Potassium in PDB 6dp7: Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 500 Mm MN2+ and 200 Mm K+ For 40 S at 21 C

Enzymatic activity of Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 500 Mm MN2+ and 200 Mm K+ For 40 S at 21 C

All present enzymatic activity of Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 500 Mm MN2+ and 200 Mm K+ For 40 S at 21 C:
3.1.26.4;

Protein crystallography data

The structure of Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 500 Mm MN2+ and 200 Mm K+ For 40 S at 21 C, PDB code: 6dp7 was solved by N.L.Samara, W.Yang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	17.98 / 1.38
*Space group*	C 1 2 1
*Cell size a, b, c (Å), α, β, γ (°)*	82.013, 37.557, 61.932, 90.00, 96.79, 90.00
*R / R_free (%)*	16.9 / 19.2

Other elements in 6dp7:

The structure of Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 500 Mm MN2+ and 200 Mm K+ For 40 S at 21 C also contains other interesting chemical elements:

Manganese	(Mn)	4 atoms
Iodine	(I)	3 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 500 Mm MN2+ and 200 Mm K+ For 40 S at 21 C (pdb code 6dp7). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total only one binding site of Potassium was determined in the Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 500 Mm MN2+ and 200 Mm K+ For 40 S at 21 C, PDB code: 6dp7:

Potassium binding site 1 out of 1 in 6dp7

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Potassium Binding Sites List in 6dp7

Potassium binding site 1 out of 1 in the Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 500 Mm MN2+ and 200 Mm K+ For 40 S at 21 C

Mono view

Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 500 Mm MN2+ and 200 Mm K+ For 40 S at 21 C within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:K204 b:32.8 occ:0.40	OP2	b:C5	2.7	20.7	1.0
	O	B:HOH103	2.8	48.6	1.0
	OE2	A:GLU188	2.9	40.7	1.0
	HG21	A:THR183	3.2	32.7	1.0
	O	A:HOH341	3.2	21.8	1.0
	O	A:HOH338	3.3	21.2	1.0
	HG1	A:THR183	3.5	29.3	1.0
	OE1	A:GLU188	3.6	64.6	1.0
	CD	A:GLU188	3.6	78.1	1.0
	O	b:HOH202	3.7	36.0	1.0
	P	b:C5	3.7	20.6	1.0
	OD2	A:ASP132	3.8	23.1	1.0
	C5'	B:U4	3.8	20.0	1.0
	OP3	b:C5	4.0	20.9	1.0
	CG2	A:THR183	4.0	27.2	1.0
	O	b:HOH204	4.1	28.3	0.5
	HG23	A:THR183	4.1	32.7	1.0
	OP1	b:C5	4.2	18.8	1.0
	OP1	B:U4	4.2	27.7	1.0
	OG1	A:THR183	4.3	24.4	1.0
	O	B:HOH108	4.4	62.4	1.0
	O5'	B:U4	4.4	28.8	1.0
	CG	A:ASP132	4.5	19.6	1.0
	HB2	A:ASP132	4.5	20.0	1.0
	MN	A:MN201	4.7	18.7	1.0
	P	B:U4	4.7	22.9	1.0
	HG22	A:THR183	4.7	32.7	1.0
	CB	A:THR183	4.7	22.7	1.0
	HB	A:THR183	4.9	27.2	1.0
	H	A:ILE189	5.0	25.3	1.0
	OP2	B:U4	5.0	29.6	1.0
	CB	A:ASP132	5.0	16.7	1.0

Reference:

N.L.Samara, W.Yang. Cation Trafficking Propels Rna Hydrolysis. Nat. Struct. Mol. Biol. V. 25 715 2018.
ISSN: ESSN 1545-9985
PubMed: 30076410
DOI: 10.1038/S41594-018-0099-4

Page generated: Mon Aug 12 15:51:48 2024

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