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Magnesium in PDB 4d0l: Phosphatidylinositol 4-Kinase III Beta-PIK93 in A Complex with RAB11A-Gtp Gammas

Enzymatic activity of Phosphatidylinositol 4-Kinase III Beta-PIK93 in A Complex with RAB11A-Gtp Gammas

All present enzymatic activity of Phosphatidylinositol 4-Kinase III Beta-PIK93 in A Complex with RAB11A-Gtp Gammas:
2.7.1.67; 3.6.5.2;

Protein crystallography data

The structure of Phosphatidylinositol 4-Kinase III Beta-PIK93 in A Complex with RAB11A-Gtp Gammas, PDB code: 4d0l was solved by J.E.Burke, A.J.Inglis, O.Perisic, G.R.Masson, S.H.Mclaughin, F.Rutaganira, K.M.Shokat, R.L.Williams, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 115.84 / 2.94
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 102.795, 146.925, 188.335, 90.00, 90.00, 90.00
R / Rfree (%) 21.626 / 25.94

Other elements in 4d0l:

The structure of Phosphatidylinositol 4-Kinase III Beta-PIK93 in A Complex with RAB11A-Gtp Gammas also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Phosphatidylinositol 4-Kinase III Beta-PIK93 in A Complex with RAB11A-Gtp Gammas (pdb code 4d0l). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Phosphatidylinositol 4-Kinase III Beta-PIK93 in A Complex with RAB11A-Gtp Gammas, PDB code: 4d0l:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 4d0l

Go back to Magnesium Binding Sites List in 4d0l
Magnesium binding site 1 out of 3 in the Phosphatidylinositol 4-Kinase III Beta-PIK93 in A Complex with RAB11A-Gtp Gammas


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Phosphatidylinositol 4-Kinase III Beta-PIK93 in A Complex with RAB11A-Gtp Gammas within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg2001

b:87.5
occ:1.00
OG1 B:THR43 1.6 78.3 1.0
OG B:SER25 1.6 64.6 1.0
O3G B:GSP2000 1.8 86.1 1.0
O2B B:GSP2000 2.3 70.3 1.0
CB B:SER25 2.8 63.7 1.0
CB B:THR43 3.0 73.6 1.0
O B:HOH3001 3.1 50.2 1.0
PG B:GSP2000 3.4 81.0 1.0
PB B:GSP2000 3.7 62.6 1.0
OD2 B:ASP66 3.7 57.9 1.0
CG2 B:THR43 3.8 71.1 1.0
N B:THR43 3.8 71.3 1.0
CA B:THR43 3.9 72.5 1.0
O3B B:GSP2000 3.9 71.9 1.0
CA B:SER25 3.9 60.1 1.0
N B:SER25 4.0 56.6 1.0
O2A B:GSP2000 4.1 58.9 1.0
OD1 B:ASP66 4.2 67.2 1.0
O2G B:GSP2000 4.3 72.2 1.0
CG B:ASP66 4.3 66.8 1.0
O B:LYS41 4.5 68.7 1.0
O3A B:GSP2000 4.5 61.2 1.0
PA B:GSP2000 4.6 61.0 1.0
S1G B:GSP2000 4.6 76.0 1.0
O1A B:GSP2000 4.6 59.2 1.0
C B:SER42 4.8 69.5 1.0
O1B B:GSP2000 4.8 58.8 1.0
OE2 B:GLU47 4.9 96.2 1.0

Magnesium binding site 2 out of 3 in 4d0l

Go back to Magnesium Binding Sites List in 4d0l
Magnesium binding site 2 out of 3 in the Phosphatidylinositol 4-Kinase III Beta-PIK93 in A Complex with RAB11A-Gtp Gammas


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Phosphatidylinositol 4-Kinase III Beta-PIK93 in A Complex with RAB11A-Gtp Gammas within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg2001

b:72.5
occ:1.00
OG1 D:THR43 1.7 69.5 1.0
O3G D:GSP2000 1.7 70.5 1.0
OG D:SER25 1.9 49.4 1.0
O2B D:GSP2000 2.0 50.8 1.0
CB D:THR43 2.9 67.7 1.0
PG D:GSP2000 3.0 61.0 1.0
CB D:SER25 3.2 46.8 1.0
PB D:GSP2000 3.3 47.3 1.0
O2G D:GSP2000 3.5 60.7 1.0
O3B D:GSP2000 3.6 52.5 1.0
CG2 D:THR43 3.8 68.5 1.0
OD2 D:ASP66 3.9 56.0 1.0
N D:THR43 3.9 61.5 1.0
CA D:THR43 4.0 64.5 1.0
OD1 D:ASP66 4.0 57.5 1.0
N D:SER25 4.0 42.6 1.0
O1B D:GSP2000 4.1 46.3 1.0
CA D:SER25 4.1 43.3 1.0
O2A D:GSP2000 4.3 50.5 1.0
CG D:ASP66 4.3 57.0 1.0
O3A D:GSP2000 4.5 47.0 1.0
S1G D:GSP2000 4.6 58.9 1.0
PA D:GSP2000 4.6 50.3 1.0
O D:THR67 4.6 67.9 1.0
O1A D:GSP2000 4.7 51.5 1.0
O D:LYS41 4.8 60.1 1.0
CB D:LYS24 4.9 43.7 1.0
C D:SER42 5.0 58.2 1.0

Magnesium binding site 3 out of 3 in 4d0l

Go back to Magnesium Binding Sites List in 4d0l
Magnesium binding site 3 out of 3 in the Phosphatidylinositol 4-Kinase III Beta-PIK93 in A Complex with RAB11A-Gtp Gammas


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Phosphatidylinositol 4-Kinase III Beta-PIK93 in A Complex with RAB11A-Gtp Gammas within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg2001

b:59.9
occ:1.00
O3G F:GSP2000 2.2 58.3 1.0
O2B F:GSP2000 2.4 50.2 1.0
OG1 F:THR43 2.7 56.3 1.0
OG F:SER25 2.8 44.9 1.0
OD1 F:ASP66 3.0 60.3 1.0
PG F:GSP2000 3.1 59.1 1.0
O2G F:GSP2000 3.1 58.9 1.0
O F:THR67 3.2 64.7 1.0
PB F:GSP2000 3.3 51.9 1.0
CB F:THR43 3.4 58.0 1.0
O3B F:GSP2000 3.6 58.8 1.0
CE F:LYS24 3.6 57.6 1.0
O1B F:GSP2000 3.7 48.0 1.0
CG F:ASP66 3.8 60.5 1.0
CB F:LYS24 3.8 49.3 1.0
OD2 F:ASP66 3.8 58.4 1.0
N F:SER25 4.0 48.5 1.0
CG2 F:THR43 4.1 56.1 1.0
CB F:SER25 4.1 49.6 1.0
NZ F:LYS24 4.3 59.2 1.0
C F:THR67 4.4 63.9 1.0
CA F:ALA68 4.5 66.4 1.0
CD F:LYS24 4.5 54.9 1.0
CA F:SER25 4.5 48.4 1.0
CG F:LYS24 4.5 51.5 1.0
C F:LYS24 4.7 49.2 1.0
CA F:THR43 4.7 59.8 1.0
O3A F:GSP2000 4.7 48.1 1.0
CA F:LYS24 4.7 49.7 1.0
N F:THR43 4.8 62.5 1.0
S1G F:GSP2000 4.9 61.3 1.0
N F:ALA68 4.9 60.5 1.0
N F:GLY69 4.9 73.1 1.0

Reference:

J.E.Burke, A.J.Inglis, O.Perisic, G.R.Masson, S.H.Mclaughlin, F.Rutaganira, K.M.Shokat, R.L.Williams. Structures of PI4KIIIBETA Complexes Show Simultaneous Recruitment of RAB11 and Its Effectors. Science V. 344 1035 2014.
ISSN: ISSN 0036-8075
PubMed: 24876499
DOI: 10.1126/SCIENCE.1253397
Page generated: Mon Dec 14 11:44:43 2020

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