Sodium in PDB 6ty6: Variant W229D/F290W-2 of the Last Common Ancestor of Gram-Negative Bacteria Beta-Lactamase Class A (GNCA4) Bound to 5(6)- Nitrobenzotriazole (Ts-Analog)

The structure of Variant W229D/F290W-2 of the Last Common Ancestor of Gram-Negative Bacteria Beta-Lactamase Class A (GNCA4) Bound to 5(6)- Nitrobenzotriazole (Ts-Analog), PDB code: 6ty6 was solved by J.A.Gavira, V.Risso, J.M.Sanchez-Ruiz, A.Romero-Rivera, S.C.L.Kamerlin, M.Ortega-Munoz, F.Santoyo-Gonzalez, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.48 / 1.80
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	78.384, 148.357, 246.008, 90.00, 90.00, 90.00
R / Rfree (%)	20.1 / 22.8

The binding sites of Sodium atom in the Variant W229D/F290W-2 of the Last Common Ancestor of Gram-Negative Bacteria Beta-Lactamase Class A (GNCA4) Bound to 5(6)- Nitrobenzotriazole (Ts-Analog) (pdb code 6ty6). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Variant W229D/F290W-2 of the Last Common Ancestor of Gram-Negative Bacteria Beta-Lactamase Class A (GNCA4) Bound to 5(6)- Nitrobenzotriazole (Ts-Analog), PDB code: 6ty6:

Sodium binding site 1 out of 1 in the Variant W229D/F290W-2 of the Last Common Ancestor of Gram-Negative Bacteria Beta-Lactamase Class A (GNCA4) Bound to 5(6)- Nitrobenzotriazole (Ts-Analog)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Variant W229D/F290W-2 of the Last Common Ancestor of Gram-Negative Bacteria Beta-Lactamase Class A (GNCA4) Bound to 5(6)- Nitrobenzotriazole (Ts-Analog) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na910 b:38.9 occ:1.00 O A:VAL113 2.3 36.2 1.0 O A:HOH1124 2.3 51.4 1.0 O A:HOH1081 2.3 36.2 1.0 O A:TYR97 2.5 40.6 1.0 O A:HOH1108 3.3 40.6 1.0 C A:TYR97 3.5 39.9 1.0 C A:VAL113 3.5 39.5 1.0 CG1 A:VAL113 4.0 41.1 1.0 CA A:GLY98 4.1 41.0 1.0 N A:TYR97 4.1 31.7 1.0 O B:HOH1563 4.2 44.7 1.0 N A:GLY98 4.2 40.1 1.0 CA A:VAL113 4.2 37.2 1.0 O3 A:GOL907 4.4 62.7 1.0 O A:GLY114 4.4 43.2 1.0 CA A:TYR97 4.5 34.6 1.0 N A:GLY114 4.5 37.8 1.0 CA A:GLY114 4.6 39.1 1.0 O A:HOH1142 4.6 31.1 1.0 C A:GLY114 4.7 42.1 1.0 O A:HOH1098 4.7 45.8 1.0 CB A:VAL113 4.8 38.7 1.0 CB A:THR96 4.8 33.7 1.0 C3 A:GOL907 4.9 63.2 1.0

V.Risso, A.Romero-Rivera, L.I.Gutierrez-Rus, M.Ortega-Munoz, F.Santoyo-Gonzalez, J.A.Gavira, J.M.Sanchez-Ruiz, S.Caroline, S.C.L.Kamerlin. Enhancing A De Novo Enzyme Activity By Computationally-Focused Ultra-Low-Throughput Screening Chem Sci 2020.
ISSN: ESSN 2041-6539
DOI: 10.1039/D0SC01935F