Sodium in PDB 5a3m: Structure of CEA1A in Complex with Chitobiose

The structure of Structure of CEA1A in Complex with Chitobiose, PDB code: 5a3m was solved by M.Kock, S.Brueckner, N.Wozniak, M.Veelders, J.Schlereth, H.-U.Moesch, L.-O.Essen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.99 / 1.75
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	101.700, 105.350, 106.470, 90.00, 90.00, 90.00
R / Rfree (%)	18.3 / 21.1

The structure of Structure of CEA1A in Complex with Chitobiose also contains other interesting chemical elements:

Calcium

(Ca)

4 atoms

The binding sites of Sodium atom in the Structure of CEA1A in Complex with Chitobiose (pdb code 5a3m). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Structure of CEA1A in Complex with Chitobiose, PDB code: 5a3m:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Structure of CEA1A in Complex with Chitobiose


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of CEA1A in Complex with Chitobiose within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1245 b:10.9 occ:1.00 OD1 B:ASN76 2.6 21.8 1.0 CB B:ASN76 3.1 17.2 1.0 CG B:ASN76 3.1 21.1 1.0 O B:HOH2543 3.4 10.8 1.0 CG B:GLN53 4.3 12.1 1.0 CB B:GLN53 4.4 11.5 1.0 CA B:ASN76 4.4 14.5 1.0 ND2 B:ASN76 4.4 23.9 1.0 N B:ASN76 4.6 12.3 1.0

Sodium binding site 2 out of 4 in the Structure of CEA1A in Complex with Chitobiose


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of CEA1A in Complex with Chitobiose within 5.0Å range: probe atom residue distance (Å) B Occ C:Na1235 b:2.1 occ:1.00 O D:HOH2448 3.1 7.0 1.0 N C:ASP222 3.3 8.3 1.0 N C:ASP223 3.4 8.3 1.0 CB C:ASP223 3.6 8.8 1.0 CA C:LEU221 3.9 7.0 1.0 CB C:LEU221 4.0 6.9 1.0 CB D:ALA219 4.0 8.4 1.0 CD2 C:LEU221 4.0 7.0 1.0 C C:LEU221 4.1 7.4 1.0 CA C:ASP223 4.1 8.4 1.0 CA C:ASP222 4.2 9.0 1.0 C C:ASP222 4.2 8.5 1.0 CB C:ASP222 4.3 10.9 1.0 CG C:LEU221 4.6 7.0 1.0 O C:ASP223 4.7 9.3 1.0 CG C:ASP223 4.9 9.1 1.0 C C:ASP223 4.9 8.8 1.0

Sodium binding site 3 out of 4 in the Structure of CEA1A in Complex with Chitobiose


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of CEA1A in Complex with Chitobiose within 5.0Å range: probe atom residue distance (Å) B Occ C:Na1236 b:12.4 occ:1.00 OG C:SER95 2.9 12.7 1.0 O C:HOH2425 3.1 7.0 1.0 CB C:PRO94 3.7 14.4 1.0 CG C:PRO94 3.8 14.7 1.0 CB C:SER95 3.9 12.6 1.0 CD C:PRO94 3.9 14.0 1.0 N C:SER95 4.0 12.6 1.0 C C:PRO94 4.3 13.4 1.0 CA C:PRO94 4.4 14.5 1.0 N C:PRO94 4.5 12.9 1.0 OD1 C:ASN93 4.5 9.0 1.0 O C:HOH2577 4.5 29.3 1.0 CA C:SER95 4.6 12.4 1.0 O C:PRO94 5.0 15.1 1.0

Sodium binding site 4 out of 4 in the Structure of CEA1A in Complex with Chitobiose


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structure of CEA1A in Complex with Chitobiose within 5.0Å range: probe atom residue distance (Å) B Occ D:Na1236 b:2.4 occ:1.00 O C:HOH2457 3.0 11.4 1.0 N D:ASP222 3.3 9.6 1.0 N D:ASP223 3.4 9.3 1.0 CB D:ASP223 3.6 9.3 1.0 CB C:ALA219 3.8 8.1 1.0 CA D:LEU221 3.9 7.8 1.0 CB D:LEU221 4.0 7.6 1.0 C D:LEU221 4.1 8.1 1.0 CA D:ASP223 4.1 9.2 1.0 CA D:ASP222 4.2 10.0 1.0 CD2 D:LEU221 4.2 7.6 1.0 C D:ASP222 4.2 9.5 1.0 CB D:ASP222 4.3 11.8 1.0 O D:HOH2493 4.4 16.8 1.0 CG D:LEU221 4.7 7.9 1.0 O D:ASP223 4.7 9.0 1.0 O D:HOH2606 4.8 16.2 1.0 CG D:ASP223 4.9 10.8 1.0 C D:ASP223 5.0 9.2 1.0

M.Kock, S.Brueckner, N.Wozniak, M.Veelders, J.Schlereth, H.-U.Moesch, L.-O.Essen. High-Affinity Recognition of Non-Reducing Chitinous Ends By the Yeast Adhesin CEA1 To Be Published.