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Magnesium in PDB 4qv3: Ycp BETA5-M45V Mutant

Enzymatic activity of Ycp BETA5-M45V Mutant

All present enzymatic activity of Ycp BETA5-M45V Mutant:
3.4.25.1;

Protein crystallography data

The structure of Ycp BETA5-M45V Mutant, PDB code: 4qv3 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 / 3.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 134.850, 301.410, 143.560, 90.00, 112.97, 90.00
R / Rfree (%) 17.1 / 21.1

Other elements in 4qv3:

The structure of Ycp BETA5-M45V Mutant also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Ycp BETA5-M45V Mutant (pdb code 4qv3). 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, PDB code: 4qv3:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 4qv3

Go back to Magnesium Binding Sites List in 4qv3
Magnesium binding site 1 out of 7 in the Ycp BETA5-M45V Mutant


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:56.9
occ:1.00
 O G:MET125 2.2 68.8 1.0
O G:ARG122 2.4 60.4 1.0
OG1 G:THR8 2.5 64.5 1.0
O G:TYR119 2.8 53.9 1.0
O G:ALA123 3.2 73.6 1.0
CG2 G:THR8 3.3 60.7 1.0
C G:MET125 3.4 64.6 1.0
CB G:THR8 3.5 60.8 1.0
C G:ALA123 3.5 67.0 1.0
C G:ARG122 3.5 62.8 1.0
CA G:ALA123 3.5 64.1 1.0
N G:ALA123 4.0 63.2 1.0
C G:TYR119 4.0 51.5 1.0
N G:THR8 4.1 61.8 1.0
N G:MET125 4.1 68.3 1.0
N G:ARG126 4.2 57.3 1.0
CA G:ARG126 4.3 57.6 1.0
CA G:MET125 4.3 69.0 1.0
CA G:THR8 4.4 61.0 1.0
N G:TYR124 4.4 68.4 1.0
CD G:PRO127 4.7 55.6 1.0
CA G:TYR119 4.8 49.6 1.0
CA G:ARG122 4.8 64.2 1.0
CB G:ALA123 4.8 63.8 1.0
C G:TYR124 4.8 64.0 1.0
N G:ARG122 4.9 62.8 1.0
CB G:MET125 4.9 74.6 1.0
C G:ARG126 4.9 59.1 1.0
N G:THR120 5.0 51.4 1.0

Magnesium binding site 2 out of 7 in 4qv3

Go back to Magnesium Binding Sites List in 4qv3
Magnesium binding site 2 out of 7 in the Ycp BETA5-M45V Mutant


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mg201

b:78.6
occ:1.00
 OE1 J:GLN118 2.9 55.8 1.0
O J:THR124 3.2 49.5 1.0
N J:ASP120 3.6 44.6 1.0
CG J:GLN118 3.6 46.8 1.0
CD J:GLN118 3.7 49.3 1.0
CB J:ASP120 3.7 50.8 1.0
CE1 J:HIS133 3.8 48.9 1.0
O J:GLN118 4.0 47.2 1.0
CG J:ASP120 4.0 53.6 1.0
C J:ILE119 4.1 43.9 1.0
OD2 J:ASP120 4.2 61.4 1.0
C J:GLN118 4.2 44.7 1.0
CA J:ASP120 4.2 46.6 1.0
CA J:ILE119 4.3 42.6 1.0
N J:ILE119 4.3 42.6 1.0
C J:THR124 4.4 46.7 1.0
CB J:THR124 4.4 45.8 1.0
CB J:GLN118 4.5 45.6 1.0
ND1 J:HIS133 4.6 47.4 1.0
CG2 J:THR124 4.7 44.3 1.0
NE2 J:HIS133 4.7 48.3 1.0
OD1 J:ASP120 4.7 56.7 1.0
CG1 I:VAL35 4.8 52.2 1.0
NE2 J:GLN118 5.0 50.7 1.0
O J:ILE119 5.0 46.6 1.0
CA J:GLN118 5.0 44.3 1.0
CA J:THR124 5.0 45.0 1.0

Magnesium binding site 3 out of 7 in 4qv3

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Magnesium binding site 3 out of 7 in the Ycp BETA5-M45V Mutant


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg201

b:52.0
occ:1.00
 O N:ILE163 2.7 55.0 1.0
O N:SER169 2.8 52.3 1.0
O N:ASP166 3.1 55.4 1.0
NH1 N:ARG19 3.5 51.0 1.0
CD1 a:LEU34 3.5 55.3 1.0
C N:ILE163 3.8 52.3 1.0
CG2 N:ILE163 3.9 51.7 1.0
C N:SER169 4.0 50.5 1.0
CZ N:ARG19 4.1 51.5 1.0
C N:ASP166 4.1 52.6 1.0
CA N:GLY167 4.2 51.9 1.0
NH2 N:ARG19 4.3 53.8 1.0
CA N:GLY170 4.4 52.8 1.0
O N:GLY167 4.5 51.3 1.0
CA N:ILE163 4.5 51.7 1.0
N N:GLY167 4.6 52.6 1.0
C N:GLY167 4.6 51.1 1.0
N N:GLY170 4.7 52.0 1.0
CG a:LEU34 4.8 56.0 1.0
N N:LYS164 4.9 55.4 1.0
CB N:ILE163 4.9 50.8 1.0
O N:LYS164 5.0 59.2 1.0

Magnesium binding site 4 out of 7 in 4qv3

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Magnesium binding site 4 out of 7 in the Ycp BETA5-M45V Mutant


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg202

b:61.5
occ:1.00
 OE1 H:GLN91 2.6 62.9 1.0
OD1 N:ASP51 3.0 40.0 1.0
O N:ASN92 3.5 57.2 1.0
CD H:GLN91 3.5 60.2 1.0
OD2 N:ASP51 3.5 50.4 1.0
CG N:ASP51 3.7 32.2 1.0
NE2 H:GLN91 3.7 61.4 1.0
C N:ASN92 4.6 56.8 1.0
CG H:GLN91 4.9 55.9 1.0
CE1 H:PHE88 4.9 43.2 1.0

Magnesium binding site 5 out of 7 in 4qv3

Go back to Magnesium Binding Sites List in 4qv3
Magnesium binding site 5 out of 7 in the Ycp BETA5-M45V Mutant


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Mg301

b:64.3
occ:1.00
 OXT L:ASP222 2.0 84.4 1.0
O V:ASP166 2.2 53.1 1.0
O V:ILE163 2.2 58.9 1.0
O V:SER169 2.8 52.7 1.0
C L:ASP222 3.0 82.6 1.0
C V:ASP166 3.1 54.1 1.0
C V:ILE163 3.4 61.2 1.0
O V:TRP164 3.7 65.0 1.0
CA V:LEU167 3.7 54.1 1.0
CA L:ASP222 3.7 81.6 1.0
N V:LEU167 3.8 53.7 1.0
C V:TRP164 3.9 62.6 1.0
O L:ASP222 3.9 83.9 1.0
C V:SER169 4.0 54.4 1.0
O V:GLY162 4.0 64.2 1.0
N V:ASP166 4.0 55.9 1.0
NH1 V:ARG19 4.1 71.3 1.0
N V:TRP164 4.2 61.9 1.0
CA V:ASP166 4.2 54.5 1.0
CA V:TRP164 4.2 62.2 1.0
C V:LEU167 4.2 54.7 1.0
CA V:ILE163 4.3 60.4 1.0
O V:LEU167 4.4 53.6 1.0
CB L:ASP222 4.4 82.0 1.0
N V:ASN165 4.4 59.4 1.0
C V:ASN165 4.6 56.2 1.0
N V:SER169 4.6 54.7 1.0
O L:ARG221 4.7 81.4 1.0
CD2 V:LEU167 4.8 52.5 1.0
CZ V:ARG19 4.8 69.8 1.0
CA V:SER169 4.8 55.0 1.0
CA V:GLY170 4.8 59.3 1.0
N V:GLY170 4.9 55.5 1.0
C V:GLY162 4.9 61.3 1.0
N L:ASP222 5.0 79.6 1.0

Magnesium binding site 6 out of 7 in 4qv3

Go back to Magnesium Binding Sites List in 4qv3
Magnesium binding site 6 out of 7 in the Ycp BETA5-M45V Mutant


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
Y:Mg301

b:67.3
occ:1.00
 O Y:ASP168 2.3 53.5 1.0
O Y:ALA165 2.3 55.6 1.0
O Y:SER171 3.1 58.6 1.0
C Y:ASP168 3.2 52.4 1.0
CB I:ASP204 3.3 71.1 1.0
CG I:ASP204 3.4 84.2 1.0
OD2 I:ASP204 3.5 95.8 1.0
C Y:ALA165 3.6 55.4 1.0
CA Y:ALA169 3.6 53.9 1.0
O Y:HIS166 3.6 46.1 1.0
CA I:ASP204 3.7 72.4 1.0
N Y:ALA169 3.8 54.5 1.0
C Y:ALA169 4.0 51.9 1.0
O Y:ALA169 4.0 53.2 1.0
O I:ASP204 4.0 95.5 1.0
C Y:HIS166 4.0 52.2 1.0
NH1 Y:ARG19 4.0 70.5 1.0
OD1 I:ASP204 4.1 88.6 1.0
C Y:SER171 4.3 58.8 1.0
C I:ASP204 4.3 86.6 1.0
N Y:ASP168 4.3 53.1 1.0
CA Y:ASP168 4.4 51.6 1.0
N Y:HIS166 4.5 55.8 1.0
CA Y:HIS166 4.5 54.4 1.0
CA Y:ALA165 4.5 53.8 1.0
C Y:ARG167 4.5 53.7 1.0
N Y:SER171 4.6 54.6 1.0
O Y:ALA164 4.7 53.9 1.0
N Y:ARG167 4.7 51.5 1.0
O Y:ARG167 4.8 52.1 1.0
N Y:TYR170 4.8 52.0 1.0
CZ Y:ARG19 4.8 68.6 1.0
CB Y:ALA169 4.9 53.1 1.0
CA Y:SER171 5.0 54.6 1.0

Magnesium binding site 7 out of 7 in 4qv3

Go back to Magnesium Binding Sites List in 4qv3
Magnesium binding site 7 out of 7 in the Ycp BETA5-M45V Mutant


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg301

b:68.8
occ:1.00
 O Z:VAL198 2.5 61.5 1.0
O Z:HIS195 2.6 53.9 1.0
O Z:THR192 2.9 67.2 1.0
O Z:ILE196 3.5 67.7 1.0
O Z:ASP222 3.6 92.1 1.0
NH2 Z:ARG28 3.6 71.8 1.0
CA Z:ILE196 3.7 60.5 1.0
C Z:HIS195 3.7 60.4 1.0
C Z:VAL198 3.7 62.2 1.0
C Z:ILE196 3.7 63.5 1.0
C Z:THR192 3.9 69.2 1.0
CG2 Z:THR192 4.0 72.5 1.0
N Z:ILE196 4.1 58.7 1.0
CA Z:THR192 4.2 69.4 1.0
N Z:VAL198 4.2 59.5 1.0
NH2 H:ARG19 4.3 76.2 1.0
CA Z:VAL198 4.5 60.4 1.0
N Z:GLN197 4.6 61.4 1.0
OD1 Z:ASP222 4.6 84.1 1.0
CZ Z:ARG28 4.7 68.7 1.0
N Z:GLY199 4.7 62.2 1.0
C Z:ASP222 4.7 91.2 1.0
CB Z:THR192 4.8 70.9 1.0
CA Z:GLY199 4.8 62.6 1.0
NH1 H:ARG19 4.8 81.0 1.0
NH1 Z:ARG28 4.9 69.8 1.0
CZ H:ARG19 4.9 75.8 1.0
CA Z:HIS195 4.9 61.3 1.0
CB Z:ILE196 4.9 59.6 1.0
N Z:HIS195 5.0 63.1 1.0
CB Z:VAL198 5.0 60.7 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 02:14:18 2024

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