Sodium in PDB 1qj3: Crystal Structure of 7,8-Diaminopelargonic Acid Synthase in Complex with 7-Keto-8-Aminopelargonic Acid

All present enzymatic activity of Crystal Structure of 7,8-Diaminopelargonic Acid Synthase in Complex with 7-Keto-8-Aminopelargonic Acid:
2.6.1.62;

The structure of Crystal Structure of 7,8-Diaminopelargonic Acid Synthase in Complex with 7-Keto-8-Aminopelargonic Acid, PDB code: 1qj3 was solved by H.Kaeck, J.Sandmark, K.J.Gibson, Y.Lindqvist, G.Schneider, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.70
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	57.970, 55.940, 120.840, 90.00, 95.69, 90.00
R / Rfree (%)	22.5 / 27.9

The binding sites of Sodium atom in the Crystal Structure of 7,8-Diaminopelargonic Acid Synthase in Complex with 7-Keto-8-Aminopelargonic Acid (pdb code 1qj3). 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 7,8-Diaminopelargonic Acid Synthase in Complex with 7-Keto-8-Aminopelargonic Acid, PDB code: 1qj3:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of 7,8-Diaminopelargonic Acid Synthase in Complex with 7-Keto-8-Aminopelargonic Acid


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 7,8-Diaminopelargonic Acid Synthase in Complex with 7-Keto-8-Aminopelargonic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1431 b:21.7 occ:1.00 O A:PRO100 2.4 53.0 1.0 O A:VAL96 2.4 35.6 1.0 OG1 A:THR99 2.5 53.6 1.0 O A:THR99 2.6 44.5 1.0 O A:LEU103 2.7 44.0 1.0 C A:THR99 3.1 46.7 1.0 C A:PRO100 3.2 51.0 1.0 C A:VAL96 3.5 39.4 1.0 CB A:THR99 3.6 48.7 1.0 C A:LEU103 3.6 43.1 1.0 CA A:THR99 3.8 47.5 1.0 O A:GLN101 3.8 47.1 1.0 N A:PRO100 3.8 47.1 1.0 CB A:LEU103 3.9 49.3 1.0 N A:GLN101 3.9 51.6 1.0 CA A:GLN101 4.0 51.4 1.0 CA A:VAL96 4.0 41.2 1.0 N A:LEU103 4.0 45.0 1.0 CA A:LEU103 4.0 44.9 1.0 N A:THR99 4.0 47.3 1.0 C A:GLN101 4.1 49.5 1.0 CA A:PRO100 4.1 49.3 1.0 CG1 A:VAL96 4.4 30.4 1.0 O A:LEU95 4.6 44.6 1.0 N A:ALA97 4.6 35.4 1.0 N A:GLU104 4.7 42.1 1.0 CB A:VAL96 4.8 43.9 1.0 CG2 A:THR99 4.8 47.3 1.0 N A:PRO102 4.9 46.6 1.0 CD A:PRO100 5.0 48.3 1.0 CG A:LEU103 5.0 49.0 1.0 CA A:GLU104 5.0 42.2 1.0 C A:PRO102 5.0 45.7 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of 7,8-Diaminopelargonic Acid Synthase in Complex with 7-Keto-8-Aminopelargonic Acid


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 7,8-Diaminopelargonic Acid Synthase in Complex with 7-Keto-8-Aminopelargonic Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1431 b:42.5 occ:1.00 O B:VAL96 2.3 35.7 1.0 OG1 B:THR99 2.3 53.4 1.0 O B:LEU103 2.6 43.8 1.0 O B:PRO100 2.7 53.0 1.0 O B:THR99 2.7 44.5 1.0 C B:VAL96 3.3 39.4 1.0 C B:THR99 3.3 46.6 1.0 C B:LEU103 3.5 43.1 1.0 C B:PRO100 3.5 50.9 1.0 CB B:THR99 3.5 48.8 1.0 CA B:VAL96 3.7 41.2 1.0 CA B:THR99 3.8 47.5 1.0 CB B:LEU103 3.9 49.3 1.0 CA B:LEU103 4.0 44.9 1.0 N B:THR99 4.0 47.6 1.0 N B:PRO100 4.0 47.0 1.0 O B:GLN101 4.1 47.1 1.0 N B:LEU103 4.1 45.0 1.0 N B:GLN101 4.2 51.8 1.0 CG1 B:VAL96 4.2 30.3 1.0 CA B:GLN101 4.3 51.5 1.0 O B:LEU95 4.3 44.8 1.0 C B:GLN101 4.3 49.5 1.0 CA B:PRO100 4.4 49.2 1.0 N B:ALA97 4.4 35.3 1.0 CB B:VAL96 4.5 44.0 1.0 N B:GLU104 4.5 42.2 1.0 CG2 B:THR99 4.7 47.4 1.0 CA B:GLU104 4.8 42.2 1.0 N B:VAL96 4.8 43.7 1.0

H.Kack, J.Sandmark, K.J.Gibson, G.Schneider, Y.Lindqvist. Crystal Structure of Diaminopelargonic Acid Synthase; Evolutionary Relationships Between Pyridoxal-5'-Phosphate Dependent Enzymes J.Mol.Biol. V. 291 857 1999.
ISSN: ISSN 0022-2836
PubMed: 10452893
DOI: 10.1006/JMBI.1999.2997