Sodium in PDB 3gvk: Crystal Structure of Endo-Neuraminidase Nf Mutant

All present enzymatic activity of Crystal Structure of Endo-Neuraminidase Nf Mutant:
3.2.1.129;

The structure of Crystal Structure of Endo-Neuraminidase Nf Mutant, PDB code: 3gvk was solved by E.C.Schulz, A.Dickmanns, R.Ficner, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	15.00 / 1.84
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	90.400, 153.700, 157.800, 90.00, 90.00, 90.00
R / Rfree (%)	26.5 / 28.2

The binding sites of Sodium atom in the Crystal Structure of Endo-Neuraminidase Nf Mutant (pdb code 3gvk). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of Endo-Neuraminidase Nf Mutant, PDB code: 3gvk:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of Endo-Neuraminidase Nf Mutant


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 Endo-Neuraminidase Nf Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Na916 b:14.8 occ:1.00 O A:HIS743 2.3 13.3 1.0 O A:THR322 2.4 12.5 1.0 O A:TYR324 2.5 13.8 1.0 O A:SER745 2.5 12.2 1.0 OD2 A:ASP746 2.8 12.7 1.0 CG A:ASP746 3.3 12.5 1.0 NH2 B:ARG772 3.4 15.0 1.0 C A:HIS743 3.5 12.9 1.0 OD1 A:ASP746 3.5 11.8 1.0 C A:SER745 3.5 12.1 1.0 OD1 A:ASN326 3.6 15.2 1.0 C A:THR322 3.6 12.7 1.0 C A:TYR324 3.7 14.0 1.0 N A:SER745 4.0 12.0 1.0 C A:PRO323 4.0 13.3 1.0 C A:PRO744 4.0 12.3 1.0 CZ B:ARG772 4.1 14.6 1.0 N A:TYR324 4.2 13.6 1.0 O A:PRO323 4.2 13.2 1.0 CA A:PRO323 4.3 13.1 1.0 CG A:ASN326 4.3 13.8 1.0 N A:ASN326 4.3 13.9 1.0 O A:PRO744 4.3 12.2 1.0 N A:PRO744 4.3 12.7 1.0 CA A:SER745 4.4 12.3 0.5 CA A:SER745 4.4 11.8 0.5 N A:PRO323 4.4 12.8 1.0 N A:ASP746 4.4 12.0 1.0 CA A:PRO744 4.4 12.3 1.0 CA A:HIS743 4.4 13.4 1.0 CB A:ASP746 4.5 11.8 1.0 N A:THR322 4.5 12.7 1.0 N A:TYR325 4.6 14.1 1.0 CA A:TYR324 4.6 14.1 1.0 CA A:ASP746 4.6 11.8 1.0 CB A:HIS743 4.6 13.4 1.0 NH1 B:ARG772 4.6 14.1 1.0 N A:HIS743 4.7 13.3 1.0 CA A:TYR325 4.7 14.2 1.0 CB A:ASN326 4.7 13.7 1.0 CA A:THR322 4.7 12.6 1.0 NE B:ARG772 4.7 14.3 1.0 O A:HOH143 4.9 13.9 1.0 OG1 A:THR322 4.9 12.7 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of Endo-Neuraminidase Nf Mutant


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 Endo-Neuraminidase Nf Mutant within 5.0Å range: probe atom residue distance (Å) B Occ B:Na916 b:14.0 occ:1.00 O B:THR322 2.4 12.8 1.0 O B:HIS743 2.4 13.0 1.0 O B:TYR324 2.4 12.9 1.0 O B:SER745 2.5 11.8 1.0 OD2 B:ASP746 2.8 12.9 1.0 CG B:ASP746 3.3 12.3 1.0 NH2 C:ARG772 3.4 14.0 1.0 OD1 B:ASN326 3.5 14.5 1.0 C B:SER745 3.5 12.3 1.0 OD1 B:ASP746 3.5 12.4 1.0 C B:HIS743 3.5 12.7 1.0 C B:THR322 3.6 12.9 1.0 C B:TYR324 3.6 13.1 1.0 C B:PRO323 3.9 12.8 1.0 N B:SER745 4.0 12.5 1.0 CZ C:ARG772 4.1 14.2 1.0 C B:PRO744 4.1 12.6 1.0 N B:TYR324 4.1 12.9 1.0 O B:PRO323 4.1 12.6 1.0 CA B:PRO323 4.2 12.8 1.0 CG B:ASN326 4.3 12.8 1.0 N B:ASN326 4.3 11.9 1.0 O B:PRO744 4.3 12.7 1.0 CA B:SER745 4.4 12.4 1.0 N B:PRO323 4.4 12.8 1.0 N B:ASP746 4.4 12.2 1.0 N B:PRO744 4.4 12.7 1.0 CB B:ASP746 4.4 12.2 1.0 CA B:HIS743 4.5 13.0 1.0 N B:THR322 4.5 12.4 1.0 CA B:PRO744 4.5 12.7 1.0 CA B:TYR324 4.5 13.0 1.0 N B:TYR325 4.6 12.7 1.0 CA B:ASP746 4.6 12.2 1.0 NH1 C:ARG772 4.6 14.2 1.0 CA B:THR322 4.6 12.7 1.0 CB B:HIS743 4.6 12.8 1.0 CB B:ASN326 4.7 12.0 1.0 N B:HIS743 4.7 13.5 1.0 CA B:TYR325 4.7 12.7 1.0 NE C:ARG772 4.7 13.7 1.0 OG1 B:THR322 4.9 13.3 1.0 O B:HOH953 4.9 11.6 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of Endo-Neuraminidase Nf Mutant


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 Endo-Neuraminidase Nf Mutant within 5.0Å range: probe atom residue distance (Å) B Occ C:Na916 b:17.1 occ:1.00 O C:HIS743 2.3 16.1 1.0 O C:THR322 2.3 14.6 1.0 O C:TYR324 2.4 15.1 1.0 O C:SER745 2.5 16.0 1.0 OD2 C:ASP746 2.9 16.1 1.0 NH2 A:ARG772 3.3 16.9 1.0 CG C:ASP746 3.4 15.4 1.0 C C:SER745 3.5 16.0 1.0 C C:HIS743 3.5 16.2 1.0 OD1 C:ASP746 3.5 14.8 1.0 OD1 C:ASN326 3.5 15.7 1.0 C C:THR322 3.6 14.9 1.0 C C:TYR324 3.6 15.2 1.0 N C:SER745 3.9 16.1 1.0 C C:PRO323 4.0 15.1 1.0 C C:PRO744 4.0 16.3 1.0 CZ A:ARG772 4.1 16.1 1.0 N C:TYR324 4.1 15.2 1.0 CG C:ASN326 4.3 15.1 1.0 CA C:PRO323 4.3 14.9 1.0 CA C:SER745 4.3 16.1 1.0 O C:PRO323 4.3 14.9 1.0 N C:ASN326 4.3 14.9 1.0 O C:PRO744 4.3 16.4 1.0 N C:PRO323 4.4 14.6 1.0 N C:PRO744 4.4 16.1 1.0 N C:ASP746 4.4 15.8 1.0 CA C:HIS743 4.4 16.3 1.0 CA C:PRO744 4.5 16.2 1.0 N C:THR322 4.5 15.1 1.0 CB C:ASP746 4.5 15.6 1.0 CA C:TYR324 4.5 15.3 1.0 N C:TYR325 4.5 15.2 1.0 CA C:THR322 4.6 15.2 1.0 CB C:HIS743 4.6 16.4 1.0 NH1 A:ARG772 4.6 16.3 1.0 CA C:ASP746 4.6 15.8 1.0 CA C:TYR325 4.6 15.0 1.0 N C:HIS743 4.7 16.4 1.0 CB C:ASN326 4.7 14.6 1.0 NE A:ARG772 4.7 15.7 1.0 O C:HOH1008 4.9 17.4 1.0 CB C:THR322 4.9 15.7 1.0 C C:TYR325 5.0 14.9 1.0

E.C.Schulz, D.Schwarzer, M.Frank, K.Stummeyer, M.Muhlenhoff, A.Dickmanns, R.Gerardy-Schahn, R.Ficner. Structural Basis For the Recognition and Cleavage of Polysialic Acid By the Bacteriophage K1F Tailspike Protein Endonf. J.Mol.Biol. V. 397 341 2010.
ISSN: ISSN 0022-2836
PubMed: 20096705
DOI: 10.1016/J.JMB.2010.01.028