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Potassium in PDB 6doi: Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid (1.54 Angstrom Wavelength): Soak in 0.5 Mm Egta and 200 Mm K+ at 21 C

Enzymatic activity of Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid (1.54 Angstrom Wavelength): Soak in 0.5 Mm Egta and 200 Mm K+ at 21 C

All present enzymatic activity of Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid (1.54 Angstrom Wavelength): Soak in 0.5 Mm Egta and 200 Mm K+ 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 (1.54 Angstrom Wavelength): Soak in 0.5 Mm Egta and 200 Mm K+ at 21 C, PDB code: 6doi 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) 22.01 / 1.95
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 81.456, 38.020, 62.071, 90.00, 96.22, 90.00
R / Rfree (%) 14.7 / 19.5

Other elements in 6doi:

The structure of Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid (1.54 Angstrom Wavelength): Soak in 0.5 Mm Egta and 200 Mm K+ at 21 C also contains other interesting chemical elements:

Iodine (I) 4 atoms
Calcium (Ca) 1 atom

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 (1.54 Angstrom Wavelength): Soak in 0.5 Mm Egta and 200 Mm K+ at 21 C (pdb code 6doi). 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 (1.54 Angstrom Wavelength): Soak in 0.5 Mm Egta and 200 Mm K+ at 21 C, PDB code: 6doi:
Jump to Potassium binding site number: 1; 2; 3;

Potassium binding site 1 out of 3 in 6doi

Go back to Potassium Binding Sites List in 6doi
Potassium binding site 1 out of 3 in the Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid (1.54 Angstrom Wavelength): Soak in 0.5 Mm Egta and 200 Mm K+ 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 (1.54 Angstrom Wavelength): Soak in 0.5 Mm Egta and 200 Mm K+ at 21 C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K201

b:21.9
occ:0.70
CA A:CA203 2.2 46.4 0.3
O A:VAL72 2.7 21.2 1.0
OP1 b:C5 2.7 23.3 1.0
OD1 A:ASP71 2.9 43.7 1.0
OP2 b:G6 2.9 24.0 1.0
OD2 A:ASP71 2.9 28.5 1.0
CG A:ASP71 3.2 40.0 1.0
HD1 A:TYR193 3.6 74.2 1.0
OD1 A:ASP192 3.8 0.9 1.0
H A:TYR193 3.8 96.4 1.0
HB2 A:TYR193 3.9 97.2 1.0
C A:VAL72 3.9 23.5 1.0
P b:C5 3.9 25.6 1.0
HA2 A:GLY73 3.9 29.3 1.0
P b:G6 4.1 25.2 1.0
C5' b:C5 4.1 17.9 1.0
H A:VAL72 4.1 30.8 1.0
O5' b:C5 4.2 24.1 1.0
K A:K202 4.2 24.3 0.7
HA A:ASP192 4.3 98.5 1.0
HG13 A:VAL72 4.4 38.4 1.0
CD1 A:TYR193 4.5 61.8 1.0
HG12 A:VAL72 4.5 38.4 1.0
O b:HOH101 4.5 40.8 1.0
OP1 b:G6 4.5 26.7 1.0
N A:VAL72 4.5 25.7 1.0
N A:TYR193 4.6 80.3 1.0
CA A:GLY73 4.7 24.4 1.0
O3' b:C5 4.7 20.6 1.0
CB A:ASP71 4.7 26.2 1.0
OP2 b:C5 4.7 22.9 1.0
N A:GLY73 4.7 25.4 1.0
CB A:TYR193 4.8 81.0 1.0
CA A:VAL72 4.9 21.4 1.0
CG A:ASP192 4.9 0.5 1.0
CG1 A:VAL72 4.9 32.0 1.0
HA3 A:GLY73 4.9 29.3 1.0
HB3 A:ASP71 4.9 31.4 1.0

Potassium binding site 2 out of 3 in 6doi

Go back to Potassium Binding Sites List in 6doi
Potassium binding site 2 out of 3 in the Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid (1.54 Angstrom Wavelength): Soak in 0.5 Mm Egta and 200 Mm K+ 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 (1.54 Angstrom Wavelength): Soak in 0.5 Mm Egta and 200 Mm K+ at 21 C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K202

b:24.3
occ:0.70
OD2 A:ASP71 2.5 28.5 1.0
OD1 A:ASP132 2.6 19.8 1.0
OP1 b:C5 2.7 23.3 1.0
OE1 A:GLU109 2.7 26.6 0.7
OD2 A:ASP132 2.7 33.7 1.0
CG A:ASP132 3.0 26.8 1.0
O A:HOH327 3.0 17.4 1.0
O3' B:U4 3.1 22.4 1.0
OE2 A:GLU109 3.4 20.7 0.3
CD A:GLU109 3.5 19.3 0.7
P b:C5 3.5 25.6 1.0
H A:VAL72 3.5 30.8 1.0
OE2 A:GLU109 3.6 21.0 0.7
HG12 A:VAL72 3.6 38.4 1.0
HA A:ASP71 3.6 24.9 1.0
CG A:ASP71 3.7 40.0 1.0
CA A:CA203 3.8 46.4 0.3
HG21 A:ILE189 3.9 64.9 1.0
K A:K201 4.2 21.9 0.7
H A:ASP132 4.2 20.4 1.0
C5' b:C5 4.3 17.9 1.0
N A:VAL72 4.4 25.7 1.0
C3' B:U4 4.4 23.1 1.0
O5' b:C5 4.4 24.1 1.0
CB A:ASP132 4.5 17.0 1.0
CA A:ASP71 4.5 20.7 1.0
CD A:GLU109 4.5 18.8 0.3
CG1 A:VAL72 4.5 32.0 1.0
HG22 A:ILE189 4.5 64.9 1.0
OD1 A:ASP71 4.6 43.7 1.0
CB A:ASP71 4.6 26.2 1.0
HB3 A:ASP132 4.7 20.4 1.0
OP2 b:C5 4.7 22.9 1.0
CG2 A:ILE189 4.7 54.1 1.0
C4' B:U4 4.7 29.1 1.0
O2' B:U4 4.7 20.4 1.0
HB2 A:ASP71 4.8 31.4 1.0
HG13 A:VAL72 4.8 38.4 1.0
O A:VAL72 4.8 21.2 1.0
HB2 A:SER133 4.8 19.1 1.0
HD13 A:ILE189 4.9 43.4 1.0
CG A:GLU109 5.0 30.5 0.7
HG11 A:VAL72 5.0 38.4 1.0
O A:VAL70 5.0 19.9 1.0
N A:ASP132 5.0 17.0 1.0

Potassium binding site 3 out of 3 in 6doi

Go back to Potassium Binding Sites List in 6doi
Potassium binding site 3 out of 3 in the Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid (1.54 Angstrom Wavelength): Soak in 0.5 Mm Egta and 200 Mm K+ 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 (1.54 Angstrom Wavelength): Soak in 0.5 Mm Egta and 200 Mm K+ at 21 C within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K101

b:32.4
occ:0.50
O C:HOH206 2.4 19.3 0.5
O6 C:DG5 2.5 28.6 1.0
O B:HOH112 2.7 51.0 1.0
O C:HOH211 3.3 28.2 1.0
O4 C:DT4 3.5 26.9 1.0
C6 C:DG5 3.6 27.6 1.0
N4 B:C2 3.9 25.6 1.0
O C:HOH203 4.1 33.2 1.0
N7 C:DG5 4.1 26.1 1.0
N6 B:A1 4.2 27.9 1.0
C5 C:DG5 4.3 26.8 1.0
C7 C:DT4 4.3 24.2 1.0
C4 C:DT4 4.3 20.9 1.0
O B:HOH111 4.4 39.8 1.0
N6 B:A3 4.6 22.5 1.0
C5 C:DT4 4.7 26.7 1.0
O4 C:DT6 4.8 32.2 1.0
N1 C:DG5 4.8 30.1 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: Mon Dec 14 00:31:59 2020

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