Sodium in PDB 7app: Structure of Lipase Tl From Capillary Grown Crystal in the Presence of Agarose

All present enzymatic activity of Structure of Lipase Tl From Capillary Grown Crystal in the Presence of Agarose:
3.1.1.3;

The structure of Structure of Lipase Tl From Capillary Grown Crystal in the Presence of Agarose, PDB code: 7app was solved by J.A.Gavira, S.Martinez-Rodriguez, R.Fernande-Penas, C.Verdugo-Escamilla, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	66.42 / 1.70
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	137.851, 137.851, 79.942, 90, 90, 120
R / Rfree (%)	12.7 / 15.4

The binding sites of Sodium atom in the Structure of Lipase Tl From Capillary Grown Crystal in the Presence of Agarose (pdb code 7app). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Structure of Lipase Tl From Capillary Grown Crystal in the Presence of Agarose, PDB code: 7app:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Structure of Lipase Tl From Capillary Grown Crystal in the Presence of Agarose


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Lipase Tl From Capillary Grown Crystal in the Presence of Agarose within 5.0Å range: probe atom residue distance (Å) B Occ A:Na302 b:30.8 occ:1.00 O A:HOH518 2.4 31.9 1.0 O A:ALA47 2.4 28.8 1.0 O A:HOH599 2.4 28.6 1.0 O A:GLU45 2.4 26.0 1.0 O A:HOH604 2.6 41.1 1.0 O A:HOH407 2.6 34.8 1.0 C A:GLU45 3.4 27.7 1.0 C A:ALA47 3.6 25.1 1.0 CA A:GLU45 3.8 21.7 1.0 O6 A:NAG301 3.8 63.7 1.0 O A:VAL44 3.9 22.3 1.0 N A:ALA49 4.1 25.9 1.0 N A:ALA47 4.3 23.5 1.0 O A:HOH620 4.3 48.9 1.0 O5 A:NAG301 4.4 51.0 1.0 C A:LYS46 4.4 27.5 0.6 CA A:ASP48 4.4 30.5 1.0 O A:HOH611 4.4 57.5 1.0 O A:ALA49 4.4 25.7 1.0 N A:ASP48 4.5 30.8 1.0 O A:ILE34 4.5 23.6 1.0 N A:LYS46 4.5 24.9 0.4 N A:LYS46 4.5 25.2 0.6 ND2 A:ASN33 4.6 40.1 1.0 CA A:ALA47 4.6 24.2 1.0 C A:LYS46 4.6 26.8 0.4 O A:LYS46 4.6 31.3 0.6 CB A:ASN33 4.7 27.5 1.0 CB A:GLU45 4.7 22.7 1.0 O A:HOH615 4.7 39.0 1.0 C A:ASP48 4.8 31.6 1.0 CG A:ASN33 4.8 33.0 1.0 N A:GLU45 4.8 22.4 1.0 C A:VAL44 4.8 21.3 1.0 C6 A:NAG301 4.9 63.4 1.0 CA A:LYS46 5.0 28.7 0.6 CA A:LYS46 5.0 26.5 0.4 CA A:ALA49 5.0 24.1 1.0

Sodium binding site 2 out of 3 in the Structure of Lipase Tl From Capillary Grown Crystal in the Presence of Agarose


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of Lipase Tl From Capillary Grown Crystal in the Presence of Agarose within 5.0Å range: probe atom residue distance (Å) B Occ B:Na302 b:25.5 occ:1.00 O B:GLU45 2.3 23.9 1.0 O B:HOH551 2.3 22.1 1.0 O B:HOH430 2.3 36.3 1.0 O B:HOH570 2.4 24.7 1.0 O B:ALA47 2.4 19.6 1.0 O B:HOH592 2.5 33.6 1.0 C B:GLU45 3.3 20.6 1.0 O B:HOH428 3.6 50.5 1.0 C B:ALA47 3.6 21.5 1.0 CA B:GLU45 3.8 21.5 1.0 O B:VAL44 3.9 19.1 1.0 O6 B:NAG301 4.0 45.9 1.0 N B:ALA49 4.1 25.5 1.0 O5 B:NAG301 4.2 32.7 1.0 N B:ALA47 4.3 18.3 1.0 O B:ALA49 4.4 23.3 1.0 N B:LYS46 4.4 19.1 0.6 N B:LYS46 4.4 20.0 0.4 O B:ILE34 4.4 21.9 1.0 C B:LYS46 4.5 21.1 0.6 CA B:ASP48 4.5 27.7 1.0 N B:ASP48 4.5 21.4 1.0 C B:LYS46 4.5 21.1 0.4 ND2 B:ASN33 4.6 32.7 1.0 CA B:ALA47 4.6 19.1 1.0 CB B:GLU45 4.7 20.2 1.0 C B:VAL44 4.8 16.7 1.0 CB B:ASN33 4.8 24.0 1.0 O B:LYS46 4.8 21.4 0.6 CG B:ASN33 4.8 26.2 1.0 C B:ASP48 4.8 28.5 1.0 N B:GLU45 4.8 18.4 1.0 CA B:LYS46 4.9 20.5 0.6 O B:HOH401 4.9 49.1 1.0 CA B:LYS46 4.9 21.6 0.4 C6 B:NAG301 4.9 40.2 1.0 O B:LYS46 5.0 21.9 0.4

Sodium binding site 3 out of 3 in the Structure of Lipase Tl From Capillary Grown Crystal in the Presence of Agarose


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of Lipase Tl From Capillary Grown Crystal in the Presence of Agarose within 5.0Å range: probe atom residue distance (Å) B Occ B:Na303 b:30.3 occ:1.00 O B:HOH564 2.2 29.9 1.0 O B:GLN188 2.5 23.2 1.0 O B:GLY191 2.5 21.4 1.0 O B:HOH602 2.5 38.0 1.0 O B:HOH544 2.6 29.6 1.0 O B:HOH535 2.8 36.9 1.0 C B:GLN188 3.6 25.3 1.0 C B:GLY191 3.7 22.4 1.0 CA B:THR189 4.2 21.6 1.0 N B:GLY191 4.2 20.2 1.0 N B:THR189 4.4 28.3 1.0 CA B:THR192 4.4 16.5 1.0 N B:THR192 4.4 18.0 1.0 O B:VAL187 4.4 25.4 1.0 OG1 B:THR192 4.5 21.1 1.0 C B:THR189 4.5 21.5 1.0 C B:VAL187 4.5 22.8 1.0 O B:HOH498 4.6 21.4 1.0 CA B:GLY191 4.6 20.1 1.0 O B:HOH435 4.6 52.6 1.0 N B:GLN188 4.6 24.5 1.0 CA B:GLN188 4.7 22.6 1.0 O B:HOH517 4.7 20.3 1.0 N B:GLY190 4.7 19.6 1.0 O B:THR186 5.0 24.3 1.0

R.Fernandez-Penas, C.Verdugo-Escamilla, S.Martinez-Rodriguez, J.A.Gavira. Production of Cross-Linked Lipase Crystals at A Preparative Scale Cryst.Growth Des. 2021.
ISSN: ESSN 1528-7505
DOI: 10.1021/ACS.CGD.0C01608