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Magnesium in PDB 4qv5: Ycp BETA5-M45I Mutant

Enzymatic activity of Ycp BETA5-M45I Mutant

All present enzymatic activity of Ycp BETA5-M45I Mutant:
3.4.25.1;

Protein crystallography data

The structure of Ycp BETA5-M45I Mutant, PDB code: 4qv5 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 (°) 134.400, 301.140, 144.120, 90.00, 112.72, 90.00
R / Rfree (%) 18.9 / 21.7

Other elements in 4qv5:

The structure of Ycp BETA5-M45I Mutant also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Ycp BETA5-M45I Mutant (pdb code 4qv5). 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-M45I Mutant, PDB code: 4qv5:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 4qv5

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Magnesium binding site 1 out of 7 in the Ycp BETA5-M45I 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-M45I Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:50.9
occ:1.00
O G:MET125 2.2 51.4 1.0
OG1 G:THR8 2.6 43.8 1.0
O G:ARG122 2.6 45.2 1.0
O G:TYR119 2.8 39.5 1.0
CG2 G:THR8 3.2 46.9 1.0
O G:ALA123 3.3 53.6 1.0
C G:MET125 3.4 51.7 1.0
CB G:THR8 3.4 46.0 1.0
C G:ALA123 3.6 51.7 1.0
CA G:ALA123 3.7 50.7 1.0
C G:ARG122 3.7 47.9 1.0
C G:TYR119 4.0 38.5 1.0
N G:THR8 4.1 49.4 1.0
N G:ALA123 4.1 49.4 1.0
CA G:ARG126 4.2 45.1 1.0
N G:ARG126 4.2 46.6 1.0
N G:MET125 4.2 54.2 1.0
CA G:MET125 4.4 55.5 1.0
CA G:THR8 4.4 47.1 1.0
CD G:PRO127 4.6 42.7 1.0
N G:TYR124 4.6 53.6 1.0
O G:HOH409 4.7 37.0 1.0
CA G:TYR119 4.7 36.8 1.0
C G:ARG126 4.9 44.3 1.0
C G:TYR124 5.0 52.2 1.0
CA G:ARG122 5.0 50.7 1.0
N G:THR120 5.0 38.8 1.0
CB G:ALA123 5.0 50.8 1.0
CB G:MET125 5.0 59.5 1.0

Magnesium binding site 2 out of 7 in 4qv5

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Magnesium binding site 2 out of 7 in the Ycp BETA5-M45I 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-M45I Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg301

b:56.4
occ:1.00
OE1 H:GLN91 2.5 47.7 1.0
O H:HOH407 2.6 44.8 1.0
OD1 N:ASP51 2.8 32.1 1.0
CD H:GLN91 3.4 46.9 1.0
NE2 H:GLN91 3.6 48.1 1.0
OD2 N:ASP51 3.6 40.8 1.0
CG N:ASP51 3.6 28.6 1.0
O N:ASN92 3.9 51.6 1.0
CE1 H:PHE88 4.7 33.5 1.0
CG H:GLN91 4.8 43.6 1.0
OG N:SER48 4.9 40.2 1.0
CZ H:PHE88 5.0 33.8 1.0

Magnesium binding site 3 out of 7 in 4qv5

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Magnesium binding site 3 out of 7 in the Ycp BETA5-M45I 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-M45I Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg301

b:48.8
occ:1.00
O W:ASP204 2.2 58.9 1.0
O K:ALA165 2.3 43.2 1.0
O K:ASP168 2.3 42.6 1.0
O K:SER171 2.7 46.8 1.0
C W:ASP204 3.1 59.2 1.0
C K:ASP168 3.3 40.3 1.0
C K:ALA165 3.4 42.2 1.0
CA W:ASP204 3.6 55.6 1.0
CA K:ALA169 3.8 39.1 1.0
NH1 K:ARG19 3.8 52.9 1.0
C K:SER171 3.9 44.0 1.0
O K:HIS166 3.9 44.3 1.0
CB W:ASP204 3.9 55.0 1.0
O K:ALA169 3.9 42.9 1.0
N K:ALA169 4.0 38.6 1.0
C K:ALA169 4.0 41.2 1.0
OXT W:ASP204 4.1 59.9 1.0
C K:HIS166 4.2 42.6 1.0
CA K:ALA165 4.3 42.8 1.0
N K:SER171 4.4 40.0 1.0
N K:HIS166 4.4 41.5 1.0
CZ K:ARG19 4.5 51.3 1.0
N K:ASP168 4.5 40.3 1.0
CA K:ASP168 4.5 40.1 1.0
CA K:HIS166 4.6 42.6 1.0
O K:ALA164 4.6 41.4 1.0
CA K:SER171 4.7 40.5 1.0
NH2 K:ARG19 4.7 53.2 1.0
C K:ARG167 4.8 41.8 1.0
N K:TYR170 4.8 41.9 1.0
N K:GLY172 4.8 46.3 1.0
N K:ARG167 4.9 41.8 1.0
CG W:ASP204 4.9 53.8 1.0
CA K:GLY172 4.9 46.5 1.0

Magnesium binding site 4 out of 7 in 4qv5

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Magnesium binding site 4 out of 7 in the Ycp BETA5-M45I 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-M45I Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg302

b:54.9
occ:1.00
O K:ILE82 2.9 37.6 1.0
CB K:ASN85 3.6 34.9 1.0
C K:ILE82 3.7 36.0 1.0
CA K:ILE82 3.8 35.8 1.0
N K:LEU86 3.8 34.3 1.0
CG2 K:ILE82 4.0 35.3 1.0
C K:ASN85 4.2 34.8 1.0
CA K:LEU86 4.3 33.1 1.0
CB K:LEU86 4.3 32.5 1.0
CB K:ILE82 4.4 35.7 1.0
CA K:ASN85 4.4 34.7 1.0
CH2 K:TRP58 4.5 35.5 1.0
O K:LYS81 4.6 36.3 1.0
CG K:ASN85 4.7 35.1 1.0
OD1 K:ASN85 4.8 38.4 1.0
CG1 K:ILE82 4.8 35.9 1.0
O K:ASN85 4.9 34.8 1.0
N K:ASN85 4.9 34.4 1.0
N K:ILE82 5.0 36.5 1.0

Magnesium binding site 5 out of 7 in 4qv5

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Magnesium binding site 5 out of 7 in the Ycp BETA5-M45I 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-M45I Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg201

b:50.5
occ:1.00
O N:ILE163 2.9 40.9 1.0
O N:SER169 3.1 37.6 1.0
CD1 a:LEU34 3.5 45.0 1.0
O N:ASP166 3.5 44.0 1.0
NH1 N:ARG19 3.6 41.6 1.0
C N:ILE163 4.0 41.5 1.0
CG2 N:ILE163 4.0 40.7 1.0
CZ N:ARG19 4.1 41.4 1.0
C N:SER169 4.2 38.6 1.0
NH2 N:ARG19 4.2 43.0 1.0
C N:ASP166 4.4 42.0 1.0
CA N:GLY167 4.4 41.0 1.0
CA N:GLY170 4.5 41.1 1.0
O N:GLY167 4.6 37.2 1.0
CA N:ILE163 4.7 41.0 1.0
CG a:LEU34 4.8 45.1 1.0
N N:GLY167 4.8 40.9 1.0
C N:GLY167 4.8 40.0 1.0
N N:GLY170 4.8 39.8 1.0
N N:LYS164 5.0 43.8 1.0
O N:LYS164 5.0 50.0 1.0
CB N:ILE163 5.0 40.5 1.0

Magnesium binding site 6 out of 7 in 4qv5

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Magnesium binding site 6 out of 7 in the Ycp BETA5-M45I 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-M45I Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Mg301

b:55.0
occ:1.00
OXT L:ASP222 2.0 68.1 1.0
O V:ILE163 2.2 44.2 1.0
O V:ASP166 2.2 43.5 1.0
O V:SER169 2.2 42.3 1.0
C L:ASP222 3.1 65.9 1.0
C V:ASP166 3.2 43.3 1.0
C V:ILE163 3.3 48.2 1.0
C V:SER169 3.4 43.8 1.0
CA L:ASP222 3.8 66.0 1.0
CA V:LEU167 3.8 42.6 1.0
NH1 V:ARG19 3.8 59.0 1.0
O V:GLY162 3.9 48.9 1.0
N V:LEU167 3.9 43.0 1.0
CA V:ILE163 4.1 49.0 1.0
O L:ASP222 4.1 63.1 1.0
C V:LEU167 4.2 42.6 1.0
O V:TRP164 4.2 51.1 1.0
N V:ASP166 4.2 44.0 1.0
N V:SER169 4.2 43.3 1.0
N V:TRP164 4.2 48.2 1.0
CB L:ASP222 4.2 66.8 1.0
C V:TRP164 4.3 49.6 1.0
O V:LEU167 4.3 42.3 1.0
N V:GLY170 4.3 45.6 1.0
CA V:ASP166 4.3 43.7 1.0
CA V:GLY170 4.3 48.1 1.0
CA V:SER169 4.3 44.0 1.0
CA V:TRP164 4.5 49.6 1.0
CZ V:ARG19 4.5 57.9 1.0
NH2 V:ARG19 4.7 60.0 1.0
N V:ASN165 4.7 47.5 1.0
CB V:SER169 4.7 45.4 1.0
C V:GLY162 4.8 49.6 1.0
N V:GLY168 4.9 43.5 1.0
C V:ASN165 4.9 45.5 1.0
N V:ILE163 4.9 49.5 1.0

Magnesium binding site 7 out of 7 in 4qv5

Go back to Magnesium Binding Sites List in 4qv5
Magnesium binding site 7 out of 7 in the Ycp BETA5-M45I 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-M45I Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
Y:Mg301

b:58.3
occ:1.00
O Y:ASP168 2.3 44.6 1.0
O I:ASP204 2.4 56.7 1.0
O Y:ALA165 2.4 42.2 1.0
O Y:SER171 3.1 42.5 1.0
C I:ASP204 3.2 57.6 1.0
C Y:ASP168 3.2 41.6 1.0
O Y:HIS166 3.6 40.5 1.0
C Y:ALA165 3.6 41.6 1.0
CA Y:ALA169 3.6 41.6 1.0
CA I:ASP204 3.7 54.8 1.0
N Y:ALA169 3.8 41.6 1.0
C Y:HIS166 4.0 40.7 1.0
C Y:ALA169 4.0 43.0 1.0
O Y:ALA169 4.1 44.1 1.0
OXT I:ASP204 4.1 60.2 1.0
NH1 Y:ARG19 4.1 57.7 1.0
CB I:ASP204 4.1 55.1 1.0
N Y:ASP168 4.3 41.1 1.0
C Y:SER171 4.3 44.0 1.0
CA Y:ASP168 4.4 40.5 1.0
N Y:HIS166 4.4 42.6 1.0
CA Y:HIS166 4.5 42.1 1.0
C Y:ARG167 4.5 40.7 1.0
CA Y:ALA165 4.5 40.6 1.0
O Y:ALA164 4.6 40.4 1.0
N Y:ARG167 4.7 40.2 1.0
N Y:SER171 4.7 42.8 1.0
O Y:ARG167 4.7 41.2 1.0
CZ Y:ARG19 4.8 55.0 1.0
N Y:TYR170 4.9 42.5 1.0
CB Y:ALA169 4.9 40.9 1.0
N I:ASP204 5.0 52.6 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 19:25:10 2020

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