Manganese in PDB 5z2r: Thdp-MN2+ Complex of R395K Variant of Ecmend Soaked with 2- Ketoglutarate For 5 Min

Enzymatic activity of Thdp-MN2+ Complex of R395K Variant of Ecmend Soaked with 2- Ketoglutarate For 5 Min

All present enzymatic activity of Thdp-MN2+ Complex of R395K Variant of Ecmend Soaked with 2- Ketoglutarate For 5 Min:
2.2.1.9;

Protein crystallography data

The structure of Thdp-MN2+ Complex of R395K Variant of Ecmend Soaked with 2- Ketoglutarate For 5 Min, PDB code: 5z2r was solved by M.M.Qin, Z.H.Guo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	38.63 / 2.30
*Space group*	P 1
*Cell size a, b, c (Å), α, β, γ (°)*	90.630, 90.750, 172.370, 82.91, 75.71, 64.20
*R / R_free (%)*	17 / 20.1

Other elements in 5z2r:

The structure of Thdp-MN2+ Complex of R395K Variant of Ecmend Soaked with 2- Ketoglutarate For 5 Min also contains other interesting chemical elements:

Magnesium

(Mg)

7 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Thdp-MN2+ Complex of R395K Variant of Ecmend Soaked with 2- Ketoglutarate For 5 Min (pdb code 5z2r). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total only one binding site of Manganese was determined in the Thdp-MN2+ Complex of R395K Variant of Ecmend Soaked with 2- Ketoglutarate For 5 Min, PDB code: 5z2r:

Manganese binding site 1 out of 1 in 5z2r

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Manganese Binding Sites List in 5z2r

Manganese binding site 1 out of 1 in the Thdp-MN2+ Complex of R395K Variant of Ecmend Soaked with 2- Ketoglutarate For 5 Min

Mono view

Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Thdp-MN2+ Complex of R395K Variant of Ecmend Soaked with 2- Ketoglutarate For 5 Min within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
G:Mn602 b:30.0 occ:1.00	O	G:GLY471	2.0	18.6	1.0
	OD1	G:ASP442	2.0	20.0	1.0
	OD1	G:ASN469	2.0	20.5	1.0
	O3B	G:TD6601	2.0	15.1	1.0
	O2A	G:TD6601	2.1	21.5	1.0
	O	G:HOH805	2.3	19.1	1.0
	CG	G:ASN469	3.0	20.7	1.0
	CG	G:ASP442	3.1	17.3	1.0
	C	G:GLY471	3.1	16.9	1.0
	PA	G:TD6601	3.3	22.4	1.0
	PB	G:TD6601	3.3	17.6	1.0
	ND2	G:ASN469	3.5	20.6	1.0
	O3A	G:TD6601	3.5	18.2	1.0
	OD2	G:ASP442	3.6	16.5	1.0
	N	G:ASP442	3.8	17.6	1.0
	N	G:GLY471	3.9	17.4	1.0
	N	G:GLY472	4.1	16.3	1.0
	CA	G:GLY471	4.1	16.8	1.0
	N	G:GLN473	4.1	18.0	1.0
	O7	G:TD6601	4.2	24.4	1.0
	CA	G:GLY472	4.2	16.4	1.0
	N	G:ASN469	4.2	18.9	1.0
	O2B	G:TD6601	4.2	14.7	1.0
	CB	G:ASP442	4.3	16.3	1.0
	O	G:VAL467	4.3	17.3	1.0
	O	G:HOH829	4.4	16.7	1.0
	O1B	G:TD6601	4.4	15.1	1.0
	CB	G:ASN469	4.4	19.1	1.0
	O1A	G:TD6601	4.4	18.4	1.0
	N	G:LEU443	4.5	19.0	1.0
	CA	G:ASP442	4.6	17.4	1.0
	C	G:ASN469	4.6	20.7	1.0
	CA	G:ASN469	4.6	19.2	1.0
	CA	G:GLY441	4.6	15.1	1.0
	N	G:ASN470	4.6	20.6	1.0
	C	G:GLY441	4.7	17.5	1.0
	CG	G:GLN473	4.7	17.1	1.0
	C	G:GLY472	4.7	17.9	1.0
	C	G:ASN470	4.9	19.8	1.0
	CG	G:LEU443	4.9	20.8	1.0
	CB	G:GLN473	4.9	18.2	1.0

Reference:

M.M.Qin, H.G.Song, X.Dai, Y.Z.Chen, Z.H.Guo. Two Active Site Arginines Are Critical Determinants of Substrate Binding and Catalysis in Mend: A Thiamine-Dependent Enzyme in Menaquinone Biosynthesis. Biochem. J. V. 475 3651 2018.
ISSN: ESSN 1470-8728
PubMed: 30341164
DOI: 10.1042/BCJ20180548

Page generated: Sun Oct 6 03:37:31 2024

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