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Potassium in PDB 6dok: Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 2 Mm MG2+ and 25 Mm K+ For 120 S at 21 C (Dataset 1)

Enzymatic activity of Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 2 Mm MG2+ and 25 Mm K+ For 120 S at 21 C (Dataset 1)

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 25 Mm K+ For 120 S at 21 C (Dataset 1):
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 25 Mm K+ For 120 S at 21 C (Dataset 1), PDB code: 6dok 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) 19.95 / 1.38
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 81.617, 37.433, 62.249, 90.00, 96.58, 90.00
R / Rfree (%) 14.9 / 17

Other elements in 6dok:

The structure of Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 2 Mm MG2+ and 25 Mm K+ For 120 S at 21 C (Dataset 1) also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Iodine (I) 2 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 25 Mm K+ For 120 S at 21 C (Dataset 1) (pdb code 6dok). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total only one binding site of Potassium was determined in the Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 2 Mm MG2+ and 25 Mm K+ For 120 S at 21 C (Dataset 1), PDB code: 6dok:

Potassium binding site 1 out of 1 in 6dok

Go back to Potassium Binding Sites List in 6dok
Potassium binding site 1 out of 1 in the Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 2 Mm MG2+ and 25 Mm K+ For 120 S at 21 C (Dataset 1)


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 25 Mm K+ For 120 S at 21 C (Dataset 1) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K203

b:32.0
occ:0.15
 N A:ARG195 2.7 66.0 0.7
O A:HOH320 2.9 35.1 0.9
HB2 A:TYR193 3.0 43.6 1.0
O A:HOH324 3.0 40.7 0.6
OP2 b:G6 3.0 31.7 1.0
O A:HOH312 3.0 28.9 1.0
OD1 A:ASP192 3.0 31.6 1.0
H A:TYR193 3.1 36.2 1.0
N A:GLY194 3.1 32.9 0.7
C A:ARG195 3.3 69.7 0.7
CG A:ARG195 3.5 51.2 0.7
CA A:ARG195 3.5 67.0 0.7
C A:TYR193 3.5 46.3 1.0
OD2 A:ASP192 3.6 33.9 1.0
N A:TYR193 3.6 30.2 1.0
CG A:ASP192 3.6 28.8 1.0
CB A:TYR193 3.7 36.4 1.0
C A:GLY194 3.7 54.3 0.7
CA A:TYR193 3.8 30.5 1.0
MG A:MG201 3.8 26.1 1.0
CA A:GLY194 3.9 43.3 0.7
HB3 A:TYR193 3.9 43.6 1.0
P b:G6 4.0 26.3 1.0
CB A:ARG195 4.0 67.6 0.7
OP1 b:G6 4.1 26.2 1.0
O A:ARG195 4.2 76.3 0.7
O A:TYR193 4.4 65.5 1.0
O b:HOH107 4.4 61.8 1.0
O5' b:G6 4.5 30.4 1.0
CD A:ARG195 4.6 49.5 0.7
C A:ASP192 4.7 26.9 1.0
HA A:TYR193 4.7 36.6 1.0
HD1 A:TYR193 4.8 34.2 1.0
O A:GLY194 4.9 58.6 0.7
HA A:ASP192 4.9 32.2 1.0
CB A:ASP192 5.0 28.6 1.0
CG A:TYR193 5.0 32.3 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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