Sodium in PDB 7bnh: Complex Structure at Atomic Resolution of SH3B Domain with Benzoic Acid

All present enzymatic activity of Complex Structure at Atomic Resolution of SH3B Domain with Benzoic Acid:
3.4.24.75;

The structure of Complex Structure at Atomic Resolution of SH3B Domain with Benzoic Acid, PDB code: 7bnh was solved by P.H.Malecki, I.Sabala, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	17.21 / 0.84
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	33.954, 54.781, 51.49, 90, 92.4, 90
R / Rfree (%)	8.5 / 10.1

The binding sites of Sodium atom in the Complex Structure at Atomic Resolution of SH3B Domain with Benzoic Acid (pdb code 7bnh). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Complex Structure at Atomic Resolution of SH3B Domain with Benzoic Acid, PDB code: 7bnh:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Complex Structure at Atomic Resolution of SH3B Domain with Benzoic Acid


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Complex Structure at Atomic Resolution of SH3B Domain with Benzoic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Na506 b:6.6 occ:0.60 OE1 A:GLN455 2.3 5.1 1.0 O A:HOH757 2.4 18.1 1.0 O A:HOH713 2.4 12.1 0.6 O A:HOH746 2.4 11.2 0.7 O A:HOH715 2.4 7.8 1.0 O A:HOH677 2.5 7.6 1.0 HE22 A:GLN455 3.2 5.5 1.0 HZ2 A:LYS480 3.3 38.9 0.3 HZ3 A:LYS480 3.3 48.3 0.7 CD A:GLN455 3.3 4.4 1.0 H A:ASP456 3.5 17.3 1.0 NE2 A:GLN455 3.6 4.9 1.0 O A:HOH731 3.8 7.0 0.3 HZ1 A:LYS480 3.9 16.7 0.7 NZ A:LYS480 4.0 8.9 0.7 NZ A:LYS480 4.1 9.1 0.3 HE2 A:PHE432 4.1 26.9 1.0 O A:HOH718 4.1 7.9 0.7 HZ1 A:LYS480 4.2 34.2 0.3 HZ3 A:LYS480 4.2 15.8 0.3 HZ2 A:LYS480 4.3 51.5 0.7 O A:HOH684 4.3 30.2 1.0 N A:ASP456 4.4 3.9 1.0 O A:HOH659 4.4 14.8 1.0 O A:HOH676 4.4 5.6 1.0 HA A:ASP456 4.5 3.8 1.0 HE21 A:GLN455 4.5 4.1 1.0 HA A:GLN455 4.5 4.0 1.0 O A:HOH731 4.5 6.0 0.7 O A:HOH795 4.5 22.2 0.7 CG A:GLN455 4.7 4.2 1.0 HG3 A:GLN455 4.7 4.3 1.0 O A:HOH612 4.9 27.3 1.0 O A:HOH823 4.9 35.3 1.0 O A:LYS407 4.9 6.3 1.0 HD2 A:LYS480 4.9 1.8 0.3 CE2 A:PHE432 4.9 8.4 1.0 CA A:ASP456 5.0 4.0 1.0

Sodium binding site 2 out of 2 in the Complex Structure at Atomic Resolution of SH3B Domain with Benzoic Acid


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Complex Structure at Atomic Resolution of SH3B Domain with Benzoic Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:Na504 b:11.7 occ:0.45 O B:HOH734 2.3 28.7 1.0 OE1 B:GLN455 2.3 6.8 1.0 O B:HOH720 2.3 39.1 1.0 O B:HOH729 2.5 12.8 1.0 O B:HOH699 2.5 15.2 1.0 O B:HOH738 2.6 37.3 1.0 HE22 B:GLN455 3.1 16.1 1.0 CD B:GLN455 3.3 6.6 1.0 NE2 B:GLN455 3.6 7.1 1.0 H B:ASP456 3.6 4.7 1.0 O B:HOH681 4.0 12.2 1.0 O B:HOH676 4.2 7.8 1.0 HZ3 B:LYS480 4.3 92.8 0.8 HD3 B:LYS480 4.3 37.2 0.2 HE1 B:PHE432 4.4 52.1 1.0 HD3 B:LYS480 4.4 61.2 0.8 HE21 B:GLN455 4.4 6.5 1.0 HA B:GLN455 4.4 3.9 1.0 N B:ASP456 4.5 5.2 1.0 O B:HOH687 4.5 30.5 1.0 O B:HOH747 4.6 24.1 0.5 HD2 B:LYS480 4.7 81.1 0.8 CG B:GLN455 4.7 6.4 1.0 O B:HOH690 4.7 31.8 1.0 HA B:ASP456 4.7 7.9 1.0 HG3 B:GLN455 4.8 7.4 1.0 HD2 B:LYS480 4.9 26.0 0.2 HZ2 B:LYS480 4.9 90.7 0.8 NZ B:LYS480 5.0 25.7 0.8 CD B:LYS480 5.0 21.0 0.8

P.H.Malecki, I.Sabala. Complex Structure of SH3B Domain with Benzoic Acid To Be Published.