Sodium in PDB 1s0a: Crystal Structure of the Y17F Mutant of 7,8-Diaminopelargonic Acid Synthase

All present enzymatic activity of Crystal Structure of the Y17F Mutant of 7,8-Diaminopelargonic Acid Synthase:
2.6.1.62;

The structure of Crystal Structure of the Y17F Mutant of 7,8-Diaminopelargonic Acid Synthase, PDB code: 1s0a 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)	19.92 / 1.71
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	58.508, 55.659, 121.396, 90.00, 97.04, 90.00
R / Rfree (%)	18.6 / 20.6

The binding sites of Sodium atom in the Crystal Structure of the Y17F Mutant of 7,8-Diaminopelargonic Acid Synthase (pdb code 1s0a). 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 Y17F Mutant of 7,8-Diaminopelargonic Acid Synthase, PDB code: 1s0a:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of the Y17F 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 Y17F Mutant of 7,8-Diaminopelargonic Acid Synthase within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1501 b:10.4 occ:1.00 O A:VAL96 2.2 17.4 1.0 O A:HOH1580 2.4 23.6 1.0 O A:LEU103 2.5 19.2 1.0 OG1 A:THR99 2.6 20.1 1.0 O A:PRO100 2.7 22.9 1.0 O A:THR99 2.7 21.6 1.0 C A:THR99 3.2 21.2 1.0 C A:VAL96 3.3 17.9 1.0 C A:PRO100 3.5 22.9 1.0 C A:LEU103 3.5 19.0 1.0 CB A:THR99 3.6 20.1 1.0 CA A:VAL96 3.8 17.6 1.0 CA A:THR99 3.8 20.5 1.0 O A:HOH1653 3.9 41.2 1.0 N A:PRO100 3.9 21.9 1.0 N A:THR99 4.0 20.4 1.0 CB A:LEU103 4.0 19.2 1.0 CA A:LEU103 4.1 19.3 1.0 O A:GLN101 4.1 23.3 1.0 N A:LEU103 4.1 20.0 1.0 CG1 A:VAL96 4.2 18.3 1.0 N A:GLN101 4.2 23.1 1.0 CA A:PRO100 4.3 22.4 1.0 C A:GLN101 4.3 23.1 1.0 O A:LEU95 4.3 17.1 1.0 CA A:GLN101 4.3 23.6 1.0 O A:HOH1609 4.4 32.1 1.0 N A:ALA97 4.5 18.2 1.0 CB A:VAL96 4.6 17.9 1.0 N A:GLU104 4.6 18.9 1.0 CG2 A:THR99 4.9 19.2 1.0 CA A:GLU104 4.9 19.2 1.0 N A:VAL96 4.9 17.9 1.0 C A:ALA97 4.9 19.5 1.0 CA A:ALA97 5.0 19.1 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of the Y17F 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 Y17F Mutant of 7,8-Diaminopelargonic Acid Synthase within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1502 b:9.4 occ:1.00 O B:VAL96 2.3 19.4 1.0 O B:LEU103 2.3 19.1 1.0 O B:HOH1583 2.4 21.2 1.0 O B:PRO100 2.5 24.2 1.0 O B:THR99 2.7 22.4 1.0 OG1 B:THR99 2.7 21.4 1.0 C B:THR99 3.2 22.4 1.0 C B:VAL96 3.3 19.4 1.0 C B:PRO100 3.4 24.2 1.0 C B:LEU103 3.4 18.7 1.0 CB B:THR99 3.7 21.7 1.0 CB B:LEU103 3.8 19.3 1.0 CA B:VAL96 3.8 18.8 1.0 CA B:THR99 3.9 22.0 1.0 CA B:LEU103 3.9 19.5 1.0 N B:LEU103 4.0 20.3 1.0 O B:HOH1653 4.0 34.5 1.0 N B:PRO100 4.0 23.2 1.0 O B:GLN101 4.0 24.6 1.0 N B:THR99 4.1 21.6 1.0 CG1 B:VAL96 4.1 18.5 1.0 N B:GLN101 4.1 24.9 1.0 CA B:GLN101 4.2 25.5 1.0 C B:GLN101 4.2 24.5 1.0 O B:HOH1612 4.2 48.9 1.0 CA B:PRO100 4.3 23.6 1.0 O B:LEU95 4.4 18.3 1.0 N B:GLU104 4.5 18.6 1.0 N B:ALA97 4.5 20.0 1.0 CB B:VAL96 4.6 18.4 1.0 CA B:GLU104 4.8 18.6 1.0 C B:ALA97 4.9 21.1 1.0 CA B:ALA97 4.9 20.6 1.0 N B:PRO102 5.0 23.7 1.0 N B:VAL96 5.0 18.8 1.0 CG2 B:THR99 5.0 21.7 1.0 C B:PRO102 5.0 21.2 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