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: Mon Dec 14 22:42:19 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy