Magnesium in PDB 6gfh: Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase From A. Thaliana in Complex with Neo-IP5 and Atp

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

All present enzymatic activity of Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase From A. Thaliana in Complex with Neo-IP5 and Atp:
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 Neo-IP5 and Atp, PDB code: 6gfh 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) 29.34 / 2.65
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 59.632, 60.563, 84.482, 87.81, 88.43, 63.01
R / Rfree (%) 19.9 / 26.8

Other elements in 6gfh:

The structure of Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase From A. Thaliana in Complex with Neo-IP5 and Atp 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 Neo-IP5 and Atp (pdb code 6gfh). 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 Neo-IP5 and Atp, PDB code: 6gfh:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 6gfh

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


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 Neo-IP5 and Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg503

b:44.9
occ:1.00
 OD2 A:ASP407 2.0 43.9 1.0
O1B A:ATP502 2.3 53.4 1.0
CG A:ASP407 2.6 44.5 1.0
OD1 A:ASP407 2.6 49.5 1.0
O33 A:K7V501 3.4 48.6 0.9
O1G A:ATP502 3.5 57.8 1.0
PB A:ATP502 3.6 49.1 1.0
O23 A:K7V501 3.8 52.0 0.9
NZ A:LYS411 3.9 45.2 1.0
CB A:ASP407 4.1 36.1 1.0
P3 A:K7V501 4.1 59.6 0.9
PG A:ATP502 4.2 72.3 1.0
O3B A:ATP502 4.2 50.5 1.0
CB A:SER409 4.3 49.8 1.0
O3G A:ATP502 4.3 51.5 1.0
O2B A:ATP502 4.4 45.0 1.0
CB A:ALA21 4.4 39.3 1.0
OG A:SER409 4.5 55.7 1.0
O13 A:K7V501 4.6 55.2 0.9
O12 A:K7V501 4.6 52.6 0.9
NH2 A:ARG40 4.7 40.9 1.0
O3A A:ATP502 4.9 50.5 1.0
H2 A:K7V501 4.9 64.6 0.9
ND2 A:ASN22 4.9 44.0 1.0

Magnesium binding site 2 out of 3 in 6gfh

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


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 Neo-IP5 and Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg503

b:44.5
occ:1.00
 O1G B:ATP502 2.2 47.6 1.0
O2G B:ATP502 2.5 58.5 1.0
PG B:ATP502 2.8 68.3 1.0
OG B:SER370 3.0 50.1 1.0
O B:ASP368 3.0 36.5 1.0
O2A B:ATP502 3.1 48.4 1.0
CB B:ASP407 3.3 44.3 1.0
OD1 B:ASP407 3.3 53.4 1.0
CG B:ASP407 3.4 47.0 1.0
O3G B:ATP502 3.9 57.7 1.0
O3B B:ATP502 4.0 52.4 1.0
C B:CYS369 4.2 39.6 1.0
N B:SER370 4.2 39.4 1.0
C B:ASP368 4.2 35.2 1.0
OD2 B:ASP407 4.2 52.2 1.0
CA B:CYS369 4.3 39.9 1.0
OD2 B:ASP368 4.3 52.3 1.0
CB B:SER370 4.4 44.8 1.0
CD B:LYS168 4.4 38.4 1.0
CE B:LYS168 4.5 38.3 1.0
PA B:ATP502 4.6 44.1 1.0
NZ B:LYS168 4.6 43.7 1.0
O B:CYS369 4.6 36.8 1.0
CA B:ASP407 4.7 40.2 1.0
N B:CYS369 4.8 31.6 1.0
CG B:ASP368 4.8 49.3 1.0
CG B:LYS168 4.8 37.4 1.0
HO3' B:ATP502 4.8 60.4 1.0
O B:ASP407 4.8 46.8 1.0
OE2 B:GLU166 4.9 51.5 1.0
O2B B:ATP502 4.9 47.9 1.0
CA B:SER370 4.9 42.1 1.0
O5' B:ATP502 4.9 52.0 1.0

Magnesium binding site 3 out of 3 in 6gfh

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


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 Neo-IP5 and Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg504

b:45.8
occ:1.00
 OD2 B:ASP407 2.3 52.2 1.0
O2B B:ATP502 2.5 47.9 1.0
OD1 B:ASP407 2.9 53.4 1.0
OG B:SER409 2.9 54.5 1.0
CG B:ASP407 2.9 47.0 1.0
O2G B:ATP502 3.2 58.5 1.0
CB B:SER409 3.4 49.1 1.0
O43 B:K7V501 3.5 52.0 1.0
OD2 B:ASP368 3.6 52.3 1.0
PB B:ATP502 3.9 44.6 1.0
ND2 B:ASN22 4.4 45.8 1.0
CB B:ASP407 4.4 44.3 1.0
PG B:ATP502 4.4 68.3 1.0
CB B:ALA21 4.5 45.1 1.0
O23 B:K7V501 4.5 39.3 1.0
P3 B:K7V501 4.6 50.1 1.0
O3B B:ATP502 4.7 52.4 1.0
CA B:SER409 4.7 46.3 1.0
N B:SER409 4.7 43.1 1.0
NH2 B:ARG40 4.7 45.4 1.0
NZ B:LYS411 4.7 35.2 1.0
O1B B:ATP502 4.8 43.5 1.0
CG B:ASP368 4.8 49.3 1.0
O2A B:ATP502 4.8 48.4 1.0
O3G B:ATP502 4.8 57.7 1.0
O B:ASP407 4.9 46.8 1.0
O3A B:ATP502 4.9 44.0 1.0
O13 B:K7V501 4.9 49.0 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 22:44:51 2020

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