Atomistry » Rubidium » PDB 5aw4-7w49 » 6dow
Atomistry »
  Rubidium »
    PDB 5aw4-7w49 »
      6dow »

Rubidium in PDB 6dow: Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 5 Mm MG2+ and 200 Mm Rb+ For 160 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 160 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 160 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 160 S at 21 C, PDB code: 6dow 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) 19.40 / 1.50
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 82.035, 37.485, 62.504, 90.00, 96.84, 90.00
R / Rfree (%) 16.4 / 19.8

Other elements in 6dow:

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 160 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 160 S at 21 C (pdb code 6dow). 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 160 S at 21 C, PDB code: 6dow:
Jump to Rubidium binding site number: 1; 2; 3; 4; 5;

Rubidium binding site 1 out of 5 in 6dow

Go back to Rubidium Binding Sites List in 6dow
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 160 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 160 S at 21 C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Rb203

b:36.0
occ:0.10
 O b:HOH102 0.9 29.8 0.7
O A:HOH355 2.5 42.5 1.0
RB A:RB204 2.8 37.9 0.1
O A:HOH328 2.8 33.7 0.3
CG A:LYS196 3.0 38.8 0.7
OP2 b:G6 3.0 33.8 1.0
N A:ARG195 3.0 42.5 0.8
N A:LYS196 3.1 53.6 0.7
NZ A:LYS196 3.1 46.1 0.7
OD1 A:ASP192 3.1 33.0 1.0
OP3 b:C5 3.4 44.0 0.7
OD2 A:ASP192 3.6 33.9 1.0
CB A:LYS196 3.6 53.5 0.7
CA A:ARG195 3.6 45.7 0.8
C A:ARG195 3.7 54.0 0.8
N A:GLY194 3.7 33.4 1.0
O A:HOH312 3.7 32.0 1.0
CD A:LYS196 3.7 45.6 0.7
CG A:ASP192 3.7 32.5 1.0
CB A:ARG195 3.9 41.2 0.8
H A:TYR193 3.9 38.6 1.0
C A:GLY194 4.0 56.7 1.0
CA A:LYS196 4.0 71.1 0.7
CE A:LYS196 4.0 42.1 0.7
HB2 A:TYR193 4.0 39.6 1.0
P b:G6 4.0 32.0 1.0
MG A:MG201 4.1 27.3 1.0
CA A:GLY194 4.2 37.4 1.0
O5' b:G6 4.2 32.5 1.0
C A:TYR193 4.4 45.4 1.0
N A:TYR193 4.4 32.2 1.0
OP1 b:G6 4.5 32.5 1.0
CG A:ARG195 4.6 36.2 0.8
CA A:TYR193 4.7 34.6 1.0
CB A:TYR193 4.7 33.0 1.0
O A:ARG195 4.7 69.2 0.8
P b:C5 4.9 37.8 0.7
HB3 A:TYR193 5.0 39.6 1.0

Rubidium binding site 2 out of 5 in 6dow

Go back to Rubidium Binding Sites List in 6dow
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 160 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 160 S at 21 C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Rb204

b:37.9
occ:0.10
 NZ A:LYS196 1.0 46.1 0.7
O A:HOH355 2.2 42.5 1.0
O A:HOH328 2.4 33.7 0.3
CE A:LYS196 2.5 42.1 0.7
RB A:RB203 2.8 36.0 0.1
OP3 b:C5 2.9 44.0 0.7
OE2 A:GLU188 2.9 89.4 1.0
OD1 A:ASP192 3.1 33.0 1.0
OE1 A:GLU188 3.2 53.6 1.0
CD A:GLU188 3.2 68.0 1.0
OD2 A:ASP192 3.3 33.9 1.0
CD A:LYS196 3.4 45.6 0.7
CG A:LYS196 3.5 38.8 0.7
O b:HOH102 3.5 29.8 0.7
CB A:LYS196 3.5 53.5 0.7
CG A:ASP192 3.5 32.5 1.0
O A:HOH309 3.8 28.6 0.3
MG A:MG201 4.0 27.3 1.0
O A:HOH319 4.1 28.1 1.0
OP2 b:C5 4.1 37.7 0.3
P b:C5 4.2 37.8 0.7
CG A:GLU188 4.3 61.1 1.0
OP2 b:C5 4.3 28.4 0.7
N A:LYS196 4.5 53.6 0.7
CA A:LYS196 4.6 71.1 0.7
OP2 b:G6 4.7 33.8 1.0
CB A:ASP192 4.9 32.3 1.0
HB2 A:ASP192 4.9 38.7 1.0
O A:HOH312 4.9 32.0 1.0

Rubidium binding site 3 out of 5 in 6dow

Go back to Rubidium Binding Sites List in 6dow
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 160 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 160 S at 21 C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Rb205

b:34.8
occ:0.10
 O A:HOH419 2.6 64.3 1.0
O A:LYS121 3.0 29.3 1.0
OD1 A:ASN124 3.0 41.2 1.0
HG2 A:LYS121 3.3 35.1 1.0
O A:HOH405 3.5 57.8 1.0
HG3 A:LYS121 3.7 35.1 1.0
CG A:LYS121 3.9 29.2 1.0
C A:LYS121 4.0 26.1 1.0
HE3 A:LYS121 4.1 47.6 1.0
CG A:ASN124 4.1 39.3 1.0
HA A:ASN124 4.2 30.3 1.0
H A:ASN124 4.3 29.4 1.0
HZ2 A:LYS121 4.3 45.5 1.0
HA A:LYS121 4.4 26.8 1.0
O A:HOH430 4.5 63.1 1.0
O A:HOH380 4.5 49.0 1.0
HD21 A:ASN124 4.6 60.6 1.0
CA A:LYS121 4.7 22.3 1.0
CE A:LYS121 4.8 39.7 1.0
ND2 A:ASN124 4.8 50.5 1.0
CA A:ASN124 4.9 25.3 1.0
N A:ASN124 4.9 24.5 1.0
O A:HOH368 4.9 38.8 1.0
NZ A:LYS121 4.9 37.9 1.0
CB A:LYS121 4.9 22.4 1.0
N A:GLU122 4.9 25.3 1.0
CD A:LYS121 5.0 29.9 1.0

Rubidium binding site 4 out of 5 in 6dow

Go back to Rubidium Binding Sites List in 6dow
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 160 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 160 S at 21 C within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Rb101

b:31.0
occ:0.30
 O A:HOH309 1.4 28.6 0.3
O B:HOH208 2.4 44.3 1.0
OP2 b:C5 2.7 37.7 0.3
OP2 b:C5 2.8 28.4 0.7
C5' B:U4 3.0 28.0 0.7
C5' B:U4 3.3 40.7 0.3
O A:HOH341 3.3 27.2 1.0
HG21 A:THR183 3.3 41.4 1.0
HG1 A:THR183 3.4 35.5 1.0
OP1 B:U4 3.4 35.8 1.0
O5' B:U4 3.4 34.0 0.3
O b:HOH101 3.5 35.9 1.0
O5' B:U4 3.5 38.0 0.7
OD2 A:ASP132 3.6 39.9 1.0
OE1 A:GLU188 3.7 53.6 1.0
O A:HOH319 3.8 28.1 1.0
P B:U4 3.8 33.3 1.0
HB2 A:ASP132 3.8 32.8 1.0
P b:C5 3.8 28.1 0.3
C3' B:U4 3.9 40.9 0.3
O3' B:U4 3.9 32.9 0.3
P b:C5 4.0 37.8 0.7
CG A:ASP132 4.0 24.6 1.0
OP2 B:U4 4.1 35.2 1.0
C4' B:U4 4.1 37.5 0.3
OE2 A:GLU188 4.1 89.4 1.0
OG1 A:THR183 4.2 29.6 1.0
CG2 A:THR183 4.2 34.5 1.0
CD A:GLU188 4.3 68.0 1.0
C4' B:U4 4.3 35.7 0.7
CB A:ASP132 4.4 27.4 1.0
OP1 b:C5 4.4 33.7 0.7
HG23 A:THR183 4.4 41.4 1.0
OP3 b:C5 4.5 44.0 0.7
OP1 b:C5 4.6 37.6 0.3
C3' B:U4 4.6 34.1 0.7
HB3 A:ASP132 4.7 32.8 1.0
OD1 A:ASP132 4.7 29.7 1.0
NZ A:LYS196 4.7 46.1 0.7
CB A:THR183 4.7 32.8 1.0
HB A:THR183 4.7 39.4 1.0
O A:HOH328 4.8 33.7 0.3
CE A:LYS196 4.8 42.1 0.7
HG22 A:THR183 4.9 41.4 1.0

Rubidium binding site 5 out of 5 in 6dow

Go back to Rubidium Binding Sites List in 6dow
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 160 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 160 S at 21 C within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Rb101

b:52.5
occ:0.40
 O C:HOH210 2.5 29.2 0.6
O6 C:DG5 2.6 34.5 1.0
O C:HOH209 3.2 36.2 1.0
C2 C:EDO103 3.5 49.1 1.0
O C:HOH202 3.5 54.5 1.0
O4 C:DT4 3.6 32.0 1.0
C6 C:DG5 3.7 36.5 1.0
N4 B:C2 4.1 35.9 1.0
O2 C:EDO103 4.2 43.1 1.0
N7 C:DG5 4.2 30.0 1.0
O B:HOH203 4.3 57.0 1.0
C5 C:DG5 4.3 31.3 1.0
N6 B:A1 4.3 32.9 1.0
C7 C:DT4 4.4 31.6 1.0
C4 C:DT4 4.4 29.9 1.0
O1 C:EDO103 4.5 67.4 1.0
C1 C:EDO103 4.6 49.4 1.0
N6 B:A3 4.7 27.8 1.0
C5 C:DT4 4.8 29.4 1.0
O4 C:DT6 4.9 40.7 1.0
N1 C:DG5 4.9 35.1 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: Thu Oct 10 12:09:57 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy