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Rubidium in PDB 6dot: Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 5 Mm MG2+ and 200 Mm Rb+ 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 5 Mm MG2+ and 200 Mm Rb+ 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 5 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 in Complex with An Rna/Dna Hybrid: Reaction in 5 Mm MG2+ and 200 Mm Rb+ For 40 S at 21 C, PDB code: 6dot 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) 23.35 / 1.42
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 81.557, 37.229, 62.052, 90.00, 96.61, 90.00
R / Rfree (%) 14.2 / 16.8

Other elements in 6dot:

The structure of Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 5 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 in Complex with An Rna/Dna Hybrid: Reaction in 5 Mm MG2+ and 200 Mm Rb+ For 40 S at 21 C (pdb code 6dot). 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 in Complex with An Rna/Dna Hybrid: Reaction in 5 Mm MG2+ and 200 Mm Rb+ For 40 S at 21 C, PDB code: 6dot:
Jump to Rubidium binding site number: 1; 2; 3;

Rubidium binding site 1 out of 3 in 6dot

Go back to Rubidium Binding Sites List in 6dot
Rubidium binding site 1 out of 3 in the Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 5 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 in Complex with An Rna/Dna Hybrid: Reaction in 5 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:40.0
occ:0.35
 O A:HOH335 2.5 45.6 1.0
O A:HOH329 2.5 43.7 1.0
O A:ARG195 2.6 58.9 0.6
N A:ARG195 2.9 43.9 0.6
OP2 b:G6 3.1 23.6 1.0
OD1 A:ASP192 3.2 31.1 1.0
C A:ARG195 3.3 61.0 0.6
O b:HOH103 3.4 50.2 1.0
O A:HOH322 3.4 24.0 1.0
N A:GLY194 3.5 31.4 0.6
CA A:ARG195 3.6 63.5 0.6
CG A:ARG195 3.6 37.9 0.6
C A:GLY194 3.7 41.1 0.6
HB2 A:TYR193 3.8 40.2 1.0
OD2 A:ASP192 3.8 34.8 1.0
H A:TYR193 3.9 31.5 1.0
MG A:MG201 3.9 20.1 1.0
CG A:ASP192 3.9 26.9 1.0
CA A:GLY194 3.9 36.0 0.6
P b:G6 4.0 22.1 1.0
C A:TYR193 4.2 45.0 1.0
CB A:ARG195 4.2 47.4 0.6
O5' b:G6 4.3 24.1 1.0
OP1 b:G6 4.3 24.1 1.0
N A:TYR193 4.4 26.2 1.0
CB A:TYR193 4.5 33.5 1.0
CA A:TYR193 4.6 25.8 1.0
HB3 A:TYR193 4.7 40.2 1.0
O A:GLY194 4.8 51.1 0.6
O A:TYR193 4.9 54.0 1.0
CD A:ARG195 5.0 44.6 0.6

Rubidium binding site 2 out of 3 in 6dot

Go back to Rubidium Binding Sites List in 6dot
Rubidium binding site 2 out of 3 in the Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 5 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 in Complex with An Rna/Dna Hybrid: Reaction in 5 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:30.5
occ:0.20
 O A:HOH420 2.5 42.7 1.0
O A:HOH402 2.6 41.0 1.0
O A:HOH451 2.7 45.3 1.0
OD1 A:ASN124 2.8 31.8 1.0
O A:HOH422 2.8 46.1 1.0
O A:LYS121 2.9 20.3 1.0
HG2 A:LYS121 3.5 24.1 1.0
CG A:ASN124 3.8 24.5 1.0
C A:LYS121 3.9 19.7 1.0
O A:HOH399 4.0 62.3 1.0
HG3 A:LYS121 4.0 24.1 1.0
H A:ASN124 4.1 20.1 1.0
CG A:LYS121 4.2 20.1 1.0
HD21 A:ASN124 4.2 42.7 1.0
HE3 A:LYS121 4.3 35.1 1.0
HA A:ASN124 4.3 20.9 1.0
ND2 A:ASN124 4.4 35.5 1.0
O A:HOH383 4.5 56.7 1.0
O A:HOH387 4.5 43.9 1.0
O A:HOH458 4.6 50.6 1.0
HA A:LYS121 4.6 21.2 1.0
O A:GLU122 4.7 23.0 1.0
CA A:GLU122 4.7 19.7 1.0
N A:GLU122 4.7 18.0 1.0
N A:ASN124 4.8 16.7 1.0
HZ2 A:LYS121 4.8 31.8 1.0
C A:GLU122 4.8 19.0 1.0
CA A:LYS121 4.8 17.6 1.0
CA A:ASN124 4.9 17.4 1.0
CB A:ASN124 4.9 20.7 1.0

Rubidium binding site 3 out of 3 in 6dot

Go back to Rubidium Binding Sites List in 6dot
Rubidium binding site 3 out of 3 in the Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 5 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 in Complex with An Rna/Dna Hybrid: Reaction in 5 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:35.9
occ:0.40
 O C:HOH213 2.4 24.6 0.5
O6 C:DG5 2.7 25.2 1.0
O B:HOH108 3.1 54.9 1.0
O4 C:DT4 3.2 21.8 1.0
O C:HOH212 3.2 28.2 1.0
C6 C:DG5 3.7 21.1 1.0
O C:HOH217 3.9 63.0 1.0
C4 C:DT4 4.1 18.4 1.0
N4 B:C2 4.1 28.4 1.0
C7 C:DT4 4.1 21.2 1.0
N7 C:DG5 4.2 21.8 1.0
C5 C:DG5 4.3 22.1 1.0
O B:HOH109 4.4 43.3 1.0
N6 B:A3 4.4 21.6 1.0
O C:HOH207 4.4 38.4 1.0
C5 C:DT4 4.5 18.3 1.0
N6 B:A1 4.5 30.2 1.0
N1 C:DG5 4.9 23.3 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 12:09:56 2024

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