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Magnesium in PDB 6fjk: Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase From A. Thaliana in Complex with Myo-IP6 and Adp

Enzymatic activity of Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase From A. Thaliana in Complex with Myo-IP6 and Adp

All present enzymatic activity of Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase From A. Thaliana in Complex with Myo-IP6 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-IP6 and Adp, PDB code: 6fjk 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) 83.95 / 2.03
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 59.810, 60.340, 83.980, 88.53, 89.18, 63.36
R / Rfree (%) 17.8 / 22.5

Other elements in 6fjk:

The structure of Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase From A. Thaliana in Complex with Myo-IP6 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-IP6 and Adp (pdb code 6fjk). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase From A. Thaliana in Complex with Myo-IP6 and Adp, PDB code: 6fjk:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 6fjk

Go back to Magnesium Binding Sites List in 6fjk
Magnesium binding site 1 out of 3 in the Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase From A. Thaliana in Complex with Myo-IP6 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-IP6 and Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg503

b:58.6
occ:1.00
 O22 A:I6P501 2.4 58.4 1.0
OD1 A:ASP407 2.8 62.6 1.0
O1B A:ADP502 2.8 87.7 1.0
O3B A:ADP502 3.0 83.7 1.0
PB A:ADP502 3.2 68.4 1.0
O33 A:I6P501 3.2 32.5 1.0
OD2 A:ASP407 3.3 72.9 1.0
CG A:ASP407 3.4 60.6 1.0
O2B A:ADP502 3.7 56.1 1.0
CB A:ALA21 3.8 34.1 1.0
P2 A:I6P501 3.8 51.7 1.0
OG A:SER409 3.9 48.1 1.0
O43 A:I6P501 3.9 31.4 1.0
P3 A:I6P501 4.0 30.5 1.0
ND2 A:ASN22 4.2 31.7 1.0
CB A:SER409 4.2 35.8 1.0
O32 A:I6P501 4.3 63.7 1.0
O A:HOH628 4.4 43.7 1.0
O13 A:I6P501 4.4 19.8 1.0
NH2 A:ARG40 4.4 37.8 1.0
N A:ALA21 4.4 22.8 1.0
OD2 A:ASP368 4.4 39.1 1.0
NZ A:LYS411 4.5 15.7 1.0
O42 A:I6P501 4.7 42.3 1.0
CA A:ALA21 4.7 31.8 1.0
O3A A:ADP502 4.7 79.0 1.0
O12 A:I6P501 4.8 25.8 1.0
CB A:ASP407 4.9 35.8 1.0

Magnesium binding site 2 out of 3 in 6fjk

Go back to Magnesium Binding Sites List in 6fjk
Magnesium binding site 2 out of 3 in the Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase From A. Thaliana in Complex with Myo-IP6 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-IP6 and Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg503

b:48.7
occ:1.00
 O32 B:I6P501 2.4 60.7 1.0
OD1 B:ASP407 2.7 71.6 1.0
O1B B:ADP502 2.8 0.9 1.0
OD2 B:ASP407 3.1 71.2 1.0
O2B B:ADP502 3.2 0.8 1.0
CG B:ASP407 3.2 65.6 1.0
O33 B:I6P501 3.3 36.6 1.0
PB B:ADP502 3.3 97.5 1.0
P2 B:I6P501 3.5 57.3 1.0
O22 B:I6P501 3.5 69.5 1.0
O3B B:ADP502 4.0 96.0 1.0
CB B:ALA21 4.0 35.7 1.0
OG B:SER409 4.1 50.1 1.0
ND2 B:ASN22 4.2 36.2 1.0
O43 B:I6P501 4.2 38.0 1.0
P3 B:I6P501 4.2 31.0 1.0
OD2 B:ASP368 4.2 33.1 1.0
NZ B:LYS411 4.3 23.9 1.0
O13 B:I6P501 4.4 25.8 1.0
O12 B:I6P501 4.5 28.0 1.0
N B:ALA21 4.5 31.6 1.0
NH2 B:ARG40 4.5 49.6 1.0
CB B:SER409 4.5 37.7 1.0
O42 B:I6P501 4.6 65.9 1.0
CB B:ASP407 4.7 44.5 1.0
O3A B:ADP502 4.8 88.7 1.0
CA B:ALA21 4.9 35.7 1.0

Magnesium binding site 3 out of 3 in 6fjk

Go back to Magnesium Binding Sites List in 6fjk
Magnesium binding site 3 out of 3 in the Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase From A. Thaliana in Complex with Myo-IP6 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-IP6 and Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg504

b:46.8
occ:1.00
 OD2 B:ASP407 2.6 71.2 1.0
OG B:SER370 2.9 34.4 1.0
O B:ASP368 2.9 26.0 1.0
O B:HOH606 3.4 44.0 1.0
CG B:ASP407 3.4 65.6 1.0
CB B:ASP407 3.5 44.5 1.0
C B:CYS369 3.5 26.3 1.0
N B:SER370 3.6 20.5 1.0
CB B:SER370 3.7 29.3 1.0
O B:CYS369 3.9 25.1 1.0
CA B:CYS369 3.9 24.0 1.0
O2A B:ADP502 3.9 68.5 1.0
C B:ASP368 4.0 26.6 1.0
CE B:LYS168 4.0 33.4 1.0
O32 B:I6P501 4.1 60.7 1.0
CD B:LYS168 4.1 23.2 1.0
O42 B:I6P501 4.1 65.9 1.0
CA B:SER370 4.2 26.8 1.0
CG B:LYS168 4.3 22.4 1.0
O B:HOH733 4.3 51.0 1.0
N B:CYS369 4.4 20.5 1.0
OD1 B:ASP407 4.6 71.6 1.0
NZ B:LYS168 4.7 34.4 1.0
O B:ILE406 4.7 25.1 1.0
P2 B:I6P501 4.7 57.3 1.0
O B:ASP407 4.8 31.7 1.0
CB B:LYS168 4.9 30.8 1.0
O2B B:ADP502 4.9 0.8 1.0
CA B:ASP407 4.9 35.2 1.0
OE2 B:GLU166 5.0 38.9 1.0
OD2 B:ASP368 5.0 33.1 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: Tue Oct 1 00:29:58 2024

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