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Zinc in PDB 6fl8: Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase From A. Thaliana in Complex with Purpurogallin and Adp

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

All present enzymatic activity of Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase From A. Thaliana in Complex with Purpurogallin 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 Purpurogallin and Adp, PDB code: 6fl8 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) 54.30 / 2.10
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 59.990, 61.450, 83.430, 89.55, 88.00, 62.08
R / Rfree (%) 19.8 / 24.7

Other elements in 6fl8:

The structure of Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase From A. Thaliana in Complex with Purpurogallin and Adp also contains other interesting chemical elements:

Magnesium (Mg) 3 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 Purpurogallin and Adp (pdb code 6fl8). 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 Purpurogallin and Adp, PDB code: 6fl8:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 6fl8

Go back to Zinc Binding Sites List in 6fl8
Zinc binding site 1 out of 2 in the Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase From A. Thaliana in Complex with Purpurogallin 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 Purpurogallin and Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn504

b:38.7
occ:1.00
NE2 A:HIS346 2.1 40.5 1.0
SG A:CYS330 2.2 36.8 1.0
SG A:CYS333 2.3 46.6 1.0
ND1 A:HIS320 2.4 30.2 1.0
CE1 A:HIS346 3.0 38.3 1.0
CD2 A:HIS346 3.1 37.9 1.0
CB A:CYS330 3.1 44.5 1.0
CE1 A:HIS320 3.3 35.8 1.0
CG A:HIS320 3.4 37.5 1.0
CB A:CYS333 3.6 52.2 1.0
CB A:HIS320 3.7 32.5 1.0
N A:CYS333 4.0 49.4 1.0
CG A:GLU342 4.2 59.1 1.0
ND1 A:HIS346 4.2 37.3 1.0
CG A:HIS346 4.2 43.7 1.0
CA A:HIS320 4.3 31.7 1.0
CA A:CYS333 4.4 54.1 1.0
NE2 A:HIS320 4.4 31.5 1.0
CD2 A:HIS320 4.5 34.6 1.0
CB A:ILE332 4.6 48.1 1.0
CA A:CYS330 4.6 46.3 1.0
CB A:GLU342 4.8 68.2 1.0
C A:ILE332 4.9 54.6 1.0

Zinc binding site 2 out of 2 in 6fl8

Go back to Zinc Binding Sites List in 6fl8
Zinc binding site 2 out of 2 in the Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase From A. Thaliana in Complex with Purpurogallin 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 Purpurogallin and Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn505

b:39.7
occ:1.00
ND1 B:HIS320 2.2 34.8 1.0
SG B:CYS330 2.2 39.2 1.0
NE2 B:HIS346 2.2 41.2 1.0
SG B:CYS333 2.4 54.7 1.0
CE1 B:HIS320 3.0 39.5 1.0
CB B:CYS330 3.1 47.0 1.0
CE1 B:HIS346 3.2 35.3 1.0
CD2 B:HIS346 3.2 41.1 1.0
CG B:HIS320 3.3 30.8 1.0
CB B:CYS333 3.4 50.0 1.0
CB B:HIS320 3.7 26.6 1.0
N B:CYS333 4.0 57.9 1.0
N B:GLU342 4.0 62.9 1.0
NE2 B:HIS320 4.2 38.1 1.0
CA B:CYS333 4.2 58.5 1.0
CA B:HIS320 4.3 29.9 1.0
ND1 B:HIS346 4.3 37.5 1.0
CD2 B:HIS320 4.3 33.1 1.0
CG B:HIS346 4.3 42.4 1.0
CA B:CYS330 4.5 53.2 1.0
C B:ILE332 4.8 55.2 1.0
CB B:ILE332 4.9 48.7 1.0
C B:CYS330 4.9 57.4 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: Wed Dec 16 11:48:39 2020

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