Sodium in PDB 1mly: Crystal Structure of 7,8-Diaminopelargonic Acid Synthase in Complex with the Cis Isomer of Amiclenomycin

All present enzymatic activity of Crystal Structure of 7,8-Diaminopelargonic Acid Synthase in Complex with the Cis Isomer of Amiclenomycin:
2.6.1.62;

The structure of Crystal Structure of 7,8-Diaminopelargonic Acid Synthase in Complex with the Cis Isomer of Amiclenomycin, PDB code: 1mly was solved by J.Sandmark, S.Mann, A.Marquet, G.Schneider, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.81
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	128.655, 56.073, 116.174, 90.00, 109.86, 90.00
R / Rfree (%)	19.4 / 22

The binding sites of Sodium atom in the Crystal Structure of 7,8-Diaminopelargonic Acid Synthase in Complex with the Cis Isomer of Amiclenomycin (pdb code 1mly). 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 the Cis Isomer of Amiclenomycin, PDB code: 1mly:
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 the Cis Isomer of Amiclenomycin


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 the Cis Isomer of Amiclenomycin within 5.0Å range: probe atom residue distance (Å) B Occ A:Na702 b:12.1 occ:1.00 O A:VAL96 2.2 20.0 1.0 O A:LEU103 2.3 23.4 1.0 O A:HOH774 2.4 28.6 1.0 O A:PRO100 2.6 24.4 1.0 OG1 A:THR99 2.6 23.7 1.0 O A:THR99 2.9 24.1 1.0 C A:VAL96 3.2 21.1 1.0 C A:LEU103 3.4 22.4 1.0 C A:THR99 3.4 24.0 1.0 C A:PRO100 3.4 24.9 1.0 CA A:VAL96 3.6 20.9 1.0 CB A:THR99 3.7 23.4 1.0 O A:HOH892 3.8 45.4 1.0 CG1 A:VAL96 3.9 21.5 1.0 CA A:THR99 4.0 23.6 1.0 CB A:LEU103 4.0 23.1 1.0 CA A:LEU103 4.0 22.9 1.0 O A:GLN101 4.0 24.1 1.0 CA A:GLN101 4.0 24.9 1.0 N A:GLN101 4.1 25.1 1.0 N A:LEU103 4.1 23.4 1.0 N A:PRO100 4.1 24.6 1.0 C A:GLN101 4.1 24.5 1.0 N A:THR99 4.2 23.6 1.0 O A:LEU95 4.3 20.8 1.0 CA A:PRO100 4.3 24.5 1.0 CB A:VAL96 4.4 21.3 1.0 N A:GLU104 4.4 22.2 1.0 O A:HOH790 4.4 33.5 1.0 N A:ALA97 4.5 21.4 1.0 CA A:GLU104 4.6 22.2 1.0 OE1 A:GLN101 4.7 36.9 0.0 N A:VAL96 4.8 20.9 1.0 N A:PRO102 4.9 24.4 1.0 CG2 A:THR99 4.9 22.9 1.0 CD2 A:LEU287 5.0 18.5 1.0 C A:PRO102 5.0 23.7 1.0 CA A:ALA97 5.0 22.1 1.0 C A:ALA97 5.0 22.9 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of 7,8-Diaminopelargonic Acid Synthase in Complex with the Cis Isomer of Amiclenomycin


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 the Cis Isomer of Amiclenomycin within 5.0Å range: probe atom residue distance (Å) B Occ B:Na701 b:15.1 occ:1.00 O B:VAL96 2.3 23.0 1.0 O B:LEU103 2.4 26.9 1.0 O B:HOH880 2.5 31.6 1.0 OG1 B:THR99 2.6 24.4 1.0 O B:PRO100 2.6 30.1 1.0 O B:THR99 2.7 26.8 1.0 C B:THR99 3.1 26.9 1.0 C B:VAL96 3.3 22.1 1.0 C B:PRO100 3.4 30.0 1.0 C B:LEU103 3.5 26.8 1.0 CB B:THR99 3.6 25.8 1.0 CA B:THR99 3.7 25.8 1.0 CA B:VAL96 3.8 21.5 1.0 N B:PRO100 3.9 28.1 1.0 N B:THR99 3.9 25.5 1.0 CB B:LEU103 4.0 27.3 1.0 CA B:LEU103 4.1 27.4 1.0 N B:LEU103 4.1 28.3 1.0 O B:GLN101 4.1 31.6 1.0 O B:HOH923 4.2 59.2 1.0 CG1 B:VAL96 4.2 22.6 1.0 N B:GLN101 4.2 30.9 1.0 CA B:PRO100 4.2 28.9 1.0 CA B:GLN101 4.3 31.8 1.0 C B:GLN101 4.3 31.1 1.0 O B:LEU95 4.3 20.2 1.0 N B:ALA97 4.5 23.1 1.0 CB B:VAL96 4.6 21.5 1.0 N B:GLU104 4.6 26.1 1.0 CG2 B:THR99 4.9 25.6 1.0 CA B:GLU104 4.9 25.8 1.0 C B:ALA97 4.9 23.9 1.0 N B:VAL96 4.9 20.8 1.0 CA B:ALA97 5.0 23.4 1.0 CD B:PRO100 5.0 28.0 1.0

J.Sandmark, S.Mann, A.Marquet, G.Schneider. Structural Basis For the Inhibition of the Biosynthesis of Biotin By the Antibiotic Amiclenomycin J.Biol.Chem. V. 277 43352 2002.
ISSN: ISSN 0021-9258
PubMed: 12218056
DOI: 10.1074/JBC.M207239200