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Gold in PDB 1w1d: Crystal Structure of the PDK1 Pleckstrin Homology (pH) Domain Bound to Inositol (1,3,4,5)-Tetrakisphosphate

Enzymatic activity of Crystal Structure of the PDK1 Pleckstrin Homology (pH) Domain Bound to Inositol (1,3,4,5)-Tetrakisphosphate

All present enzymatic activity of Crystal Structure of the PDK1 Pleckstrin Homology (pH) Domain Bound to Inositol (1,3,4,5)-Tetrakisphosphate:
2.7.1.37;

Protein crystallography data

The structure of Crystal Structure of the PDK1 Pleckstrin Homology (pH) Domain Bound to Inositol (1,3,4,5)-Tetrakisphosphate, PDB code: 1w1d was solved by D.Komander, M.Deak, D.R.Alessi, D.M.F.Van Aalten, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.00 / 1.5
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 35.399, 58.922, 36.578, 90.00, 101.48, 90.00
R / Rfree (%) 14.5 / 20

Gold Binding Sites:

The binding sites of Gold atom in the Crystal Structure of the PDK1 Pleckstrin Homology (pH) Domain Bound to Inositol (1,3,4,5)-Tetrakisphosphate (pdb code 1w1d). This binding sites where shown within 5.0 Angstroms radius around Gold atom.
In total 2 binding sites of Gold where determined in the Crystal Structure of the PDK1 Pleckstrin Homology (pH) Domain Bound to Inositol (1,3,4,5)-Tetrakisphosphate, PDB code: 1w1d:
Jump to Gold binding site number: 1; 2;

Gold binding site 1 out of 2 in 1w1d

Go back to Gold Binding Sites List in 1w1d
Gold binding site 1 out of 2 in the Crystal Structure of the PDK1 Pleckstrin Homology (pH) Domain Bound to Inositol (1,3,4,5)-Tetrakisphosphate


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 1 of Crystal Structure of the PDK1 Pleckstrin Homology (pH) Domain Bound to Inositol (1,3,4,5)-Tetrakisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Au1551

b:18.1
occ:0.85
AU A:AU1551 0.0 18.1 0.8
SG A:CYS536 2.2 14.4 1.0
O A:HOH2025 2.7 24.4 1.0
AU A:AU1551 3.0 22.1 0.1
CB A:CYS536 3.2 11.2 1.0
C A:CYS536 3.2 10.1 1.0
O A:CYS536 3.3 10.9 1.0
N A:ARG537 3.5 10.5 1.0
CA A:CYS536 3.7 9.9 1.0
CA A:ARG537 3.9 11.0 1.0
CB A:GLN540 4.1 10.7 1.0
O A:HOH2182 4.1 32.9 1.0
CG A:PRO506 4.5 11.9 1.0
CG A:ARG537 4.6 18.1 1.0
CG A:GLN540 4.7 13.5 1.0
O A:HOH2149 4.8 27.5 1.0
CB A:ARG537 4.8 13.0 1.0
O A:PRO506 4.9 14.6 1.0
C A:ARG537 4.9 10.1 1.0

Gold binding site 2 out of 2 in 1w1d

Go back to Gold Binding Sites List in 1w1d
Gold binding site 2 out of 2 in the Crystal Structure of the PDK1 Pleckstrin Homology (pH) Domain Bound to Inositol (1,3,4,5)-Tetrakisphosphate


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 2 of Crystal Structure of the PDK1 Pleckstrin Homology (pH) Domain Bound to Inositol (1,3,4,5)-Tetrakisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Au1551

b:22.1
occ:0.15
AU A:AU1551 0.0 22.1 0.1
SG A:CYS536 2.4 14.4 1.0
O A:HOH2149 2.5 27.5 1.0
AU A:AU1551 3.0 18.1 0.8
CB A:CYS536 3.3 11.2 1.0
N A:ALA508 3.3 17.1 1.0
CB A:ALA508 3.6 18.6 1.0
CA A:ALA508 4.1 18.1 1.0
C A:GLU507 4.2 16.4 1.0
CA A:GLU507 4.4 15.9 1.0
O A:ALA508 4.6 20.6 1.0
CD2 A:HIS533 4.7 25.9 1.0
CA A:CYS536 4.7 9.9 1.0
C A:ALA508 4.9 18.1 1.0

Reference:

D.Komander, A.Fairservice, M.Deak, G.S.Kular, A.R.Prescott, C.P.Downes, S.T.Safrany, D.R.Alessi, D.M.F.Van Aalten. Structural Insights Into the Regulation of PDK1 By Phosphoinositides and Inositol Phosphates Embo J. V. 23 3918 2004.
ISSN: ISSN 0261-4189
PubMed: 15457207
DOI: 10.1038/SJ.EMBOJ.7600379
Page generated: Sat Dec 12 01:53:08 2020

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