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

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

The structure of Crystal Structure of Lupinus Luteus S-Adenosyl-L-Homocysteine Hydrolase in Complex with Adenosine, PDB code: 3ond 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)	20.00 / 1.17
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	122.417, 122.417, 126.571, 90.00, 90.00, 90.00
R / Rfree (%)	12.8 / 15.9

The binding sites of Sodium atom in the Crystal Structure of Lupinus Luteus S-Adenosyl-L-Homocysteine Hydrolase in Complex with Adenosine (pdb code 3ond). 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 Adenosine, PDB code: 3ond:
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 Adenosine


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 Adenosine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na509 b:17.4 occ:1.00 O A:HOH607 2.3 17.1 1.0 O A:THR402 2.4 11.2 1.0 O A:HOH765 2.5 17.2 1.0 OG1 A:THR402 2.5 12.0 1.0 O A:HIS404 2.5 10.1 1.0 O A:GLY403 2.8 9.8 1.0 C A:THR402 3.1 9.7 1.0 C A:HIS404 3.3 9.3 1.0 CB A:THR402 3.3 11.2 1.0 C A:GLY403 3.3 8.8 1.0 CA A:THR402 3.8 10.0 1.0 OE1 A:GLN66 3.8 11.0 1.0 N A:PRO405 3.9 8.9 1.0 N A:GLY403 3.9 9.8 1.0 N A:HIS404 3.9 9.2 1.0 CA A:PRO405 4.0 9.8 1.0 N6 A:ADN506 4.1 9.8 1.0 CA A:GLY403 4.1 10.4 1.0 CA A:HIS404 4.2 9.7 1.0 CD A:GLN66 4.2 10.2 1.0 NE2 A:GLN66 4.3 12.2 1.0 O A:HOH535 4.4 11.4 1.0 O A:HOH570 4.4 11.2 1.0 CG2 A:THR402 4.6 11.8 1.0 N A:THR402 4.7 9.6 1.0 C A:PRO405 4.9 9.2 1.0 O A:HOH825 5.0 19.8 1.0

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


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 Adenosine within 5.0Å range: probe atom residue distance (Å) B Occ B:Na508 b:18.1 occ:1.00 O B:HOH603 2.3 17.4 1.0 O B:THR402 2.4 10.7 1.0 O B:HOH865 2.5 21.2 1.0 OG1 B:THR402 2.5 12.6 1.0 O B:HIS404 2.5 10.1 1.0 O B:GLY403 2.8 9.9 1.0 C B:THR402 3.1 10.1 1.0 C B:HIS404 3.3 9.1 1.0 CB B:THR402 3.3 10.7 1.0 C B:GLY403 3.3 8.7 1.0 CA B:THR402 3.8 9.4 1.0 OE1 B:GLN66 3.8 11.5 1.0 N B:GLY403 3.9 9.5 1.0 N B:PRO405 3.9 9.2 1.0 N B:HIS404 3.9 9.2 1.0 CA B:PRO405 4.0 9.9 1.0 CA B:GLY403 4.0 9.9 1.0 N6 B:ADN507 4.0 10.0 1.0 CA B:HIS404 4.2 9.7 1.0 CD B:GLN66 4.2 10.8 1.0 NE2 B:GLN66 4.2 12.7 1.0 O B:HOH575 4.4 11.1 1.0 O B:HOH494 4.4 11.4 1.0 CG2 B:THR402 4.6 12.6 1.0 N B:THR402 4.7 9.8 1.0 C B:PRO405 4.9 9.4 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