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Potassium in PDB 6doh: Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: 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: 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: 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: Soak in 0.5 Mm Egta and 200 Mm K+ at 21 C, PDB code: 6doh 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) 19.81 / 1.36
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 81.194, 37.843, 61.829, 90.00, 96.15, 90.00
R / Rfree (%) 16.8 / 20

Other elements in 6doh:

The structure of Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: 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: Soak in 0.5 Mm Egta and 200 Mm K+ at 21 C (pdb code 6doh). 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: Soak in 0.5 Mm Egta and 200 Mm K+ at 21 C, PDB code: 6doh:
Jump to Potassium binding site number: 1; 2; 3;

Potassium binding site 1 out of 3 in 6doh

Go back to Potassium Binding Sites List in 6doh
Potassium binding site 1 out of 3 in the Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: 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: 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:25.3
occ:0.70
CA A:CA201 1.8 15.8 0.3
O A:VAL72 2.6 19.6 1.0
OP1 b:C5 2.7 23.1 1.0
OD2 A:ASP71 2.7 34.2 1.0
OP2 b:G6 2.9 27.5 1.0
OD1 A:ASP71 3.0 24.7 1.0
O A:HOH403 3.2 26.4 0.4
CG A:ASP71 3.2 34.0 1.0
OD1 A:ASP192 3.5 60.4 1.0
HD1 A:TYR193 3.6 48.4 1.0
H A:TYR193 3.7 58.3 1.0
C A:VAL72 3.8 19.7 1.0
HA2 A:GLY73 3.8 25.0 1.0
HB2 A:TYR193 3.8 93.6 1.0
P b:C5 3.9 19.9 1.0
P b:G6 4.0 21.3 1.0
C5' b:C5 4.0 15.4 1.0
O A:HOH333 4.1 41.5 1.0
H A:VAL72 4.1 21.2 1.0
O5' b:C5 4.1 18.3 1.0
HA A:ASP192 4.3 53.7 1.0
HG13 A:VAL72 4.3 30.3 1.0
OP1 b:G6 4.3 20.4 1.0
O b:HOH101 4.4 45.4 1.0
K A:K203 4.4 21.9 0.7
CD1 A:TYR193 4.5 40.3 1.0
HG12 A:VAL72 4.5 30.3 1.0
N A:VAL72 4.5 17.7 1.0
N A:TYR193 4.5 48.6 1.0
CA A:GLY73 4.6 20.9 1.0
O3' b:C5 4.6 18.6 1.0
N A:GLY73 4.6 20.1 1.0
CB A:ASP71 4.7 21.6 1.0
CG A:ASP192 4.7 94.2 1.0
OP2 b:C5 4.7 23.2 1.0
CB A:TYR193 4.7 78.0 1.0
CA A:VAL72 4.8 21.0 1.0
HA3 A:GLY73 4.8 25.0 1.0
CG1 A:VAL72 4.8 25.2 1.0
HB3 A:ASP71 4.9 25.9 1.0

Potassium binding site 2 out of 3 in 6doh

Go back to Potassium Binding Sites List in 6doh
Potassium binding site 2 out of 3 in the Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: 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: 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:K203

b:21.9
occ:0.70
OD1 A:ASP71 2.5 24.7 1.0
OD1 A:ASP132 2.5 20.4 1.0
OP1 b:C5 2.7 23.1 1.0
OE1 A:GLU109 2.7 23.5 0.7
OD2 A:ASP132 2.8 26.1 1.0
CG A:ASP132 3.0 21.7 1.0
O A:HOH339 3.0 18.8 1.0
O3' B:U4 3.1 18.7 1.0
OE2 A:GLU109 3.2 17.2 0.7
CD A:GLU109 3.4 30.1 0.7
O A:HOH333 3.5 41.5 1.0
H A:VAL72 3.5 21.2 1.0
P b:C5 3.5 19.9 1.0
OE2 A:GLU109 3.5 37.8 0.3
HG12 A:VAL72 3.6 30.3 1.0
HA A:ASP71 3.6 20.6 1.0
CG A:ASP71 3.7 34.0 1.0
CA A:CA201 3.9 15.8 0.3
HG21 A:ILE189 4.1 37.9 1.0
H A:ASP132 4.2 18.5 1.0
C5' b:C5 4.3 15.4 1.0
N A:VAL72 4.3 17.7 1.0
C3' B:U4 4.3 21.6 1.0
K A:K202 4.4 25.3 0.7
CB A:ASP132 4.4 18.9 1.0
CA A:ASP71 4.4 17.1 1.0
O5' b:C5 4.5 18.3 1.0
CB A:ASP71 4.5 21.6 1.0
CG1 A:VAL72 4.5 25.2 1.0
O2' B:U4 4.6 18.9 1.0
OD2 A:ASP71 4.6 34.2 1.0
HB2 A:ASP71 4.6 25.9 1.0
HB2 A:SER133 4.7 18.4 1.0
C4' B:U4 4.7 19.5 1.0
HB3 A:ASP132 4.7 22.7 1.0
HG22 A:ILE189 4.7 37.9 1.0
OP2 b:C5 4.7 23.2 1.0
CD A:GLU109 4.7 31.4 0.3
HG13 A:VAL72 4.8 30.3 1.0
CG2 A:ILE189 4.8 31.6 1.0
O A:VAL72 4.9 19.6 1.0
CG A:GLU109 4.9 20.7 0.7
N A:ASP132 4.9 15.4 1.0
C A:ASP71 5.0 17.7 1.0
O A:VAL70 5.0 16.4 1.0
HG11 A:VAL72 5.0 30.3 1.0
HB2 A:ASP132 5.0 22.7 1.0

Potassium binding site 3 out of 3 in 6doh

Go back to Potassium Binding Sites List in 6doh
Potassium binding site 3 out of 3 in the Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: 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: 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:35.8
occ:0.50
O C:HOH204 2.5 28.5 0.5
O6 C:DG5 2.6 25.2 1.0
O C:HOH210 3.0 27.4 1.0
O4 C:DT4 3.3 20.4 1.0
C6 C:DG5 3.6 21.4 1.0
N7 C:DG5 4.0 21.4 1.0
N4 B:C2 4.1 29.7 1.0
O B:HOH107 4.1 50.9 1.0
C4 C:DT4 4.1 17.7 1.0
C7 C:DT4 4.1 22.9 1.0
C5 C:DG5 4.2 22.3 1.0
O C:HOH201 4.4 39.8 1.0
N6 B:A1 4.5 33.7 1.0
N6 B:A3 4.5 21.1 1.0
C5 C:DT4 4.5 20.8 1.0
N1 C:DG5 4.8 22.7 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 15:48:38 2024

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