Sodium in PDB 5z9t: A New PL6 Alginate Lyase Complex with Trisaccharide

The structure of A New PL6 Alginate Lyase Complex with Trisaccharide, PDB code: 5z9t was solved by W.Z.Liu, Q.Q.Lyu, K.K.Zhang, Z.J.Li, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 1.80
Space group	P 31
Cell size a, b, c (Å), α, β, γ (°)	106.086, 106.086, 101.894, 90.00, 90.00, 120.00
R / Rfree (%)	16.5 / 19.6

The binding sites of Sodium atom in the A New PL6 Alginate Lyase Complex with Trisaccharide (pdb code 5z9t). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the A New PL6 Alginate Lyase Complex with Trisaccharide, PDB code: 5z9t:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the A New PL6 Alginate Lyase Complex with Trisaccharide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of A New PL6 Alginate Lyase Complex with Trisaccharide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na601 b:19.1 occ:1.00 O6A A:LGU603 2.3 21.4 1.0 OE1 A:GLU267 2.3 18.0 1.0 OE2 A:GLU236 2.4 20.7 1.0 OE1 A:GLU265 2.5 16.2 1.0 OE2 A:GLU265 2.5 17.0 1.0 OD1 A:ASN233 2.6 22.8 1.0 CD A:GLU265 2.8 17.1 1.0 C6 A:LGU603 3.3 23.4 1.0 O A:HOH726 3.4 24.6 1.0 CD A:GLU236 3.4 18.6 1.0 CD A:GLU267 3.4 18.2 1.0 CG A:ASN233 3.5 19.9 1.0 NH2 A:ARG266 3.5 20.7 1.0 O6B A:LGU603 3.6 22.6 1.0 ND2 A:ASN233 3.9 20.0 1.0 CG A:GLU267 3.9 16.9 1.0 N A:SER234 3.9 17.8 1.0 CZ A:ARG266 4.0 22.6 1.0 NH1 A:ARG266 4.0 21.8 1.0 CG A:GLU236 4.0 16.1 1.0 CB A:GLU267 4.0 16.5 1.0 O A:HOH864 4.1 21.3 1.0 OE1 A:GLU236 4.3 18.2 1.0 CG A:GLU265 4.3 16.5 1.0 CA A:SER234 4.5 17.1 1.0 OE2 A:GLU267 4.5 20.8 1.0 C5 A:LGU603 4.7 23.7 1.0 CB A:ASN233 4.8 17.9 1.0 CA A:ASN233 4.9 18.4 1.0 C A:ASN233 4.9 18.4 1.0 O5 A:LGU603 4.9 23.1 1.0 NE A:ARG266 5.0 21.6 1.0

Sodium binding site 2 out of 2 in the A New PL6 Alginate Lyase Complex with Trisaccharide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of A New PL6 Alginate Lyase Complex with Trisaccharide within 5.0Å range: probe atom residue distance (Å) B Occ B:Na601 b:19.1 occ:1.00 OE1 B:GLU267 2.3 18.7 1.0 O6A B:LGU604 2.3 21.1 1.0 OE2 B:GLU236 2.4 20.8 1.0 OE1 B:GLU265 2.5 17.2 1.0 OE2 B:GLU265 2.5 17.0 1.0 OD1 B:ASN233 2.6 20.7 1.0 CD B:GLU265 2.8 17.6 1.0 C6 B:LGU604 3.3 22.9 1.0 CD B:GLU236 3.4 19.6 1.0 O B:HOH720 3.4 23.7 1.0 CD B:GLU267 3.4 17.9 1.0 NH2 B:ARG266 3.5 20.7 1.0 CG B:ASN233 3.5 20.3 1.0 O6B B:LGU604 3.7 22.6 1.0 ND2 B:ASN233 3.9 19.8 1.0 CG B:GLU267 3.9 16.4 1.0 N B:SER234 3.9 18.2 1.0 CZ B:ARG266 4.0 22.7 1.0 NH1 B:ARG266 4.0 21.6 1.0 CG B:GLU236 4.0 16.4 1.0 CB B:GLU267 4.1 15.6 1.0 O B:HOH864 4.1 21.7 1.0 OE1 B:GLU236 4.3 18.1 1.0 CG B:GLU265 4.4 17.5 1.0 OE2 B:GLU267 4.5 20.7 1.0 CA B:SER234 4.5 16.6 1.0 C5 B:LGU604 4.7 22.1 1.0 CB B:ASN233 4.8 18.8 1.0 CA B:ASN233 4.9 19.2 1.0 C B:ASN233 4.9 19.0 1.0 O5 B:LGU604 4.9 22.8 1.0 NE B:ARG266 5.0 21.9 1.0

Q.Lyu, K.Zhang, Y.Shi, W.Li, X.Diao, W.Liu. Structural Insights Into A Novel CA2+-Independent Pl-6 Alginate Lyase From Vibrio OU02 Identify the Possible Subsites Responsible For Product Distribution. Biochim Biophys Acta Gen V.1863 1167 2019SUBJ.
ISSN: ISSN 1872-8006
PubMed: 31004719
DOI: 10.1016/J.BBAGEN.2019.04.013