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Chlorine in PDB 6dpi: Crystal Structure of Bacillus Halodurans Ribonuclease H1 K196A in Complex with An Rna/Dna Hybrid: Reaction in 10 Mm MG2+ and 200 Mm Rb+ For 40 S at 21 C

Enzymatic activity of Crystal Structure of Bacillus Halodurans Ribonuclease H1 K196A in Complex with An Rna/Dna Hybrid: Reaction in 10 Mm MG2+ and 200 Mm Rb+ For 40 S at 21 C

All present enzymatic activity of Crystal Structure of Bacillus Halodurans Ribonuclease H1 K196A in Complex with An Rna/Dna Hybrid: Reaction in 10 Mm MG2+ and 200 Mm Rb+ For 40 S at 21 C:
3.1.26.4;

Protein crystallography data

The structure of Crystal Structure of Bacillus Halodurans Ribonuclease H1 K196A in Complex with An Rna/Dna Hybrid: Reaction in 10 Mm MG2+ and 200 Mm Rb+ For 40 S at 21 C, PDB code: 6dpi 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) 19.98 / 1.35
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 81.620, 37.290, 62.382, 90.00, 96.98, 90.00
R / Rfree (%) 14.5 / 17.4

Other elements in 6dpi:

The structure of Crystal Structure of Bacillus Halodurans Ribonuclease H1 K196A in Complex with An Rna/Dna Hybrid: Reaction in 10 Mm MG2+ and 200 Mm Rb+ For 40 S at 21 C also contains other interesting chemical elements:

Rubidium (Rb) 3 atoms
Magnesium (Mg) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Bacillus Halodurans Ribonuclease H1 K196A in Complex with An Rna/Dna Hybrid: Reaction in 10 Mm MG2+ and 200 Mm Rb+ For 40 S at 21 C (pdb code 6dpi). 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 K196A in Complex with An Rna/Dna Hybrid: Reaction in 10 Mm MG2+ and 200 Mm Rb+ For 40 S at 21 C, PDB code: 6dpi:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in 6dpi

Go back to Chlorine Binding Sites List in 6dpi
Chlorine binding site 1 out of 3 in the Crystal Structure of Bacillus Halodurans Ribonuclease H1 K196A in Complex with An Rna/Dna Hybrid: Reaction in 10 Mm MG2+ and 200 Mm Rb+ For 40 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 K196A in Complex with An Rna/Dna Hybrid: Reaction in 10 Mm MG2+ and 200 Mm Rb+ For 40 S at 21 C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl205

b:19.2
occ:0.70
 HH A:TYR83 2.3 25.2 1.0
HD22 A:LEU111 2.9 19.9 1.0
OH A:TYR83 3.1 21.0 1.0
HB3 A:LEU111 3.1 15.0 1.0
O A:HOH388 3.2 21.7 1.0
HD13 A:LEU111 3.2 18.3 1.0
HE2 A:TYR83 3.2 22.4 1.0
HD22 A:LEU161 3.2 25.7 1.0
HB3 A:LEU161 3.3 19.0 1.0
HD13 A:LEU161 3.3 26.7 1.0
O A:HOH374 3.3 19.0 1.0
HD3 A:ARG97 3.7 26.5 1.0
C3 A:GOL211 3.8 61.0 1.0
CD2 A:LEU111 3.9 16.6 1.0
CE2 A:TYR83 3.9 18.6 1.0
CZ A:TYR83 3.9 16.4 1.0
O3 A:GOL211 4.0 57.5 1.0
CB A:LEU111 4.0 12.5 1.0
CD1 A:LEU111 4.0 15.2 1.0
CD2 A:LEU161 4.1 21.4 1.0
CB A:LEU161 4.1 15.8 1.0
CG A:LEU111 4.2 13.3 1.0
CD1 A:LEU161 4.2 22.3 1.0
HH11 A:ARG97 4.3 34.7 1.0
CG A:LEU161 4.3 17.5 1.0
HD21 A:LEU111 4.4 19.9 1.0
HD23 A:LEU111 4.4 19.9 1.0
HB2 A:HIS115 4.5 16.2 1.0
HD11 A:LEU111 4.5 18.3 1.0
HG2 A:ARG97 4.6 20.2 1.0
O A:HOH398 4.6 22.1 1.0
HB2 A:LEU111 4.6 15.0 1.0
O2 A:GOL211 4.6 64.3 1.0
HD21 A:LEU161 4.6 25.7 1.0
HD12 A:LEU111 4.6 18.3 1.0
HD23 A:LEU161 4.7 25.7 1.0
HB2 A:LEU161 4.7 19.0 1.0
HD11 A:LEU161 4.7 26.7 1.0
CD A:ARG97 4.7 22.1 1.0
HA A:LEU111 4.7 14.6 1.0
HD12 A:LEU161 4.8 26.7 1.0
C2 A:GOL211 4.8 63.5 1.0
O A:LEU111 4.8 12.5 1.0
O A:HOH425 4.8 33.8 1.0
NH1 A:ARG97 4.9 28.9 1.0
CA A:LEU111 4.9 12.2 1.0
HD11 A:ILE100 4.9 25.0 1.0
HA A:LEU161 5.0 18.1 1.0
HB2 A:ALA165 5.0 17.5 1.0
O A:HOH342 5.0 21.7 1.0

Chlorine binding site 2 out of 3 in 6dpi

Go back to Chlorine Binding Sites List in 6dpi
Chlorine binding site 2 out of 3 in the Crystal Structure of Bacillus Halodurans Ribonuclease H1 K196A in Complex with An Rna/Dna Hybrid: Reaction in 10 Mm MG2+ and 200 Mm Rb+ For 40 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 K196A in Complex with An Rna/Dna Hybrid: Reaction in 10 Mm MG2+ and 200 Mm Rb+ For 40 S at 21 C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl206

b:34.0
occ:0.50
 O A:HOH443 2.4 46.9 1.0
O A:HOH357 2.7 21.7 1.0
O A:HOH455 2.8 44.6 1.0
HA A:GLN134 3.1 20.3 1.0
HB2 A:LYS180 3.2 21.3 1.0
HD12 A:ILE137 3.3 20.9 1.0
HD3 A:LYS180 3.3 23.7 1.0
HG21 A:ILE137 3.4 21.6 1.0
HB A:ILE137 3.5 17.2 1.0
HG3 A:GLN134 3.6 26.9 1.0
HD13 A:ILE137 3.6 20.9 1.0
CD1 A:ILE137 3.9 17.4 1.0
CG2 A:ILE137 4.0 18.0 1.0
CA A:GLN134 4.1 16.9 1.0
O A:HOH346 4.1 29.9 1.0
HG22 A:ILE137 4.1 21.6 1.0
CB A:LYS180 4.1 17.7 1.0
HG2 A:LYS180 4.2 23.1 1.0
CD A:LYS180 4.2 19.8 1.0
CB A:ILE137 4.2 14.3 1.0
O A:HOH457 4.2 60.2 1.0
CG A:LYS180 4.4 19.3 1.0
CG A:GLN134 4.4 22.4 1.0
HB2 A:GLN134 4.5 23.6 1.0
O A:GLN134 4.5 17.4 1.0
O A:HOH448 4.5 33.0 1.0
CB A:GLN134 4.5 19.7 1.0
HB3 A:LYS180 4.6 21.3 1.0
CG1 A:ILE137 4.6 15.0 1.0
HD11 A:ILE137 4.6 20.9 1.0
O A:HOH427 4.6 26.5 1.0
HD2 A:LYS180 4.8 23.7 1.0
C A:GLN134 4.8 17.9 1.0
HE3 A:LYS180 4.8 23.4 1.0
HG2 A:GLN134 4.8 26.9 1.0
O A:HOH452 4.9 32.2 1.0
HG23 A:ILE137 4.9 21.6 1.0
HE21 A:GLN134 5.0 32.1 1.0
N A:GLN134 5.0 15.6 1.0
CE A:LYS180 5.0 19.5 1.0
HA A:LYS180 5.0 19.3 1.0

Chlorine binding site 3 out of 3 in 6dpi

Go back to Chlorine Binding Sites List in 6dpi
Chlorine binding site 3 out of 3 in the Crystal Structure of Bacillus Halodurans Ribonuclease H1 K196A in Complex with An Rna/Dna Hybrid: Reaction in 10 Mm MG2+ and 200 Mm Rb+ For 40 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 K196A in Complex with An Rna/Dna Hybrid: Reaction in 10 Mm MG2+ and 200 Mm Rb+ For 40 S at 21 C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl207

b:34.2
occ:0.75
 O A:HOH458 2.8 26.4 1.0
O A:HOH461 2.8 24.6 0.8
HD11 A:LEU179 3.1 21.5 1.0
HG3 A:PRO128 3.1 21.4 1.0
HB3 A:PRO128 3.3 17.9 1.0
HD21 A:LEU179 3.6 23.3 1.0
CG A:PRO177 3.7 19.3 1.0
CD1 A:ILE64 3.7 29.3 1.0
CB A:PRO177 3.8 17.9 1.0
CG A:PRO128 3.9 17.8 1.0
CB A:PRO128 4.0 14.9 1.0
CD1 A:LEU179 4.0 17.9 1.0
O A:HOH463 4.3 36.7 1.0
O A:HOH462 4.3 59.0 1.0
HD3 A:PRO128 4.3 17.1 1.0
HB2 A:PRO128 4.3 17.9 1.0
HD13 A:LEU179 4.4 21.5 1.0
CD2 A:LEU179 4.4 19.4 1.0
HD12 A:LEU179 4.5 21.5 1.0
HG2 A:PRO128 4.6 21.4 1.0
HG A:LEU179 4.7 19.6 1.0
CG A:LEU179 4.7 16.4 1.0
CD A:PRO128 4.7 14.3 1.0
HD22 A:LEU179 4.7 23.3 1.0
CD A:PRO177 4.8 16.2 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 27 21:45:42 2024

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