Chlorine in PDB 6dpm: 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 1800 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 1800 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 1800 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 1800 S at 21 C, PDB code: 6dpm 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) 20.09 / 1.68
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 81.843, 37.454, 62.728, 90.00, 97.69, 90.00
R / Rfree (%) 16 / 19.9

Other elements in 6dpm:

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 1800 S at 21 C also contains other interesting chemical elements:

Rubidium (Rb) 6 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 1800 S at 21 C (pdb code 6dpm). 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 1800 S at 21 C, PDB code: 6dpm:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in 6dpm

Go back to Chlorine Binding Sites List in 6dpm
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 1800 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 1800 S at 21 C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl207

b:28.2
occ:0.70
HH A:TYR83 2.3 27.8 1.0
HD22 A:LEU111 2.9 20.4 1.0
O A:HOH360 3.0 30.2 1.0
HD22 A:LEU161 3.1 32.3 1.0
OH A:TYR83 3.1 23.1 1.0
HB3 A:LEU111 3.2 17.0 1.0
HB3 A:LEU161 3.3 18.7 1.0
HD13 A:LEU111 3.3 22.7 1.0
O A:HOH333 3.4 18.3 1.0
HE2 A:TYR83 3.4 21.6 1.0
O A:HOH324 3.5 34.5 1.0
HD13 A:LEU161 3.5 30.2 1.0
C3 A:GOL212 3.6 57.3 1.0
CD2 A:LEU111 3.8 17.0 1.0
HD3 A:ARG97 3.9 22.6 1.0
O3 A:GOL212 3.9 39.0 1.0
CB A:LEU111 4.0 14.1 1.0
CZ A:TYR83 4.0 15.7 1.0
CD2 A:LEU161 4.0 26.9 1.0
CE2 A:TYR83 4.1 18.0 1.0
CD1 A:LEU111 4.1 18.9 1.0
CB A:LEU161 4.2 15.6 1.0
CG A:LEU111 4.2 15.3 1.0
HH11 A:ARG97 4.3 52.1 1.0
HD23 A:LEU111 4.3 20.4 1.0
CD1 A:LEU161 4.4 25.2 1.0
HD21 A:LEU111 4.4 20.4 1.0
CG A:LEU161 4.4 19.0 1.0
O A:HOH401 4.5 23.3 1.0
HB2 A:HIS115 4.5 19.0 1.0
HD23 A:LEU161 4.5 32.3 1.0
HD21 A:LEU161 4.6 32.3 1.0
HB2 A:LEU111 4.6 17.0 1.0
HD11 A:LEU111 4.6 22.7 1.0
O A:HOH414 4.7 34.8 1.0
HB2 A:LEU161 4.7 18.7 1.0
HA A:LEU111 4.7 16.3 1.0
HD12 A:LEU111 4.8 22.7 1.0
O2 A:GOL212 4.8 75.1 1.0
HG2 A:ARG97 4.8 21.4 1.0
C2 A:GOL212 4.8 70.2 1.0
CD A:ARG97 4.8 18.8 1.0
O A:LEU111 4.9 14.3 1.0
O A:HOH319 4.9 19.9 1.0
HD11 A:LEU161 4.9 30.2 1.0
CA A:LEU111 4.9 13.6 1.0
HB2 A:ALA165 4.9 23.2 1.0
NH1 A:ARG97 4.9 43.4 1.0
HA A:LEU161 4.9 21.7 1.0
O A:LEU161 5.0 17.9 1.0
HD12 A:LEU161 5.0 30.2 1.0

Chlorine binding site 2 out of 3 in 6dpm

Go back to Chlorine Binding Sites List in 6dpm
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 1800 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 1800 S at 21 C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl208

b:34.9
occ:0.50
O A:HOH348 2.8 21.8 1.0
O A:HOH438 2.9 31.1 1.0
O A:HOH431 3.0 75.2 1.0
HG21 A:ILE137 3.4 25.0 1.0
HD12 A:ILE137 3.4 17.6 1.0
HA A:GLN134 3.4 18.4 1.0
HG3 A:GLN134 3.4 22.5 1.0
HB A:ILE137 3.7 18.9 1.0
HD13 A:ILE137 3.8 17.6 1.0
CD1 A:ILE137 4.0 14.6 1.0
CG2 A:ILE137 4.1 20.9 1.0
HG22 A:ILE137 4.2 25.0 1.0
O A:HOH366 4.3 23.6 1.0
CB A:ILE137 4.3 15.7 1.0
CB A:LYS180 4.3 19.4 1.0
CG A:GLN134 4.3 18.8 1.0
CA A:GLN134 4.3 15.3 1.0
O A:HOH433 4.5 31.1 1.0
O A:HOH421 4.5 25.2 1.0
HG2 A:GLN134 4.6 22.5 1.0
O A:GLN134 4.6 19.0 1.0
O A:HOH408 4.6 24.5 1.0
CD A:LYS180 4.7 29.2 1.0
CB A:GLN134 4.7 17.1 1.0
HB2 A:GLN134 4.7 20.5 1.0
CG1 A:ILE137 4.8 13.2 1.0
HD11 A:ILE137 4.8 17.6 1.0
CG A:LYS180 4.8 21.4 1.0
HE21 A:GLN134 4.9 26.4 1.0
HG23 A:ILE137 4.9 25.0 1.0
O A:HOH437 4.9 43.3 1.0
O A:HOH434 5.0 33.2 1.0
C A:GLN134 5.0 16.9 1.0

Chlorine binding site 3 out of 3 in 6dpm

Go back to Chlorine Binding Sites List in 6dpm
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 1800 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 1800 S at 21 C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl209

b:51.5
occ:0.75
HD11 A:LEU179 3.1 21.6 1.0
HB3 A:PRO128 3.2 20.6 1.0
HG3 A:PRO128 3.3 26.3 1.0
CG A:PRO177 3.6 20.0 1.0
CB A:PRO177 3.8 19.7 1.0
HD21 A:LEU179 3.8 21.1 1.0
CD1 A:ILE64 3.9 28.8 1.0
CB A:PRO128 4.0 17.2 1.0
CG A:PRO128 4.0 21.9 1.0
CD1 A:LEU179 4.1 18.0 1.0
HD3 A:PRO128 4.2 20.8 1.0
HB2 A:PRO128 4.3 20.6 1.0
HD13 A:LEU179 4.4 21.6 1.0
HD12 A:LEU179 4.6 21.6 1.0
CD2 A:LEU179 4.6 17.6 1.0
CD A:PRO128 4.6 17.3 1.0
CD A:PRO177 4.7 17.6 1.0
HG2 A:PRO128 4.8 26.3 1.0
CG A:LEU179 4.8 18.4 1.0
HG A:LEU179 4.8 22.1 1.0
HD22 A:LEU179 4.9 21.1 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 12:53:37 2020

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