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Gadolinium in PDB 6wry: Crystal Structure of Inositol Polyphosphate 1-Phosphatase INPP1 in Complex Gadolinium After Addition of Inositol 1,3,4-Trisphosphate at 2.5 Angstrom Resolution

Enzymatic activity of Crystal Structure of Inositol Polyphosphate 1-Phosphatase INPP1 in Complex Gadolinium After Addition of Inositol 1,3,4-Trisphosphate at 2.5 Angstrom Resolution

All present enzymatic activity of Crystal Structure of Inositol Polyphosphate 1-Phosphatase INPP1 in Complex Gadolinium After Addition of Inositol 1,3,4-Trisphosphate at 2.5 Angstrom Resolution:
3.1.3.57;

Protein crystallography data

The structure of Crystal Structure of Inositol Polyphosphate 1-Phosphatase INPP1 in Complex Gadolinium After Addition of Inositol 1,3,4-Trisphosphate at 2.5 Angstrom Resolution, PDB code: 6wry was solved by D.R.Dollins, S.Endo-Streeter, J.D.York, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 6.95 / 2.80
Space group P 41
Cell size a, b, c (Å), α, β, γ (°) 51.640, 51.640, 143.330, 90.00, 90.00, 90.00
R / Rfree (%) 20.5 / 25

Gadolinium Binding Sites:

The binding sites of Gadolinium atom in the Crystal Structure of Inositol Polyphosphate 1-Phosphatase INPP1 in Complex Gadolinium After Addition of Inositol 1,3,4-Trisphosphate at 2.5 Angstrom Resolution (pdb code 6wry). This binding sites where shown within 5.0 Angstroms radius around Gadolinium atom.
In total 4 binding sites of Gadolinium where determined in the Crystal Structure of Inositol Polyphosphate 1-Phosphatase INPP1 in Complex Gadolinium After Addition of Inositol 1,3,4-Trisphosphate at 2.5 Angstrom Resolution, PDB code: 6wry:
Jump to Gadolinium binding site number: 1; 2; 3; 4;

Gadolinium binding site 1 out of 4 in 6wry

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Gadolinium binding site 1 out of 4 in the Crystal Structure of Inositol Polyphosphate 1-Phosphatase INPP1 in Complex Gadolinium After Addition of Inositol 1,3,4-Trisphosphate at 2.5 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd binding site number 1 of Crystal Structure of Inositol Polyphosphate 1-Phosphatase INPP1 in Complex Gadolinium After Addition of Inositol 1,3,4-Trisphosphate at 2.5 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Gd403

b:15.7
occ:1.00
 OD1 A:ASP317 2.3 8.7 1.0
OD1 A:ASP156 2.4 9.5 1.0
OD2 A:ASP153 2.5 8.8 1.0
O2 A:SO4402 2.6 7.4 1.0
O4 A:SO4402 2.8 7.3 1.0
O A:HOH535 2.9 19.7 1.0
S A:SO4402 3.2 7.3 1.0
CG A:ASP317 3.4 8.6 1.0
CG A:ASP153 3.5 8.6 1.0
CG A:ASP156 3.6 9.6 1.0
O1 A:SO4402 3.9 7.3 1.0
OD2 A:ASP317 3.9 8.7 1.0
OD1 A:ASP153 3.9 8.7 1.0
OE1 A:GLU79 4.0 20.0 1.0
CB A:ASP156 4.3 9.7 1.0
O3 A:SO4402 4.4 7.4 1.0
CA A:ASP156 4.5 9.8 1.0
OD2 A:ASP156 4.5 9.6 1.0
NE1 A:TRP316 4.6 9.2 1.0
CD1 A:TRP316 4.6 9.1 1.0
CB A:ASP317 4.6 8.6 1.0
CB A:ASP153 4.8 8.6 1.0
N A:SER157 4.9 10.6 1.0
CD A:GLU79 5.0 19.8 1.0

Gadolinium binding site 2 out of 4 in 6wry

Go back to Gadolinium Binding Sites List in 6wry
Gadolinium binding site 2 out of 4 in the Crystal Structure of Inositol Polyphosphate 1-Phosphatase INPP1 in Complex Gadolinium After Addition of Inositol 1,3,4-Trisphosphate at 2.5 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd binding site number 2 of Crystal Structure of Inositol Polyphosphate 1-Phosphatase INPP1 in Complex Gadolinium After Addition of Inositol 1,3,4-Trisphosphate at 2.5 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Gd404

b:23.4
occ:1.00
 OE2 A:GLU79 2.2 20.2 1.0
OD2 A:ASP54 2.2 16.1 1.0
OE2 A:GLU80 2.5 20.1 1.0
CD A:GLU79 3.4 19.8 1.0
CG A:ASP54 3.4 15.9 1.0
CD A:GLU80 3.5 19.9 1.0
CG A:GLU80 3.8 19.8 1.0
CG A:GLU79 3.9 19.4 1.0
CB A:ASP54 4.0 16.1 1.0
OD1 A:ASP54 4.4 15.7 1.0
OE1 A:GLU79 4.4 20.0 1.0
O1 A:SO4402 4.5 7.3 1.0
OE1 A:GLU80 4.5 19.9 1.0
NZ A:LYS50 4.7 16.6 1.0
OG1 A:THR158 4.8 12.4 1.0
CA A:THR51 5.0 17.3 1.0

Gadolinium binding site 3 out of 4 in 6wry

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Gadolinium binding site 3 out of 4 in the Crystal Structure of Inositol Polyphosphate 1-Phosphatase INPP1 in Complex Gadolinium After Addition of Inositol 1,3,4-Trisphosphate at 2.5 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd binding site number 3 of Crystal Structure of Inositol Polyphosphate 1-Phosphatase INPP1 in Complex Gadolinium After Addition of Inositol 1,3,4-Trisphosphate at 2.5 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Gd405

b:60.2
occ:1.00
 OE2 A:GLU66 3.1 37.3 1.0
CG A:GLU63 3.7 28.6 1.0
OE1 A:GLU63 3.8 30.8 1.0
CD A:GLU63 3.8 29.8 1.0
CD A:GLU66 4.3 35.6 1.0
OE2 A:GLU63 4.6 30.2 1.0
CB A:GLU63 4.6 27.8 1.0
OE1 A:GLU66 4.9 35.6 1.0
CA A:GLU63 4.9 26.2 1.0

Gadolinium binding site 4 out of 4 in 6wry

Go back to Gadolinium Binding Sites List in 6wry
Gadolinium binding site 4 out of 4 in the Crystal Structure of Inositol Polyphosphate 1-Phosphatase INPP1 in Complex Gadolinium After Addition of Inositol 1,3,4-Trisphosphate at 2.5 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd binding site number 4 of Crystal Structure of Inositol Polyphosphate 1-Phosphatase INPP1 in Complex Gadolinium After Addition of Inositol 1,3,4-Trisphosphate at 2.5 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Gd406

b:71.0
occ:1.00
 OE2 A:GLU140 2.8 47.7 1.0
OE1 A:GLU140 3.0 42.8 1.0
CD A:GLU140 3.2 45.1 1.0
CB A:ASP3 3.8 19.7 1.0
OD2 A:ASP3 4.3 21.5 1.0
CG A:ASP3 4.5 20.5 1.0
CA A:ASP3 4.7 19.4 1.0
CG A:GLU140 4.7 44.7 1.0
OG A:SER2 4.8 19.4 1.0
N A:ASP3 5.0 19.1 1.0

Reference:

D.E.Dollins, J.P.Xiong, S.Endo-Streeter, D.E.Anderson, V.S.Bansal, J.W.Ponder, Y.Ren, J.D.York. A Structural Basis For Lithium and Substrate Binding of An Inositide Phosphatase. J.Biol.Chem. 2020.
ISSN: ESSN 1083-351X
PubMed: 33172890
DOI: 10.1074/JBC.RA120.014057
Page generated: Sat Aug 10 22:18:07 2024

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