Sodium in PDB 1s08: Crystal Structure of the D147N Mutant of 7,8-Diaminopelargonic Acid Synthase

All present enzymatic activity of Crystal Structure of the D147N Mutant of 7,8-Diaminopelargonic Acid Synthase:
2.6.1.62;

The structure of Crystal Structure of the D147N Mutant of 7,8-Diaminopelargonic Acid Synthase, PDB code: 1s08 was solved by J.Sandmark, A.C.Eliot, K.Famm, G.Schneider, J.F.Kirsch, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	58.080, 56.527, 120.993, 90.00, 96.32, 90.00
R / Rfree (%)	20.2 / 22.7

The binding sites of Sodium atom in the Crystal Structure of the D147N Mutant of 7,8-Diaminopelargonic Acid Synthase (pdb code 1s08). 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 D147N Mutant of 7,8-Diaminopelargonic Acid Synthase, PDB code: 1s08:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of the D147N 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 D147N Mutant of 7,8-Diaminopelargonic Acid Synthase within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1501 b:15.2 occ:1.00 O A:VAL96 2.3 20.0 1.0 O A:HOH1563 2.4 27.9 1.0 O A:LEU103 2.5 24.2 1.0 OG1 A:THR99 2.6 21.7 1.0 O A:PRO100 2.8 26.6 1.0 O A:THR99 2.9 25.5 1.0 C A:VAL96 3.3 21.5 1.0 C A:THR99 3.4 25.2 1.0 C A:PRO100 3.5 26.7 1.0 C A:LEU103 3.5 24.7 1.0 CB A:THR99 3.7 24.9 1.0 CA A:VAL96 3.7 21.3 1.0 O A:HOH1589 3.8 55.4 1.0 CA A:THR99 3.9 24.4 1.0 N A:THR99 4.1 24.8 1.0 O A:GLN101 4.1 29.2 1.0 N A:PRO100 4.1 25.8 1.0 CG1 A:VAL96 4.1 22.2 1.0 CB A:LEU103 4.2 24.5 1.0 CA A:LEU103 4.2 24.9 1.0 N A:GLN101 4.2 27.1 1.0 N A:LEU103 4.2 25.3 1.0 CA A:GLN101 4.3 28.1 1.0 C A:GLN101 4.3 28.1 1.0 O A:LEU95 4.3 20.8 1.0 CA A:PRO100 4.4 26.0 1.0 N A:ALA97 4.5 22.3 1.0 CB A:VAL96 4.5 21.5 1.0 O A:HOH1591 4.5 38.8 1.0 N A:GLU104 4.6 24.9 1.0 CA A:GLU104 4.8 25.3 1.0 N A:VAL96 4.9 21.6 1.0 CG2 A:THR99 4.9 23.6 1.0 CA A:ALA97 5.0 23.2 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of the D147N 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 D147N Mutant of 7,8-Diaminopelargonic Acid Synthase within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1502 b:15.4 occ:1.00 O B:VAL96 2.2 24.0 1.0 O B:LEU103 2.4 26.8 1.0 O B:HOH1559 2.4 31.5 1.0 O B:PRO100 2.5 32.4 1.0 OG1 B:THR99 2.7 27.1 1.0 O B:THR99 2.8 30.6 1.0 C B:THR99 3.3 29.9 1.0 C B:VAL96 3.3 25.1 1.0 C B:PRO100 3.3 32.3 1.0 C B:LEU103 3.5 26.8 1.0 CB B:THR99 3.7 28.5 1.0 CA B:VAL96 3.8 24.2 1.0 CA B:THR99 3.9 29.1 1.0 N B:PRO100 3.9 30.8 1.0 CB B:LEU103 4.0 26.9 1.0 O B:GLN101 4.0 33.0 1.0 N B:THR99 4.0 29.0 1.0 CG1 B:VAL96 4.1 23.9 1.0 CA B:LEU103 4.1 27.5 1.0 N B:LEU103 4.1 28.4 1.0 N B:GLN101 4.1 32.9 1.0 CA B:PRO100 4.2 31.3 1.0 CA B:GLN101 4.3 33.6 1.0 C B:GLN101 4.3 32.6 1.0 O B:LEU95 4.4 24.0 1.0 N B:ALA97 4.5 26.1 1.0 N B:GLU104 4.5 26.4 1.0 CB B:VAL96 4.6 23.8 1.0 CA B:GLU104 4.8 26.8 1.0 C B:ALA97 4.8 28.1 1.0 CA B:ALA97 4.9 27.4 1.0 CG2 B:THR99 4.9 28.2 1.0 N B:VAL96 5.0 24.1 1.0

J.Sandmark, A.C.Eliot, K.Famm, G.Schneider, J.F.Kirsch. Conserved and Nonconserved Residues in the Substrate Binding Site of 7,8-Diaminopelargonic Acid Synthase From Escherichia Coli Are Essential For Catalysis. Biochemistry V. 43 1213 2004.
ISSN: ISSN 0006-2960
PubMed: 14756557
DOI: 10.1021/BI0358059