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Rubidium in PDB 6dpp: Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 5 Mm MG2+ and 200 Mm Rb+ For 240 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 240 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 240 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 240 S at 21 C, PDB code: 6dpp 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 / 1.45
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 81.468, 37.992, 62.477, 90.00, 96.81, 90.00
R / Rfree (%) 15.1 / 17.1

Other elements in 6dpp:

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 240 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 240 S at 21 C (pdb code 6dpp). 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 240 S at 21 C, PDB code: 6dpp:
Jump to Rubidium binding site number: 1; 2; 3; 4; 5;

Rubidium binding site 1 out of 5 in 6dpp

Go back to Rubidium Binding Sites List in 6dpp
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 240 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 240 S at 21 C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Rb203

b:32.0
occ:0.10
 O b:HOH201 0.9 22.0 0.7
O A:HOH357 2.5 33.1 1.0
RB A:RB204 2.7 32.5 0.1
O A:HOH308 2.8 30.2 0.3
OP2 b:G6 3.0 22.9 1.0
N A:ARG195 3.0 29.6 0.8
N A:LYS196 3.0 35.1 0.7
CG A:LYS196 3.0 33.2 0.7
OD1 A:ASP192 3.1 20.9 1.0
NZ A:LYS196 3.4 34.4 0.7
OD2 A:ASP192 3.5 23.9 1.0
CA A:ARG195 3.6 33.8 0.8
OP3 b:C5 3.6 23.1 0.7
C A:ARG195 3.6 35.8 0.8
CB A:LYS196 3.7 34.9 0.7
N A:GLY194 3.7 25.2 1.0
CG A:ASP192 3.7 23.0 1.0
O A:HOH313 3.7 22.3 1.0
H A:TYR193 3.8 25.4 1.0
CB A:ARG195 3.8 37.0 0.8
CD A:LYS196 3.8 32.0 0.7
C A:GLY194 3.9 40.9 1.0
CA A:LYS196 3.9 41.0 0.7
HB2 A:TYR193 4.0 27.1 1.0
P b:G6 4.0 21.8 1.0
CA A:GLY194 4.1 28.1 1.0
CE A:LYS196 4.1 28.9 0.7
O5' b:G6 4.2 23.3 1.0
MG A:MG201 4.2 20.8 1.0
C A:TYR193 4.3 28.0 1.0
N A:TYR193 4.4 21.1 1.0
OP1 b:G6 4.5 21.6 1.0
CG A:ARG195 4.6 32.6 0.8
CA A:TYR193 4.7 24.4 1.0
CB A:TYR193 4.7 22.6 1.0
O A:ARG195 4.7 44.0 0.8
HB3 A:TYR193 4.9 27.1 1.0

Rubidium binding site 2 out of 5 in 6dpp

Go back to Rubidium Binding Sites List in 6dpp
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 240 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 240 S at 21 C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Rb204

b:32.5
occ:0.10
 NZ A:LYS196 1.1 34.4 0.7
O A:HOH357 1.8 33.1 1.0
CE A:LYS196 2.4 28.9 0.7
O A:HOH308 2.4 30.2 0.3
RB A:RB203 2.7 32.0 0.1
OP3 b:C5 3.0 23.1 0.7
OD1 A:ASP192 3.1 20.9 1.0
CD A:LYS196 3.2 32.0 0.7
CG A:LYS196 3.2 33.2 0.7
OE1 A:GLU188 3.2 43.8 1.0
OD2 A:ASP192 3.3 23.9 1.0
OE2 A:GLU188 3.4 63.0 1.0
CD A:GLU188 3.4 52.4 1.0
CB A:LYS196 3.4 34.9 0.7
O b:HOH201 3.4 22.0 0.7
CG A:ASP192 3.6 23.0 1.0
MG A:MG201 4.0 20.8 1.0
O A:HOH326 4.1 18.9 0.3
O A:HOH321 4.2 21.7 1.0
N A:LYS196 4.2 35.1 0.7
P b:C5 4.3 21.9 0.7
CG A:GLU188 4.4 39.0 1.0
OP2 b:C5 4.4 22.5 0.3
CA A:LYS196 4.4 41.0 0.7
OP2 b:C5 4.5 21.1 0.7
OP2 b:G6 4.6 22.9 1.0
O A:HOH313 4.8 22.3 1.0
CB A:ASP192 4.9 22.9 1.0

Rubidium binding site 3 out of 5 in 6dpp

Go back to Rubidium Binding Sites List in 6dpp
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 240 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 240 S at 21 C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Rb205

b:70.1
occ:0.20
 O A:HOH429 2.6 52.8 1.0
O A:HOH409 2.7 57.1 1.0
O A:HOH410 2.8 51.4 1.0
OD1 A:ASN124 2.9 38.0 1.0
O A:LYS121 3.5 20.7 1.0
CG A:ASN124 3.9 32.0 1.0
HG2 A:LYS121 4.0 25.3 1.0
HD21 A:ASN124 4.1 47.9 1.0
ND2 A:ASN124 4.4 39.9 1.0
O A:HOH432 4.5 54.9 1.0
HE3 A:LYS121 4.5 37.6 1.0
HG3 A:LYS121 4.5 25.3 1.0
C A:LYS121 4.6 21.0 1.0
HA A:ASN124 4.6 24.2 1.0
H A:ASN124 4.6 24.4 1.0
O A:HOH414 4.7 53.4 1.0
CG A:LYS121 4.7 21.1 1.0
HZ2 A:LYS121 4.9 39.8 1.0

Rubidium binding site 4 out of 5 in 6dpp

Go back to Rubidium Binding Sites List in 6dpp
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 240 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 240 S at 21 C within 5.0Å range:
probe atom residue distance (Å) B Occ
b:Rb101

b:25.3
occ:0.30
 O A:HOH326 1.2 18.9 0.3
O B:HOH210 2.5 32.6 1.0
OP2 b:C5 2.7 22.5 0.3
OP2 b:C5 2.8 21.1 0.7
C5' B:U4 3.0 20.4 0.7
HG21 A:THR183 3.3 33.4 1.0
HG1 A:THR183 3.4 28.4 1.0
O A:HOH366 3.4 21.1 1.0
C5' B:U4 3.4 29.3 0.3
O b:HOH202 3.4 27.4 1.0
O5' B:U4 3.4 24.5 0.3
OP1 B:U4 3.4 26.2 1.0
O5' B:U4 3.5 27.6 0.7
OD2 A:ASP132 3.7 28.9 1.0
P b:C5 3.8 17.5 0.3
O A:HOH321 3.8 21.7 1.0
OE1 A:GLU188 3.8 43.8 1.0
HB2 A:ASP132 3.8 21.2 1.0
P B:U4 3.8 24.7 1.0
P b:C5 3.9 21.9 0.7
C3' B:U4 3.9 28.2 0.3
O3' B:U4 4.0 19.0 0.3
OE2 A:GLU188 4.0 63.0 1.0
CG A:ASP132 4.1 20.7 1.0
OP2 B:U4 4.1 30.9 1.0
OG1 A:THR183 4.1 23.7 1.0
CG2 A:THR183 4.2 27.9 1.0
C4' B:U4 4.2 25.9 0.3
CD A:GLU188 4.3 52.4 1.0
C4' B:U4 4.3 25.0 0.7
OP3 b:C5 4.3 23.1 0.7
NZ A:LYS196 4.3 34.4 0.7
HG23 A:THR183 4.4 33.4 1.0
OP1 b:C5 4.4 27.2 0.3
OP1 b:C5 4.4 23.8 0.7
CB A:ASP132 4.4 17.6 1.0
CB A:THR183 4.6 26.0 1.0
C3' B:U4 4.6 22.6 0.7
OD1 A:ASP132 4.7 20.9 1.0
CE A:LYS196 4.7 28.9 0.7
HB3 A:ASP132 4.7 21.2 1.0
HB A:THR183 4.7 31.2 1.0
HG22 A:THR183 4.9 33.4 1.0
O A:HOH308 4.9 30.2 0.3

Rubidium binding site 5 out of 5 in 6dpp

Go back to Rubidium Binding Sites List in 6dpp
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 240 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 240 S at 21 C within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Rb201

b:54.9
occ:0.40
 O C:HOH307 2.5 27.9 0.6
O6 C:DG5 2.6 26.7 1.0
O C:HOH304 3.2 33.3 1.0
O4 C:DT4 3.6 25.0 1.0
O1 B:EDO101 3.6 62.5 1.0
O2 B:EDO101 3.6 47.7 1.0
C6 C:DG5 3.7 25.2 1.0
N4 B:C2 4.1 32.3 1.0
N7 C:DG5 4.1 24.6 1.0
O B:HOH208 4.2 52.9 1.0
C5 C:DG5 4.3 23.2 1.0
C4 C:DT4 4.4 20.6 1.0
C7 C:DT4 4.4 24.8 1.0
C1 B:EDO101 4.4 53.2 1.0
C2 B:EDO101 4.4 48.1 1.0
N6 B:A1 4.4 28.5 1.0
N6 B:A3 4.7 23.1 1.0
C5 C:DT4 4.8 21.9 1.0
O4 C:DT6 4.8 31.6 1.0
N1 C:DG5 4.9 24.7 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 12:12:42 2024

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