Manganese in PDB 6s2u: Structure of the Catalytic Domain of T. Thermophilus Rel in Complex with Amp and Ppgpp

Enzymatic activity of Structure of the Catalytic Domain of T. Thermophilus Rel in Complex with Amp and Ppgpp

All present enzymatic activity of Structure of the Catalytic Domain of T. Thermophilus Rel in Complex with Amp and Ppgpp:
2.7.6.5;

Protein crystallography data

The structure of Structure of the Catalytic Domain of T. Thermophilus Rel in Complex with Amp and Ppgpp, PDB code: 6s2u was solved by A.Garcia-Pino, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	56.36 / 2.95
*Space group*	C 1 2 1
*Cell size a, b, c (Å), α, β, γ (°)*	120.739, 50.346, 86.057, 90.00, 111.00, 90.00
*R / R_free (%)*	21.4 / 24.8

Other elements in 6s2u:

The structure of Structure of the Catalytic Domain of T. Thermophilus Rel in Complex with Amp and Ppgpp also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Structure of the Catalytic Domain of T. Thermophilus Rel in Complex with Amp and Ppgpp (pdb code 6s2u). 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 Structure of the Catalytic Domain of T. Thermophilus Rel in Complex with Amp and Ppgpp, PDB code: 6s2u:

Manganese binding site 1 out of 1 in 6s2u

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Manganese Binding Sites List in 6s2u

Manganese binding site 1 out of 1 in the Structure of the Catalytic Domain of T. Thermophilus Rel in Complex with Amp and Ppgpp

Mono view

Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Structure of the Catalytic Domain of T. Thermophilus Rel in Complex with Amp and Ppgpp within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mn401 b:61.4 occ:1.00	OD2	A:ASP146	2.2	82.2	1.0
	CB	A:LEU110	2.2	1.0	1.0
	NE2	A:HIS52	2.2	44.7	1.0
	NE2	A:HIS76	2.6	64.5	1.0
	OD2	A:ASP77	2.8	94.5	1.0
	CD2	A:HIS52	3.1	45.8	1.0
	CE1	A:HIS52	3.3	44.2	1.0
	OD1	A:ASP77	3.3	90.0	1.0
	CG	A:ASP146	3.3	76.5	1.0
	CD2	A:HIS76	3.3	64.8	1.0
	CG	A:ASP77	3.4	86.5	1.0
	CA	A:LEU110	3.7	0.1	1.0
	CE1	A:HIS76	3.8	64.4	1.0
	OD1	A:ASP146	3.8	82.2	1.0
	OH	A:TYR49	4.0	85.6	1.0
	N	A:LEU110	4.2	0.4	1.0
	CG	A:HIS52	4.3	45.2	1.0
	ND1	A:HIS52	4.4	45.4	1.0
	CB	A:ASP146	4.5	53.7	1.0
	CG	A:HIS76	4.6	63.6	1.0
	C	A:LEU110	4.6	0.2	1.0
	O	A:LEU110	4.6	0.2	1.0
	ND1	A:HIS76	4.8	65.1	1.0
	OD1	A:ASN150	4.9	73.1	1.0
	NH2	A:ARG43	4.9	94.5	1.0
	CB	A:ASP77	4.9	66.9	1.0

Reference:

H.Tamman, K.Van Nerom, H.Takada, N.Vandenberk, D.Scholl, Y.Polikanov, J.Hofkens, A.Talavera, V.Hauryliuk, J.Hendrix, A.Garcia-Pino. A Nucleotide-Switch Mechanism Mediates Opposing Catalytic Activities of Rel Enzymes. Nat.Chem.Biol. V. 16 834 2020.
ISSN: ESSN 1552-4469
PubMed: 32393900
DOI: 10.1038/S41589-020-0520-2

Page generated: Sun Oct 6 07:05:10 2024

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