Atomistry » Magnesium » PDB 4qq8-4qwi » 4qv3
Atomistry »
  Magnesium »
    PDB 4qq8-4qwi »
      4qv3 »

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

Go back to Magnesium Binding Sites List in 4qv3
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

Go back to Magnesium Binding Sites List in 4qv3
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

Last articles

Ca in 5UDJ
Ca in 5UDI
Ca in 5UD0
Ca in 5UBJ
Ca in 5UBO
Ca in 5U95
Ca in 5UBA
Ca in 5UB5
Ca in 5U8O
Ca in 5U6J
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy