Sodium in PDB 4c6y: Ancestral Pnca (Last Common Ancestors of Gram-Positive and Gram-Negative Bacteria) Beta-Lactamase Class A

All present enzymatic activity of Ancestral Pnca (Last Common Ancestors of Gram-Positive and Gram-Negative Bacteria) Beta-Lactamase Class A:
3.5.2.6;

The structure of Ancestral Pnca (Last Common Ancestors of Gram-Positive and Gram-Negative Bacteria) Beta-Lactamase Class A, PDB code: 4c6y was solved by J.A.Gavira, V.A.Risso, J.M.Sanchez-Ruiz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.703 / 1.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	39.581, 57.473, 240.401, 90.00, 90.00, 90.00
R / Rfree (%)	14.16 / 17

The structure of Ancestral Pnca (Last Common Ancestors of Gram-Positive and Gram-Negative Bacteria) Beta-Lactamase Class A also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the Ancestral Pnca (Last Common Ancestors of Gram-Positive and Gram-Negative Bacteria) Beta-Lactamase Class A (pdb code 4c6y). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Ancestral Pnca (Last Common Ancestors of Gram-Positive and Gram-Negative Bacteria) Beta-Lactamase Class A, PDB code: 4c6y:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Ancestral Pnca (Last Common Ancestors of Gram-Positive and Gram-Negative Bacteria) Beta-Lactamase Class A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Ancestral Pnca (Last Common Ancestors of Gram-Positive and Gram-Negative Bacteria) Beta-Lactamase Class A within 5.0Å range: probe atom residue distance (Å) B Occ A:Na293 b:27.1 occ:1.00 OE1 A:GLU273 2.0 43.5 0.5 CD A:GLU273 2.5 46.9 0.5 OE2 A:GLU273 2.5 53.6 0.5 H A:GLU273 2.9 23.1 0.5 H A:GLU273 3.0 23.1 0.5 HB1 A:ALA272 3.0 27.4 1.0 H A:ALA272 3.1 18.8 1.0 O A:HOH2186 3.2 31.9 1.0 HB2 A:ASP271 3.2 20.0 1.0 O A:HOH2188 3.2 31.0 1.0 HG2 A:GLU273 3.6 51.3 0.5 N A:ALA272 3.7 15.7 1.0 N A:GLU273 3.7 19.2 1.0 HB3 A:GLU273 3.7 31.5 0.5 CB A:ALA272 3.8 22.8 1.0 CG A:GLU273 3.8 34.6 0.5 CB A:ASP271 4.0 16.7 1.0 HG3 A:GLU273 4.1 41.5 0.5 CG A:ASP271 4.1 23.1 1.0 HB3 A:ALA272 4.1 27.4 1.0 CA A:ALA272 4.2 18.4 1.0 HB2 A:GLU273 4.2 33.3 0.5 OD1 A:ASP271 4.3 23.8 1.0 CG A:GLU273 4.4 42.8 0.5 CB A:GLU273 4.4 26.3 0.5 CB A:GLU273 4.4 27.8 0.5 C A:ALA272 4.4 16.3 1.0 HG2 A:GLU273 4.5 41.5 0.5 OD2 A:ASP271 4.5 23.8 1.0 C A:ASP271 4.5 13.3 1.0 HB2 A:ALA272 4.5 27.4 1.0 CA A:GLU273 4.7 19.8 0.5 CA A:GLU273 4.7 19.4 0.5 HB3 A:ASP271 4.7 20.0 1.0 CA A:ASP271 4.8 14.6 1.0 CD A:GLU273 4.8 49.4 0.5 HA A:ASP271 5.0 17.5 1.0

Sodium binding site 2 out of 2 in the Ancestral Pnca (Last Common Ancestors of Gram-Positive and Gram-Negative Bacteria) Beta-Lactamase Class A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Ancestral Pnca (Last Common Ancestors of Gram-Positive and Gram-Negative Bacteria) Beta-Lactamase Class A within 5.0Å range: probe atom residue distance (Å) B Occ A:Na308 b:70.8 occ:1.00 H41 A:PEG301 2.4 58.5 1.0 HH21 A:ARG184 2.4 63.8 0.7 HD2 A:ARG56 2.5 50.8 0.5 HD3 A:ARG56 2.7 53.4 0.5 O1 A:PEG301 2.7 46.4 1.0 H42 A:PEG301 2.8 58.5 1.0 HE A:ARG184 2.8 54.1 0.3 HE A:ARG184 3.0 47.3 0.7 C4 A:PEG301 3.0 48.8 1.0 HG3 A:ARG184 3.0 23.6 0.3 NH2 A:ARG184 3.1 53.2 0.7 O2 A:PEG301 3.2 47.2 1.0 HO1 A:PEG301 3.3 55.6 1.0 CD A:ARG56 3.3 42.4 0.5 NE A:ARG184 3.3 45.1 0.3 HE A:ARG56 3.5 51.0 0.5 H21 A:PEG301 3.5 54.0 1.0 HD3 A:ARG56 3.5 50.8 0.5 NE A:ARG184 3.6 39.4 0.7 C1 A:PEG301 3.6 44.3 1.0 NE A:ARG56 3.6 42.5 0.5 HH22 A:ARG184 3.6 63.8 0.7 C2 A:PEG301 3.6 45.0 1.0 CD A:ARG56 3.7 44.5 0.5 HH21 A:ARG184 3.7 56.0 0.3 CZ A:ARG184 3.7 43.5 0.7 C3 A:PEG301 3.7 32.2 1.0 H11 A:PEG301 3.8 53.2 1.0 CG A:ARG184 3.8 19.7 0.3 HE A:ARG56 3.9 52.0 0.5 CD A:ARG184 4.0 31.6 0.3 CZ A:ARG184 4.0 46.2 0.3 HD2 A:ARG56 4.1 53.4 0.5 HD3 A:ARG184 4.1 37.9 0.3 NH2 A:ARG184 4.1 46.7 0.3 O4 A:PEG301 4.1 52.2 1.0 HB3 A:ARG184 4.2 20.5 0.7 HO4 A:PEG301 4.2 62.6 1.0 NE A:ARG56 4.2 43.3 0.5 HG2 A:ARG184 4.2 23.6 0.3 H31 A:PEG301 4.2 38.7 1.0 HB3 A:ARG56 4.2 40.4 0.5 HB3 A:ARG56 4.3 40.6 0.5 O A:HOH2139 4.4 45.5 1.0 HG2 A:ARG184 4.4 27.6 0.7 H12 A:PEG301 4.5 53.2 1.0 H32 A:PEG301 4.5 38.7 1.0 CG A:ARG56 4.5 40.6 0.5 HG2 A:ARG56 4.6 49.3 0.5 H22 A:PEG301 4.6 54.0 1.0 CZ A:ARG56 4.6 46.2 0.5 CG A:ARG56 4.6 41.1 0.5 HG2 A:ARG56 4.7 48.7 0.5 HH22 A:ARG184 4.8 56.0 0.3 CD A:ARG184 4.8 32.9 0.7 CB A:ARG56 4.8 33.6 0.5 CB A:ARG56 4.8 33.8 0.5 NH1 A:ARG184 4.9 35.7 0.7 HD2 A:ARG184 4.9 37.9 0.3 CG A:ARG184 4.9 23.0 0.7 HB2 A:ARG184 4.9 22.0 0.3 HB2 A:ARG56 5.0 40.4 0.5 CB A:ARG184 5.0 17.1 0.7 HB2 A:ARG56 5.0 40.6 0.5

V.A.Risso, J.A.Gavira, E.A.Gaucher, J.M.Sanchez-Ruiz. Phenotypic Comparisons of Consensus Variants Versus Laboratory Resurrections of Precambrian Proteins. Proteins V. 82 887 2014.
ISSN: ISSN 0887-3585
PubMed: 24710963
DOI: 10.1002/PROT.24575