Sodium in PDB 6tww: Variant W229D/F290W-19 of the Last Common Ancestor of Gram-Negative Bacteria Beta-Lactamase Class A (GNCA4)

The structure of Variant W229D/F290W-19 of the Last Common Ancestor of Gram-Negative Bacteria Beta-Lactamase Class A (GNCA4), PDB code: 6tww 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)	47.31 / 1.38
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	78.230, 78.230, 198.322, 90.00, 90.00, 120.00
R / Rfree (%)	15.1 / 16.6

The structure of Variant W229D/F290W-19 of the Last Common Ancestor of Gram-Negative Bacteria Beta-Lactamase Class A (GNCA4) also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Sodium atom in the Variant W229D/F290W-19 of the Last Common Ancestor of Gram-Negative Bacteria Beta-Lactamase Class A (GNCA4) (pdb code 6tww). 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-19 of the Last Common Ancestor of Gram-Negative Bacteria Beta-Lactamase Class A (GNCA4), PDB code: 6tww:

Sodium binding site 1 out of 1 in the Variant W229D/F290W-19 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-19 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:Na1410 b:39.1 occ:1.00 O A:HOH1733 2.3 47.6 1.0 O A:TYR97 2.4 21.1 1.0 O A:HOH1762 2.4 50.3 1.0 O A:VAL113 2.6 25.4 1.0 O A:HOH1824 2.7 51.8 1.0 C A:TYR97 3.5 17.8 1.0 O A:HOH1587 3.5 32.8 1.0 CG2 A:THR96 3.6 29.2 0.4 C A:VAL113 3.7 21.9 1.0 CG1 A:VAL113 3.8 25.9 1.0 N A:TYR97 4.1 18.1 1.0 CA A:GLY98 4.2 21.3 1.0 N A:GLY98 4.3 18.4 1.0 CA A:TYR97 4.4 17.9 1.0 CA A:VAL113 4.5 20.1 1.0 O A:GLY114 4.5 34.8 1.0 C A:THR96 4.6 21.3 0.4 N A:GLY114 4.6 21.1 1.0 CA A:GLY114 4.6 26.1 1.0 O A:HOH1771 4.7 42.1 1.0 O A:HOH1680 4.7 31.2 1.0 C A:GLY114 4.8 28.0 1.0 CB A:VAL113 4.8 22.9 1.0 CB A:THR96 4.8 25.5 0.6 CB A:THR96 4.8 25.1 0.4 C A:THR96 5.0 18.4 0.6

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