Sodium in PDB 8u92: Crystal Structure of N-Acetylneuraminate Lyase (Nana) From Klebsiella Aerogenes (Pyruvate Bound, Orthorhombic P Form)

The structure of Crystal Structure of N-Acetylneuraminate Lyase (Nana) From Klebsiella Aerogenes (Pyruvate Bound, Orthorhombic P Form), PDB code: 8u92 was solved by Seattle Structural 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)	47.29 / 2.10
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	94.588, 145.738, 216.813, 90, 90, 90
R / Rfree (%)	15.3 / 19.3

The structure of Crystal Structure of N-Acetylneuraminate Lyase (Nana) From Klebsiella Aerogenes (Pyruvate Bound, Orthorhombic P Form) also contains other interesting chemical elements:

Chlorine

(Cl)

28 atoms

The binding sites of Sodium atom in the Crystal Structure of N-Acetylneuraminate Lyase (Nana) From Klebsiella Aerogenes (Pyruvate Bound, Orthorhombic P Form) (pdb code 8u92). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the Crystal Structure of N-Acetylneuraminate Lyase (Nana) From Klebsiella Aerogenes (Pyruvate Bound, Orthorhombic P Form), PDB code: 8u92:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in the Crystal Structure of N-Acetylneuraminate Lyase (Nana) From Klebsiella Aerogenes (Pyruvate Bound, Orthorhombic P Form)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of N-Acetylneuraminate Lyase (Nana) From Klebsiella Aerogenes (Pyruvate Bound, Orthorhombic P Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na303 b:44.2 occ:1.00 O A:HOH422 2.4 41.4 1.0 O A:HOH528 2.4 47.3 1.0 O A:ASP40 2.5 37.3 1.0 O A:HOH481 2.5 50.1 1.0 O A:HOH535 2.5 45.9 1.0 OG1 A:THR75 2.7 36.9 1.0 C A:ASP40 3.5 36.9 1.0 CB A:THR75 3.7 32.9 1.0 CA A:ASP40 3.9 35.6 1.0 CB A:ASP40 3.9 41.1 1.0 O A:HIS4 4.0 51.4 1.0 N A:THR75 4.0 38.3 1.0 CA A:THR75 4.5 34.6 1.0 O A:HOH480 4.7 56.7 1.0 N A:GLY41 4.7 31.4 1.0 OD1 A:ASP40 4.7 40.6 1.0 O A:ARG6 4.8 42.8 1.0 CG A:ASP40 4.8 42.0 1.0 CG2 A:THR75 4.8 33.0 1.0 CE A:MET9 4.9 37.7 1.0

Sodium binding site 2 out of 6 in the Crystal Structure of N-Acetylneuraminate Lyase (Nana) From Klebsiella Aerogenes (Pyruvate Bound, Orthorhombic P Form)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of N-Acetylneuraminate Lyase (Nana) From Klebsiella Aerogenes (Pyruvate Bound, Orthorhombic P Form) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na303 b:46.9 occ:1.00 O B:HOH542 2.2 47.7 1.0 O B:ASP40 2.3 35.8 1.0 O B:HOH541 2.4 47.0 1.0 OG1 B:THR75 2.5 36.2 1.0 O B:HOH501 2.5 53.3 1.0 O B:HOH406 2.6 42.3 1.0 C B:ASP40 3.4 33.9 1.0 CB B:THR75 3.5 34.0 1.0 CA B:ASP40 3.8 37.8 1.0 N B:THR75 3.9 38.8 1.0 CB B:ASP40 3.9 35.1 1.0 O B:HIS4 3.9 49.4 1.0 CA B:THR75 4.3 38.6 1.0 N B:GLY41 4.5 35.1 1.0 CG2 B:THR75 4.7 35.2 1.0 O B:HOH539 4.8 55.3 1.0 CE B:MET9 4.8 35.5 1.0 CG B:ASP40 4.8 38.4 1.0 C B:ILE74 4.9 39.3 1.0 OD1 B:ASP40 4.9 43.8 1.0 O B:ARG6 4.9 38.7 1.0 CA B:GLY41 5.0 32.1 1.0 CA B:ILE74 5.0 44.6 1.0

Sodium binding site 3 out of 6 in the Crystal Structure of N-Acetylneuraminate Lyase (Nana) From Klebsiella Aerogenes (Pyruvate Bound, Orthorhombic P Form)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of N-Acetylneuraminate Lyase (Nana) From Klebsiella Aerogenes (Pyruvate Bound, Orthorhombic P Form) within 5.0Å range: probe atom residue distance (Å) B Occ C:Na303 b:51.7 occ:1.00 O C:ASP40 2.2 40.0 1.0 O C:HOH514 2.3 47.1 1.0 O C:HOH522 2.4 45.8 1.0 OG1 C:THR75 2.4 42.5 1.0 O C:HOH474 2.4 51.0 1.0 O C:HOH416 2.5 41.9 1.0 C C:ASP40 3.3 41.5 1.0 CB C:THR75 3.5 40.0 1.0 CA C:ASP40 3.8 44.1 1.0 CB C:ASP40 3.8 42.2 1.0 N C:THR75 3.8 40.3 1.0 O C:HIS4 3.9 48.5 1.0 CA C:THR75 4.3 42.9 1.0 N C:GLY41 4.5 38.8 1.0 O C:HOH512 4.6 56.5 1.0 CG2 C:THR75 4.7 34.6 1.0 OD1 C:ASP40 4.7 49.2 1.0 CG C:ASP40 4.7 43.0 1.0 CE C:MET9 4.7 38.8 1.0 C C:ILE74 4.8 43.6 1.0 CA C:GLY41 4.8 37.9 1.0 O C:ARG6 4.9 42.5 1.0 CA C:ILE74 4.9 45.7 1.0

Sodium binding site 4 out of 6 in the Crystal Structure of N-Acetylneuraminate Lyase (Nana) From Klebsiella Aerogenes (Pyruvate Bound, Orthorhombic P Form)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of N-Acetylneuraminate Lyase (Nana) From Klebsiella Aerogenes (Pyruvate Bound, Orthorhombic P Form) within 5.0Å range: probe atom residue distance (Å) B Occ D:Na303 b:48.9 occ:1.00 O D:HOH532 2.3 48.4 1.0 O D:HOH497 2.3 45.8 1.0 O D:HOH452 2.4 42.8 1.0 O D:HOH531 2.5 49.2 1.0 O D:ASP40 2.5 33.5 1.0 OG1 D:THR75 2.6 35.3 1.0 C D:ASP40 3.6 31.7 1.0 CB D:THR75 3.7 32.8 1.0 O D:HIS4 3.9 50.2 1.0 N D:THR75 4.0 32.1 1.0 CA D:ASP40 4.0 35.6 1.0 CB D:ASP40 4.0 33.1 1.0 O D:HOH503 4.3 56.0 1.0 CA D:THR75 4.4 31.8 1.0 N D:GLY41 4.7 30.4 1.0 OD1 D:ASP40 4.8 39.9 1.0 CG2 D:THR75 4.8 30.7 1.0 O D:ARG6 4.8 37.3 1.0 CG D:ASP40 4.9 40.4 1.0 C D:ILE74 4.9 39.9 1.0 CE D:MET9 5.0 30.5 1.0

Sodium binding site 5 out of 6 in the Crystal Structure of N-Acetylneuraminate Lyase (Nana) From Klebsiella Aerogenes (Pyruvate Bound, Orthorhombic P Form)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of N-Acetylneuraminate Lyase (Nana) From Klebsiella Aerogenes (Pyruvate Bound, Orthorhombic P Form) within 5.0Å range: probe atom residue distance (Å) B Occ E:Na303 b:48.4 occ:1.00 O E:ASP40 2.2 38.2 1.0 O E:HOH521 2.3 54.3 1.0 O E:HOH416 2.4 43.6 1.0 O E:HOH474 2.5 49.5 1.0 OG1 E:THR75 2.5 40.8 1.0 O E:HOH459 2.7 49.3 1.0 C E:ASP40 3.3 39.7 1.0 CB E:THR75 3.5 39.2 1.0 CA E:ASP40 3.8 38.2 1.0 N E:THR75 3.8 40.2 1.0 CB E:ASP40 3.9 41.5 1.0 O E:HIS4 3.9 46.8 1.0 CA E:THR75 4.3 37.7 1.0 N E:GLY41 4.5 37.6 1.0 OD1 E:ASP40 4.6 44.9 1.0 CG2 E:THR75 4.7 36.1 1.0 CG E:ASP40 4.7 41.9 1.0 C E:ILE74 4.8 47.1 1.0 CE E:MET9 4.9 42.0 1.0 O E:ARG6 4.9 42.4 1.0 CA E:GLY41 4.9 39.0 1.0 CA E:ILE74 4.9 44.8 1.0

Sodium binding site 6 out of 6 in the Crystal Structure of N-Acetylneuraminate Lyase (Nana) From Klebsiella Aerogenes (Pyruvate Bound, Orthorhombic P Form)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Crystal Structure of N-Acetylneuraminate Lyase (Nana) From Klebsiella Aerogenes (Pyruvate Bound, Orthorhombic P Form) within 5.0Å range: probe atom residue distance (Å) B Occ F:Na303 b:55.3 occ:1.00 O F:HOH495 2.4 47.0 1.0 O F:HOH467 2.4 56.4 1.0 O F:HOH406 2.5 45.3 1.0 OG1 F:THR75 2.5 42.0 1.0 O F:HOH508 2.5 48.7 1.0 O F:ASP40 2.6 44.9 1.0 C F:ASP40 3.6 40.4 1.0 CB F:THR75 3.6 40.2 1.0 O F:HIS4 3.8 49.0 1.0 N F:THR75 3.9 42.0 1.0 CB F:ASP40 4.0 46.6 1.0 CA F:ASP40 4.0 44.0 1.0 O F:HOH469 4.3 55.7 1.0 CA F:THR75 4.4 38.4 1.0 N F:GLY41 4.8 45.0 1.0 CG2 F:THR75 4.8 37.3 1.0 C F:ILE74 4.9 44.0 1.0 OD1 F:ASP40 4.9 47.9 1.0 O F:ARG6 4.9 44.6 1.0 CE F:MET9 4.9 41.7 1.0 CG F:ASP40 4.9 47.7 1.0 C F:HIS4 4.9 52.6 1.0

S.Lovell, L.Liu, S.Seibold, K.P.Battaile. Crystal Structure of N-Acetylneuraminate Lyase (Nana) From Klebsiella Aerogenes (Pyruvate Bound, Orthorhombic P Form) To Be Published.