Atomistry » Magnesium » PDB 6g7m-6ggj » 6gfg
Atomistry »
  Magnesium »
    PDB 6g7m-6ggj »
      6gfg »

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: Wed Aug 13 06:33:33 2025

Last articles

Mg in 6WWF
Mg in 6WVR
Mg in 6WWE
Mg in 6WVM
Mg in 6WVL
Mg in 6WUU
Mg in 6WVK
Mg in 6WVJ
Mg in 6WUQ
Mg in 6WUD
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy