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Zinc 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:

Magnesium (Mg) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc 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 Zinc atom.
In total 2 binding sites of Zinc 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 Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 6gfg

Go back to Zinc Binding Sites List in 6gfg
Zinc binding site 1 out of 2 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 Zinc with other atoms in the Zn 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:Zn505

b:45.1
occ:0.94
NE2 B:HIS346 2.0 42.7 1.0
ND1 B:HIS320 2.1 38.2 1.0
SG B:CYS333 2.1 35.8 1.0
SG B:CYS330 2.2 42.9 1.0
CE1 B:HIS346 2.7 38.7 1.0
CE1 B:HIS320 2.8 39.8 1.0
CB B:CYS330 3.1 43.4 1.0
CD2 B:HIS346 3.1 40.7 1.0
CG B:HIS320 3.3 33.7 1.0
CB B:CYS333 3.6 56.1 1.0
CB B:HIS320 3.9 29.8 1.0
ND1 B:HIS346 3.9 41.7 1.0
N B:CYS333 4.0 53.2 1.0
NE2 B:HIS320 4.0 33.5 1.0
CG B:HIS346 4.1 40.1 1.0
CD2 B:HIS320 4.3 37.3 1.0
CA B:CYS333 4.3 60.0 1.0
CA B:HIS320 4.4 33.9 1.0
CA B:CYS330 4.5 53.1 1.0
CB B:ILE332 4.9 49.8 1.0
C B:ILE332 4.9 56.1 1.0
C B:CYS330 4.9 49.1 1.0
O B:CYS330 5.0 50.7 1.0

Zinc binding site 2 out of 2 in 6gfg

Go back to Zinc Binding Sites List in 6gfg
Zinc binding site 2 out of 2 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 Zinc with other atoms in the Zn 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
A:Zn505

b:42.1
occ:0.92
NE2 A:HIS346 1.9 41.1 1.0
SG A:CYS330 2.1 38.1 1.0
SG A:CYS333 2.2 44.6 1.0
ND1 A:HIS320 2.3 32.8 1.0
CE1 A:HIS346 2.6 42.7 1.0
CB A:CYS330 2.9 45.6 1.0
CD2 A:HIS346 3.0 45.6 1.0
CG A:HIS320 3.3 31.8 1.0
CE1 A:HIS320 3.3 38.0 1.0
CB A:CYS333 3.4 56.6 1.0
CB A:HIS320 3.5 30.7 1.0
ND1 A:HIS346 3.8 43.3 1.0
CA A:HIS320 4.0 31.4 1.0
N A:CYS333 4.0 61.9 1.0
CG A:HIS346 4.1 48.6 1.0
CA A:CYS333 4.2 66.7 1.0
CA A:CYS330 4.3 44.9 1.0
CB A:ILE332 4.3 50.6 1.0
C A:ILE332 4.4 57.6 1.0
CB A:GLU342 4.4 57.0 1.0
CD2 A:HIS320 4.4 35.5 1.0
NE2 A:HIS320 4.4 37.9 1.0
CA A:ILE332 4.8 56.1 1.0
C A:CYS330 4.8 49.1 1.0
N A:GLU342 4.9 63.2 1.0
O A:HIS320 4.9 31.4 1.0
O A:ILE332 4.9 57.4 1.0
O A:CYS330 4.9 53.9 1.0
C A:HIS320 4.9 31.0 1.0
N A:ILE332 4.9 54.0 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 Oct 28 21:48:07 2024

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