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Zinc in PDB 3udt: Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase From A. Thaliana in Complex with Adp and IP5.

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

All present enzymatic activity of Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase From A. Thaliana in Complex with Adp and IP5.:
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 Adp and IP5., PDB code: 3udt was solved by V.Gosein, T.-F.Leung, O.Krajden, G.J.Miller, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.63 / 3.10
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 59.362, 59.913, 83.146, 90.02, 97.04, 116.81
R / Rfree (%) 21 / 27.6

Other elements in 3udt:

The structure of Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase From A. Thaliana in Complex with Adp and IP5. also contains other interesting chemical elements:

Magnesium (Mg) 2 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 Adp and IP5. (pdb code 3udt). 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 Adp and IP5., PDB code: 3udt:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 3udt

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


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 Adp and IP5. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn914

b:39.8
occ:1.00
NE2 A:HIS346 2.1 18.2 1.0
SG A:CYS330 2.2 29.1 1.0
ND1 A:HIS320 2.2 18.2 1.0
SG A:CYS333 2.5 13.7 1.0
CE1 A:HIS346 3.0 13.8 1.0
CB A:CYS330 3.1 20.0 1.0
CE1 A:HIS320 3.2 22.3 1.0
CD2 A:HIS346 3.2 11.8 1.0
CG A:HIS320 3.2 13.4 1.0
CB A:HIS320 3.5 12.9 1.0
CB A:CYS333 3.9 23.3 1.0
CA A:HIS320 3.9 13.3 1.0
N A:CYS333 4.1 21.5 1.0
ND1 A:HIS346 4.1 16.7 1.0
CG A:HIS346 4.3 14.0 1.0
NE2 A:HIS320 4.3 14.8 1.0
CD2 A:HIS320 4.4 13.9 1.0
CB A:ILE332 4.5 18.6 1.0
CA A:CYS330 4.5 16.9 1.0
CA A:CYS333 4.6 25.7 1.0
O A:HIS320 4.7 14.3 1.0
C A:HIS320 4.8 13.1 1.0
C A:ILE332 4.9 22.2 1.0
O A:CYS330 4.9 18.8 1.0
C A:CYS330 4.9 16.3 1.0

Zinc binding site 2 out of 2 in 3udt

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


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 Adp and IP5. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn914

b:33.5
occ:1.00
NE2 B:HIS346 2.1 15.8 1.0
ND1 B:HIS320 2.2 11.5 1.0
SG B:CYS330 2.2 21.0 1.0
SG B:CYS333 2.5 14.8 1.0
CE1 B:HIS346 2.9 13.4 1.0
CB B:CYS330 2.9 16.1 1.0
CE1 B:HIS320 3.1 12.7 1.0
CG B:HIS320 3.2 10.0 1.0
CD2 B:HIS346 3.2 9.7 1.0
CB B:HIS320 3.5 9.7 1.0
CB B:CYS333 3.9 26.1 1.0
CA B:HIS320 3.9 9.8 1.0
ND1 B:HIS346 4.0 12.2 1.0
N B:CYS333 4.2 21.7 1.0
CG B:HIS346 4.2 11.8 1.0
NE2 B:HIS320 4.2 9.7 1.0
CD2 B:HIS320 4.3 10.8 1.0
CA B:CYS330 4.4 12.9 1.0
CB B:ILE332 4.5 14.5 1.0
CA B:CYS333 4.6 21.0 1.0
C B:ILE332 4.8 22.2 1.0
C B:HIS320 4.9 9.7 1.0
O B:HIS320 4.9 12.9 1.0
C B:CYS330 4.9 15.5 1.0
O B:CYS330 4.9 16.2 1.0
N B:HIS320 5.0 10.6 1.0

Reference:

V.Gosein, T.F.Leung, O.Krajden, G.J.Miller. Inositol Phosphate-Induced Stabilization of Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase and Its Role in Substrate Specificity. Protein Sci. V. 21 737 2012.
ISSN: ISSN 0961-8368
PubMed: 22362712
DOI: 10.1002/PRO.2049
Page generated: Wed Dec 16 04:54:15 2020

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