 9 in the Ycp BETA5-M45T 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-M45T Mutant in Complex with Bortezomib within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:51.8
occ:1.00
O I:ASP177 2.4 37.6 1.0
O I:SER180 2.4 41.9 1.0
O I:ALA174 2.7 42.6 1.0
C I:ASP177 3.6 38.0 1.0
C I:SER180 3.6 41.9 1.0
C I:ALA174 3.7 41.5 1.0
OXT I:ASP204 3.9 57.6 1.0
CA I:ASP175 4.1 42.0 1.0
N I:ASP175 4.3 42.5 1.0
N I:ASP177 4.4 39.5 1.0
O I:ALA178 4.4 40.3 1.0
N I:SER180 4.4 39.8 1.0
CA I:ALA178 4.4 38.3 1.0
N I:ALA178 4.4 37.7 1.0
C I:ALA178 4.4 38.6 1.0
C I:ASP175 4.4 41.1 1.0
N I:GLY181 4.5 43.0 1.0
CA I:ASP177 4.5 39.5 1.0
CA I:SER180 4.5 40.9 1.0
CA I:GLY181 4.5 44.1 1.0
O I:ASP175 4.6 41.3 1.0
NH1 Y:ARG19 4.7 52.9 1.0
CA I:ALA174 4.8 40.0 1.0
C I:ASP204 4.8 55.1 1.0
O I:ASP204 4.8 54.8 1.0
NH2 Y:ARG19 4.9 57.9 1.0
OD1 I:ASP175 4.9 45.3 1.0
CB I:SER180 5.0 42.6 1.0

Magnesium binding site 3 out of 9 in 4qvp

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Magnesium binding site 3 out of 9 in the Ycp BETA5-M45T 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-M45T Mutant in Complex with Bortezomib within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mg201

b:46.2
occ:1.00
OE1 J:GLN118 3.6 37.5 1.0
O J:THR124 3.6 36.7 1.0
CB J:ASP120 3.7 34.2 1.0
CG J:ASP120 3.8 35.7 1.0
OD2 J:ASP120 3.8 39.1 1.0
N J:ASP120 3.9 32.2 1.0
CB J:THR124 4.1 36.6 1.0
CD J:GLN118 4.3 35.7 1.0
CE1 J:HIS133 4.3 33.6 1.0
CG2 J:THR124 4.3 36.8 1.0
CG J:GLN118 4.3 34.4 1.0
CA J:ASP120 4.4 32.7 1.0
O J:GLN118 4.5 32.2 1.0
OD1 J:ASP120 4.5 36.1 1.0
C J:THR124 4.6 36.5 1.0
C J:ILE119 4.6 32.4 1.0
C J:GLN118 4.8 32.7 1.0
CA J:ILE119 4.8 30.9 1.0
CG1 I:VAL35 4.8 44.3 1.0
OG I:SER30 5.0 50.9 1.0
OG1 J:THR124 5.0 37.5 1.0

Magnesium binding site 4 out of 9 in 4qvp

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Magnesium binding site 4 out of 9 in the Ycp BETA5-M45T 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-M45T Mutant in Complex with Bortezomib within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg302

b:44.7
occ:1.00
O K:ASP168 2.2 41.2 1.0
O K:SER171 2.3 41.1 1.0
O W:ASP204 2.3 49.1 1.0
O K:ALA165 2.4 43.3 1.0
O K:HOH423 2.5 40.1 1.0
C W:ASP204 3.3 50.5 1.0
C K:ASP168 3.3 40.6 1.0
C K:SER171 3.5 40.0 1.0
NH1 K:ARG19 3.5 55.6 1.0
C K:ALA165 3.6 44.2 1.0
CA K:ALA169 3.7 41.3 1.0
CA W:ASP204 3.7 50.7 1.0
O K:ALA169 3.8 43.6 1.0
C K:ALA169 3.8 42.2 1.0
CB W:ASP204 3.9 50.5 1.0
N K:ALA169 3.9 40.3 1.0
N K:SER171 4.1 39.7 1.0
CZ K:ARG19 4.2 55.4 1.0
O K:HIS166 4.2 44.0 1.0
CA K:ALA165 4.3 44.7 1.0
OXT W:ASP204 4.3 49.7 1.0
CA K:SER171 4.3 39.1 1.0
CA K:ASP168 4.5 40.4 1.0
N K:ASP168 4.5 41.5 1.0
N K:GLY172 4.5 40.9 1.0
NH2 K:ARG19 4.5 60.2 1.0
C K:HIS166 4.5 44.0 1.0
N K:TYR170 4.6 41.3 1.0
O K:ALA164 4.6 45.0 1.0
N K:HIS166 4.6 44.0 1.0
CA K:GLY172 4.6 42.3 1.0
CB K:SER171 4.8 38.9 1.0
CA K:HIS166 4.9 44.4 1.0
CG W:ASP204 4.9 49.5 1.0
NE K:ARG19 4.9 51.8 1.0

Magnesium binding site 5 out of 9 in 4qvp

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Magnesium binding site 5 out of 9 in the Ycp BETA5-M45T 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-M45T Mutant in Complex with Bortezomib within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg303

b:45.6
occ:1.00
O K:HOH443 2.5 49.0 1.0
O K:ILE82 2.8 34.3 1.0
O K:HOH466 2.9 45.9 1.0
C K:ILE82 3.7 32.4 1.0
N K:LEU86 3.7 29.6 1.0
CG2 K:ILE82 3.8 33.1 1.0
CA K:ILE82 3.8 32.5 1.0
CB K:LEU86 4.0 29.8 1.0
CB K:ASN85 4.0 29.4 1.0
CA K:LEU86 4.1 29.6 1.0
CH2 K:TRP58 4.1 32.3 1.0
C K:ASN85 4.3 29.1 1.0
CB K:ILE82 4.3 33.1 1.0
CA K:ASN85 4.7 28.7 1.0
CG1 K:ILE82 4.8 33.9 1.0
CZ3 K:TRP58 4.8 32.1 1.0
O K:LYS81 4.9 33.9 1.0
O K:HOH428 4.9 45.3 1.0
CG K:LEU86 4.9 29.8 1.0
O K:HOH440 4.9 44.4 1.0
N K:LEU83 5.0 32.0 1.0
O K:ASN85 5.0 29.4 1.0
CD2 K:LEU86 5.0 30.1 1.0
CZ2 K:TRP58 5.0 32.3 1.0

Magnesium binding site 6 out of 9 in 4qvp

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Magnesium binding site 6 out of 9 in the Ycp BETA5-M45T 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-M45T Mutant in Complex with Bortezomib within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg202

b:41.1
occ:1.00
O N:ILE163 2.5 37.3 1.0
O N:SER169 2.5 36.9 1.0
O N:ASP166 2.7 38.2 1.0
C N:ILE163 3.6 38.7 1.0
CD1 a:LEU34 3.6 42.8 1.0
NH1 N:ARG19 3.6 40.5 1.0
C N:SER169 3.7 35.4 1.0
C N:ASP166 3.8 35.7 1.0
CG2 N:ILE163 3.9 37.6 1.0
CA N:GLY167 4.2 35.8 1.0
CA N:ILE163 4.2 38.0 1.0
CZ N:ARG19 4.4 39.5 1.0
O N:GLY167 4.4 36.3 1.0
CA N:GLY170 4.4 37.1 1.0
N N:GLY167 4.4 34.8 1.0
C N:GLY167 4.5 35.9 1.0
N N:GLY170 4.5 36.1 1.0
N N:LYS164 4.7 40.4 1.0
N N:SER169 4.7 34.6 1.0
CA N:SER169 4.7 33.9 1.0
NH2 N:ARG19 4.7 39.9 1.0
CB N:ILE163 4.7 37.4 1.0
N N:ASP166 4.8 35.7 1.0
C N:LYS164 4.8 40.8 1.0
O N:LYS164 4.8 41.4 1.0
CG a:LEU34 4.9 42.6 1.0
CA N:ASP166 4.9 35.8 1.0
CA N:LYS164 4.9 41.6 1.0

Magnesium binding site 7 out of 9 in 4qvp

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Magnesium binding site 7 out of 9 in the Ycp BETA5-M45T 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-M45T Mutant in Complex with Bortezomib within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Mg302

b:45.8
occ:1.00
O V:ASP166 2.1 36.6 1.0
O V:SER169 2.2 35.2 1.0
O V:ILE163 2.3 42.7 1.0
OXT L:ASP222 2.3 52.0 1.0
O V:HOH403 2.5 43.4 1.0
C L:ASP222 3.1 56.5 1.0
C V:ASP166 3.2 36.1 1.0
C V:ILE163 3.3 41.8 1.0
C V:SER169 3.3 36.4 1.0
NH1 V:ARG19 3.8 43.2 1.0
O V:GLY162 3.8 37.1 1.0
CA L:ASP222 3.8 57.7 1.0
CA V:LEU167 3.9 35.2 1.0
N V:LEU167 3.9 35.6 1.0
O L:ASP222 3.9 56.7 1.0
CA V:ILE163 4.1 41.0 1.0
N V:ASP166 4.1 37.9 1.0
N V:SER169 4.2 35.7 1.0
N V:GLY170 4.2 38.8 1.0
C V:LEU167 4.2 35.9 1.0
CA V:SER169 4.2 35.8 1.0
CA V:ASP166 4.2 36.6 1.0
CA V:GLY170 4.2 40.8 1.0
O V:HOH418 4.3 46.2 1.0
N V:TRP164 4.3 41.6 1.0
CB L:ASP222 4.3 58.0 1.0
C V:TRP164 4.4 43.1 1.0
CZ V:ARG19 4.4 44.5 1.0
O V:LEU167 4.4 39.0 1.0
O V:TRP164 4.5 45.2 1.0
CA V:TRP164 4.5 42.7 1.0
NH2 V:ARG19 4.6 47.1 1.0
CB V:SER169 4.7 35.9 1.0
N V:ASN165 4.7 41.1 1.0
C V:GLY162 4.8 38.2 1.0
C V:ASN165 4.9 38.5 1.0
N V:GLY168 4.9 35.1 1.0
N V:ILE163 4.9 39.4 1.0
CB V:ASP166 5.0 35.9 1.0

Magnesium binding site 8 out of 9 in 4qvp

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Magnesium binding site 8 out of 9 in the Ycp BETA5-M45T 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-M45T Mutant in Complex with Bortezomib within 5.0Å range:
probe atom residue distance (Å) B Occ
Y:Mg302

b:48.9
occ:1.00
O Y:ASP168 2.2 38.6 1.0
O Y:SER171 2.3 40.1 1.0
O I:ASP204 2.4 54.8 1.0
O Y:ALA165 2.4 39.5 1.0
O I:HOH471 3.2 53.8 1.0
C I:ASP204 3.3 55.1 1.0
C Y:ASP168 3.3 38.8 1.0
C Y:SER171 3.5 38.1 1.0
C Y:ALA165 3.5 39.8 1.0
NH1 Y:ARG19 3.6 52.9 1.0
CA I:ASP204 3.7 54.3 1.0
CA Y:ALA169 3.7 39.9 1.0
O Y:ALA169 3.8 41.4 1.0
C Y:ALA169 3.8 41.1 1.0
CB I:ASP204 3.9 54.9 1.0
N Y:ALA169 3.9 39.5 1.0
N Y:SER171 4.1 37.7 1.0
CZ Y:ARG19 4.2 53.5 1.0
O Y:HIS166 4.2 40.6 1.0
CA Y:ALA165 4.2 39.6 1.0
CA Y:SER171 4.3 36.6 1.0
OXT I:ASP204 4.3 57.6 1.0
CA Y:ASP168 4.5 38.0 1.0
N Y:GLY172 4.5 39.3 1.0
NH2 Y:ARG19 4.5 57.9 1.0
N Y:ASP168 4.5 38.4 1.0
C Y:HIS166 4.5 40.7 1.0
N Y:TYR170 4.6 40.8 1.0
N Y:HIS166 4.6 40.5 1.0
O Y:ALA164 4.6 38.5 1.0
CA Y:GLY172 4.6 40.8 1.0
CB Y:SER171 4.8 34.4 1.0
CA Y:HIS166 4.8 40.7 1.0
CG I:ASP204 4.9 53.5 1.0
NE Y:ARG19 4.9 49.9 1.0

Magnesium binding site 9 out of 9 in 4qvp

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Magnesium binding site 9 out of 9 in the Ycp BETA5-M45T 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 9 of Ycp BETA5-M45T Mutant in Complex with Bortezomib within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg301

b:58.1
occ:1.00
O Z:HOH424 2.3 38.4 1.0
O Z:VAL198 2.4 47.3 1.0
O Z:HIS195 2.5 39.6 1.0
O Z:THR192 2.8 47.9 1.0
C Z:HIS195 3.5 41.3 1.0
C Z:VAL198 3.6 46.9 1.0
NH2 Z:ARG28 3.6 55.2 1.0
CA Z:ILE196 3.6 41.9 1.0
O Z:ILE196 3.7 39.9 1.0
O Z:HOH452 3.8 41.2 1.0
C Z:ILE196 3.8 40.6 1.0
C Z:THR192 3.8 50.0 1.0
CG2 Z:THR192 3.9 53.5 1.0
N Z:ILE196 4.0 40.5 1.0
CA Z:THR192 4.1 50.8 1.0
N Z:VAL198 4.1 43.0 1.0
O Z:ASP222 4.2 57.0 1.0
CA Z:VAL198 4.4 45.2 1.0
NH2 H:ARG19 4.5 49.5 1.0
N Z:GLY199 4.6 48.0 1.0
N Z:GLN197 4.6 39.9 1.0
CZ Z:ARG28 4.6 54.8 1.0
CB Z:THR192 4.7 52.3 1.0
OD1 Z:ASP222 4.7 53.1 1.0
CA Z:GLY199 4.7 49.5 1.0
CA Z:HIS195 4.8 42.9 1.0
CB Z:VAL198 4.8 46.0 1.0
N Z:HIS195 4.9 43.5 1.0
CB Z:ILE196 4.9 41.7 1.0
NH1 Z:ARG28 4.9 55.8 1.0
C Z:ASP222 5.0 57.9 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 19:25:44 2020

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