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Rubidium in PDB 6dpm: 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 1800 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 1800 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 1800 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 1800 S at 21 C, PDB code: 6dpm 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) 20.09 / 1.68
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 81.843, 37.454, 62.728, 90.00, 97.69, 90.00
R / Rfree (%) 16 / 19.9

Other elements in 6dpm:

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 1800 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 1800 S at 21 C (pdb code 6dpm). 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 1800 S at 21 C, PDB code: 6dpm:
Jump to Rubidium binding site number: 1; 2; 3; 4; 5; 6;

Rubidium binding site 1 out of 6 in 6dpm

Go back to Rubidium Binding Sites List in 6dpm
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 1800 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 1800 S at 21 C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Rb203

b:25.9
occ:0.20
O A:TYR193 2.4 80.3 1.0
RB A:RB205 2.8 37.0 0.2
OP2 b:G6 2.8 21.2 1.0
N A:ARG195 2.9 41.0 0.8
OD1 A:ASP192 2.9 21.2 1.0
O b:HOH105 3.0 20.1 1.0
N A:ALA196 3.0 60.2 0.8
O A:HOH318 3.2 19.7 1.0
C A:TYR193 3.2 43.6 1.0
H A:TYR193 3.5 20.9 1.0
CA A:ARG195 3.5 50.1 0.8
CB A:ALA196 3.6 73.5 0.8
OD2 A:ASP192 3.6 24.4 1.0
C A:ARG195 3.6 78.4 0.8
HB2 A:TYR193 3.6 29.6 1.0
CG A:ASP192 3.6 24.9 1.0
CB A:ARG195 3.7 36.1 0.8
P b:G6 3.8 21.1 1.0
C A:GLY194 3.9 47.8 0.8
CA A:ALA196 3.9 75.8 0.8
MG A:MG201 3.9 20.5 1.0
N A:TYR193 4.0 17.5 1.0
N A:GLY194 4.0 35.1 0.8
OP1 b:G6 4.0 21.9 1.0
CA A:TYR193 4.1 25.9 1.0
CA A:GLY194 4.1 30.1 0.8
CB A:TYR193 4.3 24.7 1.0
O5' b:G6 4.3 21.4 1.0
CG A:ARG195 4.3 34.8 0.8
HB3 A:TYR193 4.6 29.6 1.0
O A:ARG195 4.6 90.7 0.8
C A:ALA196 4.9 95.5 0.8
O A:HOH371 4.9 34.0 1.0
HA A:TYR193 5.0 31.1 1.0
O A:GLY194 5.0 49.6 0.8

Rubidium binding site 2 out of 6 in 6dpm

Go back to Rubidium Binding Sites List in 6dpm
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 1800 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 1800 S at 21 C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Rb204

b:19.3
occ:0.70
OP2 b:C5 2.8 20.5 1.0
O A:HOH335 2.9 30.9 1.0
O b:HOH102 3.0 21.6 1.0
OP1 B:U4 3.0 22.0 1.0
OE1 A:GLU188 3.0 24.7 1.0
OD2 A:ASP132 3.2 22.3 1.0
HG1 A:THR183 3.5 23.5 1.0
O b:HOH101 3.5 28.9 1.0
O5' B:U4 3.5 27.9 1.0
O A:HOH337 3.5 18.2 1.0
HG21 A:THR183 3.6 33.3 1.0
O A:HOH314 3.7 16.9 1.0
P B:U4 3.8 21.5 1.0
CD A:GLU188 3.9 29.5 1.0
CG A:ASP132 3.9 16.0 1.0
P b:C5 3.9 21.6 1.0
HB2 A:ASP132 3.9 20.0 1.0
C5' B:U4 3.9 31.9 1.0
OP3 b:C5 4.1 22.7 1.0
OE2 A:GLU188 4.2 25.2 1.0
O4' B:U4 4.2 23.7 1.0
OG1 A:THR183 4.3 19.6 1.0
O A:HOH371 4.4 34.0 1.0
CB A:ASP132 4.5 16.7 1.0
CG2 A:THR183 4.5 27.8 1.0
OP1 b:C5 4.5 20.9 1.0
C6 B:U4 4.6 26.4 1.0
OD1 A:ASP132 4.6 16.4 1.0
C4' B:U4 4.7 30.5 1.0
O3' B:A3 4.7 20.6 1.0
HG23 A:THR183 4.8 33.3 1.0
O b:HOH105 4.8 20.1 1.0
HB3 A:ASP132 4.8 20.0 1.0
CB A:THR183 4.8 22.8 1.0
HB A:THR183 4.9 27.3 1.0

Rubidium binding site 3 out of 6 in 6dpm

Go back to Rubidium Binding Sites List in 6dpm
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 1800 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 1800 S at 21 C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Rb205

b:37.0
occ:0.20
OD2 A:ASP192 2.7 24.4 1.0
O A:HOH371 2.7 34.0 1.0
RB A:RB203 2.8 25.9 0.2
O b:HOH105 3.2 20.1 1.0
OD1 A:ASP192 3.3 21.2 1.0
CG A:ASP192 3.3 24.9 1.0
N A:ALA196 3.4 60.2 0.8
CB A:ALA196 3.4 73.5 0.8
CA A:ALA196 3.7 75.8 0.8
C A:ALA196 3.7 95.5 0.8
OE1 A:GLU188 3.8 24.7 1.0
OXT A:ALA196 3.9 0.9 0.8
N A:ARG195 4.1 41.0 0.8
CD A:GLU188 4.1 29.5 1.0
O A:ALA196 4.2 0.4 0.8
CG A:GLU188 4.3 31.4 1.0
O A:TYR193 4.4 80.3 1.0
MG A:MG201 4.4 20.5 1.0
CA A:GLY194 4.4 30.1 0.8
C A:ARG195 4.5 78.4 0.8
C A:GLY194 4.5 47.8 0.8
O A:HOH314 4.6 16.9 1.0
O A:HOH310 4.6 37.4 1.0
CB A:ASP192 4.7 22.4 1.0
C A:TYR193 4.8 43.6 1.0
OP2 b:G6 4.8 21.2 1.0
N A:GLY194 4.9 35.1 0.8
OE2 A:GLU188 4.9 25.2 1.0
CA A:ARG195 4.9 50.1 0.8
HB2 A:ASP192 5.0 26.9 1.0

Rubidium binding site 4 out of 6 in 6dpm

Go back to Rubidium Binding Sites List in 6dpm
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 1800 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 1800 S at 21 C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Rb206

b:38.0
occ:0.20
O A:HOH430 2.6 56.0 1.0
O A:HOH410 2.6 69.5 1.0
O A:LYS121 2.8 19.6 1.0
OD1 A:ASN124 2.9 34.9 1.0
O A:HOH352 3.4 39.3 1.0
HG2 A:LYS121 3.4 24.2 1.0
CG A:ASN124 3.9 36.1 1.0
C A:LYS121 3.9 19.8 1.0
HG3 A:LYS121 4.0 24.2 1.0
H A:ASN124 4.0 20.2 1.0
CG A:LYS121 4.1 20.2 1.0
HA A:ASN124 4.2 21.6 1.0
HD21 A:ASN124 4.3 66.1 1.0
O A:HOH361 4.3 49.2 1.0
HE3 A:LYS121 4.4 33.8 1.0
ND2 A:ASN124 4.5 55.1 1.0
O A:HOH385 4.5 40.0 1.0
HA A:LYS121 4.6 20.4 1.0
O A:GLU122 4.6 19.8 1.0
HZ2 A:LYS121 4.6 31.8 1.0
CA A:GLU122 4.6 19.4 1.0
N A:ASN124 4.7 16.9 1.0
O A:HOH435 4.7 42.4 1.0
N A:GLU122 4.7 16.0 1.0
O A:HOH407 4.7 50.2 1.0
C A:GLU122 4.7 17.9 1.0
CA A:LYS121 4.8 17.0 1.0
CA A:ASN124 4.8 18.0 1.0
CB A:ASN124 4.9 19.9 1.0

Rubidium binding site 5 out of 6 in 6dpm

Go back to Rubidium Binding Sites List in 6dpm
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 1800 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 1800 S at 21 C within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Rb101

b:30.4
occ:0.25
O B:HOH214 2.8 41.8 1.0
O2 B:U4 2.9 25.5 1.0
O C:HOH205 2.9 37.9 1.0
O2' B:U4 3.0 26.9 1.0
C2' B:U4 3.8 28.6 1.0
N6 C:DA3 4.0 24.5 1.0
O B:HOH213 4.0 25.0 1.0
C2 B:U4 4.0 22.2 1.0
C1' B:U4 4.1 25.2 1.0
O B:HOH202 4.1 40.1 1.0
N4 b:C5 4.5 21.7 1.0
N1 B:U4 4.6 20.9 1.0
O b:HOH108 4.6 35.2 1.0
O6 C:DG2 4.9 25.1 1.0
N6 B:A3 5.0 20.4 1.0

Rubidium binding site 6 out of 6 in 6dpm

Go back to Rubidium Binding Sites List in 6dpm
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 1800 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 1800 S at 21 C within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Rb101

b:48.8
occ:0.40
O C:HOH207 2.5 21.8 0.6
O6 C:DG5 2.7 20.7 1.0
O B:HOH215 3.2 41.7 1.0
O C:HOH210 3.3 27.0 1.0
O4 C:DT4 3.6 22.2 1.0
O C:HOH202 3.7 30.9 1.0
C6 C:DG5 3.8 18.6 1.0
N4 B:C2 4.1 23.0 1.0
N7 C:DG5 4.2 22.3 1.0
N6 B:A1 4.3 23.7 1.0
C5 C:DG5 4.4 18.3 1.0
C4 C:DT4 4.4 20.4 1.0
C7 C:DT4 4.4 23.6 1.0
O B:HOH208 4.5 39.2 1.0
O4 C:DT6 4.6 27.6 1.0
N6 B:A3 4.7 20.4 1.0
C5 C:DT4 4.8 17.8 1.0
N1 C:DG5 5.0 25.1 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 02:07:12 2020

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