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Magnesium in PDB 4qv4: Ycp BETA5-M45T Mutant

Enzymatic activity of Ycp BETA5-M45T Mutant

All present enzymatic activity of Ycp BETA5-M45T Mutant:
3.4.25.1;

Protein crystallography data

The structure of Ycp BETA5-M45T Mutant, PDB code: 4qv4 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 / 2.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 134.760, 301.270, 144.420, 90.00, 112.81, 90.00
R / Rfree (%) 19 / 21.3

Other elements in 4qv4:

The structure of Ycp BETA5-M45T Mutant also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Ycp BETA5-M45T Mutant (pdb code 4qv4). 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, PDB code: 4qv4:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Magnesium binding site 1 out of 9 in 4qv4

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

b:48.0
occ:1.00
 O G:MET125 2.3 51.4 1.0
O G:ARG122 2.4 48.0 1.0
OG1 G:THR8 2.6 47.6 1.0
O G:TYR119 2.7 38.2 1.0
CG2 G:THR8 3.3 46.9 1.0
O G:ALA123 3.3 51.1 1.0
C G:MET125 3.4 50.4 1.0
CB G:THR8 3.5 47.2 1.0
C G:ARG122 3.5 47.5 1.0
CA G:ALA123 3.6 48.9 1.0
C G:ALA123 3.6 50.3 1.0
C G:TYR119 3.9 38.2 1.0
N G:ALA123 4.0 47.4 1.0
N G:MET125 4.2 52.7 1.0
N G:THR8 4.2 48.6 1.0
N G:ARG126 4.2 45.9 1.0
CA G:ARG126 4.3 44.9 1.0
CA G:MET125 4.4 54.5 1.0
CA G:THR8 4.5 47.7 1.0
N G:TYR124 4.5 52.7 1.0
CD G:PRO127 4.7 41.9 1.0
CA G:TYR119 4.7 37.2 1.0
CA G:ARG122 4.8 49.1 1.0
N G:ARG122 4.9 46.2 1.0
CB G:ALA123 4.9 48.1 1.0
C G:TYR124 4.9 51.1 1.0
N G:THR120 4.9 38.3 1.0
C G:ARG126 4.9 44.0 1.0
CB G:MET125 5.0 59.4 1.0

Magnesium binding site 2 out of 9 in 4qv4

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

b:48.4
occ:1.00
 OE1 H:GLN91 2.7 52.7 1.0
O H:HOH405 2.7 42.1 1.0
OD1 N:ASP51 2.8 29.9 1.0
OD2 N:ASP51 3.5 37.7 1.0
CG N:ASP51 3.6 27.1 1.0
CD H:GLN91 3.6 51.3 1.0
NE2 H:GLN91 3.8 54.9 1.0
O N:ASN92 3.9 44.4 1.0
CE1 H:PHE88 4.7 32.5 1.0
OG N:SER48 4.8 37.1 1.0
CD2 H:HIS116 4.9 36.6 1.0
CG H:GLN91 5.0 47.5 1.0

Magnesium binding site 3 out of 9 in 4qv4

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Magnesium binding site 3 out of 9 in the Ycp BETA5-M45T 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-M45T Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:56.9
occ:1.00
 O I:ASP177 2.7 41.5 1.0
O I:SER180 2.9 47.1 1.0
O I:ALA174 3.3 45.1 1.0
OXT I:ASP204 3.4 56.7 1.0
C I:ASP177 3.7 41.6 1.0
NH1 Y:ARG19 3.9 52.8 1.0
O I:ALA178 3.9 46.4 1.0
CA I:ALA178 4.1 41.8 1.0
O I:HOH401 4.1 37.9 1.0
C I:SER180 4.1 45.1 1.0
O I:ASP204 4.1 53.2 1.0
C I:ALA178 4.2 44.0 1.0
C I:ASP204 4.2 53.5 1.0
NH2 Y:ARG19 4.3 53.0 1.0
N I:ALA178 4.3 39.8 1.0
C I:ALA174 4.4 43.8 1.0
CZ Y:ARG19 4.5 52.3 1.0
CA I:ASP175 4.6 43.7 1.0
N I:SER180 4.7 42.6 1.0
N I:ASP177 4.7 42.3 1.0
O I:ASP175 4.8 48.1 1.0
C I:ASP175 4.8 44.2 1.0
CA I:ASP177 4.8 42.5 1.0
N I:ASP175 4.9 44.1 1.0
CA I:SER180 5.0 44.0 1.0

Magnesium binding site 4 out of 9 in 4qv4

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Magnesium binding site 4 out of 9 in the Ycp BETA5-M45T 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-M45T Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mg201

b:61.5
occ:1.00
 OE1 J:GLN118 2.9 36.4 1.0
O J:THR124 3.5 40.2 1.0
CD J:GLN118 3.6 35.6 1.0
CG J:GLN118 3.6 34.9 1.0
N J:ASP120 3.7 34.1 1.0
CB J:ASP120 3.7 37.4 1.0
CE1 J:HIS133 3.8 36.8 1.0
CG J:ASP120 4.1 38.8 1.0
OD2 J:ASP120 4.1 43.3 1.0
O J:GLN118 4.1 34.5 1.0
C J:ILE119 4.3 34.2 1.0
CA J:ASP120 4.3 35.7 1.0
C J:GLN118 4.3 34.8 1.0
CA J:ILE119 4.4 33.0 1.0
CB J:THR124 4.5 35.3 1.0
N J:ILE119 4.5 34.1 1.0
ND1 J:HIS133 4.5 36.9 1.0
CB J:GLN118 4.6 34.1 1.0
C J:THR124 4.6 37.1 1.0
CG2 J:THR124 4.7 34.4 1.0
CG1 I:VAL35 4.7 43.5 1.0
NE2 J:HIS133 4.7 35.0 1.0
OD1 J:ASP120 4.8 40.0 1.0
NE2 J:GLN118 4.9 36.3 1.0

Magnesium binding site 5 out of 9 in 4qv4

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Magnesium binding site 5 out of 9 in the Ycp BETA5-M45T 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-M45T Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg301

b:49.0
occ:1.00
 O K:ALA165 2.3 43.0 1.0
O K:ASP168 2.3 40.2 1.0
O W:ASP204 2.4 58.2 1.0
O K:SER171 2.8 47.4 1.0
C W:ASP204 3.1 57.0 1.0
C K:ASP168 3.3 40.5 1.0
C K:ALA165 3.5 42.8 1.0
CA W:ASP204 3.6 53.8 1.0
CA K:ALA169 3.7 40.3 1.0
O K:HIS166 3.8 45.2 1.0
NH1 K:ARG19 3.9 53.9 1.0
N K:ALA169 3.9 39.6 1.0
CB W:ASP204 3.9 53.0 1.0
C K:SER171 4.0 43.9 1.0
OXT W:ASP204 4.0 60.6 1.0
C K:ALA169 4.0 41.3 1.0
O K:ALA169 4.0 40.7 1.0
C K:HIS166 4.2 43.2 1.0
CA K:ALA165 4.3 43.2 1.0
N K:ASP168 4.4 41.8 1.0
N K:HIS166 4.4 41.7 1.0
CA K:ASP168 4.5 40.7 1.0
N K:SER171 4.5 41.0 1.0
CZ K:ARG19 4.5 52.7 1.0
CA K:HIS166 4.5 42.9 1.0
O K:ALA164 4.6 40.5 1.0
C K:ARG167 4.7 44.0 1.0
NH2 K:ARG19 4.8 56.2 1.0
CA K:SER171 4.8 41.6 1.0
N K:ARG167 4.8 43.4 1.0
N K:TYR170 4.8 42.6 1.0
N W:ASP204 4.9 52.5 1.0
CG W:ASP204 5.0 52.8 1.0
N K:GLY172 5.0 45.3 1.0
O K:ARG167 5.0 46.4 1.0

Magnesium binding site 6 out of 9 in 4qv4

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Magnesium binding site 6 out of 9 in the Ycp BETA5-M45T 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-M45T Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg302

b:48.5
occ:1.00
 O K:HOH412 2.6 45.1 1.0
O K:HOH417 2.8 33.7 1.0
O K:ILE82 3.0 39.3 1.0
CA K:ILE82 3.7 36.6 1.0
C K:ILE82 3.7 36.8 1.0
CB K:ASN85 3.8 35.7 1.0
CG2 K:ILE82 3.9 36.0 1.0
N K:LEU86 4.0 34.1 1.0
CB K:ILE82 4.3 36.3 1.0
CB K:LEU86 4.4 34.2 1.0
C K:ASN85 4.4 34.4 1.0
O K:HOH418 4.4 36.9 1.0
CH2 K:TRP58 4.4 35.3 1.0
CA K:LEU86 4.4 34.3 1.0
CA K:ASN85 4.6 35.1 1.0
CG1 K:ILE82 4.7 36.4 1.0
O K:LYS81 4.7 37.0 1.0
OD1 K:ASN85 4.9 39.5 1.0
CG K:ASN85 4.9 36.5 1.0
N K:ILE82 5.0 36.9 1.0

Magnesium binding site 7 out of 9 in 4qv4

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Magnesium binding site 7 out of 9 in the Ycp BETA5-M45T 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-M45T Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg201

b:58.0
occ:1.00
 O N:SER169 2.9 39.3 1.0
O N:ILE163 3.0 39.2 1.0
O N:ASP166 3.4 43.4 1.0
NH1 N:ARG19 3.4 38.9 1.0
CD1 a:LEU34 3.5 45.3 1.0
CZ N:ARG19 4.0 39.5 1.0
C N:ILE163 4.1 39.8 1.0
C N:SER169 4.1 38.4 1.0
CG2 N:ILE163 4.1 38.9 1.0
NH2 N:ARG19 4.2 41.3 1.0
CA N:GLY167 4.3 38.1 1.0
C N:ASP166 4.3 39.8 1.0
O N:GLY167 4.5 37.5 1.0
CA N:GLY170 4.5 40.2 1.0
C N:GLY167 4.7 37.2 1.0
N N:GLY167 4.7 38.5 1.0
CG a:LEU34 4.8 45.3 1.0
N N:GLY170 4.8 39.5 1.0
CA N:ILE163 4.8 39.1 1.0
NE N:ARG19 5.0 39.2 1.0

Magnesium binding site 8 out of 9 in 4qv4

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Magnesium binding site 8 out of 9 in the Ycp BETA5-M45T 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-M45T Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Mg301

b:65.5
occ:1.00
 OXT L:ASP222 2.0 70.9 1.0
O V:ILE163 2.1 45.3 1.0
O V:ASP166 2.2 42.1 1.0
O V:SER169 2.3 45.4 1.0
C L:ASP222 3.1 66.4 1.0
C V:ILE163 3.2 48.6 1.0
C V:ASP166 3.3 43.0 1.0
C V:SER169 3.4 44.9 1.0
CA L:ASP222 3.7 66.3 1.0
O V:GLY162 3.8 47.7 1.0
NH1 V:ARG19 3.9 61.7 1.0
CA V:LEU167 3.9 43.2 1.0
N V:LEU167 4.0 43.7 1.0
CA V:ILE163 4.0 48.5 1.0
O L:ASP222 4.1 63.8 1.0
O V:TRP164 4.1 51.7 1.0
N V:TRP164 4.2 48.9 1.0
C V:TRP164 4.2 50.1 1.0
N V:ASP166 4.2 44.4 1.0
CB L:ASP222 4.2 67.2 1.0
C V:LEU167 4.3 43.1 1.0
N V:SER169 4.3 44.0 1.0
CA V:ASP166 4.3 43.4 1.0
CA V:GLY170 4.3 49.3 1.0
N V:GLY170 4.3 46.7 1.0
CA V:TRP164 4.4 49.5 1.0
CA V:SER169 4.4 44.0 1.0
O V:LEU167 4.4 42.6 1.0
CZ V:ARG19 4.5 59.1 1.0
N V:ASN165 4.7 48.2 1.0
NH2 V:ARG19 4.7 61.5 1.0
C V:GLY162 4.8 47.5 1.0
CB V:SER169 4.8 44.2 1.0
N V:ILE163 4.9 48.5 1.0
C V:ASN165 4.9 45.1 1.0
O L:ARG221 5.0 64.6 1.0

Magnesium binding site 9 out of 9 in 4qv4

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

b:62.9
occ:1.00
 O Y:ALA165 2.3 40.8 1.0
O Y:ASP168 2.3 44.6 1.0
O I:ASP204 2.4 53.2 1.0
O Y:SER171 2.7 45.3 1.0
C I:ASP204 3.2 53.5 1.0
C Y:ASP168 3.3 40.8 1.0
C Y:ALA165 3.5 39.9 1.0
CA I:ASP204 3.6 52.7 1.0
CA Y:ALA169 3.7 40.6 1.0
NH1 Y:ARG19 3.8 52.8 1.0
O Y:HIS166 3.9 39.2 1.0
N Y:ALA169 3.9 41.0 1.0
C Y:SER171 3.9 42.4 1.0
CB I:ASP204 4.0 53.6 1.0
O Y:ALA169 4.0 44.1 1.0
C Y:ALA169 4.0 42.2 1.0
OXT I:ASP204 4.0 56.7 1.0
C Y:HIS166 4.2 39.4 1.0
CA Y:ALA165 4.3 39.5 1.0
N Y:ASP168 4.4 40.2 1.0
N Y:SER171 4.4 40.0 1.0
N Y:HIS166 4.4 39.9 1.0
CA Y:ASP168 4.5 39.2 1.0
CZ Y:ARG19 4.5 52.3 1.0
CA Y:HIS166 4.6 40.1 1.0
O Y:ALA164 4.6 42.7 1.0
C Y:ARG167 4.7 39.9 1.0
CA Y:SER171 4.7 39.6 1.0
NH2 Y:ARG19 4.7 53.0 1.0
N Y:TYR170 4.8 41.2 1.0
N Y:ARG167 4.8 39.6 1.0
N Y:GLY172 4.9 43.5 1.0
CG I:ASP204 5.0 54.4 1.0
CA Y:GLY172 5.0 43.2 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 02:14:37 2024

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