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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 / Rfree (%) 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

Go back to 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

Go back to 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

Go back to 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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