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Rubidium in PDB 6dou: Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 5 Mm MG2+ and 200 Mm Rb+ For 120 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 120 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 120 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 120 S at 21 C, PDB code: 6dou 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) 19.94 / 1.49
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 81.541, 37.383, 62.437, 90.00, 96.57, 90.00
R / Rfree (%) 15.5 / 18.8

Other elements in 6dou:

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 120 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 120 S at 21 C (pdb code 6dou). 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 120 S at 21 C, PDB code: 6dou:
Jump to Rubidium binding site number: 1; 2; 3; 4; 5;

Rubidium binding site 1 out of 5 in 6dou

Go back to Rubidium Binding Sites List in 6dou
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 120 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 120 S at 21 C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Rb203

b:32.4
occ:0.10
 O b:HOH102 1.1 24.3 0.5
O A:HOH343 2.3 41.9 1.0
RB A:RB205 2.4 40.2 0.1
O b:HOH101 2.7 27.5 0.5
OP2 b:G6 3.0 34.0 1.0
OD1 A:ASP192 3.0 36.9 1.0
OP3 b:C5 3.0 61.4 0.5
CD A:LYS196 3.2 48.3 0.5
N A:ARG195 3.2 47.9 0.8
CG A:LYS196 3.2 42.7 0.5
OD2 A:ASP192 3.5 32.0 1.0
N A:LYS196 3.5 52.3 0.5
O A:HOH316 3.5 28.7 1.0
CB A:LYS196 3.5 54.0 0.5
CG A:ASP192 3.6 29.4 1.0
C A:ARG195 3.8 58.6 0.8
N A:GLY194 3.8 34.5 1.0
MG A:MG201 3.9 25.3 1.0
CA A:ARG195 3.9 53.8 0.8
H A:TYR193 4.0 37.0 1.0
P b:G6 4.1 33.1 1.0
CA A:LYS196 4.1 63.7 0.5
C A:GLY194 4.1 57.9 1.0
HB2 A:TYR193 4.1 41.0 1.0
CB A:ARG195 4.2 53.7 0.8
CA A:GLY194 4.2 43.1 1.0
O5' b:G6 4.2 32.2 1.0
CE A:LYS196 4.4 54.4 0.5
P b:C5 4.4 34.7 0.5
N A:TYR193 4.5 30.8 1.0
C A:TYR193 4.5 39.9 1.0
OP1 b:G6 4.6 36.2 1.0
O A:ARG195 4.7 65.2 0.8
O5' b:C5 4.9 36.9 0.5
CA A:TYR193 4.9 30.7 1.0
CB A:TYR193 4.9 34.1 1.0
CG A:ARG195 4.9 50.7 0.8
NZ A:LYS196 5.0 59.1 0.5

Rubidium binding site 2 out of 5 in 6dou

Go back to Rubidium Binding Sites List in 6dou
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 120 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 120 S at 21 C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Rb204

b:32.3
occ:0.25
 O A:HOH308 1.6 30.6 0.5
O B:HOH111 2.6 50.5 1.0
C5' B:U4 2.7 32.6 0.5
OP2 b:C5 2.7 41.9 0.5
OP2 b:C5 2.8 28.8 0.5
C5' B:U4 2.9 32.9 0.5
HG21 A:THR183 3.4 39.3 1.0
O A:HOH369 3.4 25.6 1.0
HG1 A:THR183 3.4 34.3 1.0
O A:HOH302 3.5 36.5 1.0
OD2 A:ASP132 3.5 34.7 1.0
O5' B:U4 3.5 37.8 0.5
O5' B:U4 3.6 34.5 0.5
OP1 B:U4 3.7 32.1 1.0
O A:HOH324 3.7 30.4 1.0
P b:C5 3.7 27.8 0.5
C4' B:U4 3.7 27.9 0.5
O3' B:U4 3.7 26.7 0.5
C3' B:U4 3.7 33.5 0.5
OE1 A:GLU188 3.8 65.2 1.0
HB2 A:ASP132 3.9 26.4 1.0
P B:U4 3.9 29.3 1.0
CG A:ASP132 4.0 27.9 1.0
P b:C5 4.0 34.7 0.5
OP2 B:U4 4.2 33.9 1.0
C4' B:U4 4.2 28.4 0.5
NZ A:LYS196 4.2 59.1 0.5
OG1 A:THR183 4.2 28.6 1.0
CG2 A:THR183 4.3 32.7 1.0
OP1 b:C5 4.4 34.5 0.5
OP1 b:C5 4.4 38.7 0.5
CB A:ASP132 4.5 22.0 1.0
C3' B:U4 4.5 33.0 0.5
OP3 b:C5 4.5 61.4 0.5
CD A:GLU188 4.5 82.8 1.0
OE2 A:GLU188 4.5 0.8 1.0
HG23 A:THR183 4.6 39.3 1.0
OD1 A:ASP132 4.6 25.5 1.0
O b:HOH101 4.7 27.5 0.5
HB3 A:ASP132 4.7 26.4 1.0
CB A:THR183 4.7 32.5 1.0
HB A:THR183 4.8 39.0 1.0
O4' B:U4 4.8 32.7 0.5
MG A:MG202 4.9 25.7 1.0
C2' B:U4 5.0 25.4 0.5
O4' B:U4 5.0 24.6 0.5
HG22 A:THR183 5.0 39.3 1.0

Rubidium binding site 3 out of 5 in 6dou

Go back to Rubidium Binding Sites List in 6dou
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 120 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 120 S at 21 C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Rb205

b:40.2
occ:0.10
 O A:HOH343 1.8 41.9 1.0
RB A:RB203 2.4 32.4 0.1
O b:HOH101 2.5 27.5 0.5
OE2 A:GLU188 2.8 0.8 1.0
OP3 b:C5 2.8 61.4 0.5
OD1 A:ASP192 3.1 36.9 1.0
OD2 A:ASP192 3.2 32.0 1.0
CD A:GLU188 3.3 82.8 1.0
CD A:LYS196 3.3 48.3 0.5
OE1 A:GLU188 3.4 65.2 1.0
O b:HOH102 3.4 24.3 0.5
CB A:LYS196 3.5 54.0 0.5
CG A:ASP192 3.5 29.4 1.0
CE A:LYS196 3.6 54.4 0.5
O A:HOH308 3.8 30.6 0.5
CG A:LYS196 3.8 42.7 0.5
MG A:MG201 3.9 25.3 1.0
NZ A:LYS196 4.0 59.1 0.5
P b:C5 4.1 34.7 0.5
OP2 b:C5 4.1 41.9 0.5
O A:HOH324 4.2 30.4 1.0
OP2 b:C5 4.3 28.8 0.5
N A:LYS196 4.4 52.3 0.5
CG A:GLU188 4.4 67.8 1.0
CA A:LYS196 4.5 63.7 0.5
OP2 b:G6 4.7 34.0 1.0
O A:HOH316 4.8 28.7 1.0
CB A:ASP192 4.9 31.3 1.0
HB2 A:ASP192 5.0 37.5 1.0
N A:ARG195 5.0 47.9 0.8
P b:C5 5.0 27.8 0.5

Rubidium binding site 4 out of 5 in 6dou

Go back to Rubidium Binding Sites List in 6dou
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 120 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 120 S at 21 C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Rb206

b:62.5
occ:0.20
 O A:HOH437 2.6 58.0 1.0
OD1 A:ASN124 3.0 42.1 1.0
O A:LYS121 3.2 25.8 1.0
HG2 A:LYS121 3.4 26.4 1.0
O A:HOH413 3.5 51.1 1.0
HG3 A:LYS121 3.7 26.4 1.0
O A:HOH415 3.8 63.3 1.0
HE3 A:LYS121 4.0 45.4 1.0
CG A:LYS121 4.0 22.0 1.0
CG A:ASN124 4.1 32.0 1.0
O A:HOH446 4.2 65.1 1.0
C A:LYS121 4.2 23.0 1.0
HZ2 A:LYS121 4.2 39.9 1.0
HA A:ASN124 4.3 26.7 1.0
H A:ASN124 4.5 25.0 1.0
HA A:LYS121 4.5 24.8 1.0
CE A:LYS121 4.7 37.8 1.0
HD21 A:ASN124 4.7 52.7 1.0
O A:HOH410 4.8 49.1 1.0
O A:HOH340 4.8 37.8 1.0
NZ A:LYS121 4.8 33.2 1.0
CA A:LYS121 4.8 20.6 1.0
ND2 A:ASN124 4.9 43.9 1.0
CA A:ASN124 5.0 22.3 1.0
CD A:LYS121 5.0 25.7 1.0
HZ1 A:LYS121 5.0 39.9 1.0

Rubidium binding site 5 out of 5 in 6dou

Go back to Rubidium Binding Sites List in 6dou
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 120 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 120 S at 21 C within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Rb101

b:50.1
occ:0.40
 O C:HOH208 2.5 28.0 0.6
O6 C:DG5 2.7 31.8 1.0
O1 C:EDO102 2.9 38.1 1.0
O B:HOH110 3.1 53.4 1.0
O4 C:DT4 3.4 28.7 1.0
O2 C:EDO103 3.5 51.7 1.0
C6 C:DG5 3.7 32.5 1.0
N4 B:C2 4.0 33.5 1.0
N7 C:DG5 4.2 27.2 1.0
C7 C:DT4 4.2 28.8 1.0
C4 C:DT4 4.2 24.3 1.0
O B:HOH107 4.2 56.0 1.0
C1 C:EDO102 4.3 57.9 1.0
C5 C:DG5 4.3 27.1 1.0
N6 B:A1 4.4 32.3 1.0
O1 C:EDO103 4.4 63.1 1.0
C5 C:DT4 4.6 27.4 1.0
N6 B:A3 4.6 24.4 1.0
C2 C:EDO103 4.9 43.9 1.0
C2 C:EDO102 4.9 70.3 1.0
N1 C:DG5 4.9 30.4 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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