Rubidium in PDB 6dpi: Crystal Structure of Bacillus Halodurans Ribonuclease H1 K196A in Complex with An Rna/Dna Hybrid: Reaction in 10 Mm MG2+ and 200 Mm Rb+ For 40 S at 21 C

Enzymatic activity of Crystal Structure of Bacillus Halodurans Ribonuclease H1 K196A in Complex with An Rna/Dna Hybrid: Reaction in 10 Mm MG2+ and 200 Mm Rb+ For 40 S at 21 C

All present enzymatic activity of Crystal Structure of Bacillus Halodurans Ribonuclease H1 K196A in Complex with An Rna/Dna Hybrid: Reaction in 10 Mm MG2+ and 200 Mm Rb+ For 40 S at 21 C:
3.1.26.4;

Protein crystallography data

The structure of Crystal Structure of Bacillus Halodurans Ribonuclease H1 K196A in Complex with An Rna/Dna Hybrid: Reaction in 10 Mm MG2+ and 200 Mm Rb+ For 40 S at 21 C, PDB code: 6dpi 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)*	19.98 / 1.35
*Space group*	C 1 2 1
*Cell size a, b, c (Å), α, β, γ (°)*	81.620, 37.290, 62.382, 90.00, 96.98, 90.00
*R / R_free (%)*	14.5 / 17.4

Other elements in 6dpi:

The structure of Crystal Structure of Bacillus Halodurans Ribonuclease H1 K196A in Complex with An Rna/Dna Hybrid: Reaction in 10 Mm MG2+ and 200 Mm Rb+ For 40 S at 21 C also contains other interesting chemical elements:

Magnesium	(Mg)	2 atoms
Chlorine	(Cl)	3 atoms

Rubidium Binding Sites:

The binding sites of Rubidium atom in the Crystal Structure of Bacillus Halodurans Ribonuclease H1 K196A in Complex with An Rna/Dna Hybrid: Reaction in 10 Mm MG2+ and 200 Mm Rb+ For 40 S at 21 C (pdb code 6dpi). This binding sites where shown within 5.0 Angstroms radius around Rubidium atom.
In total 3 binding sites of Rubidium where determined in the Crystal Structure of Bacillus Halodurans Ribonuclease H1 K196A in Complex with An Rna/Dna Hybrid: Reaction in 10 Mm MG2+ and 200 Mm Rb+ For 40 S at 21 C, PDB code: 6dpi:
Jump to Rubidium binding site number: 1; 2; 3;

Rubidium binding site 1 out of 3 in 6dpi

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Rubidium Binding Sites List in 6dpi

Rubidium binding site 1 out of 3 in the Crystal Structure of Bacillus Halodurans Ribonuclease H1 K196A in Complex with An Rna/Dna Hybrid: Reaction in 10 Mm MG2+ and 200 Mm Rb+ For 40 S at 21 C

Mono view

Stereo pair view

A full contact list of Rubidium with other atoms in the Rb binding site number 1 of Crystal Structure of Bacillus Halodurans Ribonuclease H1 K196A in Complex with An Rna/Dna Hybrid: Reaction in 10 Mm MG2+ and 200 Mm Rb+ For 40 S at 21 C within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Rb203 b:27.2 occ:0.30	O	A:TYR193	2.3	71.9	1.0
	O	A:HOH343	2.5	32.8	1.0
	N	A:ALA196	2.5	40.7	0.6
	N	A:ARG195	2.8	44.2	0.6
	O	A:HOH318	3.0	25.0	1.0
	OXT	A:ALA196	3.1	60.5	0.6
	OP2	b:G6	3.1	19.3	1.0
	C	A:ARG195	3.2	63.1	0.6
	C	A:ALA196	3.3	36.0	0.6
	CA	A:ALA196	3.3	41.4	0.6
	CA	A:ARG195	3.4	66.8	0.6
	OD1	A:ASP192	3.4	24.2	1.0
	O	A:HOH331	3.5	19.4	1.0
	C	A:TYR193	3.5	35.1	1.0
	CG	A:ARG195	3.6	35.9	0.6
	C	A:GLY194	3.8	54.1	0.8
	HB2	A:TYR193	3.8	34.8	1.0
	OD2	A:ASP192	3.9	29.0	1.0
	CG	A:ASP192	4.0	24.3	1.0
	P	b:G6	4.0	16.9	1.0
	CB	A:ARG195	4.1	49.9	0.6
	MG	A:MG201	4.1	16.7	1.0
	H	A:TYR193	4.1	29.3	1.0
	O	A:ARG195	4.2	72.8	0.6
	O	A:ALA196	4.2	0.6	0.6
	CA	A:GLY194	4.3	44.0	0.8
	O5'	b:G6	4.3	20.0	1.0
	OP1	b:G6	4.3	17.1	1.0
	N	A:GLY194	4.3	45.7	0.8
	CA	A:TYR193	4.4	24.7	1.0
	N	A:TYR193	4.5	24.4	1.0
	CB	A:TYR193	4.5	29.0	1.0
	CB	A:ALA196	4.7	45.3	0.6
	HB3	A:TYR193	4.8	34.8	1.0
	O	A:GLY194	4.8	56.9	0.8
	CD	A:ARG195	5.0	47.5	0.6

Rubidium binding site 2 out of 3 in 6dpi

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Rubidium Binding Sites List in 6dpi

Rubidium binding site 2 out of 3 in the Crystal Structure of Bacillus Halodurans Ribonuclease H1 K196A in Complex with An Rna/Dna Hybrid: Reaction in 10 Mm MG2+ and 200 Mm Rb+ For 40 S at 21 C

Mono view

Stereo pair view

A full contact list of Rubidium with other atoms in the Rb binding site number 2 of Crystal Structure of Bacillus Halodurans Ribonuclease H1 K196A in Complex with An Rna/Dna Hybrid: Reaction in 10 Mm MG2+ and 200 Mm Rb+ For 40 S at 21 C within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Rb204 b:33.9 occ:0.20	O	A:HOH423	2.6	55.5	1.0
	O	A:HOH387	2.6	48.8	1.0
	O	A:HOH441	2.6	59.5	1.0
	O	A:HOH413	2.7	50.8	1.0
	OD1	A:ASN124	2.8	33.9	1.0
	O	A:LYS121	2.9	19.9	1.0
	HG2	A:LYS121	3.5	23.1	1.0
	CG	A:ASN124	3.8	26.1	1.0
	C	A:LYS121	3.9	17.0	1.0
	HG3	A:LYS121	4.0	23.1	1.0
	O	A:HOH393	4.0	55.0	1.0
	H	A:ASN124	4.1	20.7	1.0
	HD21	A:ASN124	4.2	51.1	1.0
	CG	A:LYS121	4.2	19.3	1.0
	HE3	A:LYS121	4.3	36.0	1.0
	O	A:HOH414	4.3	44.8	1.0
	HA	A:ASN124	4.3	22.2	1.0
	ND2	A:ASN124	4.4	42.6	1.0
	O	A:HOH326	4.4	58.0	1.0
	O	A:HOH445	4.5	53.2	1.0
	CA	A:GLU122	4.6	21.8	1.0
	O	A:GLU122	4.6	22.5	1.0
	HA	A:LYS121	4.7	19.2	1.0
	N	A:GLU122	4.7	16.9	1.0
	C	A:GLU122	4.7	20.3	1.0
	N	A:ASN124	4.7	17.2	1.0
	HZ2	A:LYS121	4.8	32.5	1.0
	CA	A:LYS121	4.8	16.0	1.0
	CA	A:ASN124	4.9	18.5	1.0
	CB	A:ASN124	5.0	20.1	1.0

Rubidium binding site 3 out of 3 in 6dpi

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Rubidium Binding Sites List in 6dpi

Rubidium binding site 3 out of 3 in the Crystal Structure of Bacillus Halodurans Ribonuclease H1 K196A in Complex with An Rna/Dna Hybrid: Reaction in 10 Mm MG2+ and 200 Mm Rb+ For 40 S at 21 C

Mono view

Stereo pair view

A full contact list of Rubidium with other atoms in the Rb binding site number 3 of Crystal Structure of Bacillus Halodurans Ribonuclease H1 K196A in Complex with An Rna/Dna Hybrid: Reaction in 10 Mm MG2+ and 200 Mm Rb+ For 40 S at 21 C within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
C:Rb101 b:38.2 occ:0.40	O	C:HOH218	2.4	24.1	0.6
	O6	C:DG5	2.7	21.5	1.0
	O	C:HOH213	3.1	25.1	1.0
	O4	C:DT4	3.2	18.4	1.0
	O	B:HOH109	3.3	46.9	1.0
	O	C:HOH223	3.4	69.1	1.0
	C6	C:DG5	3.7	19.2	1.0
	C7	C:DT4	4.1	18.8	1.0
	C4	C:DT4	4.1	16.8	1.0
	N4	B:C2	4.1	24.0	1.0
	N7	C:DG5	4.1	18.9	1.0
	C5	C:DG5	4.3	17.5	1.0
	N6	B:A3	4.4	18.3	1.0
	O	C:HOH205	4.5	32.3	1.0
	C5	C:DT4	4.5	18.1	1.0
	O	B:HOH111	4.5	42.2	1.0
	N6	B:A1	4.5	26.0	1.0
	O	B:HOH110	4.8	54.6	1.0
	N1	C:DG5	4.9	20.2	1.0
	O	C:HOH202	5.0	58.2	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: Thu Oct 10 12:11:23 2024

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