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Rubidium in PDB 6dov: Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 5 Mm MG2+ and 200 Mm Rb+ For 80 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 80 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 80 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 80 S at 21 C, PDB code: 6dov 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) 20.06 / 1.52
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 81.656, 37.396, 61.670, 90.00, 96.51, 90.00
R / Rfree (%) 15.3 / 19

Other elements in 6dov:

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 80 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 80 S at 21 C (pdb code 6dov). 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 80 S at 21 C, PDB code: 6dov:
Jump to Rubidium binding site number: 1; 2; 3; 4; 5;

Rubidium binding site 1 out of 5 in 6dov

Go back to Rubidium Binding Sites List in 6dov
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 80 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 80 S at 21 C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Rb203

b:37.6
occ:0.15
 O A:HOH346 0.9 19.1 0.2
O A:HOH315 2.5 42.5 1.0
O A:HOH314 2.5 30.0 0.8
RB A:RB205 2.8 36.5 0.1
C A:ARG195 2.9 70.1 0.8
OP2 b:G6 3.0 29.5 1.0
N A:ARG195 3.0 64.2 0.8
OP3 b:C5 3.0 58.5 0.2
O b:HOH107 3.1 53.3 1.0
OD1 A:ASP192 3.1 35.4 1.0
O b:HOH101 3.4 27.9 1.0
CA A:ARG195 3.5 67.0 0.8
O A:ARG195 3.6 74.9 0.8
OD2 A:ASP192 3.7 35.7 1.0
N A:GLY194 3.7 42.1 1.0
CG A:ASP192 3.8 28.2 1.0
C A:GLY194 3.8 70.7 1.0
MG A:MG201 3.8 23.8 1.0
H A:TYR193 4.0 38.5 1.0
HB2 A:TYR193 4.0 39.6 1.0
P b:G6 4.0 27.9 1.0
CA A:GLY194 4.1 57.7 1.0
CB A:ARG195 4.1 53.9 0.8
CG A:ARG195 4.1 50.7 0.8
O5' b:G6 4.2 29.3 1.0
OP1 b:G6 4.4 26.8 1.0
C A:TYR193 4.5 42.0 1.0
P b:C5 4.5 41.0 0.2
N A:TYR193 4.5 32.1 1.0
CB A:TYR193 4.8 33.0 1.0
O A:GLY194 4.8 72.4 1.0
CA A:TYR193 4.8 29.6 1.0

Rubidium binding site 2 out of 5 in 6dov

Go back to Rubidium Binding Sites List in 6dov
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 80 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 80 S at 21 C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Rb204

b:37.0
occ:0.15
 O A:HOH337 1.2 32.6 0.8
C5' B:U4 2.6 21.4 0.8
O B:HOH104 2.7 35.7 1.0
OP2 b:C5 2.8 27.9 0.8
OP2 b:C5 2.8 36.3 0.2
C5' B:U4 3.0 27.6 0.2
OD2 A:ASP132 3.3 30.9 1.0
HG1 A:THR183 3.4 32.9 1.0
O A:HOH348 3.4 24.8 1.0
HG21 A:THR183 3.5 34.8 1.0
O3' B:U4 3.5 21.2 0.8
P b:C5 3.6 21.8 0.8
C4' B:U4 3.6 21.5 0.8
C3' B:U4 3.6 22.9 0.8
O5' B:U4 3.6 25.5 0.8
O5' B:U4 3.7 28.4 0.2
O b:HOH102 3.7 39.4 0.8
O b:HOH103 3.7 28.1 1.0
OE1 A:GLU188 3.8 54.2 1.0
CG A:ASP132 3.9 25.5 1.0
OP1 B:U4 3.9 25.7 1.0
HB2 A:ASP132 4.0 29.3 1.0
OP2 B:U4 4.0 25.2 1.0
P b:C5 4.0 41.0 0.2
P B:U4 4.0 23.1 1.0
OG1 A:THR183 4.2 27.4 1.0
C4' B:U4 4.2 23.5 0.2
OP1 b:C5 4.2 29.4 0.8
OP1 b:C5 4.3 34.3 0.2
CG2 A:THR183 4.4 29.0 1.0
C3' B:U4 4.4 26.7 0.2
OD1 A:ASP132 4.5 24.3 1.0
CB A:ASP132 4.5 24.4 1.0
CD A:GLU188 4.6 66.6 1.0
OE2 A:GLU188 4.6 85.1 1.0
HG23 A:THR183 4.6 34.8 1.0
CB A:THR183 4.7 31.2 1.0
HB3 A:ASP132 4.8 29.3 1.0
HB A:THR183 4.8 37.5 1.0
OP3 b:C5 4.8 58.5 0.2
O4' B:U4 4.8 24.5 0.8
O A:HOH314 4.8 30.0 0.8
MG A:MG202 4.9 19.8 1.0
C2' B:U4 4.9 20.5 0.2
O4' B:U4 5.0 21.4 0.2

Rubidium binding site 3 out of 5 in 6dov

Go back to Rubidium Binding Sites List in 6dov
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 80 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 80 S at 21 C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Rb205

b:36.5
occ:0.10
 O A:HOH315 1.8 42.5 1.0
O A:HOH314 2.1 30.0 0.8
RB A:RB203 2.8 37.6 0.1
OP3 b:C5 2.9 58.5 0.2
OE1 A:GLU188 2.9 54.2 1.0
OD1 A:ASP192 3.1 35.4 1.0
CD A:GLU188 3.2 66.6 1.0
OE2 A:GLU188 3.3 85.1 1.0
OD2 A:ASP192 3.4 35.7 1.0
O b:HOH107 3.5 53.3 1.0
O A:HOH346 3.5 19.1 0.2
CG A:ASP192 3.6 28.2 1.0
MG A:MG201 3.7 23.8 1.0
OP2 b:C5 3.8 36.3 0.2
O b:HOH103 3.9 28.1 1.0
OP2 b:C5 3.9 27.9 0.8
O A:HOH337 3.9 32.6 0.8
P b:C5 4.0 41.0 0.2
CG A:GLU188 4.3 49.2 1.0
O b:HOH101 4.7 27.9 1.0
OP2 b:G6 4.7 29.5 1.0
P b:C5 4.8 21.8 0.8
OP1 b:C5 4.8 29.4 0.8
C A:ARG195 4.9 70.1 0.8
OP1 b:C5 4.9 34.3 0.2
O A:ARG195 4.9 74.9 0.8
CB A:ASP192 4.9 29.3 1.0

Rubidium binding site 4 out of 5 in 6dov

Go back to Rubidium Binding Sites List in 6dov
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 80 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 80 S at 21 C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Rb206

b:32.1
occ:0.20
 O A:HOH421 2.5 42.5 1.0
O A:HOH446 2.6 42.4 1.0
O A:HOH425 2.6 44.5 1.0
OD1 A:ASN124 2.9 37.7 1.0
O A:LYS121 2.9 22.6 1.0
HG2 A:LYS121 3.5 28.8 1.0
C A:LYS121 3.9 21.9 1.0
CG A:ASN124 4.0 31.6 1.0
HG3 A:LYS121 4.0 28.8 1.0
O A:HOH416 4.0 55.3 1.0
H A:ASN124 4.2 23.7 1.0
CG A:LYS121 4.2 24.0 1.0
HA A:ASN124 4.3 26.0 1.0
HD21 A:ASN124 4.3 44.7 1.0
O A:HOH418 4.4 31.5 1.0
HE3 A:LYS121 4.5 36.5 1.0
HZ2 A:LYS121 4.5 39.2 1.0
ND2 A:ASN124 4.6 37.2 1.0
O A:HOH454 4.6 45.1 1.0
HA A:LYS121 4.6 21.4 1.0
CA A:GLU122 4.7 23.1 1.0
N A:GLU122 4.7 20.7 1.0
O A:GLU122 4.8 24.8 1.0
N A:ASN124 4.8 19.7 1.0
CA A:LYS121 4.8 17.9 1.0
C A:GLU122 4.8 20.3 1.0
CA A:ASN124 4.9 21.7 1.0

Rubidium binding site 5 out of 5 in 6dov

Go back to Rubidium Binding Sites List in 6dov
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 80 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 80 S at 21 C within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Rb101

b:44.7
occ:0.40
 O C:HOH212 2.4 23.5 0.6
O6 C:DG5 2.7 27.5 1.0
O B:HOH107 2.9 48.4 1.0
O C:HOH210 3.2 31.1 1.0
O4 C:DT4 3.3 27.5 1.0
C6 C:DG5 3.7 24.8 1.0
N4 B:C2 4.0 30.9 1.0
N7 C:DG5 4.2 24.8 1.0
C4 C:DT4 4.2 22.2 1.0
O B:HOH110 4.2 62.7 1.0
C7 C:DT4 4.2 26.5 1.0
O C:HOH207 4.3 38.2 1.0
C5 C:DG5 4.3 25.2 1.0
N6 B:A1 4.4 33.3 1.0
N6 B:A3 4.5 25.3 1.0
C5 C:DT4 4.6 24.5 1.0
N1 C:DG5 4.9 27.9 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 02:07:07 2020

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