Sodium in PDB 6kfn: Crystal Structure of Alginate Lyase From Paenibacillus Sp. Str. Fpu-7

All present enzymatic activity of Crystal Structure of Alginate Lyase From Paenibacillus Sp. Str. Fpu-7:
4.2.2.3;

The structure of Crystal Structure of Alginate Lyase From Paenibacillus Sp. Str. Fpu-7, PDB code: 6kfn was solved by T.Itoh, E.Nakagawa, M.Yoda, A.Nakaichi, T.Hibi, H.Kimoto, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	23.36 / 0.89
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	125.635, 57.764, 39.714, 90.00, 91.10, 90.00
R / Rfree (%)	10.5 / 12.2

The binding sites of Sodium atom in the Crystal Structure of Alginate Lyase From Paenibacillus Sp. Str. Fpu-7 (pdb code 6kfn). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Alginate Lyase From Paenibacillus Sp. Str. Fpu-7, PDB code: 6kfn:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Alginate Lyase From Paenibacillus Sp. Str. Fpu-7


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 Alginate Lyase From Paenibacillus Sp. Str. Fpu-7 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na401 b:8.1 occ:1.00 OE2 A:GLU181 2.3 7.9 1.0 O A:HOH523 2.4 15.3 1.0 O A:HOH709 2.4 10.7 1.0 O A:HOH804 2.4 21.9 1.0 OD2 A:ASP219 2.5 7.6 1.0 OE1 A:GLU216 2.5 5.6 1.0 CD A:GLU181 3.4 6.0 1.0 CD A:GLU216 3.4 4.8 1.0 HG3 A:GLU181 3.4 22.5 1.0 HZ1 A:LYS221 3.5 72.5 1.0 HG2 A:GLU181 3.5 12.1 0.7 CG A:ASP219 3.5 6.0 1.0 OE2 A:GLU216 3.7 5.7 1.0 CG A:GLU181 3.7 6.4 1.0 O A:HOH516 3.7 14.3 1.0 HB2 A:ASP219 3.7 6.8 1.0 HB2 A:ALA215 3.8 7.1 1.0 O A:HOH802 3.8 49.0 1.0 O A:HOH817 3.9 37.4 1.0 HB2 A:ALA245 4.0 6.9 1.0 CB A:ASP219 4.1 4.8 1.0 H A:GLU216 4.2 2.9 0.8 NZ A:LYS221 4.2 64.2 1.0 HB3 A:ASP219 4.3 5.4 1.0 O A:GLY178 4.4 8.1 1.0 OD1 A:ASP219 4.4 8.3 1.0 OE1 A:GLU181 4.5 6.3 1.0 HB1 A:ALA215 4.6 0.3 0.7 HZ3 A:LYS252 4.6 24.9 0.5 HD22 A:ASN243 4.6 20.3 0.7 CB A:ALA215 4.6 4.8 1.0 HE2 A:TYR184 4.6 95.1 0.8 HB2 A:GLU216 4.6 7.3 0.9 O A:ASN243 4.6 9.5 1.0 HZ1 A:LYS252 4.7 21.5 0.5 HZ3 A:LYS221 4.8 93.6 1.0 CG A:GLU216 4.8 5.0 1.0 CB A:ALA245 4.9 6.0 1.0 ND2 A:ASN243 4.9 24.4 1.0 HB1 A:ALA245 4.9 6.0 0.9 HB3 A:ALA215 5.0 4.3 0.9 O A:HOH525 5.0 25.3 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Alginate Lyase From Paenibacillus Sp. Str. Fpu-7


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 Alginate Lyase From Paenibacillus Sp. Str. Fpu-7 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:5.4 occ:1.00 O A:TYR244 2.3 6.8 1.0 O A:HOH824 2.4 15.0 1.0 O A:HOH700 2.4 5.2 1.0 O A:HOH597 2.4 9.2 1.0 OE1 A:GLN276 2.4 5.7 1.0 OD1 A:ASP246 2.4 5.5 1.0 H A:ASP246 3.2 7.0 0.9 HE21 A:GLN276 3.2 83.9 0.1 CD A:GLN276 3.4 5.2 1.0 CG A:ASP246 3.4 6.0 1.0 HE1 A:HIS278 3.5 4.1 0.7 HB3 A:TYR244 3.5 31.2 0.9 C A:TYR244 3.6 7.0 1.0 NE2 A:GLN276 3.6 8.7 1.0 OD2 A:ASP246 3.9 10.1 1.0 N A:ASP246 3.9 4.8 1.0 HA A:ALA245 3.9 2.0 0.7 O A:HOH532 4.2 15.4 1.0 CE1 A:HIS278 4.2 5.6 1.0 CB A:TYR244 4.2 23.1 1.0 HB2 A:TYR244 4.3 63.6 1.0 O A:HOH826 4.3 32.6 1.0 OE2 A:GLU216 4.4 5.7 1.0 CA A:TYR244 4.4 11.1 1.0 HA A:TYR244 4.4 2.5 1.0 N A:ALA245 4.5 5.6 1.0 CB A:ASP246 4.5 5.1 1.0 HB2 A:ASP250 4.5 3.7 0.9 HE22 A:GLN276 4.5 8.8 1.0 OG A:SER247 4.5 5.0 1.0 OD2 A:ASP250 4.5 6.3 1.0 CA A:ALA245 4.6 5.0 1.0 CA A:ASP246 4.6 4.9 1.0 HB2 A:GLN276 4.7 2.9 0.8 CG A:GLN276 4.7 4.8 1.0 HB3 A:SER247 4.7 2.2 0.6 C A:ALA245 4.8 4.8 1.0 C A:ASP246 4.8 4.5 1.0 H A:SER247 4.8 1.9 0.8 HB3 A:ASP246 4.8 4.5 1.0 O A:HOH817 4.8 37.4 1.0 CG A:ASP250 4.8 5.3 1.0 NE2 A:HIS278 4.9 6.3 1.0 N A:SER247 4.9 4.4 1.0

T.Itoh, E.Nakagawa, M.Yoda, A.Nakaichi, T.Hibi, H.Kimoto. Structural and Biochemical Characterisation of A Novel Alginate Lyase From Paenibacillus Sp. Str. Fpu-7. Sci Rep V. 9 14870 2019.
ISSN: ESSN 2045-2322
PubMed: 31619701
DOI: 10.1038/S41598-019-51006-1