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

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

The structure of Crystal Structure of 7,8-Diaminopelargonic Acid Synthase in Complex with the Trans-Isomer of Amiclenomycin., PDB code: 1mlz 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)	22.36 / 2.15
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	128.034, 55.960, 116.001, 90.00, 109.65, 90.00
R / Rfree (%)	20.5 / 24

The binding sites of Sodium atom in the Crystal Structure of 7,8-Diaminopelargonic Acid Synthase in Complex with the Trans-Isomer of Amiclenomycin. (pdb code 1mlz). 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 Trans-Isomer of Amiclenomycin., PDB code: 1mlz:
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 Trans-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 Trans-Isomer of Amiclenomycin. within 5.0Å range: probe atom residue distance (Å) B Occ A:Na501 b:20.9 occ:1.00 O A:LEU103 2.2 32.0 1.0 O A:VAL96 2.4 29.2 1.0 O A:PRO100 2.5 32.3 1.0 OG1 A:THR99 2.8 33.5 1.0 O A:THR99 2.9 33.8 1.0 C A:LEU103 3.3 31.2 1.0 C A:THR99 3.4 33.4 1.0 C A:VAL96 3.4 30.7 1.0 C A:PRO100 3.4 33.0 1.0 CB A:THR99 3.7 32.8 1.0 O A:GLN101 3.8 32.8 1.0 CA A:VAL96 3.8 29.9 1.0 CB A:LEU103 3.9 31.5 1.0 CA A:LEU103 3.9 31.6 1.0 CA A:THR99 3.9 32.9 1.0 N A:LEU103 4.0 32.2 1.0 C A:GLN101 4.0 32.5 1.0 CG1 A:VAL96 4.1 30.4 1.0 CA A:GLN101 4.1 32.2 1.0 N A:PRO100 4.1 33.3 1.0 N A:GLN101 4.1 32.3 1.0 N A:THR99 4.2 32.5 1.0 N A:GLU104 4.3 31.4 1.0 CA A:PRO100 4.4 33.3 1.0 O A:LEU95 4.5 27.8 1.0 CA A:GLU104 4.5 31.9 1.0 CB A:VAL96 4.6 30.5 1.0 N A:ALA97 4.6 31.3 1.0 O A:HOH1085 4.8 47.2 1.0 N A:PRO102 4.9 32.3 1.0 C A:PRO102 4.9 32.0 1.0 CB A:GLU104 4.9 32.9 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of 7,8-Diaminopelargonic Acid Synthase in Complex with the Trans-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 Trans-Isomer of Amiclenomycin. within 5.0Å range: probe atom residue distance (Å) B Occ B:Na502 b:21.8 occ:1.00 O B:LEU103 2.2 35.2 1.0 O B:VAL96 2.3 29.2 1.0 OG1 B:THR99 2.6 29.2 1.0 O B:HOH2057 2.6 39.5 1.0 O B:PRO100 2.6 37.6 1.0 O B:THR99 2.9 34.4 1.0 C B:VAL96 3.3 29.3 1.0 C B:LEU103 3.3 35.1 1.0 C B:THR99 3.4 34.2 1.0 C B:PRO100 3.5 37.4 1.0 CA B:VAL96 3.6 28.6 1.0 CB B:THR99 3.7 32.5 1.0 CB B:LEU103 3.8 36.0 1.0 CA B:LEU103 3.9 35.7 1.0 CA B:THR99 3.9 32.5 1.0 N B:LEU103 4.0 35.9 1.0 N B:THR99 4.0 31.6 1.0 CG1 B:VAL96 4.1 28.6 1.0 N B:PRO100 4.1 35.8 1.0 N B:GLN101 4.2 37.6 1.0 O B:GLN101 4.2 37.7 1.0 CA B:GLN101 4.2 37.5 1.0 O B:HOH2081 4.3 54.1 1.0 O B:LEU95 4.3 27.7 1.0 C B:GLN101 4.3 37.4 1.0 N B:GLU104 4.4 34.1 1.0 CA B:PRO100 4.4 36.7 1.0 CB B:VAL96 4.4 28.8 1.0 N B:ALA97 4.5 30.5 1.0 CA B:GLU104 4.7 34.0 1.0 N B:VAL96 4.8 28.4 1.0 CG2 B:THR99 4.9 33.1 1.0 CD2 B:LEU287 4.9 28.6 1.0 C B:ALA97 5.0 31.4 1.0 CA B:ALA97 5.0 30.9 1.0 C B:LEU95 5.0 27.5 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