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Rubidium in PDB 6dpl: Crystal Structure of Bacillus Halodurans Ribonuclease H1 K196A in Complex with An Rna/Dna Hybrid: Reaction in 10 Mm MG2+ and 200 Mm Rb+ For 720 S at 21 C

Enzymatic activity of Crystal Structure of Bacillus Halodurans Ribonuclease H1 K196A in Complex with An Rna/Dna Hybrid: Reaction in 10 Mm MG2+ and 200 Mm Rb+ For 720 S at 21 C

All present enzymatic activity of Crystal Structure of Bacillus Halodurans Ribonuclease H1 K196A in Complex with An Rna/Dna Hybrid: Reaction in 10 Mm MG2+ and 200 Mm Rb+ For 720 S at 21 C:
3.1.26.4;

Protein crystallography data

The structure of Crystal Structure of Bacillus Halodurans Ribonuclease H1 K196A in Complex with An Rna/Dna Hybrid: Reaction in 10 Mm MG2+ and 200 Mm Rb+ For 720 S at 21 C, PDB code: 6dpl 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) 19.50 / 1.45
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 81.856, 37.521, 62.706, 90.00, 97.31, 90.00
R / Rfree (%) 15.1 / 17.9

Other elements in 6dpl:

The structure of Crystal Structure of Bacillus Halodurans Ribonuclease H1 K196A in Complex with An Rna/Dna Hybrid: Reaction in 10 Mm MG2+ and 200 Mm Rb+ For 720 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 K196A in Complex with An Rna/Dna Hybrid: Reaction in 10 Mm MG2+ and 200 Mm Rb+ For 720 S at 21 C (pdb code 6dpl). This binding sites where shown within 5.0 Angstroms radius around Rubidium atom.
In total 6 binding sites of Rubidium where determined in the Crystal Structure of Bacillus Halodurans Ribonuclease H1 K196A in Complex with An Rna/Dna Hybrid: Reaction in 10 Mm MG2+ and 200 Mm Rb+ For 720 S at 21 C, PDB code: 6dpl:
Jump to Rubidium binding site number: 1; 2; 3; 4; 5; 6;

Rubidium binding site 1 out of 6 in 6dpl

Go back to Rubidium Binding Sites List in 6dpl
Rubidium binding site 1 out of 6 in the Crystal Structure of Bacillus Halodurans Ribonuclease H1 K196A in Complex with An Rna/Dna Hybrid: Reaction in 10 Mm MG2+ and 200 Mm Rb+ For 720 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 K196A in Complex with An Rna/Dna Hybrid: Reaction in 10 Mm MG2+ and 200 Mm Rb+ For 720 S at 21 C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Rb203

b:28.1
occ:0.25
 RB A:RB205 2.3 39.0 0.2
O A:TYR193 2.4 81.0 1.0
N A:ALA196 2.7 56.7 0.6
N A:ARG195 2.8 61.2 0.7
OP2 b:G6 3.0 20.0 1.0
O b:HOH101 3.0 26.6 1.0
OD1 A:ASP192 3.0 25.8 1.0
C A:ALA196 3.2 76.7 0.6
C A:ARG195 3.3 65.6 0.7
OXT A:ALA196 3.4 56.8 0.6
C A:TYR193 3.4 33.2 1.0
CA A:ARG195 3.4 52.7 0.7
O A:HOH317 3.5 21.4 1.0
CA A:ALA196 3.5 77.1 0.6
OD2 A:ASP192 3.5 30.1 1.0
O A:ALA196 3.6 93.8 0.6
CG A:ASP192 3.7 25.2 1.0
H A:TYR193 3.8 27.4 1.0
CB A:ARG195 3.8 53.5 0.7
C A:GLY194 3.8 0.5 1.0
HB2 A:TYR193 3.9 30.8 1.0
MG A:MG201 4.0 19.5 1.0
P b:G6 4.1 19.7 1.0
CA A:GLY194 4.1 58.8 1.0
N A:GLY194 4.2 49.6 1.0
N A:TYR193 4.3 22.8 1.0
CA A:TYR193 4.3 23.8 1.0
O A:ARG195 4.3 75.6 0.7
OP1 b:G6 4.4 19.1 1.0
O5' b:G6 4.5 20.9 1.0
CB A:TYR193 4.6 25.7 1.0
CG A:ARG195 4.6 47.9 0.7
CB A:ALA196 4.8 64.9 0.6
HB3 A:TYR193 4.8 30.8 1.0
O A:GLY194 4.9 73.5 1.0
O A:HOH303 4.9 44.3 0.6

Rubidium binding site 2 out of 6 in 6dpl

Go back to Rubidium Binding Sites List in 6dpl
Rubidium binding site 2 out of 6 in the Crystal Structure of Bacillus Halodurans Ribonuclease H1 K196A in Complex with An Rna/Dna Hybrid: Reaction in 10 Mm MG2+ and 200 Mm Rb+ For 720 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 K196A in Complex with An Rna/Dna Hybrid: Reaction in 10 Mm MG2+ and 200 Mm Rb+ For 720 S at 21 C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Rb204

b:22.5
occ:0.45
 C5' B:U4 2.5 16.9 0.6
OP2 b:C5 2.8 17.3 0.5
OP2 b:C5 2.9 37.4 0.6
OE1 A:GLU188 3.1 35.7 1.0
O5' B:U4 3.1 25.9 0.6
O A:HOH360 3.1 18.9 0.3
OD2 A:ASP132 3.2 23.8 1.0
OP1 B:U4 3.3 19.1 0.5
OP1 B:U4 3.4 37.5 0.6
O b:HOH102 3.5 48.6 1.0
HG1 A:THR183 3.5 27.2 1.0
O A:HOH348 3.6 21.2 1.0
P B:U4 3.6 19.2 0.6
O5' B:U4 3.6 18.3 0.5
HG21 A:THR183 3.6 34.2 1.0
C4' B:U4 3.6 16.1 0.6
C3' B:U4 3.8 30.9 0.6
O A:HOH326 3.8 19.3 1.0
P b:C5 3.8 16.9 0.5
OP3 b:C5 3.8 16.5 0.5
P b:C5 3.8 45.2 0.6
O3' B:U4 3.9 43.0 0.6
CG A:ASP132 3.9 20.4 1.0
C5' B:U4 3.9 22.2 0.5
HB2 A:ASP132 3.9 22.6 1.0
OP2 B:U4 3.9 53.8 0.6
P B:U4 4.1 18.7 0.5
CD A:GLU188 4.1 78.9 1.0
O4' B:U4 4.1 20.0 0.5
O A:HOH303 4.2 44.3 0.6
OG1 A:THR183 4.3 22.6 1.0
OP1 b:C5 4.4 18.0 0.5
C6 B:U4 4.4 16.1 0.5
CB A:ASP132 4.4 18.8 1.0
OP1 b:C5 4.5 38.0 0.6
CG2 A:THR183 4.5 28.5 1.0
OD1 A:ASP132 4.5 20.7 1.0
OE2 A:GLU188 4.5 51.4 1.0
O4' B:U4 4.6 19.1 0.6
C4' B:U4 4.7 24.9 0.5
O b:HOH101 4.7 26.6 1.0
HG23 A:THR183 4.8 34.2 1.0
HB3 A:ASP132 4.8 22.6 1.0
CB A:THR183 4.9 24.6 1.0
HB A:THR183 4.9 29.5 1.0
C5 B:U4 5.0 15.4 0.5
MG A:MG202 5.0 18.1 1.0

Rubidium binding site 3 out of 6 in 6dpl

Go back to Rubidium Binding Sites List in 6dpl
Rubidium binding site 3 out of 6 in the Crystal Structure of Bacillus Halodurans Ribonuclease H1 K196A in Complex with An Rna/Dna Hybrid: Reaction in 10 Mm MG2+ and 200 Mm Rb+ For 720 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 K196A in Complex with An Rna/Dna Hybrid: Reaction in 10 Mm MG2+ and 200 Mm Rb+ For 720 S at 21 C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Rb205

b:39.0
occ:0.20
 RB A:RB203 2.3 28.1 0.2
O A:ALA196 2.7 93.8 0.6
OD2 A:ASP192 2.8 30.1 1.0
O b:HOH101 3.0 26.6 1.0
C A:ALA196 3.1 76.7 0.6
N A:ALA196 3.2 56.7 0.6
O A:HOH303 3.2 44.3 0.6
OD1 A:ASP192 3.3 25.8 1.0
CA A:ALA196 3.3 77.1 0.6
CG A:ASP192 3.4 25.2 1.0
OXT A:ALA196 3.9 56.8 0.6
OE1 A:GLU188 3.9 35.7 1.0
CD A:GLU188 4.1 78.9 1.0
N A:ARG195 4.1 61.2 0.7
O A:TYR193 4.1 81.0 1.0
CG A:GLU188 4.3 64.7 1.0
MG A:MG201 4.3 19.5 1.0
C A:ARG195 4.4 65.6 0.7
CA A:GLY194 4.6 58.8 1.0
C A:GLY194 4.6 0.5 1.0
OE2 A:GLU188 4.7 51.4 1.0
O A:HOH326 4.7 19.3 1.0
OP2 b:G6 4.7 20.0 1.0
O A:HOH312 4.7 40.0 1.0
C A:TYR193 4.8 33.2 1.0
CB A:ALA196 4.8 64.9 0.6
CA A:ARG195 4.8 52.7 0.7
CB A:ASP192 4.9 24.4 1.0
O A:HOH317 4.9 21.4 1.0
OP2 b:C5 5.0 37.4 0.6

Rubidium binding site 4 out of 6 in 6dpl

Go back to Rubidium Binding Sites List in 6dpl
Rubidium binding site 4 out of 6 in the Crystal Structure of Bacillus Halodurans Ribonuclease H1 K196A in Complex with An Rna/Dna Hybrid: Reaction in 10 Mm MG2+ and 200 Mm Rb+ For 720 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 K196A in Complex with An Rna/Dna Hybrid: Reaction in 10 Mm MG2+ and 200 Mm Rb+ For 720 S at 21 C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Rb206

b:55.9
occ:0.20
 O A:HOH371 2.8 51.0 1.0
O A:HOH406 3.1 48.9 1.0
HG2 A:LYS121 3.4 24.3 1.0
O A:LYS121 3.4 19.6 1.0
OD1 A:ASN124 3.4 35.8 1.0
O A:HOH410 3.5 70.2 1.0
HE3 A:LYS121 3.8 34.1 1.0
O A:HOH425 3.9 57.5 1.0
HG3 A:LYS121 4.0 24.3 1.0
CG A:LYS121 4.1 20.3 1.0
HZ2 A:LYS121 4.3 37.0 1.0
C A:LYS121 4.3 17.5 1.0
CG A:ASN124 4.5 37.2 1.0
CE A:LYS121 4.6 28.4 1.0
HD21 A:ASN124 4.8 78.4 1.0
H A:ASN124 4.8 21.7 1.0
NZ A:LYS121 4.8 30.8 1.0
HA A:ASN124 4.9 23.5 1.0
HZ1 A:LYS121 4.9 37.0 1.0
HA A:LYS121 5.0 20.6 1.0
CD A:LYS121 5.0 24.2 1.0

Rubidium binding site 5 out of 6 in 6dpl

Go back to Rubidium Binding Sites List in 6dpl
Rubidium binding site 5 out of 6 in the Crystal Structure of Bacillus Halodurans Ribonuclease H1 K196A in Complex with An Rna/Dna Hybrid: Reaction in 10 Mm MG2+ and 200 Mm Rb+ For 720 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 K196A in Complex with An Rna/Dna Hybrid: Reaction in 10 Mm MG2+ and 200 Mm Rb+ For 720 S at 21 C within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Rb101

b:45.7
occ:0.20
 O B:HOH212 3.0 50.4 1.0
O4 B:U4 3.0 23.6 0.6
O C:HOH204 3.1 46.2 1.0
O2' B:U4 3.1 26.6 0.5
O2 B:U4 3.2 21.3 0.5
C4 B:U4 4.0 20.0 0.6
C2' B:U4 4.0 19.4 0.5
O b:HOH107 4.1 39.0 1.0
C1' B:U4 4.2 22.8 0.5
O B:HOH202 4.2 35.2 0.5
C2 B:U4 4.3 21.1 0.5
N6 C:DA3 4.3 26.7 1.0
O B:HOH205 4.4 32.5 1.0
C5 B:U4 4.4 20.5 0.6
N4 b:C5 4.4 22.8 1.0
N1 B:U4 4.8 17.8 0.5
O6 C:DG2 4.9 24.9 1.0

Rubidium binding site 6 out of 6 in 6dpl

Go back to Rubidium Binding Sites List in 6dpl
Rubidium binding site 6 out of 6 in the Crystal Structure of Bacillus Halodurans Ribonuclease H1 K196A in Complex with An Rna/Dna Hybrid: Reaction in 10 Mm MG2+ and 200 Mm Rb+ For 720 S at 21 C


Mono view


Stereo pair view

A full contact list of Rubidium with other atoms in the Rb binding site number 6 of Crystal Structure of Bacillus Halodurans Ribonuclease H1 K196A in Complex with An Rna/Dna Hybrid: Reaction in 10 Mm MG2+ and 200 Mm Rb+ For 720 S at 21 C within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Rb101

b:49.9
occ:0.40
 O C:HOH207 2.4 26.8 0.6
O6 C:DG5 2.7 24.9 1.0
O C:HOH219 3.2 80.2 1.0
O C:HOH210 3.2 30.1 1.0
O B:HOH211 3.2 58.6 1.0
O4 C:DT4 3.5 19.4 1.0
O C:HOH203 3.6 40.5 1.0
C6 C:DG5 3.7 23.5 1.0
N7 C:DG5 4.1 22.3 1.0
N4 B:C2 4.1 24.4 1.0
C5 C:DG5 4.3 21.9 1.0
C7 C:DT4 4.3 22.7 1.0
C4 C:DT4 4.3 17.9 1.0
N6 B:A1 4.4 25.3 1.0
O B:HOH210 4.7 39.5 1.0
O4 C:DT6 4.7 28.9 1.0
N6 B:A3 4.7 17.8 1.0
C5 C:DT4 4.7 18.3 1.0
N1 C:DG5 4.9 23.5 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 12:12:38 2024

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