Sodium in PDB 2qqv: Crystal Structure of A Cell-Wall Invertase (E203A) From Arabidopsis Thaliana in Complex with Sucrose

All present enzymatic activity of Crystal Structure of A Cell-Wall Invertase (E203A) From Arabidopsis Thaliana in Complex with Sucrose:
3.2.1.26;

The structure of Crystal Structure of A Cell-Wall Invertase (E203A) From Arabidopsis Thaliana in Complex with Sucrose, PDB code: 2qqv was solved by W.Lammens, K.Le Roy, A.Van Laere, A.Rabijns, W.Van Den Ende, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.63 / 3.01
Space group	P 32
Cell size a, b, c (Å), α, β, γ (°)	107.131, 107.131, 50.832, 90.00, 90.00, 120.00
R / Rfree (%)	19.9 / 23.7

The structure of Crystal Structure of A Cell-Wall Invertase (E203A) From Arabidopsis Thaliana in Complex with Sucrose also contains other interesting chemical elements:

Zinc

(Zn)

4 atoms

The binding sites of Sodium atom in the Crystal Structure of A Cell-Wall Invertase (E203A) From Arabidopsis Thaliana in Complex with Sucrose (pdb code 2qqv). 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 A Cell-Wall Invertase (E203A) From Arabidopsis Thaliana in Complex with Sucrose, PDB code: 2qqv:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of A Cell-Wall Invertase (E203A) From Arabidopsis Thaliana in Complex with Sucrose


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 A Cell-Wall Invertase (E203A) From Arabidopsis Thaliana in Complex with Sucrose within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1050 b:25.2 occ:1.00 NH1 A:ARG291 2.8 35.7 1.0 N A:ARG337 3.5 40.5 1.0 CG A:ARG337 3.6 42.0 1.0 CD A:LYS321 3.9 37.6 1.0 CD A:ARG291 4.0 34.5 1.0 CZ A:ARG291 4.0 35.6 1.0 CA A:VAL336 4.1 39.4 1.0 CB A:ARG337 4.1 41.3 1.0 CB A:LYS321 4.2 38.0 1.0 C A:VAL336 4.3 39.9 1.0 CG A:LYS321 4.3 37.8 1.0 CA A:ARG337 4.4 41.1 1.0 NE A:ARG291 4.4 35.1 1.0 CB A:VAL336 4.6 39.3 1.0 OE1 A:GLU338 4.6 43.4 1.0 CG1 A:VAL336 4.6 39.2 1.0 CE A:LYS321 4.8 37.6 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of A Cell-Wall Invertase (E203A) From Arabidopsis Thaliana in Complex with Sucrose


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 A Cell-Wall Invertase (E203A) From Arabidopsis Thaliana in Complex with Sucrose within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1051 b:34.8 occ:1.00 OG1 A:THR87 2.6 35.6 1.0 O A:THR151 3.0 37.4 1.0 O A:SER85 3.5 35.4 1.0 N A:THR87 3.6 35.7 1.0 CB A:THR87 3.8 35.8 1.0 CA A:THR152 3.8 37.8 1.0 C A:SER85 3.8 35.4 1.0 N A:ALA153 3.8 38.3 1.0 CB A:LEU97 3.9 35.8 1.0 CD1 A:LEU97 4.0 35.6 1.0 C A:THR151 4.0 37.3 1.0 CG A:LEU97 4.0 35.6 1.0 C A:ALA86 4.0 35.5 1.0 N A:LEU97 4.1 35.9 1.0 CB A:SER85 4.1 35.4 1.0 N A:ALA86 4.2 35.5 1.0 CA A:THR87 4.2 35.8 1.0 N A:THR152 4.3 37.5 1.0 C A:THR152 4.3 38.0 1.0 CA A:ALA86 4.3 35.5 1.0 O A:VAL95 4.5 36.0 1.0 CA A:SER85 4.5 35.4 1.0 CB A:ALA153 4.6 38.6 1.0 CA A:LEU97 4.6 35.9 1.0 O A:ALA86 4.7 35.5 1.0 CA A:ALA153 4.9 38.7 1.0 CZ A:PHE183 4.9 46.5 1.0 CB A:THR152 4.9 37.8 1.0 N A:SER85 5.0 35.3 1.0 CG2 A:THR87 5.0 35.9 1.0 C A:ILE96 5.0 35.8 1.0

W.Lammens, K.Le Roy, A.Van Laere, A.Rabijns, W.Van Den Ende. Crystal Structures of Arabidopsis Thaliana Cell-Wall Invertase Mutants in Complex with Sucrose. J.Mol.Biol. V. 377 378 2008.
ISSN: ISSN 0022-2836
PubMed: 18258263
DOI: 10.1016/J.JMB.2007.12.074