Sodium in PDB 4xoj: Structure of Bovine Trypsin in Complex with Analogues of Sunflower Inhibitor 1 (Sfti-1)

All present enzymatic activity of Structure of Bovine Trypsin in Complex with Analogues of Sunflower Inhibitor 1 (Sfti-1):
3.4.21.4;

The structure of Structure of Bovine Trypsin in Complex with Analogues of Sunflower Inhibitor 1 (Sfti-1), PDB code: 4xoj was solved by P.Golik, S.Malicki, P.Grudnik, N.Karna, D.Debowski, A.Legowska, B.Wladyka, A.Gitlin, K.Brzozowski, G.Dubin, K.Rolka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.60 / 0.91
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	62.390, 63.050, 69.170, 90.00, 90.00, 90.00
R / Rfree (%)	10.3 / 11.4

The structure of Structure of Bovine Trypsin in Complex with Analogues of Sunflower Inhibitor 1 (Sfti-1) also contains other interesting chemical elements:

Calcium

(Ca)

1 atom

The binding sites of Sodium atom in the Structure of Bovine Trypsin in Complex with Analogues of Sunflower Inhibitor 1 (Sfti-1) (pdb code 4xoj). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Structure of Bovine Trypsin in Complex with Analogues of Sunflower Inhibitor 1 (Sfti-1), PDB code: 4xoj:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Structure of Bovine Trypsin in Complex with Analogues of Sunflower Inhibitor 1 (Sfti-1)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Bovine Trypsin in Complex with Analogues of Sunflower Inhibitor 1 (Sfti-1) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na310 b:33.4 occ:1.00 N A:LYS215 2.9 11.9 1.0 OE1 A:GLN214 3.4 23.8 1.0 CA A:GLN214 3.5 11.7 1.0 CB A:LYS215 3.5 11.6 0.5 CG A:LYS215 3.6 17.9 0.5 C A:GLN214 3.7 10.9 1.0 CB A:LYS215 3.7 17.3 0.5 CA A:LYS215 3.8 11.4 0.5 CA A:LYS215 3.8 12.4 0.5 CD A:GLN214 4.0 17.7 1.0 CB A:GLN214 4.0 13.1 1.0 O A:HOH599 4.2 24.3 1.0 NE2 A:GLN214 4.5 19.1 1.0 O A:ALA213 4.5 11.6 1.0 CG A:GLN214 4.6 15.2 1.0 O A:HOH650 4.7 86.7 0.5 N A:GLN214 4.8 10.7 1.0 O A:GLN214 4.9 10.9 1.0 C A:LYS215 4.9 11.2 1.0 O A:LYS215 4.9 12.0 1.0 CG A:LYS215 5.0 17.1 0.5

Sodium binding site 2 out of 3 in the Structure of Bovine Trypsin in Complex with Analogues of Sunflower Inhibitor 1 (Sfti-1)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of Bovine Trypsin in Complex with Analogues of Sunflower Inhibitor 1 (Sfti-1) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na311 b:27.6 occ:1.00 O B:ILE7 2.6 16.1 1.0 O A:HOH476 2.6 17.6 0.7 O A:HOH476 2.7 14.3 0.3 NZ A:LYS58 2.7 9.1 0.5 O A:HOH402 2.8 14.9 0.8 NZ A:LYS58 2.8 9.6 0.5 OH A:TYR37 3.2 9.9 1.0 CE A:LYS58 3.3 8.2 0.5 CD B:PRO8 3.6 19.6 1.0 O A:HOH714 3.6 25.0 1.0 CE A:LYS58 3.6 9.9 0.5 O B:HOH109 3.7 16.2 0.5 C B:ILE7 3.7 12.2 1.0 CB A:PHE39 3.8 8.5 1.0 CD A:LYS58 4.0 10.1 0.5 CZ A:TYR37 4.0 8.9 1.0 CE2 A:TYR37 4.0 8.9 1.0 CG A:PHE39 4.1 7.9 1.0 N B:PRO8 4.1 13.6 1.0 O A:HOH715 4.3 44.4 1.0 CD1 A:PHE39 4.3 8.9 1.0 O B:HOH103 4.5 19.4 1.0 O A:HOH713 4.6 17.6 1.0 CD A:LYS58 4.8 7.7 0.5 CD2 A:PHE39 4.9 8.3 1.0 O B:HOH102 4.9 23.5 1.0 CG B:PRO8 4.9 19.4 1.0 CA B:ILE7 4.9 10.2 0.7 CA B:ILE7 5.0 10.5 0.3

Sodium binding site 3 out of 3 in the Structure of Bovine Trypsin in Complex with Analogues of Sunflower Inhibitor 1 (Sfti-1)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of Bovine Trypsin in Complex with Analogues of Sunflower Inhibitor 1 (Sfti-1) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na312 b:33.5 occ:1.00 O A:HOH462 2.4 35.4 1.0 O A:HOH570 2.8 17.4 1.0 O2 A:SO4301 3.1 26.7 0.8 O1 A:SO4301 3.3 22.8 0.8 S A:SO4301 3.8 11.1 0.8 CG A:GLN233 3.9 9.3 1.0 O3 A:SO4301 4.3 20.2 0.8 O A:HOH550 4.4 14.7 1.0 NE2 A:GLN233 4.5 11.2 1.0 CB A:LYS232 4.5 10.2 0.5 CD A:GLN233 4.6 10.0 1.0 CB A:LYS232 4.7 10.6 0.5 O A:SER229 4.7 9.9 1.0 O A:HOH590 4.9 19.1 1.0 N A:GLN233 4.9 8.7 1.0

N.Karna, A.Legowska, S.Malicki, D.Debowski, P.Golik, A.Gitlin, P.Grudnik, B.Wladyka, K.Brzozowski, G.Dubin, K.Rolka. Investigation of Serine-Proteinase-Catalyzed Peptide Splicing in Analogues of Sunflower Trypsin Inhibitor 1 (Sfti-1). Chembiochem V. 16 2036 2015.
ISSN: ESSN 1439-7633
PubMed: 26212347
DOI: 10.1002/CBIC.201500296