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Gadolinium in PDB 1b9x: Structural Analysis of Phosducin and Its Phosphorylation-Regulated Interaction with Transducin

Protein crystallography data

The structure of Structural Analysis of Phosducin and Its Phosphorylation-Regulated Interaction with Transducin, PDB code: 1b9x was solved by R.Gaudet, P.B.Sigler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 3.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 76.040, 89.330, 100.150, 90.00, 90.00, 90.00
R / Rfree (%) 21.7 / 26.1

Gadolinium Binding Sites:

The binding sites of Gadolinium atom in the Structural Analysis of Phosducin and Its Phosphorylation-Regulated Interaction with Transducin (pdb code 1b9x). This binding sites where shown within 5.0 Angstroms radius around Gadolinium atom.
In total 6 binding sites of Gadolinium where determined in the Structural Analysis of Phosducin and Its Phosphorylation-Regulated Interaction with Transducin, PDB code: 1b9x:
Jump to Gadolinium binding site number: 1; 2; 3; 4; 5; 6;

Gadolinium binding site 1 out of 6 in 1b9x

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Gadolinium binding site 1 out of 6 in the Structural Analysis of Phosducin and Its Phosphorylation-Regulated Interaction with Transducin


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd binding site number 1 of Structural Analysis of Phosducin and Its Phosphorylation-Regulated Interaction with Transducin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Gd341

b:42.7
occ:1.00
O A:GLN44 2.6 53.5 1.0
O A:HOH347 2.9 10.9 1.0
O A:HOH346 3.0 18.3 1.0
O A:HOH343 3.2 6.0 1.0
C A:GLN44 3.7 53.5 1.0
CA A:GLN44 4.5 53.5 1.0
N A:MET45 4.6 29.1 1.0
N A:GLN44 4.6 53.5 1.0
O A:ASN340 4.6 46.1 1.0
CB A:GLN44 4.6 43.3 1.0
CA A:MET45 4.7 29.1 1.0
OXT A:ASN340 4.8 75.1 1.0
OH C:TYR224 4.9 29.0 1.0

Gadolinium binding site 2 out of 6 in 1b9x

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Gadolinium binding site 2 out of 6 in the Structural Analysis of Phosducin and Its Phosphorylation-Regulated Interaction with Transducin


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd binding site number 2 of Structural Analysis of Phosducin and Its Phosphorylation-Regulated Interaction with Transducin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Gd342

b:0.1
occ:1.00
OD1 A:ASP228 2.6 64.8 1.0
O A:CYS204 3.2 32.6 1.0
CG A:ASP228 3.6 64.8 1.0
OD2 A:ASP228 4.0 64.8 1.0
C A:CYS204 4.4 32.6 1.0
N A:ASP228 4.7 36.0 1.0
CB A:CYS204 4.8 44.8 1.0
CB A:ASP228 4.9 64.8 1.0
CA A:CYS204 5.0 32.6 1.0

Gadolinium binding site 3 out of 6 in 1b9x

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Gadolinium binding site 3 out of 6 in the Structural Analysis of Phosducin and Its Phosphorylation-Regulated Interaction with Transducin


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd binding site number 3 of Structural Analysis of Phosducin and Its Phosphorylation-Regulated Interaction with Transducin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Gd102

b:64.3
occ:1.00
OE1 B:GLU546 2.5 80.8 1.0
OD1 B:ASP542 2.7 70.5 1.0
O B:HOH7 2.7 43.8 1.0
OE2 B:GLU546 3.1 80.8 1.0
O B:HOH8 3.1 40.2 1.0
CD B:GLU546 3.1 80.8 1.0
CG B:ASP542 3.8 70.5 1.0
GD B:GD104 4.1 65.2 1.0
OD2 B:ASP542 4.2 70.5 1.0
CG B:GLU546 4.5 80.8 1.0
O B:ASP542 5.0 47.0 1.0

Gadolinium binding site 4 out of 6 in 1b9x

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Gadolinium binding site 4 out of 6 in the Structural Analysis of Phosducin and Its Phosphorylation-Regulated Interaction with Transducin


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd binding site number 4 of Structural Analysis of Phosducin and Its Phosphorylation-Regulated Interaction with Transducin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Gd104

b:65.2
occ:1.00
OD2 B:ASP542 2.7 70.5 1.0
O B:HOH5 3.1 57.9 1.0
O B:HOH13 3.2 48.0 1.0
O B:HOH1 3.2 33.3 1.0
OE1 B:GLU546 3.5 80.8 1.0
CG B:ASP542 3.6 70.5 1.0
OD1 B:ASP542 3.7 70.5 1.0
NH2 B:ARG541 3.9 69.4 1.0
GD B:GD102 4.1 64.3 1.0
NH1 B:ARG541 4.7 69.4 1.0
CZ B:ARG541 4.8 69.4 1.0
CD B:GLU546 4.8 80.8 1.0
CB B:ASP542 4.9 70.5 1.0

Gadolinium binding site 5 out of 6 in 1b9x

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Gadolinium binding site 5 out of 6 in the Structural Analysis of Phosducin and Its Phosphorylation-Regulated Interaction with Transducin


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd binding site number 5 of Structural Analysis of Phosducin and Its Phosphorylation-Regulated Interaction with Transducin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Gd247

b:56.8
occ:1.00
OE1 C:GLU218 2.7 71.5 1.0
OE2 C:GLU161 2.8 44.2 1.0
O C:HOH250 2.8 46.8 1.0
O C:HOH252 2.9 52.5 1.0
OE1 C:GLU161 3.0 44.2 1.0
CD C:GLU161 3.3 44.2 1.0
OE2 C:GLU218 3.3 71.5 1.0
CD C:GLU218 3.4 71.5 1.0
CG C:GLU161 4.8 44.2 1.0
CG C:GLU218 4.8 71.5 1.0
OH C:TYR162 4.8 29.1 1.0

Gadolinium binding site 6 out of 6 in 1b9x

Go back to Gadolinium Binding Sites List in 1b9x
Gadolinium binding site 6 out of 6 in the Structural Analysis of Phosducin and Its Phosphorylation-Regulated Interaction with Transducin


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd binding site number 6 of Structural Analysis of Phosducin and Its Phosphorylation-Regulated Interaction with Transducin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Gd248

b:79.5
occ:1.00
OE2 C:GLU223 2.5 78.6 1.0
OE1 C:GLU223 3.1 78.6 1.0
O C:HOH251 3.1 61.9 1.0
OE1 B:GLU566 3.1 0.1 1.0
CD C:GLU223 3.1 78.6 1.0
O A:HOH349 3.4 36.5 1.0
OE2 B:GLU566 3.4 0.1 1.0
O C:HOH249 3.6 78.9 1.0
CD B:GLU566 3.7 0.1 1.0
NH2 A:ARG46 4.4 30.1 1.0
CG C:GLU223 4.6 78.6 1.0
O A:THR47 4.7 28.2 1.0
NE A:ARG46 4.9 30.1 1.0

Reference:

R.Gaudet, J.R.Savage, J.N.Mclaughlin, B.M.Willardson, P.B.Sigler. A Molecular Mechanism For the Phosphorylation-Dependent Regulation of Heterotrimeric G Proteins By Phosducin. Mol.Cell V. 3 649 1999.
ISSN: ISSN 1097-2765
PubMed: 10360181
DOI: 10.1016/S1097-2765(00)80358-5
Page generated: Sun Dec 13 18:59:10 2020

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