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Magnesium in PDB 6fl3: Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase From A. Thaliana in Complex with Myo-IP5 and Adp

Enzymatic activity of Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase From A. Thaliana in Complex with Myo-IP5 and Adp

All present enzymatic activity of Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase From A. Thaliana in Complex with Myo-IP5 and Adp:
2.7.1.158;

Protein crystallography data

The structure of Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase From A. Thaliana in Complex with Myo-IP5 and Adp, PDB code: 6fl3 was solved by H.L.Whitfield, C.A.Brearley, A.M.Hemmings, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 52.87 / 2.36
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 58.950, 59.010, 83.360, 88.98, 89.56, 63.65
R / Rfree (%) 15.4 / 21.7

Other elements in 6fl3:

The structure of Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase From A. Thaliana in Complex with Myo-IP5 and Adp also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase From A. Thaliana in Complex with Myo-IP5 and Adp (pdb code 6fl3). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase From A. Thaliana in Complex with Myo-IP5 and Adp, PDB code: 6fl3:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 6fl3

Go back to Magnesium Binding Sites List in 6fl3
Magnesium binding site 1 out of 4 in the Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase From A. Thaliana in Complex with Myo-IP5 and Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase From A. Thaliana in Complex with Myo-IP5 and Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg503

b:24.1
occ:1.00
 O2B A:ADP502 2.3 20.6 1.0
O A:HOH716 2.4 24.8 1.0
OD1 A:ASP407 2.5 23.7 1.0
OD2 A:ASP407 2.8 24.3 1.0
CG A:ASP407 3.0 27.5 1.0
PB A:ADP502 3.3 20.8 1.0
O A:HOH663 3.3 35.4 1.0
O1B A:ADP502 3.4 21.6 1.0
OG A:SER409 3.6 46.2 1.0
O43 A:5MY501 3.7 34.3 1.0
O A:HOH717 4.0 20.7 1.0
H12 A:5MY501 4.1 33.2 1.0
MG A:MG504 4.1 24.6 1.0
OD2 A:ASP368 4.1 31.7 1.0
CB A:SER409 4.1 37.6 1.0
O3B A:ADP502 4.2 25.7 1.0
CB A:ALA21 4.3 13.7 1.0
ND2 A:ASN22 4.4 25.4 1.0
NZ A:LYS411 4.5 17.8 1.0
CB A:ASP407 4.5 26.5 1.0
NH2 A:ARG40 4.5 16.4 1.0
O3A A:ADP502 4.6 25.2 1.0
O A:HOH682 4.6 25.8 1.0
P3 A:5MY501 4.8 37.1 1.0
O13 A:5MY501 4.9 30.8 1.0
O33 A:5MY501 4.9 35.8 1.0
O1A A:ADP502 4.9 26.6 1.0
O A:HOH623 5.0 33.2 1.0
N A:ALA21 5.0 22.6 1.0
O12 A:5MY501 5.0 27.7 1.0

Magnesium binding site 2 out of 4 in 6fl3

Go back to Magnesium Binding Sites List in 6fl3
Magnesium binding site 2 out of 4 in the Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase From A. Thaliana in Complex with Myo-IP5 and Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase From A. Thaliana in Complex with Myo-IP5 and Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg504

b:24.6
occ:1.00
 O A:HOH734 2.0 28.3 1.0
OD2 A:ASP407 2.0 24.3 1.0
O1A A:ADP502 2.1 26.6 1.0
O1B A:ADP502 2.1 21.6 1.0
O A:HOH644 2.3 10.6 1.0
O A:HOH717 2.3 20.7 1.0
CG A:ASP407 3.1 27.5 1.0
PB A:ADP502 3.2 20.8 1.0
PA A:ADP502 3.3 25.6 1.0
O3A A:ADP502 3.5 25.2 1.0
O2B A:ADP502 3.7 20.6 1.0
CB A:ASP407 3.7 26.5 1.0
O A:HOH708 3.9 42.5 1.0
OD1 A:ASP407 4.1 23.7 1.0
MG A:MG503 4.1 24.1 1.0
O2A A:ADP502 4.3 25.1 1.0
O A:ASP368 4.3 23.3 1.0
O5' A:ADP502 4.4 28.7 1.0
O3' A:ADP502 4.5 23.4 1.0
OG A:SER370 4.5 21.9 1.0
O3B A:ADP502 4.5 25.7 1.0
C5' A:ADP502 4.6 26.1 1.0
CA A:GLY19 4.7 24.1 1.0
H12 A:5MY501 4.9 33.2 1.0
C3' A:ADP502 4.9 19.9 1.0
O A:HOH716 5.0 24.8 1.0

Magnesium binding site 3 out of 4 in 6fl3

Go back to Magnesium Binding Sites List in 6fl3
Magnesium binding site 3 out of 4 in the Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase From A. Thaliana in Complex with Myo-IP5 and Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase From A. Thaliana in Complex with Myo-IP5 and Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg503

b:27.7
occ:1.00
 O B:HOH601 1.8 13.5 1.0
O B:HOH693 2.5 17.7 1.0
O2B B:ADP502 2.7 21.6 1.0
O33 B:5MY501 2.7 30.7 1.0
H12 B:5MY501 2.8 32.4 1.0
O3B B:ADP502 2.9 19.3 1.0
OD2 B:ASP407 3.1 30.1 1.0
PB B:ADP502 3.2 23.4 1.0
OD1 B:ASP407 3.2 17.4 1.0
OD2 B:ASP368 3.4 28.8 1.0
CG B:ASP407 3.6 26.1 1.0
O12 B:5MY501 3.8 27.0 1.0
P3 B:5MY501 3.8 29.9 1.0
O B:HOH641 3.8 30.7 1.0
O1B B:ADP502 3.9 18.7 1.0
O13 B:5MY501 3.9 26.6 1.0
O43 B:5MY501 4.0 26.6 1.0
NZ B:LYS411 4.3 19.1 1.0
CB B:ALA21 4.5 18.1 1.0
CG B:ASP368 4.5 32.9 1.0
N B:GLY20 4.6 23.6 1.0
N B:ALA21 4.6 21.9 1.0
H2 B:5MY501 4.6 28.5 1.0
O3A B:ADP502 4.7 25.4 1.0
C2 B:5MY501 4.7 23.8 1.0
O2A B:ADP502 4.9 25.7 1.0
C3 B:5MY501 4.9 23.1 1.0

Magnesium binding site 4 out of 4 in 6fl3

Go back to Magnesium Binding Sites List in 6fl3
Magnesium binding site 4 out of 4 in the Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase From A. Thaliana in Complex with Myo-IP5 and Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase From A. Thaliana in Complex with Myo-IP5 and Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg504

b:24.1
occ:1.00
 OD2 B:ASP407 2.5 30.1 1.0
OG B:SER370 2.9 25.8 1.0
O B:ASP368 3.0 16.3 1.0
O2A B:ADP502 3.1 25.7 1.0
CB B:ASP407 3.2 23.1 1.0
CG B:ASP407 3.2 26.1 1.0
CB B:SER370 3.6 23.5 1.0
C B:CYS369 3.7 18.1 1.0
N B:SER370 3.8 25.2 1.0
O3B B:ADP502 3.9 19.3 1.0
O B:CYS369 4.0 16.0 1.0
C B:ASP368 4.2 18.6 1.0
CA B:CYS369 4.2 16.8 1.0
CA B:SER370 4.2 22.3 1.0
OD1 B:ASP407 4.4 17.4 1.0
CE B:LYS168 4.4 25.9 1.0
CD B:LYS168 4.5 15.8 1.0
CG B:LYS168 4.5 19.3 1.0
OE2 B:GLU166 4.5 37.8 1.0
PA B:ADP502 4.6 23.7 1.0
O3' B:ADP502 4.7 28.4 1.0
N B:CYS369 4.7 19.4 1.0
CA B:ASP407 4.7 26.8 1.0
O B:ILE406 4.8 22.3 1.0
NZ B:LYS168 4.9 28.3 1.0
CD1 B:ILE406 5.0 20.5 1.0

Reference:

H.Whitfield, M.Gilmartin, K.Baker, A.M.Riley, H.Y.Godage, B.V.L.Potter, A.M.Hemmings, C.A.Brearley. A Fluorescent Probe Identifies Active Site Ligands of Inositol Pentakisphosphate 2-Kinase. J. Med. Chem. V. 61 8838 2018.
ISSN: ISSN 1520-4804
PubMed: 30160967
DOI: 10.1021/ACS.JMEDCHEM.8B01022
Page generated: Wed Aug 13 06:08:23 2025

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