Atomistry » Magnesium » PDB 4qq8-4qwi » 4qv0
Atomistry »
  Magnesium »
    PDB 4qq8-4qwi »
      4qv0 »

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

Go back to Magnesium Binding Sites List in 4qv0
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

Last articles

Fe in 6O7O
Fe in 6O7N
Fe in 6O7M
Fe in 6O7L
Fe in 6O5Y
Fe in 6O6M
Fe in 6O6L
Fe in 6O0B
Fe in 6O3I
Fe in 6NY6
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy