Sodium in PDB 3h7c: Crystal Structure of Arabidopsis Thaliana Agmatine Deiminase From Cell Free Expression

All present enzymatic activity of Crystal Structure of Arabidopsis Thaliana Agmatine Deiminase From Cell Free Expression:
3.5.3.12;

The structure of Crystal Structure of Arabidopsis Thaliana Agmatine Deiminase From Cell Free Expression, PDB code: 3h7c was solved by E.S.Burgie, C.A.Bingman, G.N.Phillips Jr., Center For Eukaryoticstructural Genomics (Cesg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 1.50
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	123.715, 69.932, 50.917, 90.00, 98.40, 90.00
R / Rfree (%)	14.6 / 17.4

The structure of Crystal Structure of Arabidopsis Thaliana Agmatine Deiminase From Cell Free Expression also contains other interesting chemical elements:

Magnesium	(Mg)	1 atom
Potassium	(K)	1 atom
Chlorine	(Cl)	2 atoms

The binding sites of Sodium atom in the Crystal Structure of Arabidopsis Thaliana Agmatine Deiminase From Cell Free Expression (pdb code 3h7c). 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 Arabidopsis Thaliana Agmatine Deiminase From Cell Free Expression, PDB code: 3h7c:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Arabidopsis Thaliana Agmatine Deiminase From Cell Free Expression


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 Arabidopsis Thaliana Agmatine Deiminase From Cell Free Expression within 5.0Å range: probe atom residue distance (Å) B Occ X:Na387 b:11.0 occ:1.00 O X:LEU76 2.5 14.7 1.0 O X:ARG73 2.8 11.2 1.0 O X:HOH723 2.8 25.5 1.0 O X:LYS74 3.0 14.4 1.0 C X:LYS74 3.5 11.6 1.0 C X:LEU76 3.6 12.5 1.0 CA X:LYS74 3.8 9.6 1.0 C X:ARG73 3.9 9.0 1.0 O X:HOH602 3.9 16.5 1.0 N X:LEU76 4.1 11.3 1.0 N X:LYS74 4.4 9.6 1.0 N X:GLN75 4.4 11.2 1.0 CA X:PRO77 4.5 11.9 1.0 CA X:LEU76 4.5 11.0 1.0 N X:PRO77 4.5 10.9 1.0 NH2 X:ARG73 4.5 11.4 1.0 NE X:ARG73 4.6 14.5 1.0 C X:PRO77 4.6 13.3 1.0 N X:GLU78 4.8 13.2 1.0 C X:GLN75 4.8 11.1 1.0 CZ X:ARG73 5.0 13.8 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Arabidopsis Thaliana Agmatine Deiminase From Cell Free Expression


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 Arabidopsis Thaliana Agmatine Deiminase From Cell Free Expression within 5.0Å range: probe atom residue distance (Å) B Occ X:Na388 b:15.8 occ:1.00 OH3 X:1PE391 2.7 24.7 1.0 OH5 X:1PE391 2.8 45.4 1.0 OH4 X:1PE391 2.8 35.3 1.0 OH6 X:1PE391 3.0 41.9 1.0 OH2 X:1PE391 3.1 40.7 1.0 C25 X:1PE391 3.5 41.5 1.0 C14 X:1PE391 3.5 28.3 1.0 C23 X:1PE391 3.6 19.8 1.0 C15 X:1PE391 3.6 42.5 1.0 C13 X:1PE391 3.6 33.5 1.0 C22 X:1PE391 3.7 26.7 1.0 C24 X:1PE391 3.7 32.8 1.0 C12 X:1PE391 3.9 32.1 1.0 C26 X:1PE391 4.2 41.8 1.0 CA X:GLY304 4.6 11.4 1.0

E.S.Burgie, C.A.Bingman, G.N.Phillips Jr.. Structural Insights Into the Catalytic Mechanism of Arabidopsis Thaliana Agmatine Deiminase To Be Published.