Sodium in PDB 9fcg: Medicago Truncatula 5'-Profar Isomerase (HISN3) D57N Mutant in Complex with Prfar

All present enzymatic activity of Medicago Truncatula 5'-Profar Isomerase (HISN3) D57N Mutant in Complex with Prfar:
5.3.1.16;

The structure of Medicago Truncatula 5'-Profar Isomerase (HISN3) D57N Mutant in Complex with Prfar, PDB code: 9fcg was solved by W.Witek, B.Imiolczyk, M.Ruszkowski, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.63 / 1.54
Space group	P 4
Cell size a, b, c (Å), α, β, γ (°)	87.79, 87.79, 35.633, 90, 90, 90
R / Rfree (%)	17.4 / 19.8

The structure of Medicago Truncatula 5'-Profar Isomerase (HISN3) D57N Mutant in Complex with Prfar also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Sodium atom in the Medicago Truncatula 5'-Profar Isomerase (HISN3) D57N Mutant in Complex with Prfar (pdb code 9fcg). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Medicago Truncatula 5'-Profar Isomerase (HISN3) D57N Mutant in Complex with Prfar, PDB code: 9fcg:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Medicago Truncatula 5'-Profar Isomerase (HISN3) D57N Mutant in Complex with Prfar


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Medicago Truncatula 5'-Profar Isomerase (HISN3) D57N Mutant in Complex with Prfar within 5.0Å range: probe atom residue distance (Å) B Occ A:Na406 b:19.0 occ:1.00 O A:HOH666 2.3 20.5 1.0 O A:HOH722 2.3 26.8 1.0 O A:PHE162 2.4 15.9 1.0 O A:SER159 2.4 14.7 1.0 O A:HOH604 2.4 25.0 1.0 O A:HOH696 2.6 28.0 1.0 C A:SER159 3.4 15.6 1.0 C A:PHE162 3.5 15.0 1.0 O A:HOH752 3.7 27.4 1.0 O A:HOH749 3.8 31.1 1.0 CA A:SER159 4.1 12.9 1.0 OD1 A:ASN163 4.1 20.5 1.0 N A:PHE162 4.2 15.7 1.0 CA A:PHE162 4.2 14.8 1.0 CB A:SER159 4.2 15.0 1.0 CB A:PHE162 4.2 17.6 1.0 CL A:CL408 4.3 20.5 1.0 O A:HOH564 4.4 19.2 1.0 N A:TYR160 4.4 15.5 1.0 O A:HOH649 4.5 31.8 1.0 N A:ASN163 4.5 14.0 1.0 CG A:ASN163 4.6 20.1 1.0 CA A:TYR160 4.6 16.4 1.0 OD2 A:ASP202 4.7 21.9 1.0 C A:TYR160 4.7 18.8 1.0 OD1 A:ASP202 4.7 24.0 1.0 CA A:ASN163 4.8 17.7 1.0 O A:TYR160 4.8 18.3 1.0 ND2 A:ASN163 4.9 21.7 1.0

Sodium binding site 2 out of 2 in the Medicago Truncatula 5'-Profar Isomerase (HISN3) D57N Mutant in Complex with Prfar


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Medicago Truncatula 5'-Profar Isomerase (HISN3) D57N Mutant in Complex with Prfar within 5.0Å range: probe atom residue distance (Å) B Occ A:Na407 b:17.1 occ:1.00 OE1 A:GLN65 2.5 20.7 1.0 OE2 A:GLU235 2.5 19.2 1.0 O8B A:2ER402 2.5 14.1 0.6 O A:ILE66 2.6 13.7 1.0 O A:HOH515 2.8 15.8 1.0 O4B A:2ER401 2.8 17.9 0.4 O9B A:2ER401 2.9 12.5 0.4 OG A:SER286 3.3 18.1 1.0 CD A:GLU235 3.4 15.5 1.0 O A:HOH553 3.5 16.3 1.0 CD A:GLN65 3.7 17.0 1.0 O4B A:2ER402 3.7 21.1 0.6 C A:ILE66 3.8 13.2 1.0 N A:ILE66 3.8 12.9 1.0 C5B A:2ER402 3.8 16.1 0.6 O6B A:2ER402 3.8 15.1 0.6 P7B A:2ER402 3.9 13.4 0.6 CA A:GLY236 3.9 14.8 1.0 OE1 A:GLU235 3.9 14.6 1.0 O2B A:2ER402 4.0 18.1 0.6 C4B A:2ER401 4.0 16.7 0.4 P7B A:2ER401 4.1 14.7 0.4 ND2 A:ASN57 4.3 18.1 0.4 N A:GLY236 4.3 12.4 1.0 O6B A:2ER401 4.3 13.7 0.4 C4B A:2ER402 4.4 17.6 0.6 CG A:GLU235 4.4 13.2 1.0 CB A:GLN65 4.4 13.3 1.0 CA A:ILE66 4.5 14.6 1.0 O9B A:2ER402 4.5 13.2 0.6 C5B A:2ER401 4.5 16.6 0.4 C A:GLN65 4.5 14.9 1.0 CA A:GLN65 4.6 14.4 1.0 NE2 A:GLN65 4.6 20.0 1.0 CB A:SER286 4.6 14.8 1.0 C2'' A:2ER402 4.6 18.8 0.6 CG A:GLN65 4.7 13.0 1.0 N A:SER286 4.7 13.8 1.0 O'L A:2ER401 4.7 13.6 0.4 N A:VAL67 4.9 12.4 1.0 ND2 A:ASN85 4.9 15.6 1.0

W.Witek, B.Imiolczyk, M.Ruszkowski. Structural, Kinetic, and Evolutionary Peculiarities of HISN3, A Plant 5'-Profar Isomerase. Plant Physiol Biochem. V. 215 09065 2024.
ISSN: ESSN 1873-2690
PubMed: 39186852
DOI: 10.1016/J.PLAPHY.2024.109065