Sodium in PDB 6ktr: Crystal Structure of Fibroblast Growth Factor 19 in Complex with Fab

The structure of Crystal Structure of Fibroblast Growth Factor 19 in Complex with Fab, PDB code: 6ktr was solved by H.Liu, S.Zheng, X.Hou, X.Liu, X.Lv, Y.Li, W.Li, J.Sui, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.72 / 2.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	84.968, 104.125, 165.365, 90.00, 90.00, 90.00
R / Rfree (%)	20.2 / 25.3

The binding sites of Sodium atom in the Crystal Structure of Fibroblast Growth Factor 19 in Complex with Fab (pdb code 6ktr). 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 Fibroblast Growth Factor 19 in Complex with Fab, PDB code: 6ktr:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of Fibroblast Growth Factor 19 in Complex with Fab


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 Fibroblast Growth Factor 19 in Complex with Fab within 5.0Å range: probe atom residue distance (Å) B Occ F:Na301 b:46.7 occ:1.00 O F:TRP47 2.5 31.3 1.0 O G:HOH416 2.6 35.3 1.0 O F:HOH415 2.8 32.9 1.0 O G:HOH413 3.0 44.0 1.0 CB F:ALA61 3.5 36.2 1.0 N F:TRP47 3.5 37.1 1.0 C F:TRP47 3.5 48.0 1.0 CG F:GLU46 3.5 38.9 1.0 CA F:TRP47 3.9 46.0 1.0 CE3 F:TRP47 4.0 31.5 1.0 CB F:TRP47 4.0 27.2 1.0 O G:LEU99 4.0 35.1 1.0 OE1 F:GLU46 4.3 42.6 1.0 C F:GLU46 4.3 37.6 1.0 O G:HOH424 4.4 38.6 1.0 CD F:GLU46 4.4 42.1 1.0 CA F:GLU46 4.6 34.4 1.0 CB F:GLU46 4.7 40.9 1.0 CD2 F:TRP47 4.7 28.6 1.0 N F:VAL48 4.8 39.5 1.0 CG F:TRP47 4.8 37.1 1.0 CA F:ALA61 4.8 35.3 1.0 CZ3 F:TRP47 4.9 39.1 1.0 O F:HOH450 4.9 47.4 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of Fibroblast Growth Factor 19 in Complex with Fab


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 Fibroblast Growth Factor 19 in Complex with Fab within 5.0Å range: probe atom residue distance (Å) B Occ F:Na302 b:46.7 occ:1.00 O F:GLY44 2.6 40.6 1.0 O F:HOH453 2.7 57.7 1.0 N F:ALA40 2.8 43.0 1.0 O F:HOH434 2.8 38.8 1.0 CB F:ALA40 3.4 35.4 1.0 CA F:ALA40 3.6 47.2 1.0 C F:GLN39 3.7 45.4 1.0 C F:GLY44 3.7 43.0 1.0 CA F:GLN39 3.7 43.4 1.0 CB F:LYS43 3.9 44.0 1.0 N F:GLY44 4.0 43.2 1.0 O F:ALA40 4.4 50.0 1.0 C F:LYS43 4.4 50.2 1.0 CA F:GLY44 4.4 39.6 1.0 O F:ARG38 4.4 40.9 1.0 C F:ALA40 4.5 52.6 1.0 N F:GLN39 4.6 38.0 1.0 CG F:GLN39 4.7 36.2 1.0 CB F:GLU46 4.7 40.9 1.0 N F:LEU45 4.7 43.7 1.0 CB F:GLN39 4.8 40.0 1.0 O F:HOH426 4.8 63.8 1.0 CA F:LYS43 4.8 54.7 1.0 C F:ARG38 4.8 34.3 1.0 OE2 F:GLU46 4.9 45.7 1.0 C F:LEU45 4.9 39.0 1.0 O F:GLN39 4.9 43.4 1.0 N F:GLU46 4.9 32.6 1.0 O F:LYS43 5.0 40.7 1.0 CA F:LEU45 5.0 38.7 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of Fibroblast Growth Factor 19 in Complex with Fab


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 Fibroblast Growth Factor 19 in Complex with Fab within 5.0Å range: probe atom residue distance (Å) B Occ G:Na302 b:48.4 occ:1.00 O F:HOH445 2.6 34.3 1.0 OG G:SER36 2.7 45.4 1.0 O G:TYR34 2.8 39.2 1.0 OG G:SER91 3.0 39.7 1.0 O G:SER91 3.2 32.4 1.0 O G:HOH432 3.4 27.1 1.0 CB G:SER36 3.4 29.7 1.0 CD1 G:LEU99 3.4 28.4 1.0 C G:SER91 3.4 38.8 1.0 N G:SER36 3.5 36.2 1.0 N G:SER92 3.7 43.0 1.0 CA G:SER92 3.7 43.0 1.0 O G:HOH422 3.8 37.8 1.0 C G:TYR34 3.9 40.5 1.0 C G:SER92 3.9 41.7 1.0 N G:TRP93 3.9 44.8 1.0 CB G:SER91 4.0 26.8 1.0 CA G:SER36 4.0 33.9 1.0 C G:VAL35 4.1 40.9 1.0 CA G:SER91 4.3 37.8 1.0 CA G:VAL35 4.3 29.1 1.0 N G:VAL35 4.5 46.8 1.0 O G:SER92 4.5 38.3 1.0 O F:HOH414 4.7 43.8 1.0 O F:LEU104 4.7 40.4 1.0 CB G:TYR34 4.8 39.4 1.0 CG G:LEU99 4.9 40.5 1.0 CA G:TYR34 4.9 40.2 1.0 CA G:TRP93 5.0 40.0 1.0

H.Liu, S.Zheng, X.Hou, X.Liu, K.Du, X.Lv, Y.Li, F.Yang, W.Li, J.Sui. Novel Abs Targeting the N-Terminus of Fibroblast Growth Factor 19 Inhibit Hepatocellular Carcinoma Growth Without Bile-Acid-Related Side-Effects. Cancer Sci. V. 111 1750 2020.
ISSN: ISSN 1349-7006
PubMed: 32061104
DOI: 10.1111/CAS.14353