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 Dec 12 12:53:35 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy