Chlorine in PDB 6dow: Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 5 Mm MG2+ and 200 Mm Rb+ For 160 S at 21 C

Enzymatic activity of Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 5 Mm MG2+ and 200 Mm Rb+ For 160 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 5 Mm MG2+ and 200 Mm Rb+ For 160 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 5 Mm MG2+ and 200 Mm Rb+ For 160 S at 21 C, PDB code: 6dow 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) 19.40 / 1.50
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 82.035, 37.485, 62.504, 90.00, 96.84, 90.00
R / Rfree (%) 16.4 / 19.8

Other elements in 6dow:

The structure of Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 5 Mm MG2+ and 200 Mm Rb+ For 160 S at 21 C also contains other interesting chemical elements:

Rubidium (Rb) 5 atoms
Magnesium (Mg) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 5 Mm MG2+ and 200 Mm Rb+ For 160 S at 21 C (pdb code 6dow). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 5 Mm MG2+ and 200 Mm Rb+ For 160 S at 21 C, PDB code: 6dow:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in 6dow

Go back to Chlorine Binding Sites List in 6dow
Chlorine binding site 1 out of 3 in the Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 5 Mm MG2+ and 200 Mm Rb+ For 160 S at 21 C


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 5 Mm MG2+ and 200 Mm Rb+ For 160 S at 21 C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl206

b:32.4
occ:0.75
 HH A:TYR83 2.3 34.2 1.0
HD22 A:LEU111 2.9 31.1 1.0
HB3 A:LEU111 3.1 25.3 1.0
OH A:TYR83 3.1 28.5 1.0
HD22 A:LEU161 3.2 34.1 1.0
O A:HOH371 3.2 31.6 1.0
HD13 A:LEU111 3.2 28.6 1.0
HB3 A:LEU161 3.2 27.7 1.0
HE2 A:TYR83 3.3 32.7 1.0
O A:HOH363 3.3 27.2 1.0
O A:HOH348 3.3 40.2 1.0
C3 A:GOL211 3.4 54.3 1.0
HD13 A:LEU161 3.4 33.1 1.0
CD2 A:LEU111 3.8 25.9 1.0
HD3 A:ARG97 3.9 38.0 1.0
CE2 A:TYR83 4.0 27.3 1.0
CB A:LEU111 4.0 21.1 1.0
CZ A:TYR83 4.0 24.5 1.0
CD1 A:LEU111 4.0 23.8 1.0
CD2 A:LEU161 4.1 28.4 1.0
CG A:LEU111 4.1 23.4 1.0
CB A:LEU161 4.2 23.1 1.0
O3 A:GOL211 4.2 39.4 1.0
CD1 A:LEU161 4.3 27.6 1.0
HD21 A:LEU111 4.3 31.1 1.0
HD23 A:LEU111 4.3 31.1 1.0
CG A:LEU161 4.4 27.1 1.0
HH11 A:ARG97 4.4 48.8 1.0
HB2 A:HIS115 4.5 23.7 1.0
O A:HOH387 4.5 28.4 1.0
HD11 A:LEU111 4.5 28.6 1.0
C2 A:GOL211 4.5 74.1 1.0
HB2 A:LEU111 4.6 25.3 1.0
HD23 A:LEU161 4.6 34.1 1.0
HD21 A:LEU161 4.6 34.1 1.0
HD12 A:LEU111 4.6 28.6 1.0
HB2 A:LEU161 4.6 27.7 1.0
HA A:LEU111 4.7 26.0 1.0
O A:HOH411 4.7 44.6 1.0
HG2 A:ARG97 4.8 30.5 1.0
HD11 A:LEU161 4.8 33.1 1.0
CD A:ARG97 4.8 31.6 1.0
O A:LEU111 4.9 20.2 1.0
HD12 A:LEU161 4.9 33.1 1.0
O A:HOH343 4.9 30.6 1.0
CA A:LEU111 4.9 21.7 1.0
HB2 A:ALA165 4.9 28.1 1.0
NH1 A:ARG97 4.9 40.7 1.0
O2 A:GOL211 4.9 77.5 1.0
HA A:LEU161 5.0 32.3 1.0

Chlorine binding site 2 out of 3 in 6dow

Go back to Chlorine Binding Sites List in 6dow
Chlorine binding site 2 out of 3 in the Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 5 Mm MG2+ and 200 Mm Rb+ For 160 S at 21 C


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 5 Mm MG2+ and 200 Mm Rb+ For 160 S at 21 C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl207

b:41.3
occ:0.50
 O A:HOH436 2.6 44.3 1.0
O A:HOH354 2.6 32.1 1.0
HG21 A:ILE137 3.3 32.3 1.0
HA A:GLN134 3.3 29.2 1.0
HD12 A:ILE137 3.3 30.3 1.0
HG3 A:GLN134 3.3 47.7 1.0
HB2 A:LYS180 3.4 35.7 1.0
HD3 A:LYS180 3.5 42.6 1.0
HD13 A:ILE137 3.5 30.3 1.0
HB A:ILE137 3.5 25.9 1.0
O A:HOH427 3.7 67.3 1.0
CD1 A:ILE137 3.9 25.3 1.0
CG2 A:ILE137 3.9 26.9 1.0
HG22 A:ILE137 4.0 32.3 1.0
CB A:ILE137 4.2 21.6 1.0
CG A:GLN134 4.2 39.8 1.0
CA A:GLN134 4.2 24.3 1.0
CB A:LYS180 4.3 29.8 1.0
HG2 A:GLN134 4.3 47.7 1.0
CD A:LYS180 4.4 35.5 1.0
O A:HOH315 4.4 37.3 1.0
O A:HOH429 4.4 50.8 1.0
O A:GLN134 4.5 26.6 1.0
HG2 A:LYS180 4.5 40.9 1.0
O A:HOH412 4.6 37.6 1.0
CG1 A:ILE137 4.6 23.8 1.0
CB A:GLN134 4.6 26.4 1.0
CG A:LYS180 4.7 34.0 1.0
HD11 A:ILE137 4.7 30.3 1.0
HB3 A:LYS180 4.7 35.7 1.0
HB2 A:GLN134 4.8 31.7 1.0
HG23 A:ILE137 4.8 32.3 1.0
O A:HOH433 4.8 45.0 1.0
C A:GLN134 4.9 28.6 1.0
HD2 A:LYS180 4.9 42.6 1.0

Chlorine binding site 3 out of 3 in 6dow

Go back to Chlorine Binding Sites List in 6dow
Chlorine binding site 3 out of 3 in the Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 5 Mm MG2+ and 200 Mm Rb+ For 160 S at 21 C


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 5 Mm MG2+ and 200 Mm Rb+ For 160 S at 21 C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl208

b:43.3
occ:0.70
 O A:HOH444 2.7 37.9 1.0
HD11 A:LEU179 3.1 30.1 1.0
HG3 A:PRO128 3.2 33.6 1.0
HB3 A:PRO128 3.2 28.1 1.0
HD21 A:LEU179 3.6 33.6 1.0
CG A:PRO177 3.7 29.4 1.0
CD1 A:ILE64 3.8 44.6 1.0
CB A:PRO177 3.8 25.9 1.0
CB A:PRO128 3.9 23.4 1.0
CG A:PRO128 3.9 28.0 1.0
CD1 A:LEU179 4.1 25.1 1.0
HB2 A:PRO128 4.3 28.1 1.0
O A:HOH445 4.3 55.3 0.8
HD3 A:PRO128 4.3 27.8 1.0
HD13 A:LEU179 4.4 30.1 1.0
CD2 A:LEU179 4.5 28.0 1.0
HD12 A:LEU179 4.6 30.1 1.0
HG2 A:PRO128 4.7 33.6 1.0
CG A:LEU179 4.7 24.7 1.0
HG A:LEU179 4.7 29.6 1.0
CD A:PRO128 4.7 23.1 1.0
HD22 A:LEU179 4.7 33.6 1.0
CD A:PRO177 4.8 25.5 1.0
O A:HOH437 5.0 42.5 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: Sat Dec 12 12:53:33 2020

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