Magnesium in PDB 5ze4: The Structure of Holo- Structure of Dhad Complex with [2FE-2S] Cluster

Enzymatic activity of The Structure of Holo- Structure of Dhad Complex with [2FE-2S] Cluster

All present enzymatic activity of The Structure of Holo- Structure of Dhad Complex with [2FE-2S] Cluster:
4.2.1.9;

Protein crystallography data

The structure of The Structure of Holo- Structure of Dhad Complex with [2FE-2S] Cluster, PDB code: 5ze4 was solved by J.Zhou, X.Zang, Y.Tang, Y.Yan, J.Gan, L.Wu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	30.00 / 2.11
*Space group*	P 4₂ 2₁ 2
*Cell size a, b, c (Å), α, β, γ (°)*	135.467, 135.467, 65.978, 90.00, 90.00, 90.00
*R / R_free (%)*	17.3 / 21.5

Other elements in 5ze4:

The structure of The Structure of Holo- Structure of Dhad Complex with [2FE-2S] Cluster also contains other interesting chemical elements:

Iron

(Fe)

2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the The Structure of Holo- Structure of Dhad Complex with [2FE-2S] Cluster (pdb code 5ze4). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the The Structure of Holo- Structure of Dhad Complex with [2FE-2S] Cluster, PDB code: 5ze4:

Magnesium binding site 1 out of 1 in 5ze4

Go back to

Magnesium Binding Sites List in 5ze4

Magnesium binding site 1 out of 1 in the The Structure of Holo- Structure of Dhad Complex with [2FE-2S] Cluster

Mono view

Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The Structure of Holo- Structure of Dhad Complex with [2FE-2S] Cluster within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mg606 b:57.1 occ:1.00	OD2	A:ASP140	2.2	35.8	1.0
	OE1	A:GLU463	2.5	36.2	1.0
	CG	A:ASP140	3.4	31.4	1.0
	CD	A:GLU463	3.5	34.9	1.0
	OD2	A:ASP98	3.6	31.3	1.0
	NZ	A:LYS141	3.6	25.1	1.0
	OE2	A:GLU463	3.7	39.5	1.0
	CG	A:ASP98	3.7	25.8	1.0
	O	A:HOH703	3.7	39.4	1.0
	OXT	A:ACT605	3.9	30.7	1.0
	CB	A:ASP98	3.9	22.3	1.0
	C	A:ACT605	3.9	37.2	1.0
	O	A:ACT605	4.0	41.6	1.0
	OD1	A:ASP140	4.0	33.9	1.0
	ND2	A:ASN289	4.1	22.9	1.0
	OG1	A:THR216	4.2	24.7	1.0
	OD1	A:ASP98	4.2	30.1	1.0
	O	A:HOH721	4.4	23.3	1.0
	CB	A:ASP140	4.5	27.9	1.0
	CH3	A:ACT605	4.6	38.4	1.0
	CB	A:THR216	4.6	24.6	1.0
	CG	A:GLU463	4.9	30.3	1.0
	NH1	A:ARG487	5.0	23.1	1.0

Reference:

Y.Yan, Q.Liu, X.Zang, S.Yuan, U.Bat-Erdene, C.Nguyen, J.Gan, J.Zhou, S.E.Jacobsen, Y.Tang. Resistance-Gene-Directed Discovery of A Natural-Product Herbicide with A New Mode of Action. Nature V. 559 415 2018.
ISSN: ESSN 1476-4687
PubMed: 29995859
DOI: 10.1038/S41586-018-0319-4

Page generated: Wed Aug 13 01:23:58 2025

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