Gadolinium in PDB 9b1v: Crystal Structure of Pqqt with Pqq and GD3+ Bound

The structure of Crystal Structure of Pqqt with Pqq and GD3+ Bound, PDB code: 9b1v was solved by G.D.Boggs, A.T.Bruchs, P.J.Thompson, L.Olshansky, J.Bridwell-Rabb, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.81 / 1.55
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	39.867, 53.389, 119.465, 90, 90, 90
R / Rfree (%)	17.8 / 18.6

The binding sites of Gadolinium atom in the Crystal Structure of Pqqt with Pqq and GD3+ Bound (pdb code 9b1v). This binding sites where shown within 5.0 Angstroms radius around Gadolinium atom.
In total 3 binding sites of Gadolinium where determined in the Crystal Structure of Pqqt with Pqq and GD3+ Bound, PDB code: 9b1v:
Jump to Gadolinium binding site number: 1; 2; 3;

Gadolinium binding site 1 out of 3 in the Crystal Structure of Pqqt with Pqq and GD3+ Bound


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 Pqqt with Pqq and GD3+ Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Gd405 b:23.6 occ:0.25 NE A:ARG100 3.2 25.7 1.0 N A:GLY228 3.2 18.8 1.0 N A:VAL102 3.3 20.8 1.0 O A:HOH643 3.4 22.4 1.0 NH2 A:ARG100 3.6 21.7 1.0 N A:GLY101 3.6 20.9 1.0 CA A:VAL102 3.7 18.4 1.0 OE1 A:GLU227 3.7 23.3 1.0 C A:GLY101 3.8 21.3 1.0 CE1 A:PHE77 3.8 23.0 1.0 CZ A:ARG100 3.8 26.7 1.0 CB A:VAL102 3.9 20.8 1.0 CB A:ARG100 3.9 26.5 1.0 CA A:GLU227 4.0 15.4 1.0 CZ A:PHE77 4.0 23.9 1.0 CA A:GLY228 4.1 19.8 1.0 C A:GLU227 4.1 19.6 1.0 CD A:ARG100 4.2 35.1 1.0 CA A:GLY101 4.2 22.0 1.0 C A:ARG100 4.3 21.6 1.0 O A:GLY101 4.5 22.8 1.0 CA A:ARG100 4.5 24.6 1.0 CG A:ARG100 4.5 27.4 1.0 O A:TYR226 4.6 17.6 1.0 CB A:GLU227 4.7 17.5 1.0 CD A:GLU227 4.7 19.6 1.0 CD1 A:PHE77 4.8 19.8 1.0 CG1 A:VAL102 4.9 23.2 1.0 CG2 A:VAL102 4.9 20.3 1.0

Gadolinium binding site 2 out of 3 in the Crystal Structure of Pqqt with Pqq and GD3+ Bound


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 Pqqt with Pqq and GD3+ Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Gd406 b:25.8 occ:0.25 O A:HOH502 2.6 18.4 1.0 O A:HOH515 3.1 28.6 1.0 NE A:ARG74 3.1 24.7 1.0 ND2 A:ASN70 3.3 34.5 1.0 NH2 A:ARG74 3.3 24.0 1.0 CA A:GLY87 3.4 15.9 1.0 CD2 A:PHE91 3.6 24.0 1.0 O4 A:PQQ404 3.6 17.6 1.0 CZ A:ARG74 3.7 23.6 1.0 OD1 A:ASN70 3.7 29.5 1.0 CG A:ASN70 3.9 33.1 1.0 O A:VAL86 3.9 16.3 1.0 N A:ASP88 4.0 16.1 1.0 CE2 A:PHE91 4.0 28.4 1.0 CG A:ARG74 4.2 15.7 1.0 CG A:PHE91 4.2 23.2 1.0 CD A:ARG74 4.2 21.2 1.0 C A:GLY87 4.3 17.2 1.0 OD2 A:ASP88 4.3 31.4 1.0 N A:GLY87 4.5 13.0 1.0 CD1 A:ILE85 4.5 16.0 1.0 CB A:PHE91 4.5 25.3 1.0 C A:VAL86 4.6 14.6 1.0 O A:HOH612 4.7 18.9 1.0 C4 A:PQQ404 4.8 16.6 1.0 CD2 A:LEU225 4.9 24.0 1.0 NH1 A:ARG74 5.0 29.8 1.0 CZ A:PHE91 5.0 30.4 1.0

Gadolinium binding site 3 out of 3 in the Crystal Structure of Pqqt with Pqq and GD3+ Bound


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 Pqqt with Pqq and GD3+ Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Gd407 b:17.8 occ:0.25 ND2 A:ASN58 3.2 14.9 1.0 O A:HOH580 3.2 22.7 1.0 OD1 A:ASN58 3.5 16.1 1.0 CB A:ARG243 3.7 13.0 1.0 CG A:ASN58 3.8 15.9 1.0 CD A:ARG243 4.1 12.8 1.0 NE A:ARG243 4.3 14.1 1.0 O A:ARG243 4.3 13.4 1.0 CG A:ARG243 4.4 15.2 1.0 C A:ARG243 4.4 12.1 1.0 CA A:ARG243 4.7 12.6 1.0 N A:ALA244 4.9 12.9 1.0 CB A:ALA247 5.0 13.0 1.0

P.J.Thompson, D.G.Boggs, C.A.Wilson, A.T.Bruchs, U.Velidandla, J.Bridwell-Rabb, L.Olshansky. Structure-Driven Development of A Biomimetic Rare Earth Artificial Metalloprotein. Proc.Natl.Acad.Sci.Usa V. 121 36121 2024.
ISSN: ESSN 1091-6490
PubMed: 39116128
DOI: 10.1073/PNAS.2405836121