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Potassium in PDB 6dom: Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 2 Mm MG2+ and 50 Mm K+ For 120 S at 21 C

Enzymatic activity of Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 2 Mm MG2+ and 50 Mm K+ For 120 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 2 Mm MG2+ and 50 Mm K+ For 120 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 2 Mm MG2+ and 50 Mm K+ For 120 S at 21 C, PDB code: 6dom 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 / 1.43
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 81.618, 37.341, 62.242, 90.00, 96.36, 90.00
R / Rfree (%) 14.8 / 18.4

Other elements in 6dom:

The structure of Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 2 Mm MG2+ and 50 Mm K+ For 120 S at 21 C also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Iodine (I) 3 atoms

Potassium Binding Sites:

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 50 Mm K+ For 120 S at 21 C (pdb code 6dom). 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 50 Mm K+ For 120 S at 21 C, PDB code: 6dom:
Jump to Potassium binding site number: 1; 2; 3;

Potassium binding site 1 out of 3 in 6dom

Go back to Potassium Binding Sites List in 6dom
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 50 Mm K+ For 120 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 50 Mm K+ For 120 S at 21 C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K202

b:29.2
occ:0.25
O A:HOH345 0.8 30.9 0.4
H A:ARG195 2.2 55.4 0.7
O A:HOH323 2.6 31.4 0.6
O A:HOH306 2.7 28.6 0.7
OD1 A:ASP192 2.9 28.4 1.0
OP2 b:G6 2.9 28.5 1.0
OP3 b:C5 2.9 37.1 0.3
O b:HOH301 3.0 25.6 1.0
H A:GLY194 3.0 40.8 1.0
N A:ARG195 3.1 46.2 0.7
HB2 A:ARG195 3.2 51.7 0.7
H A:TYR193 3.4 31.1 1.0
N A:GLY194 3.4 34.0 1.0
CG A:LYS196 3.5 39.9 0.7
HB2 A:TYR193 3.5 40.6 1.0
OD2 A:ASP192 3.5 29.9 1.0
CG A:ASP192 3.5 26.6 1.0
MG b:MG201 3.6 23.4 1.0
N A:LYS196 3.8 57.3 0.7
CA A:ARG195 3.8 44.6 0.7
CB A:ARG195 3.9 43.1 0.7
N A:TYR193 3.9 25.9 1.0
P b:G6 4.0 25.9 1.0
C A:GLY194 4.0 62.5 1.0
CD A:LYS196 4.0 47.1 0.7
CA A:GLY194 4.0 45.5 1.0
HA2 A:GLY194 4.0 54.6 1.0
C A:TYR193 4.0 43.2 1.0
C A:ARG195 4.1 55.8 0.7
CE A:LYS196 4.2 43.0 0.7
HG3 A:ARG195 4.2 47.2 0.7
CB A:TYR193 4.2 33.9 1.0
CA A:TYR193 4.2 27.5 1.0
CB A:LYS196 4.3 55.0 0.7
OP1 b:G6 4.3 27.5 1.0
O5' b:G6 4.4 27.2 1.0
P b:C5 4.4 47.0 0.3
HB3 A:TYR193 4.5 40.6 1.0
HD2 A:ARG195 4.5 49.6 0.7
CG A:ARG195 4.6 39.3 0.7
OP1 b:C5 4.6 28.8 0.2
CA A:LYS196 4.7 61.2 0.7
HB3 A:ARG195 4.7 51.7 0.7
HA A:ARG195 4.7 53.6 0.7
O A:TYR193 4.9 50.2 1.0
CB A:ASP192 4.9 25.9 1.0
HA3 A:GLY194 4.9 54.6 1.0
C A:ASP192 5.0 26.2 1.0
O A:ARG195 5.0 68.5 0.7

Potassium binding site 2 out of 3 in 6dom

Go back to Potassium Binding Sites List in 6dom
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 50 Mm K+ For 120 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 50 Mm K+ For 120 S at 21 C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K203

b:26.9
occ:0.25
O b:HOH303 0.9 29.0 0.6
OP2 b:C5 2.6 40.8 0.4
O B:HOH107 2.6 34.0 1.0
OP2 b:C5 2.7 45.9 0.3
OP2 b:C5 2.8 22.1 0.2
C5' B:U4 3.0 20.6 0.2
C5' B:U4 3.1 20.6 0.4
O b:HOH302 3.3 29.5 1.0
OD2 A:ASP132 3.3 30.0 1.0
C5' B:U4 3.4 34.5 0.3
OE2 A:GLU188 3.4 62.1 1.0
O A:HOH336 3.4 25.6 1.0
P b:C5 3.5 21.0 0.2
P b:C5 3.5 26.2 0.4
O3' B:U4 3.5 24.7 0.2
O A:HOH305 3.6 45.7 1.0
HG21 A:THR183 3.6 35.5 1.0
O3' B:U4 3.6 23.1 0.4
HG1 A:THR183 3.6 28.9 1.0
C3' B:U4 3.8 21.2 0.2
C3' B:U4 3.8 24.1 0.4
OP1 b:C5 3.8 28.8 0.2
P b:C5 3.9 47.0 0.3
C4' B:U4 3.9 19.4 0.2
C4' B:U4 3.9 20.5 0.4
OE1 A:GLU188 4.0 88.7 1.0
CG A:ASP132 4.0 21.9 1.0
CD A:GLU188 4.0 63.6 1.0
O5' B:U4 4.1 22.8 0.2
O5' B:U4 4.1 21.3 0.4
OP1 b:C5 4.1 30.0 0.3
OP1 b:C5 4.1 30.3 0.4
O5' B:U4 4.1 36.2 0.3
O A:HOH306 4.3 28.6 0.7
OP1 B:U4 4.3 24.9 1.0
NZ A:LYS196 4.3 57.7 0.7
OG1 A:THR183 4.4 24.1 1.0
CG2 A:THR183 4.5 29.5 1.0
P B:U4 4.5 22.6 1.0
OP2 B:U4 4.5 24.9 1.0
C4' B:U4 4.5 21.4 0.3
OP3 b:C5 4.6 37.1 0.3
OD1 A:ASP132 4.6 22.2 1.0
C3' B:U4 4.6 32.9 0.3
HG23 A:THR183 4.6 35.5 1.0
MG b:MG201 4.7 23.4 1.0
CB A:ASP132 4.7 19.5 1.0
MG A:MG201 4.8 22.3 1.0
CE A:LYS196 4.9 43.0 0.7
O5' b:C5 4.9 20.8 0.4
O5' b:C5 5.0 21.0 0.2
CB A:THR183 5.0 26.5 1.0

Potassium binding site 3 out of 3 in 6dom

Go back to Potassium Binding Sites List in 6dom
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 50 Mm K+ For 120 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 50 Mm K+ For 120 S at 21 C within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K101

b:46.2
occ:0.50
O C:HOH214 2.6 25.2 0.5
O6 C:DG5 2.6 26.6 1.0
O C:HOH213 3.0 36.4 1.0
O4 C:DT4 3.5 24.1 1.0
C6 C:DG5 3.7 24.2 1.0
O C:HOH205 4.0 38.7 1.0
N4 B:C2 4.0 32.4 1.0
N7 C:DG5 4.0 21.3 1.0
O B:HOH109 4.1 61.9 1.0
C5 C:DG5 4.2 22.7 1.0
C7 C:DT4 4.2 23.9 1.0
C4 C:DT4 4.3 22.3 1.0
N6 B:A1 4.3 29.1 1.0
C5 C:DT4 4.6 21.1 1.0
N6 B:A3 4.7 21.6 1.0
N1 C:DG5 4.8 23.5 1.0
O4 C:DT6 4.9 27.9 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: Mon Aug 12 15:49:38 2024

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