Sodium in PDB 1mgv: Crystal Structure of the R391A Mutant of 7,8-Diaminopelargonic Acid Synthase

All present enzymatic activity of Crystal Structure of the R391A Mutant of 7,8-Diaminopelargonic Acid Synthase:
2.6.1.62;

The structure of Crystal Structure of the R391A Mutant of 7,8-Diaminopelargonic Acid Synthase, PDB code: 1mgv was solved by A.C.Eliot, J.Sandmark, G.Schneider, J.F.Kirsch, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.08 / 2.10
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	127.880, 55.899, 116.237, 90.00, 110.06, 90.00
R / Rfree (%)	20.1 / 23.3

The binding sites of Sodium atom in the Crystal Structure of the R391A Mutant of 7,8-Diaminopelargonic Acid Synthase (pdb code 1mgv). 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 the R391A Mutant of 7,8-Diaminopelargonic Acid Synthase, PDB code: 1mgv:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of the R391A Mutant of 7,8-Diaminopelargonic Acid Synthase


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 the R391A Mutant of 7,8-Diaminopelargonic Acid Synthase within 5.0Å range: probe atom residue distance (Å) B Occ A:Na501 b:25.8 occ:1.00 O A:VAL96 2.1 32.0 1.0 O A:THR99 2.4 36.7 1.0 O A:PRO100 2.4 38.9 1.0 OG1 A:THR99 2.7 33.0 1.0 O A:LEU103 2.8 36.8 1.0 C A:THR99 3.1 36.6 1.0 C A:PRO100 3.2 38.6 1.0 C A:VAL96 3.2 33.2 1.0 CB A:THR99 3.7 36.1 1.0 CA A:THR99 3.7 36.0 1.0 CA A:VAL96 3.8 33.1 1.0 N A:PRO100 3.9 37.5 1.0 N A:THR99 3.9 36.0 1.0 C A:LEU103 3.9 37.5 1.0 N A:GLN101 4.0 38.6 1.0 CG1 A:VAL96 4.0 33.3 1.0 O A:GLN101 4.1 38.1 1.0 CA A:GLN101 4.1 38.4 1.0 CA A:PRO100 4.1 38.1 1.0 C A:GLN101 4.3 37.8 1.0 CB A:LEU103 4.3 37.4 1.0 O A:LEU95 4.3 32.9 1.0 N A:ALA97 4.4 33.9 1.0 N A:LEU103 4.4 38.2 1.0 CA A:LEU103 4.5 37.6 1.0 CB A:VAL96 4.6 33.6 1.0 O A:ALA97 4.7 36.8 1.0 C A:ALA97 4.7 35.7 1.0 CA A:ALA97 4.8 34.9 1.0 N A:VAL96 4.9 33.1 1.0 N A:GLU104 4.9 37.4 1.0 CG2 A:THR99 5.0 35.9 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of the R391A Mutant of 7,8-Diaminopelargonic Acid Synthase


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 the R391A Mutant of 7,8-Diaminopelargonic Acid Synthase within 5.0Å range: probe atom residue distance (Å) B Occ B:Na502 b:13.5 occ:1.00 O B:LEU103 2.2 26.0 1.0 O B:PRO100 2.4 29.4 1.0 O B:VAL96 2.5 24.4 1.0 OG1 B:THR99 2.6 23.3 1.0 O B:HOH744 2.7 27.5 1.0 O B:THR99 2.8 26.1 1.0 C B:THR99 3.3 26.2 1.0 C B:LEU103 3.3 26.5 1.0 C B:PRO100 3.3 29.7 1.0 C B:VAL96 3.5 24.1 1.0 CB B:THR99 3.6 24.7 1.0 CB B:LEU103 3.7 25.5 1.0 CA B:LEU103 3.8 26.1 1.0 CA B:VAL96 3.8 24.4 1.0 CA B:THR99 3.9 25.2 1.0 N B:LEU103 3.9 26.9 1.0 N B:PRO100 3.9 27.8 1.0 O B:HOH840 3.9 36.9 1.0 O B:GLN101 4.0 28.6 1.0 N B:THR99 4.1 25.2 1.0 N B:GLN101 4.1 29.9 1.0 CG1 B:VAL96 4.1 24.3 1.0 CA B:PRO100 4.2 28.8 1.0 C B:GLN101 4.2 29.3 1.0 CA B:GLN101 4.2 30.5 1.0 O B:LEU95 4.4 22.0 1.0 N B:GLU104 4.4 26.6 1.0 CB B:VAL96 4.6 24.8 1.0 CA B:GLU104 4.7 27.3 1.0 N B:ALA97 4.7 24.8 1.0 CG2 B:THR99 4.9 25.4 1.0 C B:PRO102 5.0 27.1 1.0 CG B:LEU103 5.0 24.5 1.0 N B:VAL96 5.0 23.6 1.0

A.C.Eliot, J.Sandmark, G.Schneider, J.F.Kirsch. The Dual-Specific Active Site of 7,8-Diaminopelargonic Acid Synthase and the Effect of the R391A Mutation Biochemistry V. 41 12582 2002.
ISSN: ISSN 0006-2960
PubMed: 12379100
DOI: 10.1021/BI026339A