Gadolinium in PDB 3txm: Crystal Structure of RPN6 From Drosophila Melanogaster, Gd(3+) Complex

The structure of Crystal Structure of RPN6 From Drosophila Melanogaster, Gd(3+) Complex, PDB code: 3txm was solved by G.R.Pathare, A.Bracher, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 3.00
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	161.251, 161.251, 42.080, 90.00, 90.00, 120.00
R / Rfree (%)	20.5 / 25.1

The binding sites of Gadolinium atom in the Crystal Structure of RPN6 From Drosophila Melanogaster, Gd(3+) Complex (pdb code 3txm). 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 RPN6 From Drosophila Melanogaster, Gd(3+) Complex, PDB code: 3txm:
Jump to Gadolinium binding site number: 1; 2; 3; 4;

Gadolinium binding site 1 out of 4 in the Crystal Structure of RPN6 From Drosophila Melanogaster, Gd(3+) Complex


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 RPN6 From Drosophila Melanogaster, Gd(3+) Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Gd1 b:0.8 occ:0.34 OD1 A:ASP266 2.4 0.1 1.0 OD2 A:ASP266 2.5 0.1 1.0 CG A:ASP266 2.8 0.5 1.0 OD1 A:ASP265 3.4 0.9 1.0 CB A:ASP266 4.2 0.9 1.0 CG A:ASP265 4.4 0.1 1.0 CG A:GLN263 4.6 0.7 1.0 CD A:GLN263 4.7 0.0 1.0 OD2 A:ASP265 4.7 0.5 1.0 NE2 A:GLN263 4.8 0.4 1.0 CA A:ASP266 5.0 0.7 1.0

Gadolinium binding site 2 out of 4 in the Crystal Structure of RPN6 From Drosophila Melanogaster, Gd(3+) Complex


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 RPN6 From Drosophila Melanogaster, Gd(3+) Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Gd2 b:0.9 occ:0.34 OE2 A:GLU234 2.5 0.9 1.0 OE1 A:GLU234 2.9 0.2 1.0 CD A:GLU234 3.1 1.0 1.0 OE1 A:GLU237 3.3 0.4 1.0 OE2 A:GLU237 3.6 0.3 1.0 CD A:GLU237 3.7 1.0 1.0 CG A:GLU234 4.6 0.3 1.0

Gadolinium binding site 3 out of 4 in the Crystal Structure of RPN6 From Drosophila Melanogaster, Gd(3+) Complex


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 RPN6 From Drosophila Melanogaster, Gd(3+) Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Gd3 b:0.5 occ:0.18 OE1 A:GLU382 2.8 0.2 1.0 CD A:GLU382 3.1 0.9 1.0 OE2 A:GLU382 3.5 0.6 1.0 CG A:GLU382 3.8 0.6 1.0 CB A:GLU382 4.7 97.6 1.0

Gadolinium binding site 4 out of 4 in the Crystal Structure of RPN6 From Drosophila Melanogaster, Gd(3+) Complex


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 RPN6 From Drosophila Melanogaster, Gd(3+) Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Gd4 b:0.5 occ:0.18 OE2 A:GLU308 2.5 0.4 1.0 CD A:GLU308 3.1 0.8 1.0 OE1 A:GLU308 3.2 0.7 1.0 O A:GLU308 4.3 0.4 1.0 CG A:GLU308 4.4 0.8 1.0 CA A:GLU308 4.7 0.3 1.0 NH1 A:ARG282 4.8 0.4 1.0 CB A:GLU308 4.9 0.3 1.0 NH2 A:ARG282 5.0 1.0 1.0 C A:GLU308 5.0 0.0 1.0

G.R.Pathare, I.Nagy, S.Bohn, P.Unverdorben, A.Hubert, R.Korner, S.Nickell, K.Lasker, A.Sali, T.Tamura, T.Nishioka, F.Forster, W.Baumeister, A.Bracher. The Proteasomal Subunit RPN6 Is A Molecular Clamp Holding the Core and Regulatory Subcomplexes Together. Proc.Natl.Acad.Sci.Usa V. 109 149 2012.
ISSN: ISSN 0027-8424
PubMed: 22187461
DOI: 10.1073/PNAS.1117648108