Sodium in PDB 1ktw: Iota-Carrageenase Complexed to Iota-Carrageenan Fragments

All present enzymatic activity of Iota-Carrageenase Complexed to Iota-Carrageenan Fragments:
3.2.1.157;

The structure of Iota-Carrageenase Complexed to Iota-Carrageenan Fragments, PDB code: 1ktw was solved by G.Michel, R.Kahn, O.Dideberg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	23.17 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	54.730, 122.310, 91.941, 90.00, 90.99, 90.00
R / Rfree (%)	20.3 / 23.8

The structure of Iota-Carrageenase Complexed to Iota-Carrageenan Fragments also contains other interesting chemical elements:

Chlorine	(Cl)	2 atoms
Calcium	(Ca)	10 atoms

The binding sites of Sodium atom in the Iota-Carrageenase Complexed to Iota-Carrageenan Fragments (pdb code 1ktw). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Iota-Carrageenase Complexed to Iota-Carrageenan Fragments, PDB code: 1ktw:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Iota-Carrageenase Complexed to Iota-Carrageenan Fragments


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Iota-Carrageenase Complexed to Iota-Carrageenan Fragments within 5.0Å range: probe atom residue distance (Å) B Occ A:Na11 b:13.5 occ:1.00 O A:LEU159 2.3 12.6 1.0 O A:PHE184 2.4 10.1 1.0 O A:HOH531 2.4 9.8 1.0 OG1 A:THR182 2.4 11.4 1.0 O A:ILE183 2.5 12.8 1.0 C A:ILE183 3.4 13.7 1.0 C A:PHE184 3.4 10.8 1.0 CB A:THR182 3.5 13.4 1.0 C A:LEU159 3.5 14.4 1.0 C A:THR182 3.9 14.4 1.0 CA A:PHE184 3.9 11.8 1.0 CB A:PHE184 3.9 13.2 1.0 O A:THR182 3.9 14.5 1.0 N A:PHE184 4.0 10.8 1.0 O A:HOH533 4.0 9.1 1.0 N A:ILE183 4.1 13.8 1.0 CA A:THR182 4.3 13.4 1.0 N A:ALA160 4.4 13.7 1.0 CA A:LEU159 4.4 15.8 1.0 CA A:ILE183 4.4 13.5 1.0 O A:ALA185 4.5 8.9 1.0 O A:HOH551 4.5 13.5 1.0 N A:ALA185 4.5 9.4 1.0 C A:ALA185 4.5 9.0 1.0 N A:LEU159 4.5 17.0 1.0 CA A:ALA160 4.5 13.0 1.0 OD2 A:ASP179 4.6 12.7 1.0 CG2 A:THR182 4.7 11.4 1.0 CE2 A:PHE151 4.7 15.1 1.0 CB A:LEU159 4.7 14.4 1.0 N A:SER186 4.8 8.6 1.0 OD1 A:ASP179 4.9 14.9 1.0 CA A:ALA185 4.9 10.0 1.0

Sodium binding site 2 out of 4 in the Iota-Carrageenase Complexed to Iota-Carrageenan Fragments


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Iota-Carrageenase Complexed to Iota-Carrageenan Fragments within 5.0Å range: probe atom residue distance (Å) B Occ A:Na13 b:14.4 occ:1.00 OD2 A:ASP178 2.0 18.5 1.0 O A:HOH724 2.6 38.1 1.0 CG A:ASP178 2.8 16.2 1.0 OD1 A:ASP178 2.9 15.8 1.0 NZ A:LYS152 4.1 17.9 1.0 CB A:ASP178 4.3 15.3 1.0 CE A:LYS152 4.7 18.9 1.0 ND2 A:ASN212 4.7 12.2 1.0 CD1 A:LEU148 5.0 10.8 1.0

Sodium binding site 3 out of 4 in the Iota-Carrageenase Complexed to Iota-Carrageenan Fragments


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Iota-Carrageenase Complexed to Iota-Carrageenan Fragments within 5.0Å range: probe atom residue distance (Å) B Occ B:Na12 b:19.7 occ:1.00 O B:LEU159 2.3 16.2 1.0 O B:PHE184 2.4 16.6 1.0 OG1 B:THR182 2.4 17.4 1.0 O B:HOH537 2.5 12.5 1.0 O B:ILE183 2.6 20.5 1.0 C B:PHE184 3.4 17.7 1.0 C B:ILE183 3.5 20.2 1.0 C B:LEU159 3.5 19.3 1.0 CB B:THR182 3.5 18.6 1.0 CB B:PHE184 3.8 18.9 1.0 CA B:PHE184 3.9 18.9 1.0 C B:THR182 3.9 20.2 1.0 N B:PHE184 4.0 19.2 1.0 O B:THR182 4.0 21.6 1.0 O B:HOH542 4.0 15.1 1.0 N B:ILE183 4.2 19.3 1.0 CA B:THR182 4.4 19.3 1.0 O B:ALA185 4.4 13.1 1.0 CA B:LEU159 4.4 19.9 1.0 N B:ALA160 4.4 18.3 1.0 C B:ALA185 4.5 13.5 1.0 N B:LEU159 4.5 21.0 1.0 N B:ALA185 4.5 16.6 1.0 CA B:ILE183 4.5 20.7 1.0 O B:HOH582 4.5 22.4 1.0 CA B:ALA160 4.6 16.8 1.0 OD2 B:ASP179 4.6 19.6 1.0 CG2 B:THR182 4.7 18.8 1.0 CB B:LEU159 4.8 19.2 1.0 OD1 B:ASP179 4.8 20.8 1.0 N B:SER186 4.8 12.9 1.0 CE2 B:PHE151 4.8 20.6 1.0 CA B:ALA185 4.8 14.3 1.0

Sodium binding site 4 out of 4 in the Iota-Carrageenase Complexed to Iota-Carrageenan Fragments


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Iota-Carrageenase Complexed to Iota-Carrageenan Fragments within 5.0Å range: probe atom residue distance (Å) B Occ B:Na14 b:19.7 occ:1.00 OD2 B:ASP178 2.1 19.8 1.0 O B:HOH748 2.4 46.3 1.0 CG B:ASP178 2.9 20.0 1.0 OD1 B:ASP178 2.9 18.6 1.0 NZ B:LYS152 4.2 27.4 1.0 CB B:ASP178 4.3 19.6 1.0 ND2 B:ASN212 4.6 18.7 1.0 CE B:LYS152 4.7 27.2 1.0 CD1 B:LEU148 5.0 15.1 1.0

G.Michel, W.Helbert, R.Kahn, O.Dideberg, B.Kloareg. The Structural Bases of the Processive Degradation of Iota-Carrageenan, A Main Cell Wall Polysaccharide of Red Algae. J.Mol.Biol. V. 334 421 2003.
ISSN: ISSN 0022-2836
PubMed: 14623184
DOI: 10.1016/J.JMB.2003.09.056