Sodium in PDB 2ppl: Human Pancreatic Lipase-Related Protein 1

All present enzymatic activity of Human Pancreatic Lipase-Related Protein 1:
3.1.1.3;

The structure of Human Pancreatic Lipase-Related Protein 1, PDB code: 2ppl was solved by J.R.Walker, T.Davis, A.Seitova, C.Butler-Cole, J.Weigelt, M.Sundstrom, C.H.Arrowsmith, A.M.Edwards, A.Bochkarev, S.Dhe-Paganon, Structural Genomics Consortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.92 / 2.20
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	62.871, 62.871, 306.280, 90.00, 90.00, 90.00
R / Rfree (%)	18 / 23.3

The structure of Human Pancreatic Lipase-Related Protein 1 also contains other interesting chemical elements:

Calcium

(Ca)

3 atoms

The binding sites of Sodium atom in the Human Pancreatic Lipase-Related Protein 1 (pdb code 2ppl). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Human Pancreatic Lipase-Related Protein 1, PDB code: 2ppl:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Human Pancreatic Lipase-Related Protein 1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Human Pancreatic Lipase-Related Protein 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na479 b:47.4 occ:1.00 O A:HOH698 2.2 48.0 1.0 O A:HOH486 2.2 52.5 1.0 O A:HOH699 2.3 48.6 1.0 O A:SER81 2.3 54.5 1.0 O A:GLU79 2.4 55.0 1.0 O A:HOH603 2.5 65.7 1.0 C A:SER81 3.5 52.7 1.0 C A:GLU79 3.6 53.7 1.0 C A:ALA80 4.0 55.0 1.0 N A:SER81 4.1 52.6 1.0 O A:ALA80 4.2 57.0 1.0 O A:ILE78 4.3 57.3 1.0 CA A:GLU79 4.4 54.7 1.0 CA A:SER81 4.4 51.7 1.0 N A:ASN82 4.4 52.2 0.5 O A:HOH595 4.5 55.3 1.0 N A:ASN82 4.5 52.3 0.5 N A:ALA80 4.5 53.5 1.0 O A:PHE83 4.5 53.2 1.0 CA A:ASN82 4.5 52.2 0.5 CA A:ALA80 4.6 54.7 1.0 CA A:ASN82 4.6 52.6 0.5 OE2 A:GLU79 4.7 58.9 1.0 C A:ASN82 4.8 51.9 0.5 N A:PHE83 4.8 51.3 1.0 CD A:GLU79 4.8 56.4 1.0 C A:ASN82 4.9 51.8 0.5

Sodium binding site 2 out of 3 in the Human Pancreatic Lipase-Related Protein 1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Human Pancreatic Lipase-Related Protein 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na480 b:49.1 occ:1.00 O A:GLY234 2.2 54.5 1.0 OE1 A:GLU197 2.2 51.4 1.0 O A:HOH589 2.3 50.6 1.0 O A:ALA225 2.3 54.3 1.0 O A:GLY232 2.3 51.1 1.0 C A:GLY232 3.3 53.5 1.0 C A:ALA225 3.4 53.7 1.0 C A:GLY234 3.4 52.6 1.0 CD A:GLU197 3.4 55.9 1.0 N A:LEU227 3.4 58.5 1.0 CB A:GLU197 3.7 51.2 1.0 C A:PRO226 3.7 57.6 1.0 CA A:PRO226 3.8 56.1 1.0 O A:ASP223 3.9 45.0 1.0 O A:ALA224 3.9 50.0 1.0 CA A:GLY232 4.0 53.8 1.0 N A:GLY234 4.0 50.3 1.0 N A:PRO226 4.0 55.4 1.0 C A:ALA224 4.1 49.0 1.0 C A:PHE233 4.1 53.0 1.0 CG A:GLU197 4.1 52.0 1.0 CA A:LEU227 4.2 60.6 1.0 N A:PHE233 4.2 52.5 1.0 CA A:GLY234 4.3 50.7 1.0 N A:THR235 4.3 54.4 1.0 O A:PHE233 4.4 54.1 1.0 N A:ALA225 4.4 49.5 1.0 OE2 A:GLU197 4.4 59.0 1.0 CA A:THR235 4.4 53.5 1.0 O A:PRO226 4.5 58.5 1.0 CB A:LEU227 4.5 60.9 1.0 CA A:PHE233 4.5 53.5 1.0 CA A:ALA225 4.5 51.0 1.0 CA A:ALA224 4.5 46.6 1.0 N A:GLY232 4.7 55.3 1.0 C A:ASP223 5.0 45.6 1.0

Sodium binding site 3 out of 3 in the Human Pancreatic Lipase-Related Protein 1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Human Pancreatic Lipase-Related Protein 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na483 b:59.5 occ:1.00 O A:HOH569 2.2 61.0 1.0 O A:HOH627 2.3 61.5 1.0 O A:HOH557 2.3 56.8 1.0 O A:LYS183 2.6 52.1 1.0 C A:LYS183 3.7 53.4 1.0 CB A:LYS183 4.1 54.8 1.0 CB A:ALA148 4.4 45.6 1.0 OD1 A:ASP152 4.4 72.5 1.0 O A:ALA148 4.4 49.2 1.0 CA A:LYS183 4.4 54.6 1.0 CB A:ASP152 4.6 55.8 1.0 N A:THR184 4.6 53.4 1.0 OG1 A:THR184 4.7 50.7 1.0 CG A:ASP152 4.7 65.7 1.0 CA A:THR184 4.8 52.2 1.0 O A:HOH666 4.8 52.0 1.0 C A:ALA148 4.8 47.8 1.0

J.R.Walker, T.Davis, A.Seitova, C.Butler-Cole, J.Weigelt, M.Sundstrom, C.H.Arrowsmith, A.M.Edwards, A.Bochkarev, S.Dhe-Paganon. Structure of the Human Pancreatic Lipase-Related Protein 1. To Be Published.