Sodium in PDB 9b1u: Crystal Structure of Pqqt with Pqq Bound

The structure of Crystal Structure of Pqqt with Pqq Bound, PDB code: 9b1u was solved by D.Boggs, A.Bruchs, P.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)	37.92 / 1.46
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	40.004, 53.191, 119.068, 90, 90, 90
R / Rfree (%)	19.9 / 20.7

The binding sites of Sodium atom in the Crystal Structure of Pqqt with Pqq Bound (pdb code 9b1u). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Pqqt with Pqq Bound, PDB code: 9b1u:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Pqqt with Pqq Bound


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Pqqt with Pqq Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:13.9 occ:1.00 O A:HOH581 3.1 21.8 1.0 ND2 A:ASN58 3.2 15.2 1.0 OD1 A:ASN58 3.5 18.0 1.0 CB A:ARG243 3.7 14.4 1.0 CG A:ASN58 3.8 15.8 1.0 CD A:ARG243 4.2 14.3 1.0 O A:ARG243 4.3 14.2 1.0 NE A:ARG243 4.3 16.1 1.0 C A:ARG243 4.4 14.6 1.0 CG A:ARG243 4.5 16.4 1.0 CA A:ARG243 4.6 17.3 1.0 N A:ALA244 4.8 15.0 1.0 CB A:ALA247 4.9 15.7 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Pqqt with Pqq Bound


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Pqqt with Pqq Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Na403 b:19.9 occ:1.00 N A:GLY228 3.2 19.9 1.0 NE A:ARG100 3.2 27.6 1.0 O A:HOH613 3.3 45.8 1.0 N A:VAL102 3.4 28.5 1.0 O A:HOH636 3.4 25.6 1.0 NH2 A:ARG100 3.6 26.3 1.0 N A:GLY101 3.6 25.1 1.0 OE1 A:GLU227 3.7 25.4 1.0 CA A:VAL102 3.7 23.6 1.0 CE1 A:PHE77 3.8 27.2 1.0 C A:GLY101 3.8 26.1 1.0 CZ A:ARG100 3.9 30.9 1.0 CB A:ARG100 3.9 30.9 1.0 CZ A:PHE77 4.0 21.6 1.0 CB A:VAL102 4.0 24.3 1.0 CA A:GLU227 4.0 17.1 1.0 CA A:GLY228 4.0 22.3 1.0 C A:GLU227 4.1 21.0 1.0 CA A:GLY101 4.2 22.8 1.0 CD A:ARG100 4.3 36.0 1.0 C A:ARG100 4.3 26.1 1.0 CA A:ARG100 4.5 26.4 1.0 O A:GLY101 4.5 28.1 1.0 CG A:ARG100 4.6 26.0 1.0 O A:TYR226 4.6 20.2 1.0 CD A:GLU227 4.7 21.2 1.0 CB A:GLU227 4.8 20.2 1.0 CD1 A:PHE77 4.8 22.0 1.0 CG1 A:VAL102 4.9 25.8 1.0 CG2 A:VAL102 5.0 25.1 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