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Rubidium in PDB 6dow: Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 5 Mm MG2+ and 200 Mm Rb+ For 160 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 160 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 160 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 160 S at 21 C, PDB code: 6dow 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) 19.40 / 1.50
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 82.035, 37.485, 62.504, 90.00, 96.84, 90.00
R / Rfree (%) 16.4 / 19.8

Other elements in 6dow:

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 160 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 160 S at 21 C (pdb code 6dow). 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 160 S at 21 C, PDB code: 6dow:
Jump to Rubidium binding site number: 1; 2; 3; 4; 5;

Rubidium binding site 1 out of 5 in 6dow

Go back to Rubidium Binding Sites List in 6dow
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 160 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 160 S at 21 C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Rb203

b:36.0
occ:0.10
 O b:HOH102 0.9 29.8 0.7
O A:HOH355 2.5 42.5 1.0
RB A:RB204 2.8 37.9 0.1
O A:HOH328 2.8 33.7 0.3
CG A:LYS196 3.0 38.8 0.7
OP2 b:G6 3.0 33.8 1.0
N A:ARG195 3.0 42.5 0.8
N A:LYS196 3.1 53.6 0.7
NZ A:LYS196 3.1 46.1 0.7
OD1 A:ASP192 3.1 33.0 1.0
OP3 b:C5 3.4 44.0 0.7
OD2 A:ASP192 3.6 33.9 1.0
CB A:LYS196 3.6 53.5 0.7
CA A:ARG195 3.6 45.7 0.8
C A:ARG195 3.7 54.0 0.8
N A:GLY194 3.7 33.4 1.0
O A:HOH312 3.7 32.0 1.0
CD A:LYS196 3.7 45.6 0.7
CG A:ASP192 3.7 32.5 1.0
CB A:ARG195 3.9 41.2 0.8
H A:TYR193 3.9 38.6 1.0
C A:GLY194 4.0 56.7 1.0
CA A:LYS196 4.0 71.1 0.7
CE A:LYS196 4.0 42.1 0.7
HB2 A:TYR193 4.0 39.6 1.0
P b:G6 4.0 32.0 1.0
MG A:MG201 4.1 27.3 1.0
CA A:GLY194 4.2 37.4 1.0
O5' b:G6 4.2 32.5 1.0
C A:TYR193 4.4 45.4 1.0
N A:TYR193 4.4 32.2 1.0
OP1 b:G6 4.5 32.5 1.0
CG A:ARG195 4.6 36.2 0.8
CA A:TYR193 4.7 34.6 1.0
CB A:TYR193 4.7 33.0 1.0
O A:ARG195 4.7 69.2 0.8
P b:C5 4.9 37.8 0.7
HB3 A:TYR193 5.0 39.6 1.0

Rubidium binding site 2 out of 5 in 6dow

Go back to Rubidium Binding Sites List in 6dow
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 160 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 160 S at 21 C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Rb204

b:37.9
occ:0.10
 NZ A:LYS196 1.0 46.1 0.7
O A:HOH355 2.2 42.5 1.0
O A:HOH328 2.4 33.7 0.3
CE A:LYS196 2.5 42.1 0.7
RB A:RB203 2.8 36.0 0.1
OP3 b:C5 2.9 44.0 0.7
OE2 A:GLU188 2.9 89.4 1.0
OD1 A:ASP192 3.1 33.0 1.0
OE1 A:GLU188 3.2 53.6 1.0
CD A:GLU188 3.2 68.0 1.0
OD2 A:ASP192 3.3 33.9 1.0
CD A:LYS196 3.4 45.6 0.7
CG A:LYS196 3.5 38.8 0.7
O b:HOH102 3.5 29.8 0.7
CB A:LYS196 3.5 53.5 0.7
CG A:ASP192 3.5 32.5 1.0
O A:HOH309 3.8 28.6 0.3
MG A:MG201 4.0 27.3 1.0
O A:HOH319 4.1 28.1 1.0
OP2 b:C5 4.1 37.7 0.3
P b:C5 4.2 37.8 0.7
CG A:GLU188 4.3 61.1 1.0
OP2 b:C5 4.3 28.4 0.7
N A:LYS196 4.5 53.6 0.7
CA A:LYS196 4.6 71.1 0.7
OP2 b:G6 4.7 33.8 1.0
CB A:ASP192 4.9 32.3 1.0
HB2 A:ASP192 4.9 38.7 1.0
O A:HOH312 4.9 32.0 1.0

Rubidium binding site 3 out of 5 in 6dow

Go back to Rubidium Binding Sites List in 6dow
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 160 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 160 S at 21 C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Rb205

b:34.8
occ:0.10
 O A:HOH419 2.6 64.3 1.0
O A:LYS121 3.0 29.3 1.0
OD1 A:ASN124 3.0 41.2 1.0
HG2 A:LYS121 3.3 35.1 1.0
O A:HOH405 3.5 57.8 1.0
HG3 A:LYS121 3.7 35.1 1.0
CG A:LYS121 3.9 29.2 1.0
C A:LYS121 4.0 26.1 1.0
HE3 A:LYS121 4.1 47.6 1.0
CG A:ASN124 4.1 39.3 1.0
HA A:ASN124 4.2 30.3 1.0
H A:ASN124 4.3 29.4 1.0
HZ2 A:LYS121 4.3 45.5 1.0
HA A:LYS121 4.4 26.8 1.0
O A:HOH430 4.5 63.1 1.0
O A:HOH380 4.5 49.0 1.0
HD21 A:ASN124 4.6 60.6 1.0
CA A:LYS121 4.7 22.3 1.0
CE A:LYS121 4.8 39.7 1.0
ND2 A:ASN124 4.8 50.5 1.0
CA A:ASN124 4.9 25.3 1.0
N A:ASN124 4.9 24.5 1.0
O A:HOH368 4.9 38.8 1.0
NZ A:LYS121 4.9 37.9 1.0
CB A:LYS121 4.9 22.4 1.0
N A:GLU122 4.9 25.3 1.0
CD A:LYS121 5.0 29.9 1.0

Rubidium binding site 4 out of 5 in 6dow

Go back to Rubidium Binding Sites List in 6dow
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 160 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 160 S at 21 C within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Rb101

b:31.0
occ:0.30
 O A:HOH309 1.4 28.6 0.3
O B:HOH208 2.4 44.3 1.0
OP2 b:C5 2.7 37.7 0.3
OP2 b:C5 2.8 28.4 0.7
C5' B:U4 3.0 28.0 0.7
C5' B:U4 3.3 40.7 0.3
O A:HOH341 3.3 27.2 1.0
HG21 A:THR183 3.3 41.4 1.0
HG1 A:THR183 3.4 35.5 1.0
OP1 B:U4 3.4 35.8 1.0
O5' B:U4 3.4 34.0 0.3
O b:HOH101 3.5 35.9 1.0
O5' B:U4 3.5 38.0 0.7
OD2 A:ASP132 3.6 39.9 1.0
OE1 A:GLU188 3.7 53.6 1.0
O A:HOH319 3.8 28.1 1.0
P B:U4 3.8 33.3 1.0
HB2 A:ASP132 3.8 32.8 1.0
P b:C5 3.8 28.1 0.3
C3' B:U4 3.9 40.9 0.3
O3' B:U4 3.9 32.9 0.3
P b:C5 4.0 37.8 0.7
CG A:ASP132 4.0 24.6 1.0
OP2 B:U4 4.1 35.2 1.0
C4' B:U4 4.1 37.5 0.3
OE2 A:GLU188 4.1 89.4 1.0
OG1 A:THR183 4.2 29.6 1.0
CG2 A:THR183 4.2 34.5 1.0
CD A:GLU188 4.3 68.0 1.0
C4' B:U4 4.3 35.7 0.7
CB A:ASP132 4.4 27.4 1.0
OP1 b:C5 4.4 33.7 0.7
HG23 A:THR183 4.4 41.4 1.0
OP3 b:C5 4.5 44.0 0.7
OP1 b:C5 4.6 37.6 0.3
C3' B:U4 4.6 34.1 0.7
HB3 A:ASP132 4.7 32.8 1.0
OD1 A:ASP132 4.7 29.7 1.0
NZ A:LYS196 4.7 46.1 0.7
CB A:THR183 4.7 32.8 1.0
HB A:THR183 4.7 39.4 1.0
O A:HOH328 4.8 33.7 0.3
CE A:LYS196 4.8 42.1 0.7
HG22 A:THR183 4.9 41.4 1.0

Rubidium binding site 5 out of 5 in 6dow

Go back to Rubidium Binding Sites List in 6dow
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 160 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 160 S at 21 C within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Rb101

b:52.5
occ:0.40
 O C:HOH210 2.5 29.2 0.6
O6 C:DG5 2.6 34.5 1.0
O C:HOH209 3.2 36.2 1.0
C2 C:EDO103 3.5 49.1 1.0
O C:HOH202 3.5 54.5 1.0
O4 C:DT4 3.6 32.0 1.0
C6 C:DG5 3.7 36.5 1.0
N4 B:C2 4.1 35.9 1.0
O2 C:EDO103 4.2 43.1 1.0
N7 C:DG5 4.2 30.0 1.0
O B:HOH203 4.3 57.0 1.0
C5 C:DG5 4.3 31.3 1.0
N6 B:A1 4.3 32.9 1.0
C7 C:DT4 4.4 31.6 1.0
C4 C:DT4 4.4 29.9 1.0
O1 C:EDO103 4.5 67.4 1.0
C1 C:EDO103 4.6 49.4 1.0
N6 B:A3 4.7 27.8 1.0
C5 C:DT4 4.8 29.4 1.0
O4 C:DT6 4.9 40.7 1.0
N1 C:DG5 4.9 35.1 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: Wed Dec 16 02:07:08 2020

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