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Chlorine in PDB 6dpp: Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 5 Mm MG2+ and 200 Mm Rb+ For 240 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 240 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 240 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 240 S at 21 C, PDB code: 6dpp 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) 19.94 / 1.45
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 81.468, 37.992, 62.477, 90.00, 96.81, 90.00
R / Rfree (%) 15.1 / 17.1

Other elements in 6dpp:

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 240 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 240 S at 21 C (pdb code 6dpp). 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 240 S at 21 C, PDB code: 6dpp:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in 6dpp

Go back to Chlorine Binding Sites List in 6dpp
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 240 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 240 S at 21 C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl206

b:29.3
occ:0.65
HH A:TYR83 2.3 28.4 1.0
HD22 A:LEU111 2.9 21.8 1.0
HB3 A:LEU111 3.1 18.9 1.0
OH A:TYR83 3.1 23.7 1.0
HD13 A:LEU111 3.1 21.4 1.0
O A:HOH384 3.2 29.4 1.0
HD22 A:LEU161 3.2 29.8 1.0
HE2 A:TYR83 3.3 24.3 1.0
HB3 A:LEU161 3.3 22.2 1.0
HD13 A:LEU161 3.3 29.5 1.0
O A:HOH370 3.5 22.0 1.0
O A:HOH343 3.5 41.9 1.0
C3 A:GOL211 3.5 51.6 1.0
CD2 A:LEU111 3.8 18.2 1.0
HD3 A:ARG97 3.9 28.7 1.0
CE2 A:TYR83 3.9 20.3 1.0
CZ A:TYR83 4.0 19.7 1.0
CB A:LEU111 4.0 15.8 1.0
CD1 A:LEU111 4.0 17.8 1.0
CD2 A:LEU161 4.1 24.8 1.0
CG A:LEU111 4.1 16.3 1.0
CB A:LEU161 4.2 18.5 1.0
CD1 A:LEU161 4.2 24.6 1.0
HH11 A:ARG97 4.3 49.4 1.0
HD21 A:LEU111 4.3 21.8 1.0
O3 A:GOL211 4.3 38.1 1.0
HD23 A:LEU111 4.4 21.8 1.0
CG A:LEU161 4.4 22.2 1.0
HD11 A:LEU111 4.5 21.4 1.0
C2 A:GOL211 4.5 71.6 1.0
HB2 A:HIS115 4.6 19.5 1.0
O A:HOH401 4.6 24.6 1.0
HB2 A:LEU111 4.6 18.9 1.0
HD12 A:LEU111 4.6 21.4 1.0
HG2 A:ARG97 4.6 25.5 1.0
HD21 A:LEU161 4.6 29.8 1.0
HB2 A:LEU161 4.7 22.2 1.0
HD23 A:LEU161 4.7 29.8 1.0
HD11 A:LEU161 4.7 29.5 1.0
HA A:LEU111 4.7 17.8 1.0
NH1 A:ARG97 4.7 41.2 1.0
HD12 A:LEU161 4.8 29.5 1.0
O A:HOH422 4.8 38.5 1.0
CD A:ARG97 4.9 23.9 1.0
O A:LEU111 4.9 14.6 1.0
CA A:LEU111 4.9 14.8 1.0
HD11 A:ILE100 4.9 29.1 1.0
O2 A:GOL211 4.9 77.3 1.0
HB2 A:ALA165 5.0 22.1 1.0

Chlorine binding site 2 out of 3 in 6dpp

Go back to Chlorine Binding Sites List in 6dpp
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 240 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 240 S at 21 C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl207

b:38.4
occ:0.50
O A:HOH440 2.7 39.0 1.0
O A:HOH360 2.9 26.5 1.0
HB2 A:LYS180 3.1 25.4 1.0
HA A:GLN134 3.2 24.7 1.0
HD12 A:ILE137 3.2 24.3 1.0
HD3 A:LYS180 3.3 28.6 1.0
HG21 A:ILE137 3.4 27.7 1.0
HG3 A:GLN134 3.4 33.3 1.0
HD13 A:ILE137 3.5 24.3 1.0
HB A:ILE137 3.6 22.6 1.0
CD1 A:ILE137 3.8 20.3 1.0
CB A:LYS180 4.1 21.2 1.0
CG2 A:ILE137 4.1 23.1 1.0
CA A:GLN134 4.1 20.6 1.0
HG22 A:ILE137 4.2 27.7 1.0
O A:HOH368 4.2 35.0 1.0
CD A:LYS180 4.2 23.8 1.0
CB A:ILE137 4.2 18.9 1.0
HG2 A:LYS180 4.2 30.0 1.0
CG A:GLN134 4.3 27.8 1.0
O A:HOH439 4.4 51.9 1.0
CG A:LYS180 4.4 25.0 1.0
HB3 A:LYS180 4.5 25.4 1.0
HB2 A:GLN134 4.5 29.0 1.0
CB A:GLN134 4.5 24.1 1.0
O A:GLN134 4.6 21.7 1.0
HD11 A:ILE137 4.6 24.3 1.0
HG2 A:GLN134 4.6 33.3 1.0
O A:HOH434 4.6 45.2 1.0
CG1 A:ILE137 4.6 17.7 1.0
O A:HOH419 4.8 34.5 1.0
HD2 A:LYS180 4.8 28.6 1.0
C A:GLN134 4.9 21.8 1.0
HE3 A:LYS180 4.9 29.9 1.0
HG23 A:ILE137 4.9 27.7 1.0
HA A:LYS180 4.9 22.0 1.0
CE A:LYS180 5.0 24.9 1.0
HE2 A:LYS180 5.0 29.9 1.0

Chlorine binding site 3 out of 3 in 6dpp

Go back to Chlorine Binding Sites List in 6dpp
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 240 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 240 S at 21 C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl208

b:39.7
occ:0.75
O A:HOH447 2.8 36.6 1.0
HG3 A:PRO128 3.2 29.7 1.0
HD11 A:LEU179 3.2 25.6 1.0
HB3 A:PRO128 3.2 24.0 1.0
CG A:PRO177 3.6 22.4 1.0
HD21 A:LEU179 3.7 28.4 1.0
CB A:PRO177 3.7 21.4 1.0
CD1 A:ILE64 3.8 36.1 1.0
CG A:PRO128 3.9 24.8 1.0
CB A:PRO128 3.9 20.0 1.0
CD1 A:LEU179 4.2 21.3 1.0
HD3 A:PRO128 4.3 20.0 1.0
HB2 A:PRO128 4.3 24.0 1.0
CD2 A:LEU179 4.5 23.6 1.0
HD13 A:LEU179 4.5 25.6 1.0
HG2 A:PRO128 4.7 29.7 1.0
CD A:PRO128 4.7 16.6 1.0
CD A:PRO177 4.7 19.3 1.0
HD12 A:LEU179 4.7 25.6 1.0
HG A:LEU179 4.7 25.1 1.0
CG A:LEU179 4.8 20.9 1.0
HD22 A:LEU179 4.8 28.4 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 Jul 12 12:59:32 2025

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