Sodium in PDB 4lov: Crystal Structure of Fimh in Complex with Heptylmannoside

The structure of Crystal Structure of Fimh in Complex with Heptylmannoside, PDB code: 4lov was solved by A.Garcia-Pino, S.Vanwetswinkel, N.Van Nuland, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.43 / 1.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	39.900, 41.820, 97.490, 90.00, 90.00, 90.00
R / Rfree (%)	16.1 / 19

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

Sodium binding site 1 out of 3 in the Crystal Structure of Fimh in Complex with Heptylmannoside


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 Fimh in Complex with Heptylmannoside within 5.0Å range: probe atom residue distance (Å) B Occ A:Na203 b:17.3 occ:1.00 O2 A:KGM201 2.7 9.0 1.0 O A:PHE1 2.7 8.9 1.0 OE1 A:GLN133 2.8 8.7 1.0 N A:GLY14 3.1 7.1 1.0 CD2 A:PHE142 3.4 9.8 1.0 CA A:ILE13 3.5 6.9 1.0 CZ A:PHE144 3.7 8.3 1.0 C A:PHE1 3.7 9.5 1.0 CE2 A:PHE142 3.7 11.7 1.0 C A:ILE13 3.8 9.9 1.0 CB A:PHE1 3.8 5.8 1.0 O3 A:KGM201 3.9 8.8 1.0 CD A:GLN133 3.9 10.1 1.0 C2 A:KGM201 3.9 9.0 1.0 CA A:GLY14 4.1 7.2 1.0 CA A:PHE1 4.1 5.8 1.0 CE1 A:PHE144 4.1 9.9 1.0 CD2 A:PHE1 4.1 8.2 1.0 CG2 A:ILE13 4.2 8.7 1.0 N A:PHE1 4.2 6.8 1.0 CB A:ILE13 4.2 9.0 1.0 NE2 A:GLN133 4.3 8.9 1.0 CG1 A:ILE13 4.4 9.1 1.0 C3 A:KGM201 4.4 7.8 1.0 CG A:PHE142 4.5 9.1 1.0 CG A:PHE1 4.5 5.5 1.0 N A:GLY15 4.5 8.9 1.0 N A:ILE13 4.6 7.8 1.0 O A:PRO12 4.6 8.5 1.0 C A:GLY14 4.7 9.8 1.0 N A:ALA2 4.8 7.2 1.0 CB A:PHE142 4.8 7.3 1.0 CE2 A:PHE144 4.8 8.4 1.0 C4 A:KGM201 4.9 7.8 1.0 O A:ILE13 5.0 10.4 1.0 CZ A:PHE142 5.0 11.6 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of Fimh in Complex with Heptylmannoside


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 Fimh in Complex with Heptylmannoside within 5.0Å range: probe atom residue distance (Å) B Occ A:Na204 b:17.3 occ:1.00 O3 A:GOL202 2.7 16.1 1.0 O A:HOH599 2.7 9.5 1.0 N A:ILE13 3.0 7.8 1.0 CB A:PRO12 3.4 10.0 1.0 CA A:PRO12 3.5 7.7 1.0 CG1 A:ILE13 3.5 9.1 1.0 C3 A:GOL202 3.6 17.7 1.0 C A:PRO12 3.7 10.3 1.0 CB A:ALA2 3.9 9.2 1.0 C2 A:GOL202 3.9 16.9 1.0 CB A:ILE13 3.9 9.0 1.0 CD1 A:ILE13 3.9 11.8 1.0 CA A:ILE13 4.1 6.9 1.0 O2 A:GOL202 4.5 17.7 1.0 N A:PRO12 4.9 8.0 1.0 CG A:PRO12 4.9 12.8 1.0 O A:PRO12 5.0 8.5 1.0 OD2 A:ASP47 5.0 11.2 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of Fimh in Complex with Heptylmannoside


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Fimh in Complex with Heptylmannoside within 5.0Å range: probe atom residue distance (Å) B Occ A:Na205 b:31.5 occ:1.00 O A:HOH508 2.4 37.8 1.0 OD1 A:ASP140 2.8 11.5 1.0 OG A:SER139 2.9 14.3 1.0 CG A:ASN138 3.2 13.5 1.0 N A:SER139 3.3 8.7 1.0 ND2 A:ASN138 3.4 15.0 1.0 CB A:ASN138 3.4 9.2 1.0 O A:HOH421 3.6 35.5 1.0 N A:ASP140 3.6 7.5 1.0 OD1 A:ASN138 3.7 9.3 1.0 CG A:ASP140 3.8 10.1 1.0 O A:HOH567 3.9 18.1 1.0 O A:HOH568 3.9 32.7 1.0 CA A:SER139 3.9 8.5 1.0 CB A:SER139 4.0 11.1 1.0 C A:SER139 4.0 11.4 1.0 C A:ASN138 4.2 10.9 1.0 O A:HOH369 4.2 24.2 1.0 CA A:ASN138 4.4 8.6 1.0 CA A:ASP140 4.4 6.9 1.0 OD2 A:ASP140 4.6 11.6 1.0 CB A:ASP140 4.6 6.4 1.0 O A:SER139 4.8 11.2 1.0

S.Vanwetswinkel, A.N.Volkov, Y.G.Sterckx, A.Garcia-Pino, L.Buts, W.F.Vranken, J.Bouckaert, R.Roy, L.Wyns, N.A.Van Nuland. Study of the Structural and Dynamic Effects in the Fimh Adhesin Upon Alpha-D-Heptyl Mannose Binding. J.Med.Chem. V. 57 1416 2014.
ISSN: ISSN 0022-2623
PubMed: 24476493
DOI: 10.1021/JM401666C