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Magnesium in PDB 4d0m: Phosphatidylinositol 4-Kinase III Beta in A Complex with RAB11A-Gtp- Gamma-S and the Rab-Binding Domain of FIP3

Enzymatic activity of Phosphatidylinositol 4-Kinase III Beta in A Complex with RAB11A-Gtp- Gamma-S and the Rab-Binding Domain of FIP3

All present enzymatic activity of Phosphatidylinositol 4-Kinase III Beta in A Complex with RAB11A-Gtp- Gamma-S and the Rab-Binding Domain of FIP3:
2.7.1.67; 3.6.5.2;

Protein crystallography data

The structure of Phosphatidylinositol 4-Kinase III Beta in A Complex with RAB11A-Gtp- Gamma-S and the Rab-Binding Domain of FIP3, PDB code: 4d0m was solved by J.E.Burke, A.J.Inglis, O.Perisic, G.R.Masson, S.H.Mclaughlin, 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) 294.32 / 6.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 199.504, 134.465, 294.328, 90.00, 90.33, 90.00
R / Rfree (%) 25.33 / 35.946

Other elements in 4d0m:

The structure of Phosphatidylinositol 4-Kinase III Beta in A Complex with RAB11A-Gtp- Gamma-S and the Rab-Binding Domain of FIP3 also contains other interesting chemical elements:

Chlorine (Cl) 12 atoms

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Magnesium atom in the Phosphatidylinositol 4-Kinase III Beta in A Complex with RAB11A-Gtp- Gamma-S and the Rab-Binding Domain of FIP3 (pdb code 4d0m). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 12 binding sites of Magnesium where determined in the Phosphatidylinositol 4-Kinase III Beta in A Complex with RAB11A-Gtp- Gamma-S and the Rab-Binding Domain of FIP3, PDB code: 4d0m:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 12 in 4d0m

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Magnesium binding site 1 out of 12 in the Phosphatidylinositol 4-Kinase III Beta in A Complex with RAB11A-Gtp- Gamma-S and the Rab-Binding Domain of FIP3


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 in A Complex with RAB11A-Gtp- Gamma-S and the Rab-Binding Domain of FIP3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg2001

b:1.0
occ:1.00
OG1 B:THR43 1.6 0.8 1.0
OG B:SER25 1.8 0.5 1.0
O3G B:GSP2000 1.8 0.4 1.0
O2B B:GSP2000 2.3 0.7 1.0
CB B:SER25 2.9 0.8 1.0
CB B:THR43 3.0 0.0 1.0
PG B:GSP2000 3.3 0.1 1.0
N B:THR43 3.6 0.1 1.0
PB B:GSP2000 3.6 0.5 1.0
CA B:THR43 3.7 0.5 1.0
O B:LYS41 3.9 0.5 1.0
O3B B:GSP2000 3.9 0.1 1.0
CG2 B:THR43 3.9 0.1 1.0
OD2 B:ASP66 3.9 0.5 1.0
CA B:SER25 4.1 0.2 1.0
N B:SER25 4.1 0.9 1.0
O2G B:GSP2000 4.1 0.4 1.0
O2A B:GSP2000 4.2 0.3 1.0
OD1 B:ASP66 4.5 0.3 1.0
C B:SER42 4.5 0.1 1.0
S1G B:GSP2000 4.5 0.7 1.0
O1A B:GSP2000 4.5 0.6 1.0
O3A B:GSP2000 4.6 0.7 1.0
CG B:ASP66 4.6 0.1 1.0
PA B:GSP2000 4.6 0.5 1.0
O1B B:GSP2000 4.7 0.2 1.0
OE2 B:GLU47 4.8 0.3 1.0
CA B:SER42 4.9 0.5 1.0
C B:LYS41 4.9 0.1 1.0

Magnesium binding site 2 out of 12 in 4d0m

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Magnesium binding site 2 out of 12 in the Phosphatidylinositol 4-Kinase III Beta in A Complex with RAB11A-Gtp- Gamma-S and the Rab-Binding Domain of FIP3


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 in A Complex with RAB11A-Gtp- Gamma-S and the Rab-Binding Domain of FIP3 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg2001

b:64.5
occ:1.00
OG1 D:THR43 1.5 0.7 1.0
OG D:SER25 1.6 0.1 1.0
O3G D:GSP2000 1.9 0.9 1.0
O2B D:GSP2000 2.3 0.0 1.0
CB D:SER25 2.9 0.6 1.0
CB D:THR43 3.0 0.8 1.0
PG D:GSP2000 3.4 0.2 1.0
OD2 D:ASP66 3.6 0.7 1.0
PB D:GSP2000 3.7 0.6 1.0
CG2 D:THR43 3.8 0.9 1.0
N D:THR43 3.8 0.6 1.0
CA D:THR43 3.8 0.1 1.0
CA D:SER25 3.9 0.0 1.0
N D:SER25 3.9 1.0 1.0
O3B D:GSP2000 4.0 0.5 1.0
OD1 D:ASP66 4.1 0.8 1.0
O2G D:GSP2000 4.2 0.7 1.0
O2A D:GSP2000 4.2 0.3 1.0
CG D:ASP66 4.2 0.6 1.0
O D:LYS41 4.3 0.8 1.0
O3A D:GSP2000 4.6 0.3 1.0
S1G D:GSP2000 4.6 0.8 1.0
O1A D:GSP2000 4.7 0.8 1.0
PA D:GSP2000 4.7 0.9 1.0
C D:SER42 4.8 0.8 1.0
OE2 D:GLU47 4.8 0.0 1.0
O1B D:GSP2000 4.8 0.8 1.0

Magnesium binding site 3 out of 12 in 4d0m

Go back to Magnesium Binding Sites List in 4d0m
Magnesium binding site 3 out of 12 in the Phosphatidylinositol 4-Kinase III Beta in A Complex with RAB11A-Gtp- Gamma-S and the Rab-Binding Domain of FIP3


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 in A Complex with RAB11A-Gtp- Gamma-S and the Rab-Binding Domain of FIP3 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg2001

b:0.1
occ:1.00
OG H:SER25 1.7 0.4 1.0
OG1 H:THR43 1.7 0.3 1.0
O3G H:GSP2000 1.7 0.8 1.0
O2B H:GSP2000 2.2 1.0 1.0
CB H:SER25 2.9 0.3 1.0
CB H:THR43 3.1 0.8 1.0
PG H:GSP2000 3.3 0.5 1.0
PB H:GSP2000 3.6 0.8 1.0
N H:THR43 3.7 0.7 1.0
O3B H:GSP2000 3.8 0.7 1.0
CA H:THR43 3.9 0.0 1.0
OD2 H:ASP66 3.9 0.8 1.0
O H:LYS41 4.0 0.1 1.0
CA H:SER25 4.0 0.5 1.0
N H:SER25 4.0 0.2 1.0
CG2 H:THR43 4.0 0.3 1.0
O2A H:GSP2000 4.0 0.6 1.0
O2G H:GSP2000 4.2 0.4 1.0
S1G H:GSP2000 4.4 0.5 1.0
OD1 H:ASP66 4.4 0.8 1.0
O1A H:GSP2000 4.5 0.8 1.0
PA H:GSP2000 4.5 0.2 1.0
O3A H:GSP2000 4.5 0.6 1.0
C H:SER42 4.6 0.6 1.0
CG H:ASP66 4.6 0.6 1.0
O1B H:GSP2000 4.8 0.6 1.0
OE2 H:GLU47 4.9 0.9 1.0

Magnesium binding site 4 out of 12 in 4d0m

Go back to Magnesium Binding Sites List in 4d0m
Magnesium binding site 4 out of 12 in the Phosphatidylinositol 4-Kinase III Beta in A Complex with RAB11A-Gtp- Gamma-S and the Rab-Binding Domain of FIP3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Phosphatidylinositol 4-Kinase III Beta in A Complex with RAB11A-Gtp- Gamma-S and the Rab-Binding Domain of FIP3 within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mg2001

b:0.5
occ:1.00
OG1 J:THR43 1.6 0.7 1.0
OG J:SER25 1.6 0.9 1.0
O3G J:GSP2000 1.8 0.6 1.0
O2B J:GSP2000 2.2 0.5 1.0
CB J:SER25 2.9 0.6 1.0
CB J:THR43 3.0 0.7 1.0
PG J:GSP2000 3.3 0.6 1.0
PB J:GSP2000 3.6 0.4 1.0
OD2 J:ASP66 3.7 0.4 1.0
N J:THR43 3.8 0.8 1.0
CA J:THR43 3.9 1.0 1.0
O3B J:GSP2000 3.9 0.4 1.0
CG2 J:THR43 3.9 0.2 1.0
CA J:SER25 3.9 0.8 1.0
N J:SER25 3.9 0.4 1.0
O2A J:GSP2000 4.1 1.0 1.0
O J:LYS41 4.1 0.1 1.0
O2G J:GSP2000 4.1 0.7 1.0
OD1 J:ASP66 4.2 0.6 1.0
CG J:ASP66 4.3 0.8 1.0
S1G J:GSP2000 4.5 0.6 1.0
O3A J:GSP2000 4.5 0.8 1.0
O1A J:GSP2000 4.5 0.1 1.0
PA J:GSP2000 4.6 0.4 1.0
C J:SER42 4.7 0.3 1.0
O1B J:GSP2000 4.7 0.8 1.0
OE2 J:GLU47 4.9 0.7 1.0

Magnesium binding site 5 out of 12 in 4d0m

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Magnesium binding site 5 out of 12 in the Phosphatidylinositol 4-Kinase III Beta in A Complex with RAB11A-Gtp- Gamma-S and the Rab-Binding Domain of FIP3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Phosphatidylinositol 4-Kinase III Beta in A Complex with RAB11A-Gtp- Gamma-S and the Rab-Binding Domain of FIP3 within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg2001

b:0.5
occ:1.00
OG1 N:THR43 1.6 0.5 1.0
OG N:SER25 1.6 0.4 1.0
O3G N:GSP2000 1.9 0.4 1.0
O2B N:GSP2000 2.4 0.6 1.0
CB N:SER25 2.8 0.6 1.0
CB N:THR43 3.0 0.9 1.0
PG N:GSP2000 3.4 0.6 1.0
N N:THR43 3.6 0.1 1.0
CA N:THR43 3.7 0.1 1.0
PB N:GSP2000 3.7 0.6 1.0
O N:LYS41 3.8 1.0 1.0
OD2 N:ASP66 3.8 0.6 1.0
CG2 N:THR43 3.8 0.1 1.0
O3B N:GSP2000 4.0 0.9 1.0
CA N:SER25 4.0 0.4 1.0
O2A N:GSP2000 4.0 98.2 1.0
N N:SER25 4.2 0.9 1.0
O2G N:GSP2000 4.4 0.6 1.0
C N:SER42 4.4 0.8 1.0
S1G N:GSP2000 4.4 0.0 1.0
O1A N:GSP2000 4.5 97.2 1.0
OD1 N:ASP66 4.5 0.1 1.0
PA N:GSP2000 4.5 0.4 1.0
OE2 N:GLU47 4.5 0.0 1.0
CG N:ASP66 4.6 0.4 1.0
O3A N:GSP2000 4.6 0.9 1.0
C N:LYS41 4.9 0.5 1.0
CA N:SER42 4.9 0.6 1.0
O1B N:GSP2000 4.9 0.6 1.0

Magnesium binding site 6 out of 12 in 4d0m

Go back to Magnesium Binding Sites List in 4d0m
Magnesium binding site 6 out of 12 in the Phosphatidylinositol 4-Kinase III Beta in A Complex with RAB11A-Gtp- Gamma-S and the Rab-Binding Domain of FIP3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Phosphatidylinositol 4-Kinase III Beta in A Complex with RAB11A-Gtp- Gamma-S and the Rab-Binding Domain of FIP3 within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Mg2001

b:0.3
occ:1.00
OG1 P:THR43 1.5 0.6 1.0
OG P:SER25 1.6 0.6 1.0
O3G P:GSP2000 1.9 0.4 1.0
O2B P:GSP2000 2.4 0.5 1.0
CB P:SER25 2.8 0.2 1.0
CB P:THR43 2.9 0.5 1.0
PG P:GSP2000 3.5 0.3 1.0
N P:THR43 3.6 0.1 1.0
CA P:THR43 3.6 0.1 1.0
OD2 P:ASP66 3.7 0.9 1.0
CG2 P:THR43 3.7 0.8 1.0
PB P:GSP2000 3.8 0.6 1.0
O P:LYS41 3.8 0.9 1.0
O3B P:GSP2000 4.0 0.3 1.0
CA P:SER25 4.0 0.3 1.0
O2A P:GSP2000 4.1 0.2 1.0
N P:SER25 4.2 0.2 1.0
OD1 P:ASP66 4.4 0.8 1.0
O2G P:GSP2000 4.4 0.5 1.0
C P:SER42 4.4 0.9 1.0
OE2 P:GLU47 4.4 0.1 1.0
CG P:ASP66 4.4 0.7 1.0
S1G P:GSP2000 4.5 0.5 1.0
O1A P:GSP2000 4.6 0.7 1.0
PA P:GSP2000 4.6 0.4 1.0
O3A P:GSP2000 4.7 0.6 1.0
O1B P:GSP2000 4.9 0.8 1.0
C P:LYS41 5.0 0.2 1.0
CA P:SER42 5.0 0.0 1.0

Magnesium binding site 7 out of 12 in 4d0m

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Magnesium binding site 7 out of 12 in the Phosphatidylinositol 4-Kinase III Beta in A Complex with RAB11A-Gtp- Gamma-S and the Rab-Binding Domain of FIP3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Phosphatidylinositol 4-Kinase III Beta in A Complex with RAB11A-Gtp- Gamma-S and the Rab-Binding Domain of FIP3 within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Mg2001

b:0.2
occ:1.00
OG R:SER25 1.7 0.6 1.0
OG1 R:THR43 1.7 0.1 1.0
O3G R:GSP2000 1.8 0.2 1.0
O2B R:GSP2000 2.3 0.4 1.0
CB R:SER25 2.9 0.5 1.0
CB R:THR43 3.1 0.3 1.0
PG R:GSP2000 3.4 0.2 1.0
PB R:GSP2000 3.6 0.9 1.0
N R:THR43 3.7 0.5 1.0
CA R:THR43 3.9 0.9 1.0
O3B R:GSP2000 3.9 0.6 1.0
OD2 R:ASP66 3.9 0.7 1.0
O2A R:GSP2000 3.9 0.0 1.0
O R:LYS41 4.0 0.0 1.0
CA R:SER25 4.0 0.7 1.0
CG2 R:THR43 4.0 0.9 1.0
N R:SER25 4.0 0.9 1.0
O1A R:GSP2000 4.3 0.3 1.0
O2G R:GSP2000 4.3 0.9 1.0
PA R:GSP2000 4.3 0.1 1.0
O3A R:GSP2000 4.4 0.1 1.0
OD1 R:ASP66 4.5 0.5 1.0
S1G R:GSP2000 4.5 0.7 1.0
C R:SER42 4.6 0.7 1.0
CG R:ASP66 4.6 0.4 1.0
O1B R:GSP2000 4.8 0.0 1.0
OE2 R:GLU47 4.8 0.4 1.0

Magnesium binding site 8 out of 12 in 4d0m

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Magnesium binding site 8 out of 12 in the Phosphatidylinositol 4-Kinase III Beta in A Complex with RAB11A-Gtp- Gamma-S and the Rab-Binding Domain of FIP3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Phosphatidylinositol 4-Kinase III Beta in A Complex with RAB11A-Gtp- Gamma-S and the Rab-Binding Domain of FIP3 within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Mg2001

b:1.0
occ:1.00
OG T:SER25 1.5 0.9 1.0
O3G T:GSP2000 1.8 0.0 1.0
OG1 T:THR43 1.8 0.7 1.0
O2B T:GSP2000 2.3 0.5 1.0
CB T:SER25 2.7 0.1 1.0
CB T:THR43 3.2 0.0 1.0
PG T:GSP2000 3.3 0.0 1.0
PB T:GSP2000 3.6 0.7 1.0
CA T:SER25 3.8 0.5 1.0
OD2 T:ASP66 3.8 0.3 1.0
O3B T:GSP2000 3.8 0.7 1.0
N T:THR43 3.8 0.9 1.0
N T:SER25 3.9 0.9 1.0
CA T:THR43 4.0 0.9 1.0
O T:LYS41 4.0 1.0 1.0
O2A T:GSP2000 4.0 0.2 1.0
CG2 T:THR43 4.1 0.3 1.0
O2G T:GSP2000 4.3 0.3 1.0
S1G T:GSP2000 4.3 1.0 1.0
OD1 T:ASP66 4.4 0.5 1.0
O1A T:GSP2000 4.4 0.8 1.0
O3A T:GSP2000 4.5 0.9 1.0
PA T:GSP2000 4.5 0.4 1.0
CG T:ASP66 4.5 0.3 1.0
C T:SER42 4.7 0.6 1.0
O1B T:GSP2000 4.8 0.7 1.0
OE2 T:GLU47 4.9 0.6 1.0

Magnesium binding site 9 out of 12 in 4d0m

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Magnesium binding site 9 out of 12 in the Phosphatidylinositol 4-Kinase III Beta in A Complex with RAB11A-Gtp- Gamma-S and the Rab-Binding Domain of FIP3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Phosphatidylinositol 4-Kinase III Beta in A Complex with RAB11A-Gtp- Gamma-S and the Rab-Binding Domain of FIP3 within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Mg2001

b:0.1
occ:1.00
OG1 X:THR43 1.6 1.0 1.0
OG X:SER25 1.6 0.7 1.0
O3G X:GSP2000 1.9 0.2 1.0
O2B X:GSP2000 2.4 0.7 1.0
CB X:SER25 2.8 0.4 1.0
CB X:THR43 3.0 0.3 1.0
PG X:GSP2000 3.4 0.0 1.0
N X:THR43 3.6 0.2 1.0
PB X:GSP2000 3.7 0.7 1.0
CA X:THR43 3.7 0.1 1.0
O X:LYS41 3.8 0.6 1.0
OD2 X:ASP66 3.8 0.3 1.0
CG2 X:THR43 3.9 0.1 1.0
CA X:SER25 3.9 0.3 1.0
O3B X:GSP2000 4.0 0.0 1.0
N X:SER25 4.1 0.6 1.0
O2A X:GSP2000 4.2 0.6 1.0
O2G X:GSP2000 4.4 0.5 1.0
O1A X:GSP2000 4.4 0.6 1.0
C X:SER42 4.4 0.7 1.0
OD1 X:ASP66 4.5 0.1 1.0
CG X:ASP66 4.5 0.4 1.0
S1G X:GSP2000 4.6 0.6 1.0
O3A X:GSP2000 4.6 0.5 1.0
PA X:GSP2000 4.6 1.0 1.0
OE2 X:GLU47 4.6 0.7 1.0
C X:LYS41 4.9 0.5 1.0
O1B X:GSP2000 4.9 0.8 1.0
CA X:SER42 4.9 0.4 1.0

Magnesium binding site 10 out of 12 in 4d0m

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Magnesium binding site 10 out of 12 in the Phosphatidylinositol 4-Kinase III Beta in A Complex with RAB11A-Gtp- Gamma-S and the Rab-Binding Domain of FIP3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Phosphatidylinositol 4-Kinase III Beta in A Complex with RAB11A-Gtp- Gamma-S and the Rab-Binding Domain of FIP3 within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg2001

b:0.4
occ:1.00
OG Z:SER25 1.4 0.7 1.0
OG1 Z:THR43 1.5 0.6 1.0
O3G Z:GSP2000 1.9 0.2 1.0
O2B Z:GSP2000 2.4 0.6 1.0
CB Z:SER25 2.7 0.3 1.0
CB Z:THR43 3.0 0.6 1.0
OD2 Z:ASP66 3.5 0.6 1.0
PG Z:GSP2000 3.5 0.1 1.0
CG2 Z:THR43 3.7 0.1 1.0
N Z:THR43 3.8 0.1 1.0
CA Z:THR43 3.8 1.0 1.0
CA Z:SER25 3.8 0.1 1.0
PB Z:GSP2000 3.8 0.5 1.0
N Z:SER25 3.9 0.5 1.0
O3B Z:GSP2000 4.0 0.5 1.0
O Z:LYS41 4.1 0.9 1.0
O2A Z:GSP2000 4.1 0.6 1.0
OD1 Z:ASP66 4.2 0.1 1.0
CG Z:ASP66 4.2 0.4 1.0
OE2 Z:GLU47 4.4 0.2 1.0
O1A Z:GSP2000 4.4 0.2 1.0
O2G Z:GSP2000 4.5 0.5 1.0
PA Z:GSP2000 4.5 0.4 1.0
S1G Z:GSP2000 4.6 0.5 1.0
O3A Z:GSP2000 4.6 0.4 1.0
C Z:SER42 4.6 1.0 1.0
O1B Z:GSP2000 5.0 0.9 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 11:46:29 2020

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