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Magnesium in PDB 4qv0: Ycp BETA5-A49T-A50V-Double Mutant

Enzymatic activity of Ycp BETA5-A49T-A50V-Double Mutant

All present enzymatic activity of Ycp BETA5-A49T-A50V-Double Mutant:
3.4.25.1;

Protein crystallography data

The structure of Ycp BETA5-A49T-A50V-Double Mutant, PDB code: 4qv0 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 / 3.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 134.800, 300.210, 144.400, 90.00, 112.86, 90.00
R / Rfree (%) 15.9 / 19.7

Other elements in 4qv0:

The structure of Ycp BETA5-A49T-A50V-Double Mutant also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Ycp BETA5-A49T-A50V-Double Mutant (pdb code 4qv0). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Ycp BETA5-A49T-A50V-Double Mutant, PDB code: 4qv0:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 4qv0

Go back to Magnesium Binding Sites List in 4qv0
Magnesium binding site 1 out of 6 in the Ycp BETA5-A49T-A50V-Double 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-A50V-Double Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:66.2
occ:1.00
 O G:MET125 2.2 64.9 1.0
OG1 G:THR8 2.7 58.9 1.0
O G:ARG122 2.8 62.4 1.0
O G:ALA123 3.1 70.4 1.0
O G:TYR119 3.1 59.5 1.0
CG2 G:THR8 3.3 60.7 1.0
C G:MET125 3.3 64.6 1.0
C G:ALA123 3.5 68.0 1.0
CB G:THR8 3.5 59.2 1.0
CA G:ALA123 3.6 66.6 1.0
C G:ARG122 3.8 64.0 1.0
N G:THR8 4.0 59.9 1.0
CA G:ARG126 4.1 58.2 1.0
N G:ARG126 4.1 58.6 1.0
N G:MET125 4.2 69.9 1.0
N G:ALA123 4.2 65.2 1.0
C G:TYR119 4.3 56.0 1.0
CA G:MET125 4.4 70.0 1.0
CA G:THR8 4.4 61.4 1.0
N G:TYR124 4.5 69.5 1.0
CD G:PRO127 4.6 55.8 1.0
C G:TYR124 4.8 67.6 1.0
C G:ARG126 4.8 57.7 1.0
CB G:ALA123 4.9 67.7 1.0

Magnesium binding site 2 out of 6 in 4qv0

Go back to Magnesium Binding Sites List in 4qv0
Magnesium binding site 2 out of 6 in the Ycp BETA5-A49T-A50V-Double 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-A50V-Double Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg301

b:58.9
occ:1.00
 O H:HOH401 2.4 34.4 1.0
OD1 N:ASP51 2.8 34.8 1.0
OE1 H:GLN91 3.2 85.2 1.0
CG N:ASP51 3.6 27.0 1.0
OD2 N:ASP51 3.6 62.5 1.0
CD H:GLN91 3.6 73.5 1.0
NE2 H:GLN91 3.9 82.2 1.0
O N:ASN92 4.1 61.5 1.0
CE1 H:PHE88 4.4 49.0 1.0
CG H:GLN91 4.5 64.5 1.0
OG N:SER48 4.7 55.2 1.0
CZ H:PHE88 4.8 49.5 1.0
CD2 H:HIS116 4.8 50.4 1.0
CB H:GLN91 4.8 57.8 1.0

Magnesium binding site 3 out of 6 in 4qv0

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Magnesium binding site 3 out of 6 in the Ycp BETA5-A49T-A50V-Double 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-A50V-Double Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg301

b:59.9
occ:1.00
 O K:ASP168 2.3 53.0 1.0
O K:ALA165 2.3 64.4 1.0
O W:ASP204 2.5 81.8 1.0
O K:SER171 2.9 64.6 1.0
C W:ASP204 3.2 83.5 1.0
C K:ASP168 3.2 55.6 1.0
C K:ALA165 3.5 58.1 1.0
CA W:ASP204 3.5 77.8 1.0
O K:HIS166 3.6 60.3 1.0
CA K:ALA169 3.6 58.9 1.0
N K:ALA169 3.8 59.1 1.0
CB W:ASP204 3.9 77.1 1.0
C K:ALA169 4.0 58.9 1.0
O K:ALA169 4.0 57.2 1.0
NH1 K:ARG19 4.0 79.3 1.0
C K:HIS166 4.0 59.0 1.0
C K:SER171 4.1 59.6 1.0
OXT W:ASP204 4.2 92.0 1.0
N K:ASP168 4.3 54.8 1.0
CA K:ASP168 4.3 54.4 1.0
CA K:ALA165 4.4 58.0 1.0
N K:HIS166 4.4 56.1 1.0
CA K:HIS166 4.5 58.8 1.0
C K:ARG167 4.5 57.8 1.0
N K:SER171 4.5 55.9 1.0
O K:ALA164 4.6 56.3 1.0
O K:ARG167 4.7 57.0 1.0
CZ K:ARG19 4.7 76.9 1.0
N K:ARG167 4.7 57.8 1.0
N K:TYR170 4.8 59.8 1.0
CA K:SER171 4.9 53.9 1.0
N W:ASP204 4.9 74.9 1.0
CB K:ALA169 5.0 57.8 1.0
NH2 K:ARG19 5.0 84.2 1.0

Magnesium binding site 4 out of 6 in 4qv0

Go back to Magnesium Binding Sites List in 4qv0
Magnesium binding site 4 out of 6 in the Ycp BETA5-A49T-A50V-Double 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-A50V-Double Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg201

b:55.0
occ:1.00
 O N:ILE163 2.8 50.7 1.0
O N:SER169 2.9 59.8 1.0
O N:ASP166 3.3 52.5 1.0
NH1 N:ARG19 3.5 54.0 1.0
CD1 a:LEU34 3.5 59.5 1.0
C N:ILE163 3.9 51.7 1.0
CG2 N:ILE163 3.9 53.1 1.0
CZ N:ARG19 4.0 52.8 1.0
C N:SER169 4.1 54.7 1.0
NH2 N:ARG19 4.1 55.8 1.0
C N:ASP166 4.3 51.5 1.0
CA N:GLY170 4.4 56.9 1.0
CA N:GLY167 4.4 49.4 1.0
CA N:ILE163 4.6 53.0 1.0
O N:GLY167 4.6 45.5 1.0
N N:GLY170 4.7 55.1 1.0
N N:GLY167 4.8 49.4 1.0
C N:GLY167 4.8 49.0 1.0
CG a:LEU34 4.8 59.6 1.0
N N:LYS164 4.9 54.2 1.0
CB N:ILE163 4.9 52.4 1.0
NE N:ARG19 5.0 51.8 1.0

Magnesium binding site 5 out of 6 in 4qv0

Go back to Magnesium Binding Sites List in 4qv0
Magnesium binding site 5 out of 6 in the Ycp BETA5-A49T-A50V-Double 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-A50V-Double Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Mg301

b:77.4
occ:1.00
 OXT L:ASP222 2.0 90.2 1.0
O V:ASP166 2.2 52.5 1.0
O V:ILE163 2.3 55.6 1.0
O V:SER169 2.8 52.6 1.0
C L:ASP222 3.0 85.7 1.0
C V:ASP166 3.1 53.3 1.0
C V:ILE163 3.4 59.7 1.0
O V:TRP164 3.5 58.7 1.0
CA L:ASP222 3.7 83.8 1.0
CA V:LEU167 3.7 51.6 1.0
N V:LEU167 3.8 52.2 1.0
C V:TRP164 3.8 60.9 1.0
O L:ASP222 3.9 85.6 1.0
O V:GLY162 4.0 60.9 1.0
C V:SER169 4.0 53.3 1.0
N V:ASP166 4.0 53.2 1.0
NH1 V:ARG19 4.0 81.2 1.0
N V:TRP164 4.2 61.3 1.0
CA V:ASP166 4.2 53.1 1.0
CA V:TRP164 4.2 60.0 1.0
C V:LEU167 4.3 50.1 1.0
CA V:ILE163 4.4 59.5 1.0
N V:ASN165 4.4 58.0 1.0
CB L:ASP222 4.4 84.1 1.0
O V:LEU167 4.5 48.6 1.0
C V:ASN165 4.5 56.4 1.0
CD2 V:LEU167 4.6 52.0 1.0
O L:ARG221 4.7 72.3 1.0
N V:SER169 4.7 54.2 1.0
CZ V:ARG19 4.8 76.4 1.0
CA V:GLY170 4.8 59.1 1.0
N V:GLY170 4.9 53.4 1.0
CA V:SER169 4.9 53.2 1.0
NH2 V:ARG19 4.9 83.2 1.0
N L:ASP222 4.9 79.2 1.0
C V:GLY162 5.0 59.2 1.0
CB V:LEU167 5.0 51.6 1.0
CA V:ASN165 5.0 57.1 1.0

Magnesium binding site 6 out of 6 in 4qv0

Go back to Magnesium Binding Sites List in 4qv0
Magnesium binding site 6 out of 6 in the Ycp BETA5-A49T-A50V-Double 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-A50V-Double Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
Y:Mg301

b:74.1
occ:1.00
 O Y:ASP168 2.1 54.9 1.0
O I:ASP204 2.4 86.8 1.0
O Y:ALA165 2.6 54.5 1.0
O Y:SER171 2.7 61.5 1.0
C Y:ASP168 3.1 54.9 1.0
C I:ASP204 3.3 82.7 1.0
CA Y:ALA169 3.4 53.0 1.0
O Y:ALA169 3.5 51.4 1.0
C Y:ALA169 3.6 50.7 1.0
NH1 Y:ARG19 3.7 81.4 1.0
N Y:ALA169 3.7 56.2 1.0
C Y:ALA165 3.8 54.4 1.0
CA I:ASP204 3.8 77.9 1.0
C Y:SER171 3.9 56.8 1.0
O Y:HIS166 4.1 54.6 1.0
CB I:ASP204 4.1 76.9 1.0
N Y:SER171 4.2 53.1 1.0
OXT I:ASP204 4.2 90.0 1.0
CZ Y:ARG19 4.4 77.9 1.0
CA Y:ASP168 4.4 53.0 1.0
N Y:TYR170 4.4 49.0 1.0
N Y:ASP168 4.5 54.1 1.0
C Y:HIS166 4.5 54.0 1.0
CA Y:ALA165 4.5 54.2 1.0
CA Y:SER171 4.6 51.6 1.0
CB Y:ALA169 4.7 52.0 1.0
C Y:ARG167 4.8 55.1 1.0
N Y:HIS166 4.8 55.6 1.0
NH2 Y:ARG19 4.8 78.7 1.0
O Y:ALA164 4.8 60.1 1.0
N Y:GLY172 4.9 60.9 1.0
O Y:ARG167 4.9 52.7 1.0
CA Y:HIS166 4.9 54.7 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 02:12:02 2024

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