Sodium in PDB 4d52: Crystal Structure of Fucose Binding Lectin From Aspergillus Fumigatus (Afl) in Complex with L-Galactopyranose.

The structure of Crystal Structure of Fucose Binding Lectin From Aspergillus Fumigatus (Afl) in Complex with L-Galactopyranose., PDB code: 4d52 was solved by J.Houser, G.Cioci, J.Komarek, M.Wimmerowa, N.Kostlanova, M.Lahmann, A.Varrot, A.Imberty, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	111.82 / 1.76
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	80.030, 70.440, 117.800, 90.00, 108.34, 90.00
R / Rfree (%)	15.374 / 17.78

The structure of Crystal Structure of Fucose Binding Lectin From Aspergillus Fumigatus (Afl) in Complex with L-Galactopyranose. also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Sodium atom in the Crystal Structure of Fucose Binding Lectin From Aspergillus Fumigatus (Afl) in Complex with L-Galactopyranose. (pdb code 4d52). 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 Fucose Binding Lectin From Aspergillus Fumigatus (Afl) in Complex with L-Galactopyranose., PDB code: 4d52:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of Fucose Binding Lectin From Aspergillus Fumigatus (Afl) in Complex with L-Galactopyranose.


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 Fucose Binding Lectin From Aspergillus Fumigatus (Afl) in Complex with L-Galactopyranose. within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1318 b:13.4 occ:1.00 O B:HOH3057 2.4 27.5 1.0 O B:HOH3011 2.5 16.1 1.0 O B:HOH3010 2.5 17.1 1.0 O B:HOH3058 2.5 25.3 1.0 O B:GLY59 2.5 14.4 1.0 O B:HOH3059 2.6 33.2 1.0 O B:HOH3198 3.0 37.1 1.0 C B:GLY59 3.5 14.4 1.0 CA B:GLY59 3.9 15.2 1.0 O B:ARG12 4.2 10.8 1.0 OE2 B:GLU265 4.3 20.2 1.0 O B:HOH3236 4.3 35.7 1.0 O A:HOH3025 4.3 29.8 1.0 O B:HOH3195 4.4 21.5 1.0 O B:SER60 4.5 12.5 1.0 O B:HOH3016 4.6 11.4 1.0 O A:HOH3009 4.7 28.8 1.0 C B:SER60 4.7 12.1 1.0 O A:HOH3010 4.7 29.2 1.0 N B:SER60 4.7 13.3 1.0 O B:HOH3007 4.7 29.4 1.0 O A:HOH3026 4.9 21.9 1.0 O A:HOH3020 4.9 26.2 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of Fucose Binding Lectin From Aspergillus Fumigatus (Afl) in Complex with L-Galactopyranose.


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 Fucose Binding Lectin From Aspergillus Fumigatus (Afl) in Complex with L-Galactopyranose. within 5.0Å range: probe atom residue distance (Å) B Occ C:Na1318 b:20.9 occ:1.00 O C:HOH3069 2.4 36.5 1.0 O C:HOH3068 2.5 28.6 1.0 O C:HOH3015 2.5 15.5 1.0 O C:GLY59 2.6 14.9 1.0 O C:HOH3014 2.6 16.4 1.0 C C:GLY59 3.5 13.4 1.0 O C:HOH3213 3.8 43.3 1.0 CA C:GLY59 3.9 14.0 1.0 O C:ARG12 4.2 11.6 1.0 O D:HOH3010 4.2 29.9 1.0 OE2 C:GLU265 4.3 19.5 1.0 O C:HOH3117 4.4 46.6 1.0 O C:HOH3210 4.5 19.2 1.0 O C:HOH3012 4.5 23.9 1.0 O C:SER60 4.5 12.0 1.0 O C:HOH3050 4.6 24.3 1.0 O C:HOH3021 4.6 13.5 1.0 O D:HOH3007 4.7 40.5 1.0 N C:SER60 4.7 12.8 1.0 C C:SER60 4.7 12.4 1.0 O C:HOH3039 4.8 31.6 1.0 O D:HOH3011 4.8 31.9 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of Fucose Binding Lectin From Aspergillus Fumigatus (Afl) in Complex with L-Galactopyranose.


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 Fucose Binding Lectin From Aspergillus Fumigatus (Afl) in Complex with L-Galactopyranose. within 5.0Å range: probe atom residue distance (Å) B Occ D:Na1317 b:15.5 occ:1.00 O D:HOH3049 2.4 28.1 1.0 O D:HOH3048 2.5 20.2 1.0 O D:HOH3050 2.5 35.4 1.0 O D:GLY59 2.6 14.0 1.0 O D:HOH3008 2.6 12.5 1.0 O D:HOH3009 2.6 16.6 1.0 O D:HOH3185 3.4 37.1 1.0 C D:GLY59 3.6 14.3 1.0 CA D:GLY59 4.0 14.7 1.0 OE2 D:GLU265 4.3 20.6 1.0 O D:ARG12 4.3 12.6 1.0 O D:HOH3211 4.3 41.9 1.0 O C:HOH3016 4.4 22.5 1.0 O D:HOH3182 4.4 21.0 1.0 O C:HOH3007 4.5 21.3 1.0 O D:SER60 4.5 12.0 1.0 O D:HOH3013 4.6 11.9 1.0 O C:HOH3017 4.6 25.9 1.0 C D:SER60 4.7 11.6 1.0 O C:HOH3005 4.7 28.1 1.0 O C:HOH3013 4.7 23.5 1.0 N D:SER60 4.7 12.7 1.0 O D:HOH3006 4.7 22.2 1.0 O D:HOH3045 4.9 21.9 1.0

J.Houser, J.Komarek, G.Cioci, A.Varrot, A.Imberty, M.Wimmerova. Structural Insights Into Aspergillus Fumigatus Lectin Specificity: Afl Binding Sites Are Functionally Non-Equivalent Acta Crystallogr.,Sect.D V. 71 442 2015.
ISSN: ISSN 0907-4449
DOI: 10.1107/S1399004714026595