Sodium in PDB 8ur1: Crystal Structure N-Acetylneuraminate Lyase (Nana) From Klebsiella Aerogenes (Pyruvate Bound Halide Free Active Site)

The structure of Crystal Structure N-Acetylneuraminate Lyase (Nana) From Klebsiella Aerogenes (Pyruvate Bound Halide Free Active Site), PDB code: 8ur1 was solved by Seattle Structural Genomics Center For Infectious Disease, Seattlestructural Genomics Center For Infectious Disease (Ssgcid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.93 / 2.10
Space group	P 62 2 2
Cell size a, b, c (Å), α, β, γ (°)	96.4, 96.4, 205.596, 90, 90, 120
R / Rfree (%)	18.3 / 21.4

The structure of Crystal Structure N-Acetylneuraminate Lyase (Nana) From Klebsiella Aerogenes (Pyruvate Bound Halide Free Active Site) also contains other interesting chemical elements:

Chlorine

(Cl)

4 atoms

The binding sites of Sodium atom in the Crystal Structure N-Acetylneuraminate Lyase (Nana) From Klebsiella Aerogenes (Pyruvate Bound Halide Free Active Site) (pdb code 8ur1). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure N-Acetylneuraminate Lyase (Nana) From Klebsiella Aerogenes (Pyruvate Bound Halide Free Active Site), PDB code: 8ur1:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Crystal Structure N-Acetylneuraminate Lyase (Nana) From Klebsiella Aerogenes (Pyruvate Bound Halide Free Active Site)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure N-Acetylneuraminate Lyase (Nana) From Klebsiella Aerogenes (Pyruvate Bound Halide Free Active Site) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na301 b:31.0 occ:1.00 O A:HOH546 2.2 27.3 1.0 OG1 A:THR75 2.3 27.3 1.0 O A:HOH500 2.3 34.4 1.0 O A:ASP40 2.3 29.6 1.0 O A:HOH541 2.4 27.7 1.0 O A:HOH444 2.4 31.6 1.0 CB A:THR75 3.3 27.7 1.0 C A:ASP40 3.4 27.0 1.0 N A:THR75 3.7 29.0 1.0 CB A:ASP40 3.8 27.5 1.0 CA A:ASP40 3.9 27.5 1.0 O A:HIS4 3.9 36.3 1.0 O A:HOH572 4.1 40.9 1.0 O A:HOH555 4.1 46.1 1.0 CA A:THR75 4.1 28.7 1.0 O A:HOH556 4.4 44.0 1.0 CG2 A:THR75 4.5 26.0 1.0 N A:GLY41 4.5 24.7 1.0 O A:HOH509 4.6 37.9 1.0 CE A:MET9 4.7 30.9 1.0 C A:ILE74 4.8 36.4 1.0 O A:ARG6 4.8 30.4 1.0 CG A:ASP40 4.8 27.2 1.0 CA A:GLY41 4.9 30.3 1.0 OD1 A:ASP40 4.9 34.4 1.0 CA A:ILE74 5.0 28.8 1.0

Sodium binding site 2 out of 4 in the Crystal Structure N-Acetylneuraminate Lyase (Nana) From Klebsiella Aerogenes (Pyruvate Bound Halide Free Active Site)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure N-Acetylneuraminate Lyase (Nana) From Klebsiella Aerogenes (Pyruvate Bound Halide Free Active Site) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na302 b:31.2 occ:1.00 OG A:SER143 2.6 22.9 1.0 OG1 A:THR107 2.8 20.5 1.0 N A:ILE139 2.9 20.6 1.0 OD1 A:ASN138 3.0 24.0 1.0 O A:VAL145 3.2 36.1 1.0 C A:ILE139 3.4 24.7 1.0 CB A:SER143 3.5 22.8 1.0 O A:ILE139 3.6 23.9 1.0 N A:PRO140 3.6 28.2 1.0 CA A:ASN138 3.7 26.4 1.0 C A:ASN138 3.7 24.7 1.0 CA A:ILE139 3.7 24.8 1.0 CG2 A:THR107 3.9 22.8 1.0 CB A:THR107 3.9 22.3 1.0 CA A:PRO140 3.9 23.8 1.0 CB A:VAL145 4.0 23.7 1.0 CD A:PRO140 4.0 23.4 1.0 CG A:ASN138 4.0 27.0 1.0 C A:VAL145 4.2 30.2 1.0 CG2 A:ILE139 4.3 22.2 1.0 O A:TYR137 4.3 23.7 1.0 CB A:ASN138 4.4 26.8 1.0 CG A:PRO140 4.5 24.8 1.0 CA A:VAL145 4.5 24.0 1.0 CG1 A:VAL145 4.6 21.2 1.0 N A:VAL145 4.6 26.9 1.0 CB A:ILE139 4.7 19.7 1.0 CB A:PRO140 4.8 22.1 1.0 N A:THR107 4.8 26.5 1.0 N A:ASN138 4.8 26.8 1.0 CA A:SER143 4.8 26.8 1.0 O A:ASN138 4.9 23.1 1.0 CG2 A:VAL145 5.0 30.0 1.0 CA A:THR107 5.0 25.2 1.0

Sodium binding site 3 out of 4 in the Crystal Structure N-Acetylneuraminate Lyase (Nana) From Klebsiella Aerogenes (Pyruvate Bound Halide Free Active Site)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure N-Acetylneuraminate Lyase (Nana) From Klebsiella Aerogenes (Pyruvate Bound Halide Free Active Site) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na303 b:30.1 occ:1.00 OD1 A:ASP191 2.7 22.0 1.0 O A:ASN188 2.8 20.5 1.0 OH A:TYR210 2.8 24.8 1.0 ND2 A:ASN188 3.2 20.2 1.0 N A:ASP191 3.4 22.9 1.0 CA A:ASP191 3.5 21.7 1.0 C A:GLY189 3.5 31.1 1.0 CZ A:TYR210 3.6 25.6 1.0 C A:TYR190 3.6 23.4 1.0 C A:ASN188 3.6 27.5 1.0 O A:GLY189 3.6 22.2 1.0 O A:ILE206 3.6 29.8 1.0 CG A:ASP191 3.7 26.0 1.0 CE1 A:TYR210 3.8 23.4 1.0 N A:TYR190 3.8 22.9 1.0 CA A:GLY189 3.9 23.0 1.0 O A:TYR190 3.9 20.4 1.0 N A:GLY189 4.1 23.0 1.0 C A:ILE206 4.1 26.9 1.0 CB A:ASP191 4.1 24.4 1.0 CD1 A:PHE194 4.1 34.0 1.0 CA A:GLY207 4.2 26.9 1.0 CA A:TYR190 4.2 22.3 1.0 CG A:ASN188 4.3 21.0 1.0 N A:ILE206 4.3 28.4 1.0 N A:GLY207 4.4 28.5 1.0 CB A:ASN188 4.5 20.1 1.0 CA A:GLY205 4.6 28.2 1.0 CA A:ASN188 4.7 20.6 1.0 CE2 A:TYR210 4.7 27.0 1.0 OD2 A:ASP191 4.7 23.4 1.0 C A:ASP191 4.7 23.0 1.0 CE1 A:PHE194 4.8 31.2 1.0 C A:GLY205 4.8 24.5 1.0 OH7 A:1PE318 4.9 47.4 1.0 CA A:ILE206 4.9 28.6 1.0 CB A:PHE194 4.9 28.3 1.0 CG A:PHE194 5.0 22.4 1.0

Sodium binding site 4 out of 4 in the Crystal Structure N-Acetylneuraminate Lyase (Nana) From Klebsiella Aerogenes (Pyruvate Bound Halide Free Active Site)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure N-Acetylneuraminate Lyase (Nana) From Klebsiella Aerogenes (Pyruvate Bound Halide Free Active Site) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na304 b:32.8 occ:1.00 O A:VAL267 2.7 26.6 1.0 O A:LEU269 2.7 17.5 1.0 N A:PHE16 3.0 23.4 1.0 N A:LEU269 3.3 30.8 1.0 NZ A:LYS256 3.4 22.5 1.0 O A:PHE16 3.4 29.1 1.0 CD A:LYS256 3.4 22.3 1.0 CA A:PRO15 3.6 25.5 1.0 C A:PRO268 3.6 25.2 1.0 CE A:LYS256 3.7 24.4 1.0 C A:LEU269 3.7 25.9 1.0 C A:VAL267 3.7 29.7 1.0 C A:PRO15 3.8 27.6 1.0 CA A:PRO268 3.8 31.6 1.0 CA A:PHE16 3.9 28.5 1.0 CA A:LEU269 4.0 23.5 1.0 C A:PHE16 4.1 24.3 1.0 CB A:PHE16 4.2 25.5 1.0 N A:PRO268 4.2 29.1 1.0 O A:HOH460 4.3 24.0 1.0 CG A:LYS256 4.3 21.1 1.0 O A:PRO268 4.3 26.1 1.0 CB A:PRO15 4.3 25.0 1.0 O A:THR14 4.4 21.9 1.0 CD1 A:LEU265 4.4 29.1 1.0 CD2 A:PHE16 4.5 29.9 1.0 CB A:LYS256 4.6 20.7 1.0 CB A:LEU269 4.7 25.2 1.0 CG A:PHE16 4.7 22.6 1.0 N A:PRO15 4.8 27.8 1.0 N A:CYS270 4.9 26.7 1.0 CA A:VAL267 4.9 22.4 1.0

S.Lovell, L.Liu, S.Seibold, M.R.Mian. Crystal Structure N-Acetylneuraminate Lyase (Nana) From Klebsiella Aerogenes (Pyruvate Bound Halide Free Active Site) To Be Published.