Manganese in PDB 8ak4: Structure of the C-Terminally Truncated Nad+-Dependent Dna Ligase From the Poly-Extremophile Deinococcus Radiodurans

Enzymatic activity of Structure of the C-Terminally Truncated Nad+-Dependent Dna Ligase From the Poly-Extremophile Deinococcus Radiodurans

All present enzymatic activity of Structure of the C-Terminally Truncated Nad+-Dependent Dna Ligase From the Poly-Extremophile Deinococcus Radiodurans:
6.5.1.2;

Protein crystallography data

The structure of Structure of the C-Terminally Truncated Nad+-Dependent Dna Ligase From the Poly-Extremophile Deinococcus Radiodurans, PDB code: 8ak4 was solved by A.Fernandes, A.K.Williamson, P.M.Matias, E.Moe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	74.97 / 3.36
*Space group*	P 2₁ 2 2₁
*Cell size a, b, c (Å), α, β, γ (°)*	70.844, 73.434, 149.942, 90, 90, 90
*R / R_free (%)*	21.5 / 27.5

Other elements in 8ak4:

The structure of Structure of the C-Terminally Truncated Nad+-Dependent Dna Ligase From the Poly-Extremophile Deinococcus Radiodurans also contains other interesting chemical elements:

Zinc

(Zn)

4 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Structure of the C-Terminally Truncated Nad+-Dependent Dna Ligase From the Poly-Extremophile Deinococcus Radiodurans (pdb code 8ak4). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Structure of the C-Terminally Truncated Nad+-Dependent Dna Ligase From the Poly-Extremophile Deinococcus Radiodurans, PDB code: 8ak4:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in 8ak4

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Manganese Binding Sites List in 8ak4

Manganese binding site 1 out of 2 in the Structure of the C-Terminally Truncated Nad+-Dependent Dna Ligase From the Poly-Extremophile Deinococcus Radiodurans

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 C-Terminally Truncated Nad+-Dependent Dna Ligase From the Poly-Extremophile Deinococcus Radiodurans within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mn801 b:59.0 occ:1.00	OD1	A:ASP295	2.1	63.8	1.0
	OD1	A:ASP293	2.2	77.1	1.0
	NE2	A:HIS287	2.2	86.9	1.0
	CE1	A:HIS287	2.9	73.4	1.0
	CG	A:ASP293	3.2	81.7	1.0
	CD2	A:HIS287	3.3	85.9	1.0
	CG	A:ASP295	3.4	74.5	1.0
	O	A:ALA294	3.4	88.9	1.0
	OD2	A:ASP293	3.6	83.5	1.0
	C	A:ALA294	3.9	88.1	1.0
	ND1	A:HIS287	4.0	73.3	1.0
	MN	A:MN802	4.0	61.9	1.0
	NH2	A:ARG189	4.1	85.5	1.0
	CA	A:ASP295	4.1	98.9	1.0
	OD2	A:ASP295	4.2	71.5	1.0
	N	A:ASP295	4.2	89.6	1.0
	CG	A:HIS287	4.2	89.0	1.0
	N	A:ALA294	4.3	87.7	1.0
	CB	A:ASP295	4.3	98.9	1.0
	CB	A:ASP293	4.5	79.1	1.0
	O	A:GLY391	4.6	84.3	1.0
	C	A:GLY391	4.6	89.5	1.0
	CA	A:ALA294	4.8	80.1	1.0
	CA	A:ASP293	4.8	85.8	1.0
	C	A:ASP293	4.8	93.1	1.0
	N	A:GLY392	4.9	100.3	1.0

Manganese binding site 2 out of 2 in 8ak4

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Manganese Binding Sites List in 8ak4

Manganese binding site 2 out of 2 in the Structure of the C-Terminally Truncated Nad+-Dependent Dna Ligase From the Poly-Extremophile Deinococcus Radiodurans

Mono view

Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Structure of the C-Terminally Truncated Nad+-Dependent Dna Ligase From the Poly-Extremophile Deinococcus Radiodurans within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mn802 b:61.9 occ:1.00	OD2	A:ASP293	2.1	83.5	1.0
	OD2	A:ASP130	2.2	85.3	1.0
	OD2	A:ASP295	2.2	71.5	1.0
	CG	A:ASP295	2.9	74.5	1.0
	OD1	A:ASP295	3.0	63.8	1.0
	CG	A:ASP293	3.3	81.7	1.0
	CG	A:ASP130	3.4	83.4	1.0
	CA	A:GLY391	3.7	90.4	1.0
	OD1	A:ASP293	3.7	77.1	1.0
	MN	A:MN801	4.0	59.0	1.0
	N	A:GLY391	4.1	92.2	1.0
	CB	A:ASP130	4.3	88.6	1.0
	OD1	A:ASP130	4.3	76.7	1.0
	CB	A:ASP295	4.4	98.9	1.0
	C	A:GLY391	4.5	89.5	1.0
	CB	A:ASP293	4.5	79.1	1.0
	CD	A:PRO210	4.6	84.4	1.0
	CG	A:PRO210	4.7	80.5	1.0
	O	A:GLY391	4.9	84.3	1.0

Reference:

A.Fernandes, A.Williamson, P.M.Matias, E.Moe. Structure/Function Studies of the Nad + -Dependent Dna Ligase From the Poly-Extremophile Deinococcus Radiodurans Reveal Importance of the Brct Domain For Dna Binding. Extremophiles V. 27 26 2023.
ISSN: ESSN 1433-4909
PubMed: 37712998
DOI: 10.1007/S00792-023-01309-Z

Page generated: Sun Oct 6 11:19:05 2024

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