Sodium in PDB 5e7h: Crystal Structure of Domains Cd (Residues 230-489) of BACOVA_02650

The structure of Crystal Structure of Domains Cd (Residues 230-489) of BACOVA_02650, PDB code: 5e7h was solved by N.M.Koropatkin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.69 / 1.57
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	87.090, 87.090, 201.560, 90.00, 90.00, 120.00
R / Rfree (%)	15.6 / 17.1

The binding sites of Sodium atom in the Crystal Structure of Domains Cd (Residues 230-489) of BACOVA_02650 (pdb code 5e7h). 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 Domains Cd (Residues 230-489) of BACOVA_02650, PDB code: 5e7h:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Domains Cd (Residues 230-489) of BACOVA_02650


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 Domains Cd (Residues 230-489) of BACOVA_02650 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na508 b:24.6 occ:1.00 OD2 A:ASP482 2.5 18.6 1.0 O A:THR350 2.5 15.4 1.0 O A:ASN348 2.6 21.0 1.0 O A:HOH747 2.6 27.7 1.0 OD1 A:ASP482 2.6 14.6 1.0 O A:ASN321 2.8 17.1 1.0 CG A:ASP482 2.9 15.4 1.0 HB2 A:ASN321 3.0 16.4 1.0 OD2 A:ASP323 3.3 23.9 1.0 C A:THR350 3.6 15.6 1.0 H A:THR350 3.6 19.3 1.0 N A:THR350 3.7 16.1 1.0 C A:ASN348 3.8 17.1 1.0 O A:HOH852 3.8 40.5 1.0 C A:ASN321 3.8 16.5 1.0 CB A:ASN321 3.9 13.7 1.0 HB2 A:ASP323 4.0 26.6 1.0 HA3 A:GLY349 4.0 20.3 1.0 C A:GLY349 4.1 16.1 1.0 HA A:ASN321 4.1 15.0 1.0 CA A:THR350 4.2 14.9 1.0 CG A:ASP323 4.2 21.3 1.0 CA A:ASN321 4.3 12.5 1.0 HB A:THR350 4.3 19.4 1.0 HB2 A:ASN348 4.3 20.7 1.0 HA A:CYS351 4.3 17.3 1.0 CA A:GLY349 4.4 16.9 1.0 CB A:ASP482 4.4 12.1 1.0 HB2 A:TYR322 4.5 24.7 1.0 HB3 A:ASN348 4.5 20.7 1.0 H A:ASN483 4.5 13.5 1.0 HB3 A:ASN321 4.5 16.4 1.0 N A:GLY349 4.6 17.2 1.0 CG A:ASN321 4.6 14.3 1.0 OD1 A:ASN483 4.6 18.1 1.0 CB A:ASP323 4.6 22.1 1.0 N A:CYS351 4.6 14.4 1.0 HD21 A:ASN483 4.6 24.3 1.0 O A:GLY349 4.7 18.0 1.0 CB A:ASN348 4.7 17.2 1.0 HB2 A:ASP482 4.8 14.5 1.0 HB3 A:CYS351 4.8 22.8 1.0 O A:HOH623 4.8 20.4 1.0 CB A:THR350 4.8 16.1 1.0 HB3 A:ASP482 4.8 14.5 1.0 CA A:ASN348 4.8 17.6 1.0 CA A:CYS351 4.9 14.4 1.0 H A:ASP323 5.0 21.9 1.0 ND2 A:ASN483 5.0 20.2 1.0 CG A:ASN483 5.0 16.7 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Domains Cd (Residues 230-489) of BACOVA_02650


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 Domains Cd (Residues 230-489) of BACOVA_02650 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na509 b:57.1 occ:0.50 HA A:ASN459 2.6 22.8 1.0 OD1 A:ASN459 2.7 24.0 1.0 O A:LEU456 2.9 15.3 1.0 O A:HOH713 3.0 18.9 0.5 O A:HOH782 3.4 22.9 1.0 CA A:ASN459 3.5 19.0 1.0 H A:ASN459 3.6 21.5 1.0 CG A:ASN459 3.7 20.0 1.0 C A:LEU456 4.0 14.8 1.0 CB A:ASN459 4.0 19.3 1.0 N A:ASN459 4.0 17.9 1.0 HA A:ASN457 4.1 19.6 1.0 HB3 A:ASN459 4.1 23.1 1.0 HB3 A:LEU456 4.1 17.7 1.0 C A:ASN459 4.6 18.6 1.0 H A:SER460 4.6 19.8 1.0 HA A:LEU456 4.7 17.1 1.0 CA A:LEU456 4.8 14.2 1.0 N A:ASN457 4.8 15.4 1.0 ND2 A:ASN459 4.8 24.5 1.0 CA A:ASN457 4.9 16.3 1.0 N A:SER460 4.9 16.5 1.0 CB A:LEU456 4.9 14.7 1.0 HB2 A:ASN459 4.9 23.1 1.0

A.S.Tauzin, K.J.Kwiatkowski, N.I.Orlovsky, C.J.Smith, A.L.Creagh, C.A.Haynes, Z.Wawrzak, H.Brumer, N.M.Koropatkin. Molecular Dissection of Xyloglucan Recognition in A Prominent Human Gut Symbiont. Mbio V. 7 02134 2016.
ISSN: ESSN 2150-7511
PubMed: 27118585
DOI: 10.1128/MBIO.02134-15