Sodium in PDB 3onf: Crystal Structure of Lupinus Luteus S-Adenosyl-L-Homocysteine Hydrolase in Complex with Cordycepin

All present enzymatic activity of Crystal Structure of Lupinus Luteus S-Adenosyl-L-Homocysteine Hydrolase in Complex with Cordycepin:
3.3.1.1;

The structure of Crystal Structure of Lupinus Luteus S-Adenosyl-L-Homocysteine Hydrolase in Complex with Cordycepin, PDB code: 3onf was solved by K.Brzezinski, M.Jaskolski, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.00
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	122.623, 122.623, 126.622, 90.00, 90.00, 90.00
R / Rfree (%)	15.6 / 20.1

The binding sites of Sodium atom in the Crystal Structure of Lupinus Luteus S-Adenosyl-L-Homocysteine Hydrolase in Complex with Cordycepin (pdb code 3onf). 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 Lupinus Luteus S-Adenosyl-L-Homocysteine Hydrolase in Complex with Cordycepin, PDB code: 3onf:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Lupinus Luteus S-Adenosyl-L-Homocysteine Hydrolase in Complex with Cordycepin


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 Lupinus Luteus S-Adenosyl-L-Homocysteine Hydrolase in Complex with Cordycepin within 5.0Å range: probe atom residue distance (Å) B Occ A:Na507 b:29.2 occ:1.00 O A:HOH783 2.4 29.4 1.0 O A:THR402 2.5 12.9 1.0 O A:HOH554 2.6 20.2 1.0 OG1 A:THR402 2.7 15.4 1.0 O A:HIS404 2.8 14.0 1.0 CB A:THR402 3.3 14.3 1.0 C A:THR402 3.3 13.2 1.0 OE1 A:GLN66 3.4 17.6 1.0 O A:GLY403 3.5 11.9 1.0 C A:HIS404 3.6 12.9 1.0 CD A:GLN66 3.8 16.8 1.0 NE2 A:GLN66 3.8 12.3 1.0 C A:GLY403 3.9 13.0 1.0 N6 A:3AD504 4.0 10.6 1.0 CA A:THR402 4.0 14.3 1.0 CA A:PRO405 4.1 13.1 1.0 N A:PRO405 4.2 12.4 1.0 N A:GLY403 4.2 13.2 1.0 N A:HIS404 4.3 12.9 1.0 O A:HOH784 4.5 26.6 1.0 CA A:GLY403 4.5 13.5 1.0 CA A:HIS404 4.6 13.2 1.0 CG2 A:THR402 4.7 15.2 1.0 C A:PRO405 4.9 13.4 1.0 CG A:GLN66 4.9 14.4 1.0 O A:HOH578 4.9 17.5 1.0 OE1 A:GLN92 5.0 18.7 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Lupinus Luteus S-Adenosyl-L-Homocysteine Hydrolase in Complex with Cordycepin


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 Lupinus Luteus S-Adenosyl-L-Homocysteine Hydrolase in Complex with Cordycepin within 5.0Å range: probe atom residue distance (Å) B Occ B:Na506 b:28.1 occ:1.00 O B:HOH605 2.5 18.4 1.0 O B:THR402 2.6 12.1 1.0 O B:HIS404 2.6 13.8 1.0 O B:HOH489 2.7 32.3 1.0 OG1 B:THR402 2.7 17.0 1.0 O B:GLY403 3.2 14.0 1.0 C B:THR402 3.4 13.6 1.0 CB B:THR402 3.4 15.3 1.0 C B:HIS404 3.4 13.5 1.0 OE1 B:GLN66 3.6 18.4 1.0 C B:GLY403 3.7 13.5 1.0 CD B:GLN66 3.9 17.0 1.0 NE2 B:GLN66 3.9 12.6 1.0 CA B:PRO405 4.0 12.8 1.0 N6 B:3AD505 4.0 16.6 1.0 N B:PRO405 4.1 12.3 1.0 CA B:THR402 4.1 13.9 1.0 N B:HIS404 4.2 14.0 1.0 N B:GLY403 4.2 13.5 1.0 CA B:GLY403 4.4 13.3 1.0 CA B:HIS404 4.4 14.2 1.0 O B:HOH797 4.6 22.3 1.0 O B:HOH606 4.6 18.9 1.0 CG2 B:THR402 4.8 14.7 1.0 C B:PRO405 4.8 13.6 1.0 O B:HOH529 4.8 14.4 1.0 CG B:GLN66 5.0 11.4 1.0

K.Brzezinski, Z.Dauter, M.Jaskolski. High-Resolution Structures of Complexes of Plant S-Adenosyl-L-Homocysteine Hydrolase (Lupinus Luteus). Acta Crystallogr.,Sect.D V. 68 218 2012.
ISSN: ISSN 0907-4449
PubMed: 22349223
DOI: 10.1107/S0907444911055090