Sodium in PDB 6txd: Variant W229D/F290W-12 of the Last Common Ancestor of Gram-Negative Bacteria Beta-Lactamase Class A (GNCA4)

The structure of Variant W229D/F290W-12 of the Last Common Ancestor of Gram-Negative Bacteria Beta-Lactamase Class A (GNCA4), PDB code: 6txd was solved by J.A.Gavira, V.Risso, J.M.Sanchez-Ruiz, A.Romero-Rivera, S.C.L.Kamerlin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	71.74 / 2.00
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	77.314, 148.228, 245.962, 90.00, 90.00, 90.00
R / Rfree (%)	21.2 / 23.5

The binding sites of Sodium atom in the Variant W229D/F290W-12 of the Last Common Ancestor of Gram-Negative Bacteria Beta-Lactamase Class A (GNCA4) (pdb code 6txd). 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-12 of the Last Common Ancestor of Gram-Negative Bacteria Beta-Lactamase Class A (GNCA4), PDB code: 6txd:

Sodium binding site 1 out of 1 in the Variant W229D/F290W-12 of the Last Common Ancestor of Gram-Negative Bacteria Beta-Lactamase Class A (GNCA4)


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-12 of the Last Common Ancestor of Gram-Negative Bacteria Beta-Lactamase Class A (GNCA4) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na306 b:35.4 occ:1.00 O A:VAL113 2.4 31.3 1.0 O A:HOH534 2.4 30.8 1.0 O A:HOH538 2.5 50.9 1.0 O A:HOH442 2.5 37.5 1.0 O A:TYR97 2.5 35.1 1.0 O A:HOH454 3.3 29.8 1.0 C A:TYR97 3.5 30.4 1.0 C A:VAL113 3.6 32.1 1.0 CG1 A:VAL113 4.1 37.6 1.0 O B:HOH472 4.1 39.8 1.0 N A:TYR97 4.2 27.2 1.0 N A:GLY98 4.3 30.5 1.0 CA A:GLY98 4.3 35.5 1.0 O A:GLY114 4.4 40.3 1.0 CA A:VAL113 4.5 32.4 1.0 CA A:TYR97 4.5 27.8 1.0 O A:HOH473 4.5 27.7 1.0 N A:GLY114 4.5 31.5 1.0 CA A:GLY114 4.5 37.3 1.0 C A:GLY114 4.7 39.6 1.0 CB A:THR96 4.9 29.3 1.0 O A:HOH509 5.0 36.5 1.0 CB A:VAL113 5.0 35.2 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