Sodium in PDB 1vbw: Crystal Structure of Bitter Gourd Trypsin Inhibitor

The structure of Crystal Structure of Bitter Gourd Trypsin Inhibitor, PDB code: 1vbw was solved by K.Suto, M.Furuichi, E.Nishimoto, K.Meno, K.Horii, H.Mizuno, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.00 / 0.93
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	22.662, 23.023, 27.685, 92.05, 100.11, 101.80
R / Rfree (%)	11.4 / 14.3

The structure of Crystal Structure of Bitter Gourd Trypsin Inhibitor also contains other interesting chemical elements:

Potassium

(K)

1 atom

The binding sites of Sodium atom in the Crystal Structure of Bitter Gourd Trypsin Inhibitor (pdb code 1vbw). 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 Bitter Gourd Trypsin Inhibitor, PDB code: 1vbw:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Bitter Gourd Trypsin Inhibitor


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 Bitter Gourd Trypsin Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1103 b:11.6 occ:1.00 O A:GLY68 2.7 8.5 1.0 O A:THR66 2.7 8.1 1.0 O A:HOH3037 2.7 19.3 1.0 N A:ARG52 2.9 6.3 1.0 N A:GLY68 3.3 6.8 1.0 C A:GLY68 3.5 8.7 1.0 O A:HOH3001 3.6 8.0 1.0 CB A:ARG52 3.6 8.4 1.0 O A:ARG50 3.6 6.0 1.0 CA A:VAL51 3.6 5.5 1.0 CG A:ARG52 3.6 12.8 1.0 C A:VAL51 3.7 5.5 1.0 CA A:GLY68 3.7 8.4 1.0 CA A:ARG52 3.8 6.7 1.0 C A:ILE67 3.8 6.5 1.0 C A:THR66 3.9 6.6 1.0 C A:ARG50 4.1 5.3 1.0 O A:HOH3090 4.2 29.6 1.0 CD A:ARG52 4.2 19.1 1.0 N A:VAL51 4.2 5.1 1.0 CA A:ILE67 4.3 6.2 1.0 O A:ILE67 4.5 8.8 1.0 O A:ARG52 4.5 7.8 1.0 CG A:ARG50 4.6 8.4 1.0 OXT A:GLY68 4.6 11.2 1.0 N A:ILE67 4.6 6.4 1.0 C A:ARG52 4.7 6.2 1.0 O A:HOH3062 4.7 27.0 1.0 NE A:ARG50 4.8 9.5 1.0 OG1 A:THR66 4.8 12.3 0.4 CB A:VAL51 4.8 5.5 1.0 O A:VAL51 4.9 6.7 1.0 N A:THR66 4.9 6.0 1.0 CG1 A:VAL51 4.9 6.6 1.0 CA A:THR66 5.0 7.3 0.6 CB A:ARG50 5.0 7.0 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Bitter Gourd Trypsin Inhibitor


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 Bitter Gourd Trypsin Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1104 b:13.2 occ:1.00 O A:HOH3076 2.9 24.1 1.0 NZ A:LYS6 3.3 9.5 1.0 N A:GLN11 3.4 6.3 1.0 CA A:TRP9 3.4 5.5 1.0 C A:TRP9 3.5 5.9 1.0 CB A:GLN11 3.6 8.7 1.0 N A:PRO10 3.6 6.4 1.0 CD A:PRO10 3.7 8.2 1.0 CG A:GLN11 3.8 11.9 1.0 CE A:LYS6 3.9 8.5 1.0 CD2 A:LEU12 4.0 6.5 0.1 CB A:TRP9 4.0 5.7 1.0 CA A:GLN11 4.0 6.6 1.0 O A:TRP9 4.1 6.1 1.0 CD1 A:TRP9 4.2 6.2 1.0 CG A:PRO10 4.3 9.5 1.0 NE2 A:GLN11 4.3 45.2 1.0 C A:PRO10 4.4 6.3 1.0 CG A:TRP9 4.4 5.5 1.0 CD A:GLN11 4.4 18.4 1.0 O A:SER8 4.5 6.8 1.0 O A:HOH3002 4.5 26.9 1.0 CA A:PRO10 4.5 7.2 1.0 N A:LEU12 4.6 6.0 1.0 N A:TRP9 4.6 5.7 1.0 C A:GLN11 4.7 6.9 1.0 O A:HOH3028 4.7 23.1 0.5 CG A:LEU12 5.0 6.2 0.9 C A:SER8 5.0 6.0 1.0

K.Suto, M.Furuichi, E.Nishimoto, K.Meno, K.Horii, H.Mizuno. Crystal Structure of Bitter Gourd Trypsin Inhibitor To Be Published.