Sodium in PDB 4hes: Structure of A Beta-Lactamase Class A-Like Protein From Veillonella Parvula.

The structure of Structure of A Beta-Lactamase Class A-Like Protein From Veillonella Parvula., PDB code: 4hes was solved by M.E.Cuff, H.Li, S.Clancy, A.Joachimiak, Midwest Center For Structuralgenomics (Mcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.49 / 1.90
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	117.398, 163.106, 113.009, 90.00, 90.38, 90.00
R / Rfree (%)	13.7 / 16

The binding sites of Sodium atom in the Structure of A Beta-Lactamase Class A-Like Protein From Veillonella Parvula. (pdb code 4hes). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Structure of A Beta-Lactamase Class A-Like Protein From Veillonella Parvula., PDB code: 4hes:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Structure of A Beta-Lactamase Class A-Like Protein From Veillonella Parvula.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of A Beta-Lactamase Class A-Like Protein From Veillonella Parvula. within 5.0Å range: probe atom residue distance (Å) B Occ A:Na303 b:28.3 occ:1.00 O1 B:FMT304 2.5 26.5 1.0 O2 A:FMT304 2.6 21.9 1.0 O B:HOH414 2.9 23.2 1.0 O A:HOH419 3.0 21.8 1.0 CB B:ASP202 3.4 17.1 1.0 CB A:ASP202 3.5 16.1 1.0 C B:FMT304 3.6 31.6 1.0 C A:FMT304 3.7 29.2 1.0 CE1 A:PHE206 3.8 15.7 1.0 CE1 B:PHE206 3.8 15.3 1.0 O1 A:FMT304 4.1 24.2 1.0 O2 B:FMT304 4.1 26.0 1.0 CD1 A:PHE206 4.1 15.1 1.0 CA B:ASP202 4.2 15.7 1.0 CD1 B:PHE206 4.2 15.2 1.0 CA A:ASP202 4.2 15.4 1.0 O A:ASP202 4.2 16.9 1.0 O B:ASP202 4.2 16.9 1.0 CG B:ASP202 4.6 17.9 1.0 OD2 B:ASP202 4.7 19.1 1.0 CG A:ASP202 4.7 16.4 1.0 OD2 A:ASP202 4.7 17.7 1.0 CZ B:PHE206 4.7 15.1 1.0 C B:ASP202 4.7 15.6 1.0 C A:ASP202 4.7 16.1 1.0 CZ A:PHE206 4.7 16.0 1.0 CD A:LYS253 4.9 18.6 1.0 CD B:LYS253 5.0 18.9 1.0 O A:HOH503 5.0 24.5 1.0

Sodium binding site 2 out of 3 in the Structure of A Beta-Lactamase Class A-Like Protein From Veillonella Parvula.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of A Beta-Lactamase Class A-Like Protein From Veillonella Parvula. within 5.0Å range: probe atom residue distance (Å) B Occ D:Na306 b:30.3 occ:1.00 O2 C:FMT303 2.5 28.3 1.0 O1 D:FMT305 2.5 28.5 1.0 O D:HOH464 3.0 24.0 1.0 O C:HOH414 3.0 24.1 1.0 CB D:ASP202 3.5 19.2 1.0 CB C:ASP202 3.5 19.9 1.0 C D:FMT305 3.6 39.3 1.0 C C:FMT303 3.6 34.5 1.0 CE1 C:PHE206 3.7 18.4 1.0 CE1 D:PHE206 3.8 20.3 1.0 O2 D:FMT305 4.0 32.3 1.0 O1 C:FMT303 4.0 28.5 1.0 CD1 C:PHE206 4.1 18.6 1.0 CD1 D:PHE206 4.1 19.4 1.0 O D:ASP202 4.2 18.6 1.0 CA D:ASP202 4.2 18.8 1.0 CA C:ASP202 4.3 18.7 1.0 O C:ASP202 4.3 19.4 1.0 OD2 D:ASP202 4.7 21.0 1.0 CG D:ASP202 4.7 19.9 1.0 CZ C:PHE206 4.7 19.5 1.0 C D:ASP202 4.7 18.1 1.0 OD2 C:ASP202 4.7 20.7 1.0 CG C:ASP202 4.7 20.0 1.0 CZ D:PHE206 4.7 21.3 1.0 C C:ASP202 4.8 19.0 1.0 CD D:LYS253 4.9 20.3 1.0

Sodium binding site 3 out of 3 in the Structure of A Beta-Lactamase Class A-Like Protein From Veillonella Parvula.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of A Beta-Lactamase Class A-Like Protein From Veillonella Parvula. within 5.0Å range: probe atom residue distance (Å) B Occ E:Na307 b:29.6 occ:0.50 O1 E:FMT308 2.6 26.5 1.0 O E:HOH437 3.0 22.3 1.0 CB E:ASP202 3.5 18.3 1.0 C E:FMT308 3.7 31.3 1.0 CE1 E:PHE206 3.8 17.4 1.0 O2 E:FMT308 4.1 27.7 1.0 CD1 E:PHE206 4.1 17.1 1.0 CA E:ASP202 4.2 17.6 1.0 O E:ASP202 4.3 17.6 1.0 OD2 E:ASP202 4.7 21.5 1.0 CG E:ASP202 4.7 19.3 1.0 C E:ASP202 4.8 17.0 1.0 CZ E:PHE206 4.8 18.0 1.0 CD E:LYS253 5.0 20.4 1.0

M.E.Cuff, H.Li, S.Clancy, A.Joachimiak. Structure of A Beta-Lactamase Class A-Like Protein From Veillonella Parvula. To Be Published.