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

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

All present enzymatic activity of Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase From A. Thaliana in Complex with D-Chiro-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 D-Chiro-IP6 and Adp, PDB code: 6gfg 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) 29.02 / 3.00
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 59.566, 60.820, 82.439, 89.50, 88.34, 62.54
R / Rfree (%) 19.7 / 26.5

Other elements in 6gfg:

The structure of Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase From A. Thaliana in Complex with D-Chiro-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 D-Chiro-IP6 and Adp (pdb code 6gfg). 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 D-Chiro-IP6 and Adp, PDB code: 6gfg:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 6gfg

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

b:45.5
occ:1.00
 OD1 B:ASP407 2.2 38.9 1.0
O1B B:ADP502 2.4 52.2 0.9
CG B:ASP407 3.0 43.0 1.0
OD2 B:ASP407 3.1 47.5 1.0
PB B:ADP502 3.7 44.4 0.9
OD2 B:ASP368 3.8 46.1 1.0
O22 B:KGN501 3.9 76.7 0.9
NZ B:LYS411 3.9 46.8 1.0
CB B:SER409 3.9 45.1 1.0
O2B B:ADP502 3.9 45.6 0.9
OG B:SER409 4.1 56.4 1.0
CB B:ALA21 4.1 48.1 1.0
OD1 B:ASP368 4.2 65.8 1.0
CG B:ASP368 4.4 57.2 1.0
CB B:ASP407 4.5 39.4 1.0
NH2 B:ARG40 4.5 45.6 1.0
O3A B:ADP502 4.6 44.3 0.9
OD1 B:ASN22 4.8 53.2 1.0
P2 B:KGN501 4.9 76.2 0.9
O3B B:ADP502 4.9 42.0 0.9
O B:ASP407 4.9 30.0 1.0
O12 B:KGN501 4.9 77.9 0.9
O1A B:ADP502 4.9 38.5 0.9
O42 B:KGN501 4.9 77.9 0.9
CA B:ASP407 5.0 38.7 1.0

Magnesium binding site 2 out of 4 in 6gfg

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

b:43.5
occ:1.00
 O2B B:ADP502 2.3 45.6 0.9
OD2 B:ASP407 2.6 47.5 1.0
O1A B:ADP502 2.6 38.5 0.9
O5' B:ADP502 3.4 49.5 0.9
PA B:ADP502 3.6 46.3 0.9
PB B:ADP502 3.7 44.4 0.9
CG B:ASP407 3.7 43.0 1.0
HO3' B:ADP502 3.8 44.2 0.9
O31 B:KGN501 3.9 74.9 0.9
O3' B:ADP502 3.9 36.8 0.9
H3' B:ADP502 4.0 51.8 0.9
O3A B:ADP502 4.0 44.3 0.9
CB B:ASP407 4.1 39.4 1.0
OG B:SER370 4.3 41.5 1.0
C3' B:ADP502 4.5 43.1 0.9
O1B B:ADP502 4.5 52.2 0.9
O3B B:ADP502 4.7 42.0 0.9
CA B:GLY19 4.7 50.0 1.0
OD1 B:ASP407 4.7 38.9 1.0
C5' B:ADP502 4.7 48.2 0.9
CD B:LYS168 4.8 33.8 1.0
O B:ASP368 4.8 35.0 1.0
NZ B:LYS168 4.8 55.8 1.0
OD1 B:ASP368 4.9 65.8 1.0
CE B:LYS168 5.0 42.2 1.0
O2A B:ADP502 5.0 48.6 0.9

Magnesium binding site 3 out of 4 in 6gfg

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

b:53.4
occ:1.00
 OD2 A:ASP407 2.2 61.8 1.0
O3A A:ADP502 2.6 57.1 0.9
O3B A:ADP502 3.0 61.7 0.9
CG A:ASP407 3.1 56.3 1.0
CB A:ASP407 3.3 48.5 1.0
HO3' A:ADP502 3.5 64.8 0.9
PB A:ADP502 3.5 64.5 0.9
O31 A:KGN501 3.6 67.2 0.9
PA A:ADP502 3.7 57.0 0.9
O3' A:ADP502 3.7 54.0 0.9
O5' A:ADP502 3.8 65.3 0.9
OG A:SER370 4.0 47.6 1.0
O1A A:ADP502 4.0 52.8 0.9
H3' A:ADP502 4.1 66.1 0.9
OD1 A:ASP407 4.2 55.1 1.0
O A:ASP368 4.2 45.0 1.0
O2B A:ADP502 4.3 62.6 0.9
CE A:LYS168 4.5 45.7 1.0
C3' A:ADP502 4.5 55.1 0.9
O1B A:ADP502 4.7 51.1 0.9
P1 A:KGN501 4.7 65.6 0.9
NZ A:LYS168 4.7 51.2 1.0
CD A:LYS168 4.8 47.4 1.0
CA A:ASP407 4.8 47.9 1.0
MG A:MG504 4.9 53.6 1.0
CA A:GLY19 4.9 54.9 1.0
O41 A:KGN501 4.9 66.8 0.9
O2A A:ADP502 5.0 56.0 0.9
OD2 A:ASP368 5.0 60.7 1.0

Magnesium binding site 4 out of 4 in 6gfg

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

b:53.6
occ:1.00
 OD1 A:ASP407 2.0 55.1 1.0
O2B A:ADP502 2.6 62.6 0.9
CG A:ASP407 2.7 56.3 1.0
OD2 A:ASP407 2.7 61.8 1.0
O42 A:KGN501 3.3 75.0 0.9
O22 A:KGN501 3.3 75.5 0.9
OD2 A:ASP368 3.6 60.7 1.0
PB A:ADP502 3.7 64.5 0.9
O3B A:ADP502 3.8 61.7 0.9
P2 A:KGN501 3.8 79.2 0.9
CB A:SER409 3.9 54.9 1.0
CB A:ASP407 4.2 48.5 1.0
O3A A:ADP502 4.3 57.1 0.9
OG A:SER409 4.4 53.9 1.0
O A:ASP407 4.4 45.0 1.0
CE A:LYS411 4.5 40.5 1.0
NZ A:LYS411 4.5 49.5 1.0
O12 A:KGN501 4.5 76.4 0.9
CA A:ASP407 4.7 47.9 1.0
N A:SER409 4.7 49.8 1.0
CG A:ASP368 4.8 58.3 1.0
C A:ASP407 4.8 49.7 1.0
NH2 A:ARG40 4.8 50.8 1.0
MG A:MG503 4.9 53.4 1.0
CA A:SER409 4.9 50.2 1.0
O1B A:ADP502 5.0 51.1 0.9

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 22:44:50 2020

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