Sodium in PDB 8qaw: Medicago Truncatula HISN5 (Igpd) in Complex with Mn, Imd, Edo, Fmt, Gol and Trs

The structure of Medicago Truncatula HISN5 (Igpd) in Complex with Mn, Imd, Edo, Fmt, Gol and Trs, PDB code: 8qaw was solved by W.Witek, M.Ruszkowski, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	58.06 / 1.55
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	137.68, 137.68, 265.907, 90, 90, 120
R / Rfree (%)	12.9 / 16.1

The structure of Medicago Truncatula HISN5 (Igpd) in Complex with Mn, Imd, Edo, Fmt, Gol and Trs also contains other interesting chemical elements:

Manganese	(Mn)	16 atoms
Chlorine	(Cl)	2 atoms

The binding sites of Sodium atom in the Medicago Truncatula HISN5 (Igpd) in Complex with Mn, Imd, Edo, Fmt, Gol and Trs (pdb code 8qaw). 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 HISN5 (Igpd) in Complex with Mn, Imd, Edo, Fmt, Gol and Trs, PDB code: 8qaw:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Medicago Truncatula HISN5 (Igpd) in Complex with Mn, Imd, Edo, Fmt, Gol and Trs


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Medicago Truncatula HISN5 (Igpd) in Complex with Mn, Imd, Edo, Fmt, Gol and Trs within 5.0Å range: probe atom residue distance (Å) B Occ A:Na311 b:40.3 occ:1.00 O A:HOH564 2.2 46.8 1.0 O A:ASN106 2.4 27.4 1.0 O A:HOH494 2.5 43.7 1.0 O A:HOH477 2.5 40.4 1.0 O A:HOH522 2.6 43.6 1.0 O A:HOH440 2.6 32.1 1.0 C A:ASN106 3.5 25.0 1.0 N A:ASN106 4.0 24.8 1.0 CA A:ASN106 4.2 24.2 1.0 CB A:ASP114 4.2 24.7 1.0 O A:HOH426 4.4 46.5 1.0 CB A:ASN106 4.4 24.7 1.0 OD1 A:ASP118 4.4 25.9 1.0 OD2 A:ASP118 4.4 28.6 1.0 OG A:SER107 4.5 25.9 0.5 OD2 A:ASP114 4.5 30.1 1.0 O B:HOH556 4.5 65.4 1.0 CG A:ASP114 4.6 28.1 1.0 N A:SER107 4.6 24.7 0.5 N A:SER107 4.6 23.7 0.5 O A:HOH526 4.6 49.0 1.0 O A:HOH444 4.6 58.2 1.0 CA A:SER107 4.9 26.1 0.5 CG A:ASP118 4.9 25.9 1.0 CA A:SER107 5.0 24.7 0.5

Sodium binding site 2 out of 2 in the Medicago Truncatula HISN5 (Igpd) in Complex with Mn, Imd, Edo, Fmt, Gol and Trs


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Medicago Truncatula HISN5 (Igpd) in Complex with Mn, Imd, Edo, Fmt, Gol and Trs within 5.0Å range: probe atom residue distance (Å) B Occ B:Na311 b:37.3 occ:1.00 O B:TYR194 2.4 24.7 1.0 O B:HOH585 2.4 42.1 1.0 O B:HOH506 2.4 33.1 1.0 O B:HOH432 2.4 40.5 1.0 O B:HOH548 2.4 39.3 1.0 O B:HOH436 2.6 39.7 1.0 C B:TYR194 3.5 21.8 1.0 N B:TYR194 4.0 22.7 1.0 CB B:TYR194 4.0 24.1 1.0 CA B:TYR194 4.0 22.1 1.0 O B:HOH577 4.0 59.5 1.0 O B:HOH408 4.2 56.5 1.0 O B:HOH420 4.4 47.7 1.0 O B:HOH461 4.4 46.7 1.0 OD1 B:ASP195 4.5 55.4 1.0 CD2 B:TYR194 4.5 23.7 1.0 N B:ASP195 4.6 22.3 1.0 OE2 B:GLU212 4.7 30.2 1.0 CG B:TYR194 4.8 22.4 1.0 CG B:ASP195 4.9 49.6 1.0 O B:HOH495 4.9 33.3 1.0

W.Witek, J.Sliwiak, M.Rawski, M.Ruszkowski. Targeting Imidazole-Glycerol Phosphate Dehydratase in Plants: Novel Approach For Structural and Functional Studies, and Inhibitor Blueprinting. Front Plant Sci V. 15 43980 2024.
ISSN: ESSN 1664-462X
PubMed: 38559763
DOI: 10.3389/FPLS.2024.1343980