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Magnesium in PDB 4qux: Ycp BETA5-A49T-Mutant

Enzymatic activity of Ycp BETA5-A49T-Mutant

All present enzymatic activity of Ycp BETA5-A49T-Mutant:
3.4.25.1;

Protein crystallography data

The structure of Ycp BETA5-A49T-Mutant, PDB code: 4qux 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 (°) 135.640, 301.150, 145.230, 90.00, 112.89, 90.00
R / Rfree (%) 16.8 / 19.7

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Ycp BETA5-A49T-Mutant (pdb code 4qux). 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-A49T-Mutant, PDB code: 4qux:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Magnesium binding site 1 out of 9 in 4qux

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Magnesium binding site 1 out of 9 in the Ycp BETA5-A49T-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-A49T-Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:63.2
occ:1.00
 O G:MET125 2.1 60.0 1.0
OG1 G:THR8 2.6 56.1 1.0
O G:ARG122 2.6 52.4 1.0
O G:TYR119 2.6 50.2 1.0
CG2 G:THR8 3.2 56.2 1.0
C G:MET125 3.3 57.5 1.0
CB G:THR8 3.4 55.0 1.0
O G:ALA123 3.5 65.2 1.0
C G:ARG122 3.7 54.2 1.0
C G:ALA123 3.8 58.8 1.0
CA G:ALA123 3.8 56.8 1.0
C G:TYR119 3.8 50.1 1.0
CA G:ARG126 4.1 52.4 1.0
N G:ARG126 4.1 52.2 1.0
N G:THR8 4.2 57.4 1.0
N G:ALA123 4.2 55.6 1.0
N G:MET125 4.2 60.1 1.0
CA G:MET125 4.3 62.0 1.0
CA G:THR8 4.4 56.4 1.0
CD G:PRO127 4.5 49.8 1.0
CA G:TYR119 4.6 48.4 1.0
N G:TYR124 4.7 59.2 1.0
C G:ARG126 4.7 52.9 1.0
N G:THR120 4.8 49.8 1.0
CB G:MET125 4.9 67.2 1.0
N G:PRO127 4.9 50.6 1.0
CA G:ARG122 4.9 55.9 1.0
CA G:THR120 4.9 48.7 1.0
N G:ARG122 5.0 54.6 1.0

Magnesium binding site 2 out of 9 in 4qux

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Magnesium binding site 2 out of 9 in the Ycp BETA5-A49T-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-A49T-Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:72.0
occ:1.00
 O I:ASP177 2.7 54.3 1.0
O I:SER180 2.8 53.3 1.0
O I:ALA174 3.0 56.2 1.0
OXT I:ASP204 3.7 72.7 1.0
C I:ASP177 3.8 53.3 1.0
C I:ALA174 4.0 56.6 1.0
C I:SER180 4.0 53.9 1.0
CA I:ASP175 4.2 56.2 1.0
NH1 Y:ARG19 4.3 62.8 1.0
O I:ASP204 4.3 64.2 1.0
O I:ALA178 4.4 60.3 1.0
C I:ASP204 4.4 66.1 1.0
CA I:ALA178 4.4 52.4 1.0
C I:ASP175 4.5 56.0 1.0
NH2 Y:ARG19 4.5 64.1 1.0
O I:ASP175 4.5 59.1 1.0
C I:ALA178 4.5 54.1 1.0
N I:ALA178 4.5 49.7 1.0
N I:ASP175 4.5 57.0 1.0
N I:ASP177 4.6 53.8 1.0
CZ Y:ARG19 4.8 62.5 1.0
N I:SER180 4.8 50.5 1.0
CA I:ASP177 4.8 53.2 1.0
OD1 I:ASP175 4.8 54.9 1.0
CA I:GLY181 4.8 56.0 1.0
N I:GLY181 4.9 53.9 1.0
CA I:SER180 5.0 52.8 1.0

Magnesium binding site 3 out of 9 in 4qux

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Magnesium binding site 3 out of 9 in the Ycp BETA5-A49T-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-A49T-Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mg201

b:68.9
occ:1.00
 O J:THR124 3.2 47.0 1.0
OE1 J:GLN118 3.2 52.2 1.0
N J:ASP120 3.4 43.2 1.0
CB J:ASP120 3.6 46.5 1.0
CG J:ASP120 3.8 48.4 1.0
CG J:GLN118 3.8 46.1 1.0
CE1 J:HIS133 3.9 44.2 1.0
CD J:GLN118 3.9 47.5 1.0
OD2 J:ASP120 4.0 51.3 1.0
O J:GLN118 4.0 44.6 1.0
C J:ILE119 4.1 42.8 1.0
CA J:ASP120 4.1 44.1 1.0
CB J:THR124 4.2 46.3 1.0
CA J:ILE119 4.2 41.9 1.0
C J:THR124 4.2 45.8 1.0
C J:GLN118 4.3 42.9 1.0
OD1 J:ASP120 4.4 53.2 1.0
N J:ILE119 4.4 41.5 1.0
CG2 J:THR124 4.5 45.4 1.0
CB J:GLN118 4.7 44.6 1.0
ND1 J:HIS133 4.7 44.4 1.0
NE2 J:HIS133 4.8 43.0 1.0
CA J:THR124 4.8 44.5 1.0
O J:ILE119 5.0 44.8 1.0
CG1 I:VAL35 5.0 53.4 1.0

Magnesium binding site 4 out of 9 in 4qux

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Magnesium binding site 4 out of 9 in the Ycp BETA5-A49T-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-A49T-Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg301

b:48.5
occ:1.00
 O K:ALA165 2.2 51.2 1.0
O K:ASP168 2.2 48.8 1.0
O W:ASP204 2.6 58.4 1.0
O K:SER171 2.9 56.9 1.0
C K:ASP168 3.2 47.7 1.0
C W:ASP204 3.2 61.6 1.0
C K:ALA165 3.3 50.2 1.0
CA W:ASP204 3.6 62.4 1.0
O K:HIS166 3.7 52.1 1.0
CA K:ALA169 3.7 49.4 1.0
N K:ALA169 3.8 48.7 1.0
CB W:ASP204 4.0 61.8 1.0
C K:HIS166 4.0 50.2 1.0
C K:ALA169 4.0 50.3 1.0
C K:SER171 4.1 53.4 1.0
NH1 K:ARG19 4.1 61.5 1.0
O K:ALA169 4.1 50.3 1.0
OXT W:ASP204 4.1 64.4 1.0
N K:ASP168 4.2 46.6 1.0
CA K:ALA165 4.2 50.4 1.0
N K:HIS166 4.3 50.5 1.0
CA K:ASP168 4.3 47.3 1.0
CA K:HIS166 4.4 51.0 1.0
N K:SER171 4.5 48.3 1.0
O K:ALA164 4.5 47.6 1.0
C K:ARG167 4.5 48.6 1.0
N K:ARG167 4.6 49.5 1.0
N K:TYR170 4.8 51.3 1.0
CA K:SER171 4.8 49.5 1.0
CZ K:ARG19 4.8 60.0 1.0
O K:ARG167 4.9 49.4 1.0
N W:ASP204 5.0 63.2 1.0

Magnesium binding site 5 out of 9 in 4qux

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Magnesium binding site 5 out of 9 in the Ycp BETA5-A49T-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-A49T-Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg201

b:49.2
occ:1.00
 O N:ILE163 2.8 47.5 1.0
O N:SER169 2.8 47.1 1.0
O N:ASP166 3.2 55.4 1.0
CD1 a:LEU34 3.5 53.9 1.0
NH1 N:ARG19 3.6 50.9 1.0
C N:ILE163 3.9 48.6 1.0
CG2 N:ILE163 4.0 49.2 1.0
C N:SER169 4.0 48.2 1.0
CZ N:ARG19 4.2 50.9 1.0
C N:ASP166 4.2 49.5 1.0
NH2 N:ARG19 4.3 52.5 1.0
CA N:GLY167 4.3 48.4 1.0
CA N:GLY170 4.5 51.0 1.0
O N:GLY167 4.5 50.2 1.0
CA N:ILE163 4.6 49.6 1.0
N N:GLY167 4.7 48.3 1.0
C N:GLY167 4.7 48.4 1.0
N N:GLY170 4.7 49.3 1.0
CG a:LEU34 4.8 54.4 1.0
N N:LYS164 4.9 50.1 1.0
CB N:ILE163 4.9 48.4 1.0

Magnesium binding site 6 out of 9 in 4qux

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Magnesium binding site 6 out of 9 in the Ycp BETA5-A49T-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-A49T-Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg202

b:54.9
occ:1.00
 OD1 N:ASP51 3.1 43.4 1.0
NE2 H:GLN91 3.6 82.8 1.0
OD2 N:ASP51 3.7 43.8 1.0
O N:ASN92 3.8 53.3 1.0
CG N:ASP51 3.8 31.1 1.0
CD H:GLN91 4.7 77.5 1.0
CD2 H:HIS116 4.9 48.8 1.0
C N:ASN92 4.9 52.9 1.0
CG H:GLN91 5.0 65.5 1.0
CE1 H:PHE88 5.0 40.4 1.0

Magnesium binding site 7 out of 9 in 4qux

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Magnesium binding site 7 out of 9 in the Ycp BETA5-A49T-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-A49T-Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Mg301

b:72.1
occ:1.00
 OXT L:ASP222 2.1 71.2 1.0
O V:ILE163 2.2 51.8 1.0
O V:ASP166 2.3 48.9 1.0
O V:SER169 2.8 49.0 1.0
C L:ASP222 3.0 71.5 1.0
C V:ASP166 3.2 51.3 1.0
C V:ILE163 3.3 57.3 1.0
CA L:ASP222 3.7 70.2 1.0
O V:TRP164 3.8 59.5 1.0
O L:ASP222 3.8 73.3 1.0
CA V:LEU167 3.9 52.8 1.0
N V:LEU167 3.9 52.3 1.0
C V:TRP164 3.9 57.8 1.0
C V:SER169 3.9 52.7 1.0
O V:GLY162 3.9 60.1 1.0
N V:ASP166 4.0 51.7 1.0
N V:TRP164 4.1 59.2 1.0
NH1 V:ARG19 4.2 71.0 1.0
CA V:ASP166 4.2 51.5 1.0
CA V:TRP164 4.2 57.4 1.0
CA V:ILE163 4.2 56.8 1.0
CB L:ASP222 4.3 73.3 1.0
N V:ASN165 4.3 55.1 1.0
C V:LEU167 4.4 52.1 1.0
C V:ASN165 4.5 53.2 1.0
O V:LEU167 4.6 48.4 1.0
N V:SER169 4.6 53.5 1.0
O L:ARG221 4.7 69.2 1.0
CA V:SER169 4.8 53.0 1.0
CA V:GLY170 4.8 59.4 1.0
N V:GLY170 4.8 53.7 1.0
CD2 V:LEU167 4.8 51.1 1.0
CZ V:ARG19 4.8 67.6 1.0
C V:GLY162 4.9 56.8 1.0
N L:ASP222 4.9 69.2 1.0
CA V:ASN165 4.9 54.8 1.0
NH2 V:ARG19 5.0 70.3 1.0

Magnesium binding site 8 out of 9 in 4qux

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Magnesium binding site 8 out of 9 in the Ycp BETA5-A49T-Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Ycp BETA5-A49T-Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
Y:Mg301

b:55.9
occ:1.00
 O Y:ASP168 2.3 50.2 1.0
O I:ASP204 2.5 64.2 1.0
O Y:ALA165 2.5 51.5 1.0
O Y:SER171 3.0 54.6 1.0
C I:ASP204 3.2 66.1 1.0
C Y:ASP168 3.2 48.9 1.0
CA Y:ALA169 3.5 48.1 1.0
C Y:ALA165 3.7 49.5 1.0
CA I:ASP204 3.7 63.5 1.0
N Y:ALA169 3.7 48.5 1.0
C Y:ALA169 3.8 47.5 1.0
O Y:ALA169 3.8 47.7 1.0
NH1 Y:ARG19 3.9 62.8 1.0
O Y:HIS166 3.9 49.0 1.0
OXT I:ASP204 4.0 72.7 1.0
CB I:ASP204 4.1 64.5 1.0
C Y:SER171 4.2 51.5 1.0
C Y:HIS166 4.2 48.4 1.0
N Y:ASP168 4.4 49.7 1.0
CA Y:ASP168 4.4 48.1 1.0
N Y:SER171 4.5 49.6 1.0
CA Y:ALA165 4.6 48.4 1.0
N Y:HIS166 4.6 49.5 1.0
N Y:TYR170 4.6 48.4 1.0
C Y:ARG167 4.6 49.7 1.0
CA Y:HIS166 4.7 48.2 1.0
CZ Y:ARG19 4.7 62.5 1.0
O Y:ALA164 4.8 47.7 1.0
CB Y:ALA169 4.8 47.6 1.0
N Y:ARG167 4.8 46.8 1.0
O Y:ARG167 4.9 49.8 1.0
CA Y:SER171 4.9 49.1 1.0

Magnesium binding site 9 out of 9 in 4qux

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Magnesium binding site 9 out of 9 in the Ycp BETA5-A49T-Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Ycp BETA5-A49T-Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg301

b:56.0
occ:1.00
 O Z:VAL198 2.6 57.8 1.0
O Z:HIS195 2.6 54.0 1.0
O Z:THR192 2.9 67.9 1.0
O Z:ILE196 3.5 56.7 1.0
C Z:HIS195 3.6 56.3 1.0
CA Z:ILE196 3.6 56.0 1.0
C Z:ILE196 3.7 55.1 1.0
C Z:VAL198 3.8 57.1 1.0
NH2 Z:ARG28 3.8 65.7 1.0
O Z:ASP222 3.8 83.3 1.0
C Z:THR192 3.9 67.9 1.0
N Z:ILE196 4.1 55.7 1.0
CG2 Z:THR192 4.1 67.2 1.0
N Z:VAL198 4.2 54.8 1.0
NH2 H:ARG19 4.2 69.8 1.0
CA Z:THR192 4.2 66.1 1.0
CA Z:VAL198 4.5 56.3 1.0
N Z:GLN197 4.6 53.3 1.0
OD1 Z:ASP222 4.6 79.5 1.0
N Z:GLY199 4.8 56.6 1.0
CZ Z:ARG28 4.8 64.9 1.0
C Z:ASP222 4.8 80.2 1.0
NH1 H:ARG19 4.8 69.4 1.0
CB Z:THR192 4.8 65.4 1.0
CA Z:HIS195 4.9 56.4 1.0
CZ H:ARG19 4.9 67.9 1.0
CA Z:GLY199 4.9 60.8 1.0
N Z:HIS195 4.9 58.6 1.0
CB Z:ILE196 4.9 54.1 1.0
CB Z:VAL198 5.0 56.9 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 Aug 11 22:34:54 2025

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