Sodium in PDB 6nib: Crystal Structure of Medicago Truncatula Agmatine Iminohydrolase (Deiminase)

All present enzymatic activity of Crystal Structure of Medicago Truncatula Agmatine Iminohydrolase (Deiminase):
3.5.3.12;

The structure of Crystal Structure of Medicago Truncatula Agmatine Iminohydrolase (Deiminase), PDB code: 6nib was solved by B.Sekula, Z.Dauter, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.70 / 1.20
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	146.996, 75.504, 47.103, 90.00, 108.56, 90.00
R / Rfree (%)	11.2 / 13.7

The binding sites of Sodium atom in the Crystal Structure of Medicago Truncatula Agmatine Iminohydrolase (Deiminase) (pdb code 6nib). 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 Medicago Truncatula Agmatine Iminohydrolase (Deiminase), PDB code: 6nib:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Medicago Truncatula Agmatine Iminohydrolase (Deiminase)


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 Medicago Truncatula Agmatine Iminohydrolase (Deiminase) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na404 b:16.2 occ:1.00 O A:ASP220 2.7 20.3 1.0 O A:TRP125 2.7 12.6 1.0 OD1 A:ASN222 2.8 10.5 1.0 O A:HOH886 2.9 33.0 1.0 O A:HOH979 2.9 45.7 1.0 O A:HOH854 3.0 42.4 1.0 O A:ASP219 3.3 24.6 1.0 C A:ASP220 3.4 15.9 1.0 O A:HOH670 3.6 56.2 1.0 CG A:ASN222 3.6 10.4 1.0 C A:TRP125 3.9 10.2 1.0 ND2 A:ASN222 3.9 13.6 1.0 CA A:ASP220 4.0 23.6 1.0 ND2 A:ASN185 4.1 11.9 1.0 CB A:TRP125 4.3 10.5 1.0 N A:THR221 4.3 10.8 1.0 C A:ASP219 4.3 21.6 1.0 N A:ASN222 4.4 9.4 1.0 C A:THR221 4.5 9.7 1.0 CA A:THR221 4.5 10.1 1.0 NH1 A:ARG186 4.6 9.6 1.0 N A:ASP220 4.7 19.5 1.0 O A:HOH536 4.7 38.4 1.0 O A:HOH862 4.7 54.1 1.0 CA A:TRP125 4.7 10.1 1.0 O A:HOH502 4.8 48.4 1.0 CB A:ASN222 4.8 10.3 1.0 N A:GLY126 4.9 11.0 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Medicago Truncatula Agmatine Iminohydrolase (Deiminase)


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 Medicago Truncatula Agmatine Iminohydrolase (Deiminase) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na405 b:14.2 occ:1.00 O A:LEU76 2.3 13.9 1.0 O A:HOH913 2.3 20.3 1.0 O A:HOH636 2.4 15.7 1.0 O A:ARG73 2.4 11.7 1.0 O A:HOH926 2.4 19.6 1.0 O A:ASN74 2.6 13.3 1.0 C A:ASN74 3.2 12.1 1.0 O A:HOH530 3.4 15.9 1.0 C A:LEU76 3.5 12.3 1.0 C A:ARG73 3.5 11.2 1.0 CA A:ASN74 3.6 12.0 1.0 N A:LEU76 3.9 12.1 1.0 N A:ASN74 4.0 11.3 1.0 O A:HOH880 4.1 39.7 1.0 N A:GLN75 4.2 11.5 1.0 C A:GLN75 4.2 11.8 1.0 O A:HOH717 4.3 38.9 1.0 O A:HOH971 4.3 46.6 1.0 CA A:LEU76 4.3 12.2 1.0 OD1 A:ASP78 4.3 20.4 1.0 NE A:ARG73 4.3 10.4 1.0 NH2 A:ARG73 4.4 11.4 1.0 N A:PRO77 4.4 13.2 1.0 CA A:PRO77 4.5 14.6 1.0 O A:HOH981 4.5 20.0 1.0 O A:HOH977 4.6 29.5 1.0 O A:GLN75 4.7 13.4 1.0 C A:PRO77 4.7 12.7 1.0 CA A:GLN75 4.7 13.0 1.0 CA A:ARG73 4.8 10.2 1.0 OD1 A:ASN74 4.8 19.8 1.0 CZ A:ARG73 4.9 10.2 1.0 N A:ASP78 4.9 14.1 1.0 CB A:ASN74 5.0 12.9 1.0

B.Sekula, Z.Dauter. Structural Study of Agmatine Iminohydrolase Frommedicago Truncatula, the Second Enzyme of the Agmatine Route of Putrescine Biosynthesis in Plants. Front Plant Sci V. 10 320 2019.
ISSN: ESSN 1664-462X
PubMed: 30984210
DOI: 10.3389/FPLS.2019.00320