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Rubidium in PDB 6dox: Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 5 Mm MG2+ and 200 Mm Rb+ For 360 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 360 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 360 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 360 S at 21 C, PDB code: 6dox 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) 19.89 / 1.45
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 81.324, 37.894, 62.145, 90.00, 96.71, 90.00
R / Rfree (%) 15.4 / 17.5

Other elements in 6dox:

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 360 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 360 S at 21 C (pdb code 6dox). This binding sites where shown within 5.0 Angstroms radius around Rubidium atom.
In total 5 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 360 S at 21 C, PDB code: 6dox:
Jump to Rubidium binding site number: 1; 2; 3; 4; 5;

Rubidium binding site 1 out of 5 in 6dox

Go back to Rubidium Binding Sites List in 6dox
Rubidium binding site 1 out of 5 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 360 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 360 S at 21 C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Rb203

b:31.1
occ:0.10
 O b:HOH203 0.9 22.9 0.7
O A:HOH358 2.5 31.2 1.0
RB A:RB205 2.8 33.2 0.1
O A:HOH307 2.8 33.1 0.3
N A:LYS196 2.9 35.0 0.7
OP2 b:G6 3.0 21.3 1.0
N A:ARG195 3.0 29.7 0.8
CG A:LYS196 3.1 29.8 0.7
OD1 A:ASP192 3.1 20.6 1.0
NZ A:LYS196 3.3 28.4 0.7
OD2 A:ASP192 3.5 23.6 1.0
CA A:ARG195 3.6 31.9 0.8
OP3 b:C5 3.6 22.4 0.7
C A:ARG195 3.6 35.9 0.8
CB A:LYS196 3.7 37.3 0.7
N A:GLY194 3.7 26.7 1.0
O A:HOH315 3.7 22.6 1.0
CG A:ASP192 3.7 20.8 1.0
H A:TYR193 3.8 26.0 1.0
CB A:ARG195 3.8 35.2 0.8
CA A:LYS196 3.9 51.7 0.7
C A:GLY194 3.9 35.3 1.0
HB2 A:TYR193 3.9 28.2 1.0
CD A:LYS196 4.0 27.6 0.7
P b:G6 4.0 20.9 1.0
CA A:GLY194 4.1 27.1 1.0
CE A:LYS196 4.2 26.2 0.7
O5' b:G6 4.2 23.3 1.0
MG A:MG201 4.2 19.7 1.0
C A:TYR193 4.3 28.7 1.0
N A:TYR193 4.3 21.7 1.0
OP1 b:G6 4.5 20.2 1.0
CG A:ARG195 4.6 31.6 0.8
CA A:TYR193 4.6 25.3 1.0
CB A:TYR193 4.6 23.5 1.0
O A:ARG195 4.8 42.4 0.8
HB3 A:TYR193 4.9 28.2 1.0
C A:LYS196 4.9 77.5 0.7
O A:GLY194 5.0 39.7 1.0

Rubidium binding site 2 out of 5 in 6dox

Go back to Rubidium Binding Sites List in 6dox
Rubidium binding site 2 out of 5 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 360 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 360 S at 21 C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Rb204

b:48.7
occ:0.20
 O A:HOH427 2.6 50.3 1.0
O A:HOH409 2.7 46.7 1.0
O A:HOH412 2.8 51.8 1.0
OD1 A:ASN124 2.9 36.5 1.0
O A:LYS121 3.0 20.3 1.0
HG2 A:LYS121 3.5 24.1 1.0
CG A:ASN124 3.9 29.6 1.0
C A:LYS121 4.1 18.1 1.0
HG3 A:LYS121 4.2 24.1 1.0
HD21 A:ASN124 4.2 44.2 1.0
HE3 A:LYS121 4.2 33.5 1.0
CG A:LYS121 4.2 20.1 1.0
H A:ASN124 4.3 23.5 1.0
O A:HOH379 4.3 47.9 1.0
HA A:ASN124 4.4 24.4 1.0
O A:HOH405 4.4 55.0 1.0
O A:HOH353 4.4 52.8 1.0
ND2 A:ASN124 4.4 36.8 1.0
HA A:LYS121 4.7 21.8 1.0
HZ2 A:LYS121 4.8 31.4 1.0
CA A:GLU122 4.9 22.5 1.0
N A:ASN124 4.9 19.6 1.0
O A:GLU122 4.9 24.3 1.0
N A:GLU122 4.9 18.0 1.0
CA A:LYS121 4.9 18.1 1.0
CA A:ASN124 4.9 20.4 1.0
C A:GLU122 5.0 22.0 1.0

Rubidium binding site 3 out of 5 in 6dox

Go back to Rubidium Binding Sites List in 6dox
Rubidium binding site 3 out of 5 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 360 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 360 S at 21 C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Rb205

b:33.2
occ:0.10
 NZ A:LYS196 1.0 28.4 0.7
O A:HOH358 1.9 31.2 1.0
CE A:LYS196 2.3 26.2 0.7
O A:HOH307 2.4 33.1 0.3
RB A:RB203 2.8 31.1 0.1
OP3 b:C5 2.9 22.4 0.7
OD1 A:ASP192 3.1 20.6 1.0
OE2 A:GLU188 3.2 51.5 1.0
CD A:LYS196 3.2 27.6 0.7
OE1 A:GLU188 3.2 40.2 1.0
CG A:LYS196 3.2 29.8 0.7
CD A:GLU188 3.3 42.9 1.0
OD2 A:ASP192 3.3 23.6 1.0
CB A:LYS196 3.4 37.3 0.7
O b:HOH203 3.5 22.9 0.7
CG A:ASP192 3.5 20.8 1.0
MG A:MG201 4.0 19.7 1.0
O b:HOH201 4.1 16.0 0.3
O A:HOH318 4.1 21.8 1.0
P b:C5 4.2 21.8 0.7
CG A:GLU188 4.2 36.1 1.0
N A:LYS196 4.2 35.0 0.7
OP2 b:C5 4.3 23.8 0.3
CA A:LYS196 4.4 51.7 0.7
OP2 b:C5 4.5 18.9 0.7
OXT A:LYS196 4.6 95.8 1.0
OP2 b:G6 4.7 21.3 1.0
O A:HOH315 4.9 22.6 1.0
CB A:ASP192 4.9 21.9 1.0
HB2 A:ASP192 5.0 26.3 1.0

Rubidium binding site 4 out of 5 in 6dox

Go back to Rubidium Binding Sites List in 6dox
Rubidium binding site 4 out of 5 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 360 S at 21 C


Mono view


Stereo pair view

A full contact list of Rubidium with other atoms in the Rb binding site number 4 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 360 S at 21 C within 5.0Å range:
probe atom residue distance (Å) B Occ
b:Rb101

b:22.6
occ:0.30
 O b:HOH201 1.1 16.0 0.3
O B:HOH206 2.4 29.2 1.0
OP2 b:C5 2.7 23.8 0.3
OP2 b:C5 2.8 18.9 0.7
C5' B:U4 3.0 20.2 0.7
HG21 A:THR183 3.3 30.7 1.0
HG1 A:THR183 3.3 27.2 1.0
O A:HOH360 3.4 19.7 1.0
O5' B:U4 3.4 23.9 0.3
O b:HOH202 3.4 25.6 1.0
OP1 B:U4 3.4 24.3 1.0
C5' B:U4 3.4 29.8 0.3
O5' B:U4 3.5 27.4 0.7
P b:C5 3.7 17.3 0.3
OE1 A:GLU188 3.7 40.2 1.0
O A:HOH318 3.8 21.8 1.0
OD2 A:ASP132 3.8 29.9 1.0
HB2 A:ASP132 3.8 20.5 1.0
P B:U4 3.9 23.4 1.0
P b:C5 3.9 21.8 0.7
O3' B:U4 3.9 25.0 0.3
C3' B:U4 3.9 28.1 0.3
OE2 A:GLU188 3.9 51.5 1.0
OP2 B:U4 4.1 27.1 1.0
CG A:ASP132 4.1 20.3 1.0
OG1 A:THR183 4.1 22.6 1.0
CG2 A:THR183 4.2 25.6 1.0
CD A:GLU188 4.2 42.9 1.0
C4' B:U4 4.2 23.9 0.3
OP3 b:C5 4.3 22.4 0.7
C4' B:U4 4.3 23.3 0.7
OP1 b:C5 4.3 27.3 0.3
OP1 b:C5 4.3 21.7 0.7
NZ A:LYS196 4.3 28.4 0.7
HG23 A:THR183 4.4 30.7 1.0
CB A:ASP132 4.4 17.1 1.0
CE A:LYS196 4.6 26.2 0.7
C3' B:U4 4.6 19.0 0.7
CB A:THR183 4.6 25.5 1.0
OD1 A:ASP132 4.7 20.3 1.0
HB3 A:ASP132 4.7 20.5 1.0
HB A:THR183 4.7 30.6 1.0
O A:HOH307 4.8 33.1 0.3
HG22 A:THR183 4.9 30.7 1.0

Rubidium binding site 5 out of 5 in 6dox

Go back to Rubidium Binding Sites List in 6dox
Rubidium binding site 5 out of 5 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 360 S at 21 C


Mono view


Stereo pair view

A full contact list of Rubidium with other atoms in the Rb binding site number 5 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 360 S at 21 C within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Rb101

b:53.2
occ:0.40
 O C:HOH211 2.6 26.0 0.6
O6 C:DG5 2.6 27.6 1.0
O2 C:EDO102 3.1 32.4 1.0
O2 B:EDO101 3.3 64.0 1.0
O4 C:DT4 3.6 24.1 1.0
C6 C:DG5 3.7 25.9 1.0
O1 B:EDO101 3.8 45.5 1.0
N4 B:C2 4.1 32.3 1.0
C2 C:EDO102 4.1 50.6 1.0
N7 C:DG5 4.2 23.1 1.0
C2 B:EDO101 4.3 52.1 1.0
C5 C:DG5 4.3 24.6 1.0
N6 B:A1 4.3 29.3 1.0
O B:HOH204 4.4 50.0 1.0
C1 B:EDO101 4.4 45.1 1.0
C4 C:DT4 4.4 20.4 1.0
C7 C:DT4 4.5 24.7 1.0
N6 B:A3 4.8 22.6 1.0
O4 C:DT6 4.8 30.6 1.0
C5 C:DT4 4.9 21.6 1.0
N1 C:DG5 4.9 23.7 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: Thu Oct 10 12:09:59 2024

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