Chlorine in PDB 6dox: Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 5 Mm MG2+ and 200 Mm Rb+ For 360 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 360 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 360 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 360 S at 21 C, PDB code: 6dox 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) 19.89 / 1.45
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 81.324, 37.894, 62.145, 90.00, 96.71, 90.00
R / Rfree (%) 15.4 / 17.5

Other elements in 6dox:

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 360 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 360 S at 21 C (pdb code 6dox). 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 360 S at 21 C, PDB code: 6dox:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in 6dox

Go back to Chlorine Binding Sites List in 6dox
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 360 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 360 S at 21 C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl206

b:28.9
occ:0.65
 HH A:TYR83 2.3 26.5 1.0
HD22 A:LEU111 2.9 20.7 1.0
HB3 A:LEU111 3.0 17.9 1.0
OH A:TYR83 3.1 22.1 1.0
HD13 A:LEU111 3.1 19.6 1.0
O A:HOH383 3.2 30.1 1.0
HE2 A:TYR83 3.2 23.4 1.0
HD22 A:LEU161 3.3 29.2 1.0
HB3 A:LEU161 3.3 21.6 1.0
O A:HOH329 3.3 40.0 1.0
HD13 A:LEU161 3.3 26.8 1.0
C3 A:GOL212 3.5 44.5 1.0
O A:HOH369 3.6 20.3 1.0
CD2 A:LEU111 3.8 17.2 1.0
CE2 A:TYR83 3.9 19.5 1.0
CZ A:TYR83 3.9 17.8 1.0
CB A:LEU111 3.9 14.9 1.0
HD3 A:ARG97 3.9 26.4 1.0
CD1 A:LEU111 4.0 16.3 1.0
CG A:LEU111 4.1 15.8 1.0
CD2 A:LEU161 4.2 24.3 1.0
CB A:LEU161 4.2 18.0 1.0
CD1 A:LEU161 4.2 22.3 1.0
HH11 A:ARG97 4.4 44.0 1.0
O3 A:GOL212 4.4 34.4 1.0
HD23 A:LEU111 4.4 20.7 1.0
HD21 A:LEU111 4.4 20.7 1.0
CG A:LEU161 4.4 20.5 1.0
HB2 A:LEU111 4.5 17.9 1.0
HD11 A:LEU111 4.5 19.6 1.0
HB2 A:HIS115 4.5 19.1 1.0
C2 A:GOL212 4.6 64.6 1.0
HD12 A:LEU111 4.6 19.6 1.0
O A:HOH398 4.6 23.1 1.0
HB2 A:LEU161 4.7 21.6 1.0
HG2 A:ARG97 4.7 24.1 1.0
HA A:LEU111 4.7 16.9 1.0
O A:HOH422 4.7 35.2 1.0
HD21 A:LEU161 4.7 29.2 1.0
HD23 A:LEU161 4.7 29.2 1.0
HD11 A:LEU161 4.7 26.8 1.0
HD12 A:LEU161 4.8 26.8 1.0
O A:LEU111 4.8 14.4 1.0
CA A:LEU111 4.8 14.1 1.0
NH1 A:ARG97 4.8 36.7 1.0
CD A:ARG97 4.9 22.0 1.0
O2 A:GOL212 4.9 73.1 1.0
HD11 A:ILE100 4.9 27.0 1.0
HB2 A:ALA165 5.0 20.0 1.0

Chlorine binding site 2 out of 3 in 6dox

Go back to Chlorine Binding Sites List in 6dox
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 360 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 360 S at 21 C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl207

b:37.6
occ:0.50
 O A:HOH443 2.7 37.3 1.0
O A:HOH354 2.8 23.7 1.0
HD12 A:ILE137 3.1 22.5 1.0
HA A:GLN134 3.1 22.7 1.0
HB2 A:LYS180 3.2 23.2 1.0
HD3 A:LYS180 3.3 28.0 1.0
HG3 A:GLN134 3.4 32.5 1.0
HG21 A:ILE137 3.4 26.7 1.0
HD13 A:ILE137 3.5 22.5 1.0
HB A:ILE137 3.5 22.2 1.0
CD1 A:ILE137 3.8 18.8 1.0
CA A:GLN134 4.1 18.9 1.0
CB A:LYS180 4.1 19.3 1.0
CG2 A:ILE137 4.1 22.3 1.0
CD A:LYS180 4.2 23.3 1.0
CB A:ILE137 4.2 18.5 1.0
HG22 A:ILE137 4.2 26.7 1.0
O A:HOH366 4.2 34.8 1.0
CG A:GLN134 4.3 27.1 1.0
HG2 A:LYS180 4.3 27.2 1.0
O A:HOH440 4.4 54.0 1.0
CG A:LYS180 4.4 22.6 1.0
HB2 A:GLN134 4.5 27.6 1.0
O A:GLN134 4.5 20.9 1.0
CB A:GLN134 4.5 23.0 1.0
HD11 A:ILE137 4.5 22.5 1.0
HB3 A:LYS180 4.6 23.2 1.0
O A:HOH436 4.6 40.7 1.0
CG1 A:ILE137 4.6 17.8 1.0
HG2 A:GLN134 4.6 32.5 1.0
O A:HOH420 4.6 30.4 1.0
HD2 A:LYS180 4.8 28.0 1.0
C A:GLN134 4.8 21.9 1.0
HA A:LYS180 4.9 21.1 1.0
HE3 A:LYS180 5.0 31.9 1.0
HE2 A:LYS180 5.0 31.9 1.0
HG23 A:ILE137 5.0 26.7 1.0
N A:GLN134 5.0 18.1 1.0

Chlorine binding site 3 out of 3 in 6dox

Go back to Chlorine Binding Sites List in 6dox
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 360 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 360 S at 21 C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl208

b:37.2
occ:0.75
 O A:HOH450 2.7 33.3 1.0
HD11 A:LEU179 3.2 25.7 1.0
HG3 A:PRO128 3.2 28.0 1.0
HB3 A:PRO128 3.2 22.2 1.0
CG A:PRO177 3.6 20.2 1.0
HD21 A:LEU179 3.7 25.4 1.0
CB A:PRO177 3.7 18.2 1.0
CD1 A:ILE64 3.8 36.2 1.0
CG A:PRO128 3.9 23.3 1.0
CB A:PRO128 4.0 18.5 1.0
CD1 A:LEU179 4.1 21.4 1.0
HD3 A:PRO128 4.2 22.6 1.0
O A:HOH448 4.3 49.5 0.8
HB2 A:PRO128 4.3 22.2 1.0
HD13 A:LEU179 4.5 25.7 1.0
CD2 A:LEU179 4.5 21.2 1.0
HD12 A:LEU179 4.6 25.7 1.0
CD A:PRO128 4.7 18.9 1.0
HG2 A:PRO128 4.7 28.0 1.0
CD A:PRO177 4.7 18.8 1.0
HG A:LEU179 4.7 23.2 1.0
CG A:LEU179 4.7 19.4 1.0
HD22 A:LEU179 4.9 25.4 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 12:53:34 2020

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