Sodium in PDB 8qay: Medicago Truncatula HISN5 (Igpd) in Complex with Mn, Fmt, Act, Cit, Edo, SO4

Enzymatic activity of Medicago Truncatula HISN5 (Igpd) in Complex with Mn, Fmt, Act, Cit, Edo, SO4

All present enzymatic activity of Medicago Truncatula HISN5 (Igpd) in Complex with Mn, Fmt, Act, Cit, Edo, SO4:
4.2.1.19;

Protein crystallography data

The structure of Medicago Truncatula HISN5 (Igpd) in Complex with Mn, Fmt, Act, Cit, Edo, SO4, PDB code: 8qay 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)*	36.40 / 2.20
*Space group*	H 3
*Cell size a, b, c (Å), α, β, γ (°)*	137.6, 137.6, 265.65, 90, 90, 120
*R / R_free (%)*	18.9 / 23.1

Other elements in 8qay:

The structure of Medicago Truncatula HISN5 (Igpd) in Complex with Mn, Fmt, Act, Cit, Edo, SO4 also contains other interesting chemical elements:

Manganese

(Mn)

16 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Medicago Truncatula HISN5 (Igpd) in Complex with Mn, Fmt, Act, Cit, Edo, SO4 (pdb code 8qay). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Medicago Truncatula HISN5 (Igpd) in Complex with Mn, Fmt, Act, Cit, Edo, SO4, PDB code: 8qay:

Sodium binding site 1 out of 1 in 8qay

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Sodium Binding Sites List in 8qay

Sodium binding site 1 out of 1 in the Medicago Truncatula HISN5 (Igpd) in Complex with Mn, Fmt, Act, Cit, Edo, SO4

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, Fmt, Act, Cit, Edo, SO4 within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
C:Na308 b:44.1 occ:1.00	O	C:HOH497	2.3	53.7	1.0
	O	C:HOH417	2.5	34.3	1.0
	O	C:HOH469	2.5	37.8	1.0
	O	C:HOH484	2.5	48.1	1.0
	O	C:ASN106	2.6	38.2	1.0
	O	C:HOH432	2.7	32.6	1.0
	C	C:ASN106	3.7	38.5	1.0
	O	C:HOH481	3.9	47.3	1.0
	CB	C:ASP114	4.2	29.0	1.0
	N	C:ASN106	4.3	40.2	1.0
	OD2	C:ASP114	4.4	33.8	1.0
	CA	C:ASN106	4.5	36.2	1.0
	OD2	C:ASP118	4.5	34.6	1.0
	CG	C:ASP114	4.6	35.6	1.0
	OD1	C:ASP118	4.7	33.1	1.0
	N	C:SER107	4.7	32.3	1.0
	CB	C:ASN106	4.8	31.8	1.0
	CA	C:SER107	5.0	35.8	1.0

Reference:

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

Page generated: Mon Aug 18 15:11:07 2025

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