Sodium in PDB 5a3l: Structure of CEA1A in Complex with N-Acetylglucosamine

The structure of Structure of CEA1A in Complex with N-Acetylglucosamine, PDB code: 5a3l 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)	19.84 / 1.66
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	102.340, 106.210, 107.600, 90.00, 90.00, 90.00
R / Rfree (%)	17.1 / 20.2

The structure of Structure of CEA1A in Complex with N-Acetylglucosamine also contains other interesting chemical elements:

Calcium

(Ca)

4 atoms

The binding sites of Sodium atom in the Structure of CEA1A in Complex with N-Acetylglucosamine (pdb code 5a3l). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the Structure of CEA1A in Complex with N-Acetylglucosamine, PDB code: 5a3l:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in the Structure of CEA1A in Complex with N-Acetylglucosamine


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 N-Acetylglucosamine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1246 b:7.5 occ:1.00 NH1 A:ARG208 3.3 11.7 1.0 O A:HOH525 3.3 10.9 1.0 CD2 A:HIS134 3.6 9.6 1.0 CG A:HIS134 3.7 9.4 1.0 CG2 A:VAL177 3.8 11.9 1.0 O A:ASN178 3.9 8.5 1.0 CB A:HIS134 4.1 8.4 1.0 NE2 A:HIS134 4.2 11.1 1.0 CZ A:ARG208 4.4 11.3 1.0 ND1 A:HIS134 4.4 10.6 1.0 NH2 A:ARG208 4.5 11.5 1.0 CE1 A:HIS134 4.6 10.0 1.0 O A:HOH421 4.7 13.8 1.0 O A:HOH646 4.8 20.8 1.0 C A:ASN178 4.8 8.6 1.0

Sodium binding site 2 out of 5 in the Structure of CEA1A in Complex with N-Acetylglucosamine


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 N-Acetylglucosamine within 5.0Å range: probe atom residue distance (Å) B Occ C:Na1239 b:3.8 occ:1.00 O D:HOH433 3.2 12.0 1.0 N C:ASP222 3.3 9.7 1.0 N C:ASP223 3.4 9.3 1.0 CB C:ASP223 3.6 9.6 1.0 CA C:LEU221 3.9 8.6 1.0 CB C:LEU221 4.0 9.0 1.0 CB D:ALA219 4.0 8.2 1.0 CD2 C:LEU221 4.1 10.1 1.0 C C:LEU221 4.1 8.8 1.0 CA C:ASP223 4.1 9.5 1.0 CA C:ASP222 4.1 10.6 1.0 C C:ASP222 4.2 9.8 1.0 CB C:ASP222 4.3 13.2 1.0 CG C:LEU221 4.6 9.8 1.0 O C:ASP223 4.7 9.5 1.0 CG C:ASP223 4.9 10.0 1.0 C C:ASP223 5.0 9.6 1.0

Sodium binding site 3 out of 5 in the Structure of CEA1A in Complex with N-Acetylglucosamine


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 N-Acetylglucosamine within 5.0Å range: probe atom residue distance (Å) B Occ C:Na1240 b:15.2 occ:1.00 OG C:SER95 3.0 16.1 1.0 O C:HOH449 3.1 9.5 1.0 CB C:PRO94 3.6 14.0 1.0 CG C:PRO94 3.8 14.1 1.0 CD C:PRO94 3.9 13.9 1.0 CB C:SER95 4.0 14.8 1.0 N C:SER95 4.0 14.4 1.0 C C:PRO94 4.3 14.7 1.0 CA C:PRO94 4.4 14.0 1.0 N C:PRO94 4.4 13.0 1.0 OD1 C:ASN93 4.5 10.3 1.0 CA C:SER95 4.7 14.5 1.0 O C:HOH575 4.7 39.5 1.0

Sodium binding site 4 out of 5 in the Structure of CEA1A in Complex with N-Acetylglucosamine


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 N-Acetylglucosamine within 5.0Å range: probe atom residue distance (Å) B Occ D:Na1240 b:17.0 occ:1.00 O D:HOH605 2.6 17.7 1.0 O D:HOH506 2.9 20.9 1.0 NA D:NA1241 3.2 3.8 1.0 O C:HOH440 3.5 11.0 1.0 CB D:ASP223 3.5 11.4 1.0 OD2 D:ASP223 3.6 14.8 1.0 CG D:ASP223 4.0 12.8 1.0 CA D:ASP223 4.8 11.2 1.0 N D:ASP223 4.8 10.6 1.0

Sodium binding site 5 out of 5 in the Structure of CEA1A in Complex with N-Acetylglucosamine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Structure of CEA1A in Complex with N-Acetylglucosamine within 5.0Å range: probe atom residue distance (Å) B Occ D:Na1241 b:3.8 occ:1.00 O C:HOH440 3.2 11.0 1.0 NA D:NA1240 3.2 17.0 1.0 N D:ASP222 3.3 9.9 1.0 N D:ASP223 3.4 10.6 1.0 CB D:ASP223 3.6 11.4 1.0 CA D:LEU221 3.9 8.5 1.0 CB C:ALA219 3.9 9.3 1.0 CB D:LEU221 4.0 8.8 1.0 C D:LEU221 4.1 9.2 1.0 CD2 D:LEU221 4.1 10.0 1.0 CA D:ASP222 4.1 11.5 1.0 CA D:ASP223 4.2 11.2 1.0 C D:ASP222 4.2 11.0 1.0 CB D:ASP222 4.3 13.0 1.0 O D:HOH506 4.4 20.9 1.0 CG D:LEU221 4.6 9.5 1.0 O D:ASP223 4.8 11.6 1.0 O D:HOH605 4.8 17.7 1.0 CG D:ASP223 4.9 12.8 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.