Sodium in PDB 1s07: Crystal Structure of the R253A Mutant of 7,8-Diaminopelargonic Acid Synthase

All present enzymatic activity of Crystal Structure of the R253A Mutant of 7,8-Diaminopelargonic Acid Synthase:
2.6.1.62;

The structure of Crystal Structure of the R253A Mutant of 7,8-Diaminopelargonic Acid Synthase, PDB code: 1s07 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 / 2.42
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 (%)	18.8 / 22.4

The binding sites of Sodium atom in the Crystal Structure of the R253A Mutant of 7,8-Diaminopelargonic Acid Synthase (pdb code 1s07). 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 R253A Mutant of 7,8-Diaminopelargonic Acid Synthase, PDB code: 1s07:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of the R253A 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 R253A Mutant of 7,8-Diaminopelargonic Acid Synthase within 5.0Å range: probe atom residue distance (Å) B Occ A:Na501 b:10.4 occ:1.00 O A:VAL96 2.3 18.6 1.0 O A:HOH595 2.4 34.8 1.0 O A:PRO100 2.5 26.3 1.0 O A:LEU103 2.6 24.5 1.0 O A:THR99 2.7 25.3 1.0 OG1 A:THR99 2.8 23.7 1.0 C A:THR99 3.2 24.4 1.0 C A:PRO100 3.2 25.3 1.0 C A:VAL96 3.4 20.1 1.0 C A:LEU103 3.7 23.8 1.0 CB A:THR99 3.8 24.8 1.0 O A:HOH510 3.8 37.0 1.0 CA A:THR99 3.8 24.2 1.0 CA A:VAL96 3.9 19.8 1.0 N A:PRO100 3.9 24.8 1.0 N A:GLN101 3.9 24.8 1.0 N A:THR99 4.0 23.9 1.0 O A:GLN101 4.0 22.7 1.0 CA A:GLN101 4.0 24.6 1.0 N A:LEU103 4.1 23.7 1.0 CB A:LEU103 4.1 23.7 1.0 C A:GLN101 4.1 23.6 1.0 CA A:PRO100 4.1 24.9 1.0 CG1 A:VAL96 4.2 19.3 1.0 CA A:LEU103 4.2 23.7 1.0 O A:LEU95 4.4 21.4 1.0 N A:ALA97 4.5 20.4 1.0 CB A:VAL96 4.7 20.1 1.0 N A:GLU104 4.7 24.1 1.0 C A:ALA97 4.8 22.1 1.0 CA A:GLU104 4.9 24.7 1.0 O A:ALA97 4.9 21.4 1.0 CA A:ALA97 4.9 21.4 1.0 N A:PRO102 5.0 23.4 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of the R253A 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 R253A Mutant of 7,8-Diaminopelargonic Acid Synthase within 5.0Å range: probe atom residue distance (Å) B Occ B:Na502 b:14.0 occ:1.00 O B:VAL96 1.9 22.1 1.0 O B:HOH685 2.4 30.5 1.0 OG1 B:THR99 2.5 21.2 1.0 O B:THR99 2.5 23.5 1.0 O B:LEU103 2.7 24.3 1.0 O B:PRO100 2.7 26.5 1.0 C B:VAL96 3.0 22.3 1.0 C B:THR99 3.2 23.5 1.0 CB B:THR99 3.5 22.5 1.0 CA B:VAL96 3.5 22.3 1.0 C B:PRO100 3.6 26.1 1.0 CA B:THR99 3.7 22.7 1.0 C B:LEU103 3.7 23.6 1.0 N B:THR99 3.7 22.6 1.0 CG1 B:VAL96 3.8 21.8 1.0 O B:LEU95 4.0 22.0 1.0 N B:PRO100 4.1 24.2 1.0 N B:ALA97 4.1 22.5 1.0 CB B:LEU103 4.2 23.4 1.0 N B:GLN101 4.3 26.4 1.0 CA B:LEU103 4.3 23.5 1.0 CB B:VAL96 4.3 22.5 1.0 N B:LEU103 4.4 24.1 1.0 CA B:GLN101 4.4 27.9 1.0 O B:GLN101 4.4 27.3 1.0 CA B:PRO100 4.4 24.5 1.0 C B:ALA97 4.6 22.8 1.0 C B:GLN101 4.6 26.8 1.0 CA B:ALA97 4.6 23.1 1.0 N B:VAL96 4.7 21.5 1.0 CG2 B:THR99 4.7 23.9 1.0 N B:MET98 4.8 22.7 1.0 N B:GLU104 4.8 23.6 1.0 C B:LEU95 4.8 21.9 1.0 O B:ALA97 4.8 23.5 1.0 CA B:GLU104 5.0 24.3 1.0 C B:MET98 5.0 22.5 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