Potassium in PDB 6doa: Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 2 Mm MG2+ and 200 Mm K+ For 480 S at 21 C

The structure of Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 2 Mm MG2+ and 200 Mm K+ For 480 S at 21 C, PDB code: 6doa 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)	31.14 / 1.47
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	81.731, 37.890, 62.695, 90.00, 96.66, 90.00
R / Rfree (%)	16 / 18.6

The structure of Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 2 Mm MG2+ and 200 Mm K+ For 480 S at 21 C also contains other interesting chemical elements:

Magnesium	(Mg)	2 atoms
Iodine	(I)	4 atoms

The binding sites of Potassium atom in the Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 2 Mm MG2+ and 200 Mm K+ For 480 S at 21 C (pdb code 6doa). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 3 binding sites of Potassium where determined in the Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 2 Mm MG2+ and 200 Mm K+ For 480 S at 21 C, PDB code: 6doa:
Jump to Potassium binding site number: 1; 2; 3;

Potassium binding site 1 out of 3 in the Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 2 Mm MG2+ and 200 Mm K+ For 480 S at 21 C


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 2 Mm MG2+ and 200 Mm K+ For 480 S at 21 C within 5.0Å range: probe atom residue distance (Å) B Occ A:K203 b:24.5 occ:0.10 O b:HOH101 0.6 26.1 0.9 H A:ARG195 2.1 32.0 0.9 O A:HOH337 2.6 30.5 1.0 OD1 A:ASP192 2.8 19.4 1.0 OP2 b:G6 2.9 21.4 1.0 N A:ARG195 3.0 26.6 0.9 H A:GLY194 3.1 28.7 1.0 HB2 A:ARG195 3.1 45.1 0.9 O A:HOH301 3.1 21.6 0.3 H A:TYR193 3.3 22.3 1.0 OD2 A:ASP192 3.3 21.6 1.0 N A:GLY194 3.4 23.9 1.0 O A:HOH307 3.4 20.2 1.0 CG A:ASP192 3.4 18.6 1.0 N A:LYS196 3.4 38.4 0.7 HB2 A:TYR193 3.5 28.9 1.0 NZ A:LYS196 3.5 24.7 0.7 CG A:LYS196 3.6 29.8 0.7 OP3 b:C5 3.7 22.3 0.7 CA A:ARG195 3.7 33.2 0.9 CB A:ARG195 3.8 37.6 0.9 N A:TYR193 3.9 18.6 1.0 C A:GLY194 3.9 34.7 1.0 C A:TYR193 3.9 28.5 1.0 C A:ARG195 3.9 37.6 0.9 MG A:MG201 3.9 16.9 1.0 CA A:GLY194 4.0 28.0 1.0 P b:G6 4.0 18.5 1.0 HA2 A:GLY194 4.0 33.6 1.0 HG3 A:ARG195 4.1 40.9 0.9 CA A:TYR193 4.1 21.0 1.0 CB A:TYR193 4.2 24.1 1.0 CB A:LYS196 4.2 33.9 0.7 O5' b:G6 4.3 23.2 1.0 CD A:LYS196 4.3 28.6 0.7 CA A:LYS196 4.4 44.2 0.7 OP1 b:G6 4.4 17.9 1.0 HB3 A:TYR193 4.5 28.9 1.0 CG A:ARG195 4.5 34.1 0.9 CE A:LYS196 4.5 24.0 0.7 HB3 A:ARG195 4.5 45.1 0.9 HD2 A:ARG195 4.6 45.6 0.9 HA A:ARG195 4.6 39.8 0.9 O A:TYR193 4.7 29.8 1.0 CB A:ASP192 4.8 18.5 1.0 C A:ASP192 4.9 20.4 1.0 HA3 A:GLY194 4.9 33.6 1.0 HA A:ASP192 5.0 22.0 1.0 O A:ARG195 5.0 44.3 0.9

Potassium binding site 2 out of 3 in the Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 2 Mm MG2+ and 200 Mm K+ For 480 S at 21 C


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 2 Mm MG2+ and 200 Mm K+ For 480 S at 21 C within 5.0Å range: probe atom residue distance (Å) B Occ A:K216 b:18.5 occ:0.35 O A:HOH308 1.3 15.9 0.3 OP2 b:C5 2.6 15.7 0.7 O B:HOH208 2.6 27.0 1.0 OP2 b:C5 2.6 19.0 0.3 C5' B:U4 3.0 15.4 0.7 OD2 A:ASP132 3.3 30.2 1.0 O A:HOH368 3.4 17.6 1.0 O5' B:U4 3.5 19.4 0.3 HG1 A:THR183 3.5 22.4 1.0 O b:HOH102 3.5 25.6 1.0 HG21 A:THR183 3.5 29.3 1.0 O A:HOH320 3.6 17.8 1.0 OP1 B:U4 3.6 21.3 1.0 P b:C5 3.6 15.0 0.3 O5' B:U4 3.6 26.3 0.7 C5' B:U4 3.6 30.2 0.3 OE2 A:GLU188 3.7 44.5 1.0 P b:C5 3.7 18.3 0.7 O3' B:U4 3.8 18.1 0.3 C3' B:U4 3.8 31.5 0.3 HB2 A:ASP132 3.8 18.1 1.0 CG A:ASP132 3.9 18.4 1.0 OE1 A:GLU188 3.9 62.4 1.0 P B:U4 4.0 19.0 1.0 OP1 b:C5 4.1 24.5 0.3 OP3 b:C5 4.2 22.3 0.7 CD A:GLU188 4.2 53.5 1.0 OP2 B:U4 4.3 24.3 1.0 OP1 b:C5 4.3 20.1 0.7 C4' B:U4 4.3 24.9 0.3 C4' B:U4 4.3 23.0 0.7 OG1 A:THR183 4.3 18.7 1.0 CB A:ASP132 4.4 15.1 1.0 NZ A:LYS196 4.4 24.7 0.7 CG2 A:THR183 4.4 24.4 1.0 OD1 A:ASP132 4.5 18.0 1.0 O A:HOH301 4.5 21.6 0.3 CE A:LYS196 4.6 24.0 0.7 C3' B:U4 4.6 21.3 0.7 HG23 A:THR183 4.6 29.3 1.0 HB3 A:ASP132 4.6 18.1 1.0 CB A:THR183 4.8 21.2 1.0 MG A:MG202 4.9 14.9 1.0 MG A:MG201 4.9 16.9 1.0 HB A:THR183 4.9 25.4 1.0 O5' b:C5 5.0 17.5 0.3

Potassium binding site 3 out of 3 in the Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 2 Mm MG2+ and 200 Mm K+ For 480 S at 21 C


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 2 Mm MG2+ and 200 Mm K+ For 480 S at 21 C within 5.0Å range: probe atom residue distance (Å) B Occ C:K101 b:34.6 occ:0.50 O C:HOH210 1.9 24.8 0.6 O6 C:DG5 2.6 22.7 1.0 O C:HOH211 3.2 28.6 1.0 O4 C:DT4 3.5 21.4 1.0 C6 C:DG5 3.7 20.6 1.0 O C:HOH205 3.8 42.9 1.0 N4 B:C2 4.0 30.2 1.0 N7 C:DG5 4.2 21.9 1.0 C4 C:DT4 4.3 18.9 1.0 C5 C:DG5 4.3 20.6 1.0 C7 C:DT4 4.4 21.8 1.0 N6 B:A1 4.4 28.1 1.0 O B:HOH211 4.6 46.1 1.0 N6 B:A3 4.6 19.1 1.0 C5 C:DT4 4.7 19.3 1.0 O4 C:DT6 4.8 27.7 1.0 N1 C:DG5 4.9 23.1 1.0

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