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Potassium in PDB 6dpa: Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 4 Mm MN2+ and 200 Mm K+ For 40 S at 21 C

Enzymatic activity of Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 4 Mm MN2+ and 200 Mm K+ For 40 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 4 Mm MN2+ and 200 Mm K+ For 40 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 4 Mm MN2+ and 200 Mm K+ For 40 S at 21 C, PDB code: 6dpa 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) 19.83 / 1.49
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 81.199, 37.746, 62.051, 90.00, 96.25, 90.00
R / Rfree (%) 15.5 / 18.6

Other elements in 6dpa:

The structure of Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 4 Mm MN2+ and 200 Mm K+ For 40 S at 21 C also contains other interesting chemical elements:

Manganese (Mn) 2 atoms
Iodine (I) 4 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 4 Mm MN2+ and 200 Mm K+ For 40 S at 21 C (pdb code 6dpa). 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 4 Mm MN2+ and 200 Mm K+ For 40 S at 21 C, PDB code: 6dpa:
Jump to Potassium binding site number: 1; 2; 3;

Potassium binding site 1 out of 3 in 6dpa

Go back to Potassium Binding Sites List in 6dpa
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 4 Mm MN2+ and 200 Mm K+ For 40 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 4 Mm MN2+ and 200 Mm K+ For 40 S at 21 C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K203

b:40.5
occ:0.20
O A:HOH305 2.6 29.8 0.7
N A:GLY194 2.9 35.2 0.7
OP2 b:G6 3.2 23.4 1.0
HB2 A:TYR193 3.2 54.5 1.0
OD1 A:ASP192 3.2 35.5 1.0
H A:TYR193 3.4 46.8 1.0
CA A:GLY194 3.4 42.2 0.7
O A:HOH315 3.5 21.5 1.0
C A:TYR193 3.6 56.5 1.0
OP3 b:C5 3.6 30.8 0.3
C A:GLY194 3.7 36.4 0.7
OD2 A:ASP192 3.7 36.0 1.0
CG A:ASP192 3.8 40.2 1.0
N A:TYR193 3.8 39.0 1.0
CB A:TYR193 3.9 45.4 1.0
CA A:TYR193 4.0 36.5 1.0
P b:G6 4.0 21.6 1.0
HB3 A:TYR193 4.1 54.5 1.0
OP1 b:G6 4.1 20.1 1.0
MN A:MN201 4.1 28.1 0.9
O A:GLY194 4.4 43.4 0.7
O5' b:G6 4.5 26.4 1.0
O A:TYR193 4.5 51.8 1.0
C A:ASP192 4.9 28.5 1.0
HA A:TYR193 4.9 43.7 1.0

Potassium binding site 2 out of 3 in 6dpa

Go back to Potassium Binding Sites List in 6dpa
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 4 Mm MN2+ and 200 Mm K+ For 40 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 4 Mm MN2+ and 200 Mm K+ For 40 S at 21 C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K214

b:27.3
occ:0.20
O b:HOH103 1.2 34.8 0.8
C5' B:U4 2.6 20.9 0.7
OP2 b:C5 2.7 30.9 0.7
O B:HOH206 2.8 35.4 1.0
OP2 b:C5 2.8 16.0 0.3
C5' B:U4 3.0 24.3 0.3
OD2 A:ASP132 3.3 30.6 1.0
O3' B:U4 3.3 23.0 0.7
P b:C5 3.4 17.5 0.7
O A:HOH346 3.4 25.5 1.0
O A:HOH318 3.5 27.8 1.0
C4' B:U4 3.5 20.2 0.7
C3' B:U4 3.6 20.7 0.7
O b:HOH102 3.6 40.4 1.0
HG1 A:THR183 3.6 32.1 1.0
HG21 A:THR183 3.7 42.4 1.0
O5' B:U4 3.7 43.7 0.3
O5' B:U4 3.7 24.6 0.7
CG A:ASP132 3.9 22.7 1.0
OP1 b:C5 3.9 36.6 0.7
P b:C5 3.9 30.1 0.3
OP1 B:U4 3.9 27.4 1.0
OE2 A:GLU188 4.0 57.6 1.0
HB2 A:ASP132 4.1 22.7 1.0
P B:U4 4.1 22.1 1.0
OP1 b:C5 4.1 16.3 0.3
OP2 B:U4 4.2 24.5 1.0
OE1 A:GLU188 4.2 79.7 1.0
C4' B:U4 4.2 23.5 0.3
C3' B:U4 4.4 14.1 0.3
OG1 A:THR183 4.4 26.7 1.0
OD1 A:ASP132 4.4 23.0 1.0
CD A:GLU188 4.5 64.8 1.0
CB A:ASP132 4.5 18.9 1.0
OP3 b:C5 4.5 30.8 0.3
CG2 A:THR183 4.5 35.4 1.0
HG23 A:THR183 4.7 42.4 1.0
HB3 A:ASP132 4.8 22.7 1.0
O4' B:U4 4.8 32.5 0.7
MN A:MN202 4.8 26.3 0.9
C2' B:U4 4.8 14.3 0.3
O5' b:C5 4.9 15.2 0.7
O4' B:U4 5.0 14.9 0.3
CB A:THR183 5.0 32.5 1.0

Potassium binding site 3 out of 3 in 6dpa

Go back to Potassium Binding Sites List in 6dpa
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 4 Mm MN2+ and 200 Mm K+ For 40 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 4 Mm MN2+ and 200 Mm K+ For 40 S at 21 C within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K101

b:45.8
occ:0.50
O C:HOH202 2.0 29.4 0.5
O6 C:DG5 2.7 27.8 1.0
O4 C:DT4 3.1 22.2 1.0
O C:HOH211 3.2 32.9 1.0
O B:HOH209 3.5 61.8 1.0
C6 C:DG5 3.7 24.2 1.0
N4 B:C2 4.0 27.4 1.0
C4 C:DT4 4.0 20.8 1.0
O C:HOH213 4.0 60.4 1.0
C7 C:DT4 4.0 22.4 1.0
N7 C:DG5 4.1 22.0 1.0
C5 C:DG5 4.3 22.8 1.0
N6 B:A3 4.3 19.4 1.0
O B:HOH205 4.4 46.8 1.0
C5 C:DT4 4.4 24.6 1.0
O C:HOH201 4.5 39.8 1.0
N6 B:A1 4.7 28.3 1.0
N1 C:DG5 4.9 23.5 1.0
O B:HOH210 5.0 50.0 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 Dec 14 00:33:32 2020

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